Basic Microbiology Terms

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Extremophiles

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Microorganisms that live in extreme environments, such as high temperature, high acidity, or high salt.

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Pili

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Protein fibers allowing cells to attach to surfaces.

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Genome

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The complete set of genetic information in a human cell.

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Pathogen

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Disease-causing agents.

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Animalcules

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A microscopic organism observed by Leeuwenhoek; probably protozoa.

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Spontaneous Generation

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the idea that living things could be born from nonliving things.

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Miasma

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idea of the 1700s-1800s that provided diseases were caused by an altered chemical quality of the atmosphere.

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Variolation

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a 14th-18th century method to inoculate a susceptible person with material from a smallpox vesicle.

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Bacteria

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All organisms NOT classified as Archaea or Eukarya; a domain of living things.

(bakterion="little rod")

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Cell Theory

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All things are made up of cells.

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Fermentation

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a splitting of sugar molecules into simpler products, including alcohol, acid, and gas (carbon dioxide);

a metabolic pathway where carbohydrates serve as electron donors, the final electron acceptor is NOT oxygen gas, and NADH is reoxydized to NAD+ for reuse in glycolysis for generation of ATP.

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Antisepsis

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the use of chemical methods for disinfection of external living surfaces, such as the skin.

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Bacilli

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ANY rod-shaped prokaryotic cell;

when referring to the genus Bacillus, it referes to an aerobic or facultatively anaerobic, rod-shaped, endospore-producing gram-positive bacterial cell.

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Attenuate

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to reduce or weaken.

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Nitrogen Fixation

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chemical process where microorganisms convert nitrogen gas into ammonia.

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Antibiotic

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antimicrobial substances naturally produced by mold and bacterial species that inhibit growth or kill other microorganisms.

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Biotechnology

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the commercial application of genetic engineering using living organisms.

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Polymicrobial Diseases

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diseases caused by more than one infectious agent.

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Biofilm

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a complex community of microorganisms that form a protective and adhesive matrix that attaches to a surface, like a catheter or industrial pipeline.

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Bioremediation

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the use of microorganisms to remove or decontaminate toxic materials in the environment.

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Ribosomal RNA; (rRNA)

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RNA types that are major components of the ribosome.

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Eukaryotic

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cells that have a cell nucleus and a membrane envelope.

(a). All plants, animals, and the microorganisms that comprise the fungi and protists are eukaryotes.

(eu = "true", karyon = "nucleus")

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Prokaryotic

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cells that have few of the cellular compartments typical of eukaryotic cells; cells with NO cell nucleus and NO membrane envelope.

(a). Bacteria and Archaea are prokaryotes.

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Phytoplankton

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floating communities of prokaryotic cyanobacteria and eukaryotic algae.

(phyto = "plant", plankto = "wandering")

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Ecotype

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a subgroup of species having special characteristics to survive in its ecological surroundings.

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Chlorophyll

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the major pigment used to convert sunlight into sugar.

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Myxobacteria

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a group of soil-dwelling bacterial species that exhibit multicellular behaviors.

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Quorum Sensing (QS)

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the ability of bacteria to chemically communicate and coordinate behaviro via signaling molecules.

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Cell Membrane

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a thin bilayer of phospholipids and proteins that surrounds the prokaryotic cell cytoplasm;

Also known as plasma membrane in eukaryotes.

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Metabolism

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all the chemical reactions occurring in an organism or cell.

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Cytoplasm

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the complex of chemicals and structures within a cell; in plant and animal cells (eukaryotic) excluding the nucleus.

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Cytosol

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the fluid, ions, and compounds of a cell's cytoplasm excluding organelles and other structures.

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Ribosome

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an RNA protein machine that cranks out proteins based ont eh genetic instructions it receives from the DNA; it is made of RNA and proteins that participates in protein synthesis.

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Organelles

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a special compartment in cells that has a particular function;

membrane-enclosed subcellular compartments (eukarotes have organelles).

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Endomembrane System

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a system that is designed to transport protein and lipids through and out the cell;

a cytoplasmic set of membranes that function in the transport, modification, and sorting of proteins and lipids in eukaryotic cells.

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Endoplasmic Reticulum (ER)

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a network of membranous plates and tubes in the eukaryotic cell cytoplasm responsible for the synthesis and transport of materials from the cell.

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Gogi Apparatus

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a stack of flattened, membrane-enclosed compartments in eukaryotic cells involved in the modification and sorting of lipids and proteins.

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Lysosome

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a membrane-enclosed compartment in eukaryotic cells that contains enzymes to degrade or digest substances.

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Microcompartments

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cellular compartments in prokaryotic cells surrounded by a protein shell;

represents a type of organelle, since the shell proteinscan control transport (prokaryotic cells).

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Cellular Respiration

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a process where all cells convert chemical energy into cellular energy for cellular work;

the process of converting chemical energy into cellular energy in the form of ATP (adenosine triphosphate).

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Mitochondria

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a double membrane-enclosed compartment in eukaryotic cells that carries out aerobic respiration.

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Photosynthesis

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the conversion of light energy into chemical energy.

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Chloroplast(s)

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a double membrane-enclosed compartment in algae that contains chlorophyll and other pigments for photosynthesis.

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Taxonomy

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the science of classification involving a systematized arrangement or cateloging of related organisms into logical categories.

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Endosymbiotic Theory

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the idea that mitochondria and chloroplasts originated from bacterial cells and cyanobacteria that took up residence in a primitive eukaryotic cell proposed by Lynn Margelis.

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Genus

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a rank in the classification system of organisms composed of one or more species; a collection of genera = a family.

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Specific Epithet

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a descriptor that further describes the genus name.

(Genus + Specific Epithet = Species Name).

Ex.: Escherichia coli = Escherichia is the genus, coli is the specific epithet for colon.

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Biotype

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a population or group of individuals having the same genetic constitution (genotype).

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Taxa

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subdivisions used to classify organisms.

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Five Kingdon System

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Monera, Protista, Animalia, Fungi, and Plantae.

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Domain

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Archaea, Bacteria, and Eukarya;

proposed by Carl Woese.

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Three Domain System

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the classification scheme by Carl Woese placing all living organisms into one of three groups based in part, on ribosomal RNA (rRNA) sequences;

1. Archaea Domain
2. Bacteria Domain
3. Eukarya Domain (protista, plantae, fungi, and animalia).

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Antigenic

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microorganisms that are capable of triggering the production of antibodies.

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Antisera

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a blood-derived fluid containing antibodies and used to provide temporary immunity.

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Molecular Taxonomy

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the systematized arrangement of related organisms based on molecular characteristics, such as ribosomal RNA (rRNA) nucleotide sequences;

it is based on the universal presence of ribosomes in all living organisms, of most importance is the RNAs in the ribosome.

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Dichotomous Key

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a method of deducing the correct species assignment of a living organism by offering two alternatives at each juncture, with the choice of one of those alternatives determining the next step.

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Index of Refraction

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a measure of the light-bending ability of a medium.

Also known as Refractive Index.

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Koch's Postulates

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1. the same microorganisms are present in every case of the disease;

2. the microorganisms are isolated from the tissues of a dead animal and a pure culture is prepared;

3. microorganisms from the pure culture are inoculated into a healthy, susceptible animal. The disease is reproduced; and

4. the identical microorganisms are isolated and recultivated from the tissue specimens of the experimental animal.

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Molecular Postulates

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1. the virulence factor gene or its products should be found in the pathogenic strains but NOT in nonpathogenic strains.

2. introduction of cloned virulence gene into nonpathogenic strain should make it pathogenic;

3. genes of virulence must be expressed during disease process; and

4. antibiotics or immune cells specific for the virulence gene products must be protective.

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Pili

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protein fibers allowing cells to attach to surfaces.

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Flagella

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protein appendages used for motility.

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Glycocalyx

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a carbohydrate-rich layer to prevent desiccation, allow attachment, or evade immune system defenses.

Also known as: Capsule or Slime Layer.

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Cell Envelope

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consists of the cell wall, which maintains cell shape and prevents cell rupture.

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Cell Membrane

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a typical phospholipid bilayer that separate environment from cell interior and regulates transport of materials into or out of the cell.

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Nucleoid

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a subcompartment in the cytoplasm that contains the genetic information in the form of a circular bacterial chromosome.

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Plasmids

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small cytoplasmic loops of DNA that carry nonessential genetic information.

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Ribosome

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a cellular structure made of RNA and protein that participates in protein synthesis.

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Inclusion Body

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a granule-like storage structure found in the prokaryotic cell cytoplasm;

a virus in the cytoplasm or nucleus of an infected cell.

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Gas Vesicle

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a cytoplasmic compartment in some prokaryotic cells used to regulate buoyancy.

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Magnetosomes

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a cytoplasmic inclusion body in some prokaryotic cells that assists orientation to the environment by aligning with the magnetic field.

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Cytoskeleton

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the structural proteins in a prokaryotic cell that help control cell shape and cell division;

in a eukaryotic cell, the internal network of protein filaments and microtubules that control the cell's shape and movement.

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Anabolism

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an energy-requiring involving the synthesis of larger organic compounds from smaller ones.

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Catabolism

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an energy-liberating process in which larger organic compounds are broken down into smaller ones.

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Endergonic Reaction

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a chemical process that requires energy.

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Exergonic Reaction

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a chemical process releasing energy.

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Enzyme

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a reusable protein molecule that brings about a chemical change while itself remaining unchanged;

protein catalysts that speed up chemical reactions by lowering the activation energy of reactions.

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Activation Energy

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the energy required for a chemical reaction to occur.

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Active Site

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the region of an enzyme where the substrate binds.

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Enzyme-Substrate Complex

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the association of an enzyme with its substrate at the active site.

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Metabolic Pathways

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a sequence of linked enzyme-catalyzed reactions in a cell.

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Noncompetitive Inhibition

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the prevention of a chemical reaction by a chemical that binds elsewhere than to active site of an enzyme.

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Competitive Inhibition

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the prevention of a chemical reaction by a chemical that competes with the normal substrate for an enzyme's active site.

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Glycolysis

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a metabolic pathway in which glucose is broken down into two molecules of pyruvate with a net gain of two ATP molecules.

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Kreb's Cycle

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a cyclic metabolic pathway in which carbon from acetyl-CoA (coenzyme A) is released as carbon dioxide;

the reactions yield ATP as well as protons and high-energy electrons that are transferred to coenzymes; also called Citric Acid Cycle.

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Electron Transport Chain

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a series of proteins that transfer electrons in cellular respiration to generate ATP.

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Chemiosmosis

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the use of a proton gradient across a membrane to generate cellular energy in the form of ATP.

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Autotrophy

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an organism that uses carbon dioxide as a carbon source.

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Heterotrophy

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an organism that requires performed organic matter for its energy and carbon needs.

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Asexual Reproduction

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the form of rproduction that maintains genetic constancy while increasing cell numbers.

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Binary Fission

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an asexual process in prokaryotic cells by which a cell divides to form two new cells while maintaining genetic constancy.

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Cytokinesis

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division of the cytoplasm of a cell during binary fission or mitosis.

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Bacterial Growth Curve

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the events occurring over time within a population of growing and dividing prokaryotic cells.

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Lag Phase

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a portion of a bacterial growth curve encompassing the first few hours of the population's history when no growth occurs.

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Logarithmic (Log) Phase

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the portion of a bacterial growth curve during which active growth leads to a rapid rise in cell numbers.

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Decline Phase

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the final portion of a bacterial growth curve in which environmental factors overwhelm the population and induce death;

Also called Death Phase.

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Sporulation

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the process of spore formation.

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Dipicolinic Acid

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an organic substance that helps stabilize the proteins and DNA in a bacterial spore, thereby increasing spore resistance.

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Generation Time

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the time interval for a cell population to double in number.

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Endospore

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an extremely resistant dormat cell produced by some gram-positive bacterial species.

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Viable But Not Culturable (VBNC)

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referring to prokaryotes that are viable but not culturable.

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Pure Culture

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an accumulation or colony of microorganisms of one species.

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Pour-Plate Method

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a process by which a mixed culture can be separated into pure colonies and the colonies isolated.

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Streak-Plate Method

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a process by which a mixed culture can be streaked onto an agar plate and pure colonies isolated.

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Direct Microscopic Count

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estimation of the number of cells by observation with the light microscope.

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Most Probable Number (MPN)

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a laboratory test in which a statistical evaluation is used to estimate the number of bacterial cells in a sample of fluid;

often employed in determinations of coliform bacteria in water.

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Standard Plate Count

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a procedure to estimate the number of cells in a sample dilution spread on an agar plate.

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Mold

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a type of fungus that consists of chains of cells and appears as a fuzzy mass of thin filaments in culture.

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Yeast

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a type of unicellular, nonfilamentous fungus that resembles bacterial colonies when grown in culture;

a term sometimes used to denote the unicellular form of pathogenic fungi.

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Coccus

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a spherical-shaped prokaryotic cell.

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Bacillus

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any rod-shaped prokaryotic cell; when referring to the genus Bacillus, it refers to an aerobic or facultatively anaerobic, rod-shaped, endospore-producing, gram-positive bacterial cell.

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Streptococci

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a chain of bacterial cocci; a genus of facultatively anaerobic, nonmotile, nonspore-forming, gram-positive spheres in chains.

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Diplococci

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a pair of spherical-shaped prokaryotic cells.

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Staphylococci

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an arrangement of bacterial cells characterized by spheres in a grapelike cluster;

a genus of facultatively anaerobic, nonmotile, nonsporeforming, gram-positive spheres in clusters.

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Streptobacilli

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a chain of bacterial rods; a genus of facultatively anaerobic, nonmotile, gram-negative rods.

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Spirochetes

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a twisted bacterial rod with a flexible cell wall containing endoflagella for motility.

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Spirillum

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a bacterial cell shape characterized by twisted or curved rods;

a genus of aerobic, helical cells usually with many flagella.

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Capsule

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a layer polysaccharides and small proteins covalently bound some prokaryotic cells.

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Cell Wall

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a carbohydrate-containing structure surrounding fungal, algal, and most prokaryotic cells.

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Algae

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an organism in the kingdom of Protista that performs photosynthesis.

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Protozoa

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a single-celled eukaryotic organism that lacks a cell wall and usually exhibits chemoheterotrophic metabolism.

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Amoeba

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a protozoan that undergoes a crawling movement by forming cytoplasmic projections into the environment.

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Apicomplexan

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a protozoan containing a number of organelles at one end of the cell that are used for host penetration;

NO motion is observed in adult forms.

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Hypha

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a microscopic filament of cells representing the vegetative portion of a fungus.

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Mycelium

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a mass of fungal filaments from which most fungi are built.