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Chapter 3
Alcamo's Microbiology
100
Microbiology
Undergraduate 1
09/19/2010

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Term
ecotypes
Definition
Subgroups of a species that have special characteristics to survive in their ecological surroundings
Term
Biosphere
Definition
that part of the earth-including the air, soil, and water- where life occurs
Term
Homeostasis
Definition
the ability to adjust yet maintain a relatively steady internal state
-factors include of external environment: temperature, sunlight, or toxic chemicals
Term
Biofilms
Definition
a “multicellular state” where survival required chemical communication and cooperation between cells; the cells become embedded in a matrix of excreted polymeric substances produced by the bacterial cells, theses stick substances are composed of charged and neutral polysaccharides that hold the it together, and cement it to nonliving or living surfaces such as metals, plastics, soil particles, medical indwelling devices, or human tissue
Ie: fatal lung infections, middle ear infections, and tooth decay
-they can also develop on improperly cleaned medical devices, like artificial joints, mechanical heart valves, and catheters
Term
Quorum Sensing
Definition
involves the ability of bacteria to sense their numbers, and then communicate and coordinate behavior, including gene expression, via signaling molecules
Term
Bioremediation
Definition
uses microorganisms to remove or clean up chemically contaminated environments like oil spills, or toxic waste sites
Term
Cell theory
Definition
The tenent that all organisms are made of cells and arise from preexisting cells
Term
Chromosomes
Definition
A structure in the nucleoid or cell nucleus that carries hereditary information in the form of genes
-most bacteria have a single, circular DNA molecule without an enclosing membrane, but Eukaryotic cells have multiple, linear chromosomes enclosed by the membrane envelope of the cell nucleus
Term
Cell membrane
Definition
A thin bilayer of phosopholipids and proteins that surrounds the prokaryotic cell cytoplasm
Term
Plasma Membrane
Definition
the phosopholipid bilayer with proteins that surrounds the eukaryotic cell cytoplasm
Term
Metabolism
Definition
all the chemical reactions occurring in an organisms or cell
Term
Cytoplasm
Definition
the complex of chemicals and structures within a cell; in plant and animal cells excluding the nucleus
Term
Cytosol
Definition
the fluid, ions, and compounds of a cell’s cytoplasm excluding organelles and other structures
Term
Ribosome
Definition
a cellular structure made of RNA and protein that participates in protein synthesis based on the genetic instructions it receives from the DNA
Term
Organelles
Definition
a specialized compartment in cells that has a particular function
Term
Endomembrane System
Definition
A cytoplasmic set of membranes that function in the transport, modification, and sorting of proteins and lipids in eukaryotic cells
Term
Endoplasmic Reticulum (ER)
Definition
A network of membranous plates and tubes in the eukaryotic cells cytoplasm responsible for the synthesis and transport of materials from the cell
Term
Rough ER
Definition
flat membranes to which ribosomes are attached to
Term
Smooth ER
Definition
tube-like membranes without ribosomes
Term
Golgi Appartatus
Definition
A stack of flattened, membrane-enclosed compartments in eukaryotic cells involved in the modification and sorting of lipids and proteins
Term
Vesicles
Definition
membrane-enclosed spheres involved with secretion and storage
Term
Lysosomes
Definition
A membrane-enclosed compartment in many eukaryotic cells that contains enzymes to degrade or digest substances
Term
Microcompartments
Definition
A region in some bacterial cells surrounded by a protein shell
Term
Cellular Respiration
Definition
the process of converting chemical energy into cellular energy in the form of ATP
Term
Mitochondria
Definition
A double membrane-enclosed compartment in eukaryotic cells that carries out aerobic respiration
Term
Photosynthesis
Definition
A biochemical process in which light energy is converted to chemical energy which is then used for carbohydrate synthesis
Term
Chloroplasts
Definition
a double membrane-enclosed compartment in algae that contains chlorophyll and other pigments for photosynthesis
Term
Cytoskeleton
Definition
1.) the structural proteins in a prokaryotic cells that help control cell shape and cell division 2.) In a eukaryotic cell, the internal network of protein filaments and microtubules that control the cell’s shape and movement
Term
Centrosome
Definition
the microtubule-organizing center of a eukaryotic cell
Term
Flagella
Definition
A long, hair-like appendage-composed of protein and responsible for motion in microorganisms; found in some bacterial, archaeal, protozoal , algal, and fungal cells
Term
Cilia
Definition
a hair-like projection on some eukaryotic ells that along with many others assist in the motion of some protozoa and beat rhythmically to aid the movement of a fluid past the respiratory epithelial cells in humans
Term
Diffusion
Definition
the movement of a substance from where it is in a higher concentration to where it is in a lower concentration
Term
Osmosis
Definition
the net movement of water molecules from where they are in high concentration through a semi-permeable membrane to a region where they are in a lower concentration
Term
Cell Wall
Definition
A carbohydrate-containing structure surrounding fungal, algal, and most bacterial and archaeal cells
Term
Carolus Linnaeus
Definition
18th century, began identifying living organisms by their similarities in form and placing organisms in two kingdoms, “Vegetalia” and “Animalia”

popularized Systema Naturae, which is a two word scheme of nomenclature derived from Greek or Latin stems
Term
Ernst Haeckel
Definition
noticed that unicellular (microscopic) organisms didn’t fit into the two kingdoms, so he made a third kingdom named Protista, where unicellular organisms fit into
Term
Edouard Chatton
Definition
1937, noticed that bacteria are in the prokaryotic nature of cells, and should be separated from the rest of the protists because they are eukaryotic in nature
Term
Robert Whitaker
Definition
saw the fungi as another kingdom of organisms since they are eukaryotic but they must digest food externally prior to absorption and live in the food source, so he named a fourth kingdom as fungi, which are multicellular, eukaryotic, absorptive mode of nutrition
Term
Carl Woese
Definition
1970s studied the nucleotide sequences of gene coding for the small subunit ribosomal RNA and dichotomy of the prokaryotes, then 1990, kingdom Monera contained two different unrelated groups, Bacteria, and Archaebacteria
Term
Systematics
Definition
studying the diversity of life and its evolutionary relationships
Term
Systematic Biologists- Systematists
Definition
identify, describe, name, and classify organisms and organize their observations within a framework that shows taxonomic relationships
Term
Taxonomy
Definition
the science dealing with the systematized arrangements of related living things in categories
Term
Domain
Definition
1.) the most inclusive taxonomic level of classification; consists of the Archaea, Bacteria, and Eukarya
Term
Phylogeny
Definition
the evolutionary history of a species or group of species
Term
Phylogenetic trees
Definition
identify inferred relationships among species
Term
Three Domain System
Definition
the classification scheme placing all living organisms into one of three groups based in part on ribosomal RNA sequences
Term
Archaea
Definition
The domain of living organisms that excludes the Bacteria and Eukarya
Term
Eukarya
Definition
The domain of living organisms that includes all organisms not classified as Archaea or Bacteria
Term
Eukarya
Definition
the taxonomic domain encompassing all eukaryotic organisms
Term
Genus
Definition
A rank in the classification system of organisms composed of one or more species a collection of genera constitute a family
Term
Specific Epithet
Definition
The second of the two scientific names for a species
Term
Species
Definition
the fundamental rank in the classification system of organisms
Term
Family
Definition
A category of related organisms consisting of one or more genera
Term
Order
Definition
A category of related organisms consisting of one or more families
Term
Class
Definition
a category of related organisms consisting of one or more orders
Term
Phylum
Definition
A category of related organisms consisting of one or more classes
Term
Biotypes
Definition
Populations or groups of individuals having the same genetic constitution (genotype)
Term
David Hendricks Bergey
Definition
devised one of the first systems of classification for the bacteria species in 1923 and today there is a proper taxonomic classification for Bacteria and Archaea called Bergey’s Manual of Systematic Bacteriology
Term
Physical Characteristics
Definition
includes differential staining reactions to help determine the organism’s shape (morphology) and the size and arrangement of cells, others include: oxygen, pH, and growth temperature requirements.; spore-forming ability and motility
Term
Biochemical Tests
Definition
fermentation of carbohydrates, the use of a specific substrate, and the production of specific products or waste products,
Term
Serological Tests
Definition
microorganisms are antigenic, meaning they cannot trigger the production of antibodies
Term
Antibodies
Definition
proteins produced by the immune system in response to a specific chemical configuration (antigen)
Term
Antisera
Definition
solutions of collected antibodies
Term
Molecular Taxonomy
Definition
the systemized arrangement of related organisms base don molecular characteristics, such as ribosomal DNA nucleotide sequences
Term
Dichotomous Key
Definition
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
Term
Micrometer (µm)
Definition
common unit of measuring is the equivalent to a millionth of a meter (10-6)
Term
Nanometer (nm)
Definition
common unit of measuring is the equivalent to a billionth of a meter (10-9)
Term
Light/Compound Microscope
Definition
An instrument that uses visible light and a system of glass lenses to produce a magnified image of an object
Term
Bright-field Microscopy
Definition
an instrument that magnifies an object by passing visible light directly through the lenses and object
Term
Magnification
Definition
the increase in the apparent size of the specimen being observed
Term
Total Magnification
Definition
the magnification of the ocular multiplied by the magnification of the objective lens being used
Term
Resolving Power
Definition
the numerical value of a lens system indicating the size of the smallest object that can be seen clearly when using that system
Term
Index of Refraction
Definition
A measure of the light bending ability of a medium through which light passes
Term
Simple Stain Technique
Definition
the use of a single cationic dye to contrast cells
-bacterial cells in a droplet of water or broth are smeared on a glass slide and the slide air-dried using heat fixation, bonding the cells to the slide, killing any organisms still alive, and increases stain absorption, then the slide is flooded with a basic dye like methylene blue, since basic dyes have a positive charge, the dye is attracted to the cytoplasm and cell wall, which have negative charges
Term
Heat Fixation
Definition
the use of warm temperature to prepare microorganisms for staining and viewing with the light microscope
Term
Basic Dye
Definition
A positively charged colored substance in solution that is used to stain cells
Term
Negative Stain Techinque
Definition
A staining process that results in colorless bacterial cells on a stained background when viewed with the light microscope
-bacterial cells are mixed on a slide with an acidic (anionic) dye like nigrosin or India ink, the mixture is then pushed across the face of the slide and allowed to air dry; the anionic dye carries negative charge and it is repelled from the cell wall and cytoplasm, the stain does not enter the cells and the observer sees clear or white cells on a black or gray background
Term
Acidic Dye
Definition
A negatively charged colored substance in solution that is used to stain an area around cells
Term
Gram Stain Technique
Definition
A staining procedure used to identify bacterial cells are gram negative or gram positive
Term
Differential Staining Procedure
Definition
A technique using two dyes to differentiate cells or cellular objects based on their staining
-it allows the observer to differentiate (separate) bacterial cells visually into two groups based on staining differences
Term
Step 1 of Gram Staining
Definition
stained with crystal violet rinsed then
Term
Step 2 of Gram Staining
Definition
a special Gram’s iodine solution is added, All bacterial cells would appear blue-purple if the procedure was stopped and the sample viewed with the light microscope,
Term
Step 3 of Gram Staining
Definition
next the smear is rinsed with a decolorizer, like 95% alcohol or an alcohol-acetone mixture, certain cells may lose their color while others don’t, so they are either gram negative or positive
Term
Step 4 of Gram Staining
Definition
uses safranin, a red cationic dye, to counterstain the orange-red color
Term
Gram Negative
Definition
Referring to a bacterial cell that stains red after gram staining (more susceptible to tetracycline, more complex cells wells)
Term
Gram Positive
Definition
referring to a bacterial cell that stains purple after gram staining (more susceptible to penicillin)
Term
Toxins
Definition
chemical substances that are poisonous (both gram positive ad gram negative bacterial species can produce different types)
Term
Acid-Fast Techniques
Definition
a staining process in which mycobacteria resist decolorization with acid alcohol
-used to identify members of genus Mycobacterium, which causes TB, this technique will stain red when treated with carbol-fuchsin (red dye) and heat (or lipid solubilizer)
Term
Phase-Contrast Microscopy
Definition
An optical system on the light microscope that uses a special condenser and objective lenses to examine cell structure
-it can see structures of yeasts, molds, and protozoa and while they are living
Term
Dark Field Microscopy
Definition
an optical system on the light microscope that scatters light such that the specimen appears white on a black background
Term
Fluorescence Microscopy
Definition
An optical system on the light microscope that uses ultraviolet light to excite dye-containing objects to fluoresce
Term
Fluorescent Antibody Technique
Definition
A diagnostic tool that uses fluorescent antibodies with the fluorescence microscope to identify an unknown organism
Term
Electron Microscope
Definition
an instrument that uses electrons and a system of electromagnetic lenses to produce a greatly magnified image of an object
Term
ultrastructure
Definition
the detailed structure of an cell, virus, or other object when viewed with the electron microscope
Term
Transmission Electron Microscope (TEM)
Definition
the type of electron microscope that allows electrons to pass through a thin section of the object, resulting in a detailed view of the object’s structure

Gives you more of a slice of a specimen
Term
Scanning Electron Microscope (SEM)
Definition
the type of electron microscope that allows electrons to scan across an object, generating a 3D image of the object

gives you a 3D appearance and overview of the surface
Term
Stage 1: Initial Attachment of Biofilms
Definition
Formation begins with the reversible attachement of free-floating bacteria to a surface
Term
Stage 2: Irreversible Attachment
Definition
Many pioneer cells anchor themselves irreversibly using cell adhesion structures as they secrete sticky, extracellular polysaccharides
Term
Stage 3: Maturation I
Definition
The first colonists faciliate the arrival of other cells by providing more diverse adhesion sites and beginning to build the polysaccharide matrix that holds the biofilm together. As nutrients accumulate, the cells start to divide.
Term
Stage 4: Maturation II
Definition
A fully mature biofilm is now established and may only change in shape and size. The matrix acts as a protective coating for the cells and is a barrier to chemicals, antibiotics, and other potentially toxic substances.
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