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ecotypes

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Subgroups of a species that have special characteristics to survive in their ecological surroundings

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Biosphere

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that part of the earth-including the air, soil, and water- where life occurs

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Homeostasis

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the ability to adjust yet maintain a relatively steady internal state
-factors include of external environment: temperature, sunlight, or toxic chemicals

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Biofilms

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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

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Quorum Sensing

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involves the ability of bacteria to sense their numbers, and then communicate and coordinate behavior, including gene expression, via signaling molecules

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Bioremediation

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uses microorganisms to remove or clean up chemically contaminated environments like oil spills, or toxic waste sites

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Cell theory

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The tenent that all organisms are made of cells and arise from preexisting cells

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Chromosomes

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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

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Cell membrane

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A thin bilayer of phosopholipids and proteins that surrounds the prokaryotic cell cytoplasm

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Plasma Membrane

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the phosopholipid bilayer with proteins that surrounds the eukaryotic cell cytoplasm

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Metabolism

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all the chemical reactions occurring in an organisms 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 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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a cellular structure made of RNA and protein that participates in protein synthesis based on the genetic instructions it receives from the DNA

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Organelles

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a specialized compartment in cells that has a particular function

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Endomembrane System

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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 cells cytoplasm responsible for the synthesis and transport of materials from the cell

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Rough ER

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flat membranes to which ribosomes are attached to

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Smooth ER

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tube-like membranes without ribosomes

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Golgi Appartatus

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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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Vesicles

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membrane-enclosed spheres involved with secretion and storage

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Lysosomes

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A membrane-enclosed compartment in many eukaryotic cells that contains enzymes to degrade or digest substances

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Microcompartments

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A region in some bacterial cells surrounded by a protein shell

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Cellular Respiration

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the process of converting chemical energy into cellular energy in the form of ATP

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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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A biochemical process in which light energy is converted to chemical energy which is then used for carbohydrate synthesis

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Chloroplasts

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

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Cytoskeleton

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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

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Centrosome

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the microtubule-organizing center of a eukaryotic cell

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Flagella

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A long, hair-like appendage-composed of protein and responsible for motion in microorganisms; found in some bacterial, archaeal, protozoal , algal, and fungal cells

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Cilia

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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

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Diffusion

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the movement of a substance from where it is in a higher concentration to where it is in a lower concentration

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Osmosis

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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

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Cell Wall

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A carbohydrate-containing structure surrounding fungal, algal, and most bacterial and archaeal cells

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Carolus Linnaeus

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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

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Ernst Haeckel

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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

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Edouard Chatton

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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

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Robert Whitaker

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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

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Carl Woese

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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

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Systematics

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studying the diversity of life and its evolutionary relationships

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Systematic Biologists- Systematists

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identify, describe, name, and classify organisms and organize their observations within a framework that shows taxonomic relationships

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Taxonomy

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the science dealing with the systematized arrangements of related living things in categories

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Domain

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1.) the most inclusive taxonomic level of classification; consists of the Archaea, Bacteria, and Eukarya

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Phylogeny

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the evolutionary history of a species or group of species

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Phylogenetic trees

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identify inferred relationships among species

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Three Domain System

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the classification scheme placing all living organisms into one of three groups based in part on ribosomal RNA sequences

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Archaea

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The domain of living organisms that excludes the Bacteria and Eukarya

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Eukarya

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The domain of living organisms that includes all organisms not classified as Archaea or Bacteria

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Eukarya

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the taxonomic domain encompassing all eukaryotic organisms

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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 constitute a family

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Specific Epithet

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The second of the two scientific names for a species

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Species

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the fundamental rank in the classification system of organisms

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Family

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A category of related organisms consisting of one or more genera

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Order

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A category of related organisms consisting of one or more families

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Class

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a category of related organisms consisting of one or more orders

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Phylum

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A category of related organisms consisting of one or more classes

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Biotypes

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Populations or groups of individuals having the same genetic constitution (genotype)

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David Hendricks Bergey

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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

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Physical Characteristics

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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

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Biochemical Tests

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fermentation of carbohydrates, the use of a specific substrate, and the production of specific products or waste products,

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Serological Tests

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microorganisms are antigenic, meaning they cannot trigger the production of antibodies

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Antibodies

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proteins produced by the immune system in response to a specific chemical configuration (antigen)

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Antisera

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solutions of collected antibodies

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Molecular Taxonomy

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the systemized arrangement of related organisms base don molecular characteristics, such as ribosomal DNA nucleotide sequences

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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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Micrometer (µm)

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common unit of measuring is the equivalent to a millionth of a meter (10-6)

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Nanometer (nm)

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common unit of measuring is the equivalent to a billionth of a meter (10-9)

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Light/Compound Microscope

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An instrument that uses visible light and a system of glass lenses to produce a magnified image of an object

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Bright-field Microscopy

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an instrument that magnifies an object by passing visible light directly through the lenses and object

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Magnification

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the increase in the apparent size of the specimen being observed

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Total Magnification

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the magnification of the ocular multiplied by the magnification of the objective lens being used

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Resolving Power

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the numerical value of a lens system indicating the size of the smallest object that can be seen clearly when using that system

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Index of Refraction

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A measure of the light bending ability of a medium through which light passes

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Simple Stain Technique

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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

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Heat Fixation

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the use of warm temperature to prepare microorganisms for staining and viewing with the light microscope

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Basic Dye

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A positively charged colored substance in solution that is used to stain cells

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Negative Stain Techinque

answer

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

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Acidic Dye

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A negatively charged colored substance in solution that is used to stain an area around cells

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Gram Stain Technique

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A staining procedure used to identify bacterial cells are gram negative or gram positive

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Differential Staining Procedure

answer

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

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Step 1 of Gram Staining

answer

stained with crystal violet rinsed then

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Step 2 of Gram Staining

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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,

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Step 3 of Gram Staining

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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

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Step 4 of Gram Staining

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uses safranin, a red cationic dye, to counterstain the orange-red color

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Gram Negative

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Referring to a bacterial cell that stains red after gram staining (more susceptible to tetracycline, more complex cells wells)

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Gram Positive

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referring to a bacterial cell that stains purple after gram staining (more susceptible to penicillin)

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Toxins

answer

chemical substances that are poisonous (both gram positive ad gram negative bacterial species can produce different types)

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Acid-Fast Techniques

answer

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)

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Phase-Contrast Microscopy

answer

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

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Dark Field Microscopy

answer

an optical system on the light microscope that scatters light such that the specimen appears white on a black background

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Fluorescence Microscopy

answer

An optical system on the light microscope that uses ultraviolet light to excite dye-containing objects to fluoresce

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Fluorescent Antibody Technique

answer

A diagnostic tool that uses fluorescent antibodies with the fluorescence microscope to identify an unknown organism

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Electron Microscope

answer

an instrument that uses electrons and a system of electromagnetic lenses to produce a greatly magnified image of an object

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ultrastructure

answer

the detailed structure of an cell, virus, or other object when viewed with the electron microscope

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Transmission Electron Microscope (TEM)

answer

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

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Scanning Electron Microscope (SEM)

answer

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

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Stage 1: Initial Attachment of Biofilms

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Formation begins with the reversible attachement of free-floating bacteria to a surface

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Stage 2: Irreversible Attachment

answer

Many pioneer cells anchor themselves irreversibly using cell adhesion structures as they secrete sticky, extracellular polysaccharides

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Stage 3: Maturation I

answer

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.

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Stage 4: Maturation II

answer

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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