Microbiology Chapters 3, 4, 5

Term Definition
Bacteria Prokaryotic microorganisms typically having cell walls composed of peptidoglycan. In Woese's taxonomy, domain which includes all prokaryotic cells having bacterial rRNA sequences.
Archaea In Woese's taxonomy, domain that includes all prokaryotic cells having archaeal rRNA sequences.
Eucarya In Woese's taxonomy, domain that includes all eukaryotic cells.
Prokaryote Any unicellular microorganism that lacks a nucleus. Classification includes bacteria and archaea.
Eukaryote Any organism made up of cells containing a nucleus composed of genetic material surrounded by a distinct membrane. Classification includes animals, plants, algae, fungi, and protozoa.
Pathogenicity A microorganism's ability to cause disease.
Virulence A measure of pathogenicity.
Taxis Bacterial movement in response to stimuli.
Phototaxis Cell movement that occurs in response to chemical stimulus.
Chemotaxis Cell movement that occurs in response to chemical stimulus.
Positive taxis Movement toward a favorable stimulus.
Negative Taxis Movement away from an unfavorable stimulus
Peritrichous Term used to describe a cell having flagella projecting in all directions. eg; E. coli
Monotrichous Bacteria having multiple flagellum. eg; Vibrio cholerae
Lophotrichous Bacteria having multiple flagella located at the same spot, which act in concert to drive the bacteria in a single direction. eg; Helicobacter pylori
Conjugation pili Proteinaceous, rodlike structure extending from the surface of a cell, mediates conjunction.
Pilin A class of fibrous proteins that are found in pilus structures in bacteria.
Conjugation In genetics: method of horizontal gene transfer in which a bacterium containing a fertility plasmid forms a conjugation pilus that attaches and transfers plasmid genes to a recipient, in reproduction of ciliates: coupling of mating cells.
Conjugation Mediates the transfer of DNA from one cell to another.
Hans Christian Gram Invented the staining procedure called the gram stain.
Gram Stain Technique for staining microbial samples by applying a series of dyes that leave some microbes purple and others pink.
Peptidoglycan Large, interconnected polysaccharides composed of chains of two alternating sugars and crossbridges of amino acids. Main component of bacterial cell walls.
Mycolic Acid Long carbon chain waxy lipids found in the walls of cells in the genus Mycobacterium that makes them resistant to desiccation and staining with water-based dyes.
Lipid A (Endotoxin) The lipid component of lipopolysaccharide, which is released from dead Gram-negative bacterial cells and can trigger shock and other symptoms in human hosts.
Endotoxin (lipid A) Potentially fatal toxin released from the lipopolysaccharide layer of the outer membrane of the cell wall of dead and dying gram-negative bacteria
Phospholipid bilayer Two layered structure of a cell's membrane. Bacteria Cytoplasmic Membranes: structure.
Integral proteins Composed of phospholipids and associated proteins inserted among the phospholipids. Function as recognition proteins, enzymes, receptors, carriers, etc.
Peripheral proteins Composed of phospholipids and associated proteins loosely attached to the membrane on one side or the other. Function as recognition proteins, enzymes, receptors, carriers, etc.
Permeable Allowing substances through; allowing liquids, gases or magnetic fields to pass through.
Impermeable Not permitting passage through; not permitting the passage of liquid, gas or other fluid.
Selectively permeable In cell physiology, characteristic of a membrane that allows some substances to cross while preventing the crossing of others.
Concentration gradient (chemical gradient) The difference in concentration of a chemical on the two sides of a membrane.
Electrical Gradient Voltage across a membrane created by the electrical charges of the chemicals on either side.
Passive transport Movement of molecules across the cytoplasmic membrane by requiring no cell energy to be used by cell.
Active transport The movement of a substance against its electrochemical gradient via carrier proteins and requiring cell energy from ATP.
Diffusion The net movement of a chemical down its concentration gradient.
Osmosis The diffusion of water molecules across a semipermeable membrane.
Solution A homogeneous mixture composed of only one phase. The solution more or less takes on the characteristics of the solvent including its phase.
Solute A substance dissolved in another substance, known as a solvent. The solvent does the dissolving. The solvent is commonly the major fraction of the mixture.
Bacillus anthracis The slimy or mucoid appearance of a bacterial colony is usually evidence of capsule production. The capsule is often involved in virulence.
Streptococcus pneumonia Is in a similar situation with Bacillus anthracis.
Candida Albicans A diploid fungus that grows as yeast and filamentous cells and a casual agent of opportunistic oral and genital infections in humans. RNA binding proteins were recently discovered to play a role in instigating the hyphal formation & virulence.
Candida Albicans Have emerged as important causes of morbidity and mortality in immune-compromised patients. eg; AIDS, cancer chemotherapy, organ or bone marrow transplantation.
Candida Albicans biofilms may form where? On the surface of implantable medical devices. In addition, hospital acquired infections have become a cause of major health concerns. Normal in the mouth and gut without causing harmful effects.
What are common forms of Candida Albicans? thrush and yeast infections
Streptococcus mutans Biofilm construction by the oral bacterium which forms dental plaque. The biofilm layer is about 300-500 cells in thickness. The bacteria can break down the polysaccharide of the glycocalyx to glucose as a nutrient source, releasing lactic acid.
Treponema pallidum The causative agent of syphllis, which uses the corkscrew mechanism to help burrow through mucus and into host tissue. It is a spirochetes.
Neiserria gonorrhoeae Bacteria that use fimbria to adhear to one another, to hosts, and to substrates in environments.
Staphylococcus aureus Is coccus in shape. A bacterium that is a member of the firmicutes, and is frequently found in the human respiratory tract and on the skin.
Microbacterium Tuberculosis Mycobacterium spp. Also have mycolid acid, a wax that helps the cells survive desiccation (not stained with gram stain). Grape-cluster berry, is a facultative anerobi gram-positive coccal bacterium.
Bacillus subtilis Endospores form subterminally, have an internal network of protein fibers that have essential roles in cell division, protection, shape determination, etc. (cytoskeleton)
Clostridium Botulinum (food posioning) Endospores form terminally. Gram positive, rod-shaped bacterium that produces several toxins. The best known are its neurotoxins.
Total magnification a multiple of the magnification achieved by the objective and ocular lenses of a compound microscope.
Resolution The ability to distinguish between objects that are close together.
Refraction The bending of waves, such as light waves, when they pass from one substance to another.
Refractive Index (RI) a measure of light-bending ability of the medium. RI is actually a measure of the speed of light in a particular medium.
Immunofluorescence Uses a combination of fluorescent microscopy and fluorescent dyes bound to antibodies to identify organisms and cellular components.
Chromophore Colored portions of the stain.
Methylene blue The stain methylene blue chloride consists of the chromophore methylene blue (cation) and a chloride ion (anion).
Simple stain In microscopy, a stain composed of a single dye such as crystal violet.
Differential stain In microscopy, a stain using more than one dye so that different structures can be distinguished. The gram stain is the most commonly used.
Primary stain In staining, the initial dye, which colors all cells.
Decolorizing agent In a stain, a solution that washes the primary stain away.
Counterstain In a gram stain, red stain that provides contrasting color to the primary stain, causing gram-negative cells to appear pink.
Mordant In microscopy, a substance that binds to a dye, forming a complex with it and making it less soluble.
Negative stain (capsule stain) In microscopy,a substance that binds to a dye, forming a complex with it and making it less soluble.
Gram stain Technique for staining microbial samples by applying a series of dyes that leave some microbes purple and others pink.
Gram positive Prokaryotic cells having thick wall; in bacteria, composed of a thick layer of peptidoglycan containing teichoic acids; Gram-positive cells retain the crystal violet dye used in the gram-staining procedure, appearing purple.
Gram negative Generally, a prokaryotic call having a wall composed of a thin layer of wall material, an external membrane and a periplasmic space between; appears pink after the gram staining procedure.
Acid-fast In microscopy, a differential stain used to penetrate waxy cell walls. It is used to stain cells of mycobacterium and other species that have large amounts of wax in their cell walls and therefore do not stain with the gram stain.
Acid-fast stains retain what? the red carbol fuchsin because the acid can't penetrate through the waxy layer of the cells.
Non-acid fast Methylene blue (stains the non-acid fast cells blue. HCL + alcohol (removes the primary stain from the non-acid-fast cells).
Metabolism The sum of all chemical reactions, both anabolic and catabolic, within an organism.
Catabolism All of the decomposition reactions in an organism taken together.
Catabolic Reaction Break larger molecules into smaller products; released energy can then be stored as ATP. Catabolism breaks down proteins to amino acids.
Anabolic Reaction Synthesize large molecules from the smaller products of catabolism. Synthesis's amino acids to proteins.
Exergonic Reaction Released energy = outside
Endergonic Reaction Requires more energy than they release.
Electron A negatively charged subatomic particle.
Electron Donor A molecule that donates an electron.
Electron Acceptor A molecule that accepts an electron.
Reduction Reactions in which electrons are accepted. Since electrons are negatively charged, when they accept an electron they become even more negatively charged.
Oxidation Reactions in which electrons are donated. An electron donor is said to be oxidized because frequently their electrons are donated to oxygen atoms.
Redox Reaction(oxidation-reduction reaction) Any metabolic reaction involving the transfer of electrons from an electron donor to an electron acceptor.
Electron Carrier Any of various molecules that are capable of accepting one or two electrons from one molecule and donating them to another in the process.
Enzyme An organic catalyst. Grouped into functional classes based on the chemical reactions they catalyze. Enzyme changes its shape to bind to its substrate more tightly.
Substrate The molecule upon which an enzyme acts.
Activation Energy The amount of energy needed to trigger a chemical reaction.
Catalyst Increases the rate of a reaction without being consumed in the process.
Induced fit model Description of way in which an enzyme changes its shape slightly after binding to its substrate so as to bind it more tightly.
Metabolic pathway Have multiple reactions. Each chemical reaction in the pathway is catalyzed by a specific enzyme. Usually the end-product of one reaction serves as the substrate for the next reaction.
Feedback inhibition (negative feedback) Method of controlling the action of enzyme in which the end product of a series of reactions inhibits an enzyme in an earlier part of the pathway.
Allosteric Site A binding site on the surface of an enzyme other than the active site.
What are the three basic shapes of bacteria? Rod, sphere or corkscrew
Scanning electron microscope Focuses electrons across specimen surfaces. Can use whole organisms and get 3D images in great detail.
Transmission electron microscope Passes electrons through very thin slices of specimen.
Fluorescent Microscope Uses ultraviolet light; Molecules in specimen absorb energy from UV light and then radiate the energy back as longer, visible wavelengths. Some cells and molecules are naturally fluorescent.
Dark-Field Microscope Best for observing pale objects; light is directed toward an object at an angle, rather than from the bottom, increases contrast and enables observation or more details, very useful in spirochetes.
Compound Bright-Field Microscopes The microscope we use in the lab; Series of lenses for magnification, light passes through specimen into objective lens, have one or two ocular lenses. They also have condenser lens.
Simple Bright-Field Microscope Contains a single magnifying lens, Leeuwenhoek used a simple microscope to observe microorganisms.
Ocular lens Remagnifies the image formed by the objective lens.
Body Transmits the image from the objective lens to the ocular lens using prisms.
Arm The piece that you carry the microscope with that connects the eye piece to the stage and base.
Objective lenses Primary objective lenses
Stage Holds the microscope slide in position.
Condenser Focuses light through specimen
Diaphragm Controls the amount of light entering the condenser
Illuminator Light source.
Coarse Focusing knob Moves the stage up and down to focus the image.
Fine Focusing knob Fine focuses the image once you have coarse focused the image.
Base The bottom part of the microscope where the on/off switch, power cord and the illuminator is.
Why is immersion oil used for microscopy? Immersion oil used for microscopy has been formulate so that it has a refractive index identical to that of glass, no refraction of light when it passes from glass to oil or vise versa and oil immersion lens increases resolution.
Why is staining necessary for microscopy observation of many cells/tissue? To make microorganisms and their parts more visible; Stains increase the contrast between structures and between a specimen and its background.
Describe the protocol for preparing smears for staining. Before staining, a smear of the microorganism is made and air dried, then pass slide through flame to fix it.
Why must smears be thin? Thick smears cells crowd too close together and are difficult to stain properly
Why is heat fixation used? Ensures the microorganism are dead and are firmly attached to the slide. It also helps preserve the shape and size of the microorganisms.
Differentiate between simple stains and differential stains. Simple stains are used to increase contrast and differential stains used more than one dye to stain different cells or structures, which can then be differentiated from each other based on color.
Give an example of differential gram stains. E. coli
Give an example of differetial acid-fast stain. Mycobacterium
Give an example of differential endospores stain. Bacillus anthracie
Give an example of simple stains. Staphylococcus aureus
Give an example of special stains. Nigrosin
How are gram stains interpreted? The gram stain differentiates between purple-staining gram stain bacteria and pink staining gram negative cells.
Describe the acid-fast stain procedure. Carbol fuchsin is applied with heat, then decolorizing agent (HCL + alcohol) is applied, then counterstain (methylene blue stain) is applied.
Describe how results of acid-fast stain are interpreted. HCL + alcohol removes the primary stain from the non-acid fast cells and the counterstain(methelyen blue) stains the non-acid fast cells blue. Acid-fast cells retain the red carbol fuchsin because the acid can't penetrate the waxy layer on the cell
Describe in detail the gram stain procedure. apply crystal violet and leave on for 60s then rinse off, apply iodine and leave on for 60s then wash of with water, apply alcohol was 10s then rinse off with water, apply safranin and leave on for 30s, then wash off with water and blot off excess water
How is gram stain results interpreted? The gram stain differentiates between purple-staining gram stain bacteria and pink-staining gram negative cell.
Nucleus An internal membrane-enclosed region that contains the genetic material.
Nucleiod A region in bacteria which has a single circular dsDNA organized as chromosome.
Glycocalyx Gelatinous, sticky substance surrounding the outside of the cell. Composed mainly of polysaccharides (and some polypeptides).
Capsule A type of glycocalyx; composed of organized repeating units or organic chemicals. Ridgid and firmly attached to cell surface which may prevent bacteria from being recognized and destroyed.
What is the function of capsules? Help protect bacteria from engulfment by protozoa WBC's. May also protect them from anitmicrobial agents.
Slime layer A type of glycocalyx that is loosely attached to cell surfaces, water soluble, with a sticky layer that allows prokaryotes to attach to surfaces.
What is the function of a slime layer? Attach bacteria to a surface or substrate. These bacteria attach to a surface, produce slime, divide and produce microcolonies within the slime layer and construct a biofilm.
Biofilm Organisms that have divided and expanded into microcolonies and have created a proctective barrier.
Flagella Long structures that extend beyond cell surfaces, composed of protein subunits.
What is the function of a flagella? They are responsible for movement, rotation propels bacterium through environment, bacterial movement in response to stimuli.
Endoflagella Special flagella of spirochetes that spiral tightly around the cell instead of protruding into the environment.
Fimbria Rod-like proteinaceous extensions with sticky, bristle like projections, used by bacteria to adhere to one another, to hosts, and to substrate in environment. Shorter than flagella.
Pili (conjugation pili) rod-like proteinaceous extension tubules composed of pilin, longer than fimbriae but shorter than glagella. Bacteria typically only have one or two per cell. Mediate the transfer of DNA from one cell to another.
Cell Wall Provides structure to cells, prtects cell from osmotic forces, assist some cells in attaching to other cells, gives bacterial cells characteristic shapes.
Cell(cytoplasmic) membrane (phospholipid bilayer) Composed of phospholipids and associated proteins. The integral proteins and peripheral proteins functions as recognition proteins, enzymes, receptors, carriers, etc.
Outer membrane Bilayer outside the peptidoglycan that contains phospholipids, proteins and lipopolysaccharides
Cystosol The fluid portion of the cytoplasm where a part of the cell metabolism occurs. No single function, is instead the part of the cell where a variety of processes take place.
Cytoplasm 70-80% water; some ions, carbohydrates, proteins lipids and wastes. Site for cell's biochemical activities and have ribosomes.
Ribosomes Protein synthesis; Bacterial ribosomes (70S) are composed of two subunits. A smaller 30S subunit and a larger 50S subunit. Riboomes from prokaryotes and eukaryotes have significantly different structures and RNA sequences.
Bacterial chromosome A singular circular double stranded dsDNA (DNA organized as a chromosome).
Plasmid Small DNA circles which replicate independently of the chromosome and can exist in the cell as one copy or many copies. They carry genes to encode toxins or proteins that promote the transfer of the plasmid to other cells.
Inclusions Cytoplasm of bacteria have deposits that act as storage structures for nutrients.
Endospores Unique structures produced by some bacteria that are defensive strategy against unfavorable conditions. A single bacterial cell transforms into an endospore, which then germinates to grow into a single bacterial cell.
Cytoskeleton An internal network of protein fibers that has essential roles in cell division, protection, shape determination, etc.
Prokaryotes Are bacteria and archeae. Have a simple structure, lack a nucleus but instead have a nucleoid, lack internal structures bound with phospholipid membrane, and are smaller than eukaryote cells.
Eukaryotes Are organisms such as fungi, protozoa, algae, animals and plants. They have a more complex structure, a nucleus and internal membrane-bound organelles; they are larger than prokaryotes.
What is the clinical significance of biofilms? Believed to be caused by the introduction of foreign organisms, mainly bacteria. Once on the surface these organisms secrete polysaccharides that allow them to anchor themselves on the surface; once attached they create a protective barrier.
Gram Positive bacterial cell walls have what? thick layer of peptidoglycan (up to 90% of the cell wall), also contain teichoic acids and/or lipoteichoic acids which provide additional rigidity; They appear purple with gram staining procedures.
Gram Negative bacterial cell walls have what? thin layer of peptidoglycan, the bilayer (outer membrane) outside the peptidoglycan contains phospholipids, proteins and lipopolysaccharies; They appear pink with gram staining procedures.

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