Microbiology Study Guide Chpt 1-6

Microbiology Study Guide Chapters 1-6
Chapter 1 Main Themes of Microbiology Microorganisms Most are not Pathogens Prokaryotic-no nucleus or organelles Very simplistic—like bacteria Eukaryotic-has nucleus and organelles like mitochondria Includes fungus, and animals Acellular-not even a complete cell Includes viruses and prions like those that cause Mad Cow disease Six main types of microorganisms Bacterium (prokaryotic) Fungus (eukaryotic) Algae (eukaryotic) Virus (acellular) Protozoan (eukaryotic) Helminth (eukaryotic) Most common infectious diseases worldwide Respiratory #1 AIDS #2 Diarrheal #3 Antonie van Leeuwenhoek Fashioned together a primitive microscope—he was the first to observe microorganisms Scientific method-an experimental system that answered questions objectively Hypothesis- tentative explanation to account for what has been observed or measured; predicts specific explanations that may or may not be borne out by testing; best written as a statement Experimentation-outlines particular events predicted by hypothesis, then sets up experiments to test for the events Results-support or refute hypothesis (you never prove anything), some part of hypothesis may be discarded or modified to fit results Conclusion or theory-repeated investigation of results History of Microbiology Spores and Sterilization Some microbes in dust and air were resistant to high heat—later identified as spores The term “sterile” was introduced which meant completely eliminating all life forms from objects and materials Spontaneous generation Early belief that some forms of life could arise from vital forces present in nonliving or decomposing matter (Ex. Flies from manure, etc) Louis Pasteur-showed microbes caused fermentation and spoilage, and disproved spontaneous generation by use of swan neck flasks in his experiments Aseptic technique Joseph Lister (think listerene)-introduced aseptic technique in order to reduce microbes in a medical setting and prevent wound infections Introduced using disinfectant on hands prior to surgery Germ theory of disease Many diseases are caused by the growth of microbes in the body and not by sins, bad character, or poverty Koch’s Postulates-formed by Robert Koch which verified the Germ Theory; still used today and links microbes with specific diseases Microbes present in samples of diseased animals Grow organism in pure culture Inject healthy animal with cultured cells Animal develops same disease Taxonomy-system for organizing, classifying & naming living things Levels of classification-Do kings play chess or find games silly? Domain-largest; there are three Bacteria-prokaryotic, true bacteria, has peptidoglycan cell wall Archaea-prokaryotic, odd bacteria that live in extreme environments, high salt, heat, etc. Eukarya-eukaryotic, has nucleus and organelles Kingdom Phylum or Division Class Order Family Genus-Bacillus, always capitalized, always italicized or underlined Species-most specific; subtilis, always lowercase, always italicized or underlined
Chapter 2 Chemistry Atoms-What are subatomic particles? Proton-positively charged; in nucleus Neutron-neutrally charged; in nucleus Electron-negatively charged; in outer shell; electron shell=electron cloud Atomic number=no. of protons Atomic Mass number/Mass number=number of protons and neutrons Atomic Mass=mass of subatomic particles at rest Elements & Stuff Element-varied subatomic particles (atomic number and mass) make-up specific elements as they come together; very pure; elements are important for structure and function of the cell Molecule-combination of 2 or more elements (Ex. H2) held together by chemical bonds (covalent) Inorganic-carbon OR hydrogen is present (Ex. CO2, H2) Organic- carbon AND hydrogen is present (Ex. CH3) Compound-combination of 2 or more different elements (Ex. H2O); chemically combined Isotope-a version of an element that is virtually identical in all chemical properties to another version except that their atoms have slightly different atomic masses (differ in the number of neutrons)---so some have unstable nuclei that spontaneously release energy in the form of radiation Chemical bonds Covalent-shares electrons; typically hydrophobic Polarity-can occur with different types of covalent bonding (Ex. H2O) Polar has a positive + and negative – pole, nonpolar electrons are evenly distributed Ionic –electron transfer among atoms to complement valence; hydrophilic; Ex.-sodium chloride Ionic bonding molecules breakup (ionization) when dissolved in a solvent like water producing separate positive and negative particles Hydrogen-weakest bond; formed between hydrogen covalently bound to a molecule and an oxygen or nitrogen atom on the same or different molecule…results from polar covalent bonds; Ex. DNA-placed right between strands of double helix Best example are water molecules pH scale-measurement of the H+ ion concentration Acidic-excess H+ ions in solution Basic-excess OH- ions in solution (hydroxide) Neutral-equal amounts of H+ and OH- ions Macromolecules Carbohydrates-sugars, polysaccharides Monosaccharides-have 6 carbons; include glucose, galactose, fructose Disaccharides- maltose, lactose, sucrose Polysaccharides-several sugars bonded together by glycosidic bonds Water is released (dehydration) after the bond is formed; therefore the forming of polysaccharides is called dehydration synthesis and is anabolic Hydrolysis-is the catabolic breaking down of polysaccharides into more basic forms Peptidoglycan-is an example of polysaccharide; it is a combination of a protein component and sugar Lipids-triglycerides, phospholipids, steroids Triglyceride-important storage lipid (Ex. Fats and oils) Glycerol backbone + 3 fatty acids (hydrocarbon chains)-bound by an ester bond Phospholipids-serve as a major structural component of cell membranes Phosphate head + glycerol neck + 2 fatty acid tails The head is polar and hydrophilic and therefore loves water The tail is nonpolar and hydrophobic and hates water Phospholipids in a single layer it forms a circle Bilayer=heads on the outside, tails inside Proteins-consist of a series of amino acids (Ex. Peptides, polypeptides) The predominant organic molecule in cells Peptide=short chains of amino acids Polypeptides=usually more than 20 amino acids Protein=more than 50 amino acids (Ex. Enzymes, antibodies) Peptide bond forms between the amino group on one amino acid and the carboxyl group on another amino acid Shapes of proteins Primary-chain of amino acids stuck together by peptide bonds Secondary structure-helix or pleated shape Tertiary structure-helix and pleated shape Quaternary structure-major folding into 3-D shape; conformational changes (binding site shapes can change positions) Nucleic acids-are polymers of repeating units called nucleotides (building blocks of nucleic acids) DNA-deoxyribonucleic acid; double stranded; contains genetic information and transfers it to RNA Rails consist of a phosphate covalently bonded with a pentose sugar (5 carbons) Rungs consist of nitrogen bases that are hydrogen bonded (2 bonds hold together the adenine and thymine; 3 bonds hold together the guanine and cytosine) Nucleoside-the combination of the pentose sugar and nitrogen base (it is an incomplete nucleotide) Purines-nitrogen bases that are formed in 2 rings; adenine and guanine Pyrimidines-nitrogen bases that are formed in 3 rings; thymine, cytosine, and uracil (only found in RNA) The sides of the DNA strand are anti-parallel The DNA configuration is a double helix DNA serves as a template for the synthesis of new DNA, mRNA, tRNA, and rRNA RNA-ribonucleic acid Single stranded Translates the DNA information into proteins (transcription)
Chapter 3 The Microscope Methods of Culturing Microorganisms Five basic techniques Inoculate-introduce a tiny sample into a container of medium Incubate-let grow (we use 37°C), varied temperatures, atmospheric states Isolation-take one colony and put it on a plate by itself; 3 basic methods for isolating; using sterilized tools (121°C, 15 minutes, 15 psi) Streak plate-dilute manually Loop dilution or pour plate-dilute in a series of tubes with final being poured onto plate Spread plate-small volume of liquid, diluted sample is put on surface of a medium and spread evenly with sterile “hockey stick” Inspection-staining such as simple stain, wet mount (giggle); most colonies are heat fixed Identification-look at characteristics via microscope Media classified according to 3 properties Physical state Liquid media-0% agar; termed broths, milks and infusions; we use tryptic soy broth Semi-solid media-less than 1% of agar; used for motility testing; if cloudy it shows motility Solid-1%-5% of agar; enables the formation of discrete colonies; we use TSA Chemical content Synthetic media-exact chemical formula (Ex. TSA) Nonsynthetic or complex media-contain ingredients that are not chemically defined (Ex. Blood or chocolate agar) Functional types of growth media Minimal-like TSA plate Enriched media/complex-like blood agar Selective media-selects a certain group to grow Differential media-allows multiple types but designed to display visible differences Selective and Differential Examples of differential media Blood agar-differentiates between types of hemolysis by different species of Streptococcus MSA (mannitol salt agar)-diff. between species of Staphylcoccus MacConkey agar-diff. between bacteria that ferment lactose (lowering the pH) from those that do not Urea broth-diff. between bacteria that hydrolyze urea to ammonia SIM (sulfur indole motility)-diff. between H2S gas producers from nonproducers TSIA (triple-sugar iron agar)-diff. between fermentation of sugars, H2S production Microscopy-Properties of Light Electromagnetic waves-visible light (400-500 provide best resolution) is between 400-700nm Reflection-light hits an opaque object-rays bounce off object Transmission-light rays pass through the object; must be transparent Absorption-some light does not pass through; certain wavelengths can be absorbed Diffraction-light rays bend when they pass near an opaque object Refraction-bending of light Refractive Index-determines the speed of light through a medium Magnification-enlargement of an image Contrast-property of specimen (whether or not specimen absorbs light) Resolution-ability to distinguish between 2 points; measured as resolving power; dependent upon: Size of objective lens Wavelength of light Refractive index of material between objective lens and specimen (Ex. Oil=1.5 vs. Air=1.0) Microscopes Optical all have a maximum magnification of 2000X Brightfield-most common; use live or preserved specimens; best with stains Darkfield-use with live, unstained specimens; backround is dark, specimen is light Phase-Contrast-observe live specimens; view internal cellular detail Flourescent-uses fluorescence stain or dye; diagnostic tool Confocal-flourescence or unstained specimen images are combined to form a 3-D image Electron microscopes-very high magnification (100,000X) TEM (Transmission electron microscope)-view internal structures of cells via a beam of electrons are transmitted through specimen; can view viruses SEM (Scanning electron microscope)-compiles 3-D images Stains-used after microorganism are fixed (killed) usually by heat fixation; can use chemicals like formaldehyde Positive stains-basic dyes (positive charge) that bind negative charge cells Dye binds to specimen Ex. Include crystal violet, hematoxylin, safranin Subtypes of positive stains Simple-uses one dye Differential-uses two different colored dyes (primary and counterstain); includes Gram stains, Acid-fast stains & Spore stains Special/Structural stains-includes Capsule, Flagella, & Spore Stains

Negative stains-acidic dyes (negative charge) that bind to the backround Acidic dyes (eosin) stain positive structures like collagen There are a few types of negative stains: Capsule & Spore use India ink
Chapter 4 Prokaryotes Methods to Classify Prokaryotes Morphology-what are the three basic bacterial cell morphologies (shapes)? Cocci (Coccus)-spherical shaped Diplococcus-pair of cocci Streptococcus-chain of cocci Staphylcoccus-cluster of cocci Bacilli (Bacillus)-rod shaped Diplobacillus-pair of rods Streptobacillus-chain of rods Spirilla-spiral shaped Vibrio-comma shaped Spirochetes-corkscrew shaped Other-square or star shaped Biochemistry & Physiology Gram staining tells you something about the cell wall (physiology) Biochemistry example: Can it ferment lactose? Is it motile? Serology-does your body form antibodies to it? If so, to which parts of it? Comparing genomes-we’ll attack that later Cell Structure of Prokaryotes-from the outermost to the innermost Appendages Pili-straight hair-like projections of the cell A pilus is an elongate, rigid tubular structure made of a special protein called pilin Typically not involved with movement, used for attachment This attachment could be for conjugation, or mating Sexual conjugation-F or sex pilus; is for the transfer of DNA Fimbriae-small, bristlelike fibers sprouting off the surface Primary function is for attachment—they have an inherent tendency to stick to each other and to surfaces Responsible for biofilms Flagella-bacterial propeller Three main parts-basal body (the point of attachment), the hook (the part that rotates 360°), and the filament (a helical structure composed of proteins) Chemically “taste” the environment; respond to food or toxins; then “get there” by chemotaxis Arrangement of flagella Polar arrangement-the flagella are attached to one or both ends of cell; include monotrichous lophotrichous and amphitrichous Peritrichous-flagella are dispersed randomly over the surface of the cell Movement of cell Chemotaxis-sense chemicals “on the move for food” Phototaxis-sense light intensity “walk into the light” Aerotaxis-seek out oxygen Magnetotaxis-move along magnetic lines Bacterial Surface Coating, or Glycocalyx (outermost layer) Coating of repeating polysaccharide units, proteins, or both Some bacteria are covered with a loose shield called a slime layer Easily washed off Slimy or gummy substance Protects bacteria from loss of water and nutrients Helps it adhere to surfaces=creates biofilm A glycocalyx is called a capsule when it is bound more tightly to the cell than a slime layer and it is denser and thicker Protection against drying out and against phagocytes Encapsulated bacteria generally have greater pathogenicity or are more virulent d/t blocking the mechanisms that phagocytes use to attach to and engulf bacteria The cell envelope: the boundary layer of bacteria-composed of 2 or 3 basic layers Outer membrane-only Gram negative bacteria has this membrane Contains specialized types of polysaccharides and proteins The uppermost layer of the OM contains lipopolysaccharide (LPS); the lipid portion of LPS has been referred to as endotoxin because it stimulates fever and shock in gram-negative infections The innermost layer of the OM is a phospholipid layer anchored to the cell wall Cell wall-made from peptidoglycan Provides shape; helps withstand turgor pressure Made up of chains of alternating polysaccharides NAG & NAM cross-linked with peptides Gram-positive cell walls are thick; also contains teichoic acid and lipoteichoic acid—looks like a thick slice of cheese on a cracker (the cell wall plus the cell membrane); stain purple Gram-negative cells walls are thinner and sandwiched between the outer membrane and the cell membrane—looks like a nutter butter; stain pink Cell membrane (cytoplasmic membrane) Holds in the cytoplasm; regulates passage into and out of the cell (selectively permeable) Made of phospholipid bilayer; fluid like a waterbed Cytoplasm Primarily made of water This is where metabolism takes place Does not contain nucleus—the region where the DNA hangs out is called a nucleoid Contains ribosomes-the site of protein synthesis; they are generally a different size than that of eukaryotes-- that is why antibiotics can be made to target ribosomes of bacteria to interrupt protein synthesis and not effect our own ribosomes Bacterial Division Divide by binary fission If divide along the same plane it will form chains (Diplococcus, Streptococcus) If it divides along 3 planes irregularly it will form clusters (Staphylcoccus) Sporulation Occurs when conditions are unfavorable for growth like extreme heat, cold, dehydration, presence of toxic chemicals or radiation Makes for long term survival—spores can survive for hundreds of years Process: Unequal cell division begins Cytoplasm divides into the vegetative (mommy) cell and the forespore (baby spore)—each containing DNA Thick protective wall forms around baby spore made up of peptidoglycan that is different than the vegetative cell; it is keratinlike as to its hardness The spore contains all essential cell components The vegetative cell lyses and releases endospore The endospore then germinates when conditions become more favorable Prokaryotic Taxonomy-2 main domains Archea and Bacteria Archea-2 phyla Bacteria-23 phyla B12 Proteobacteria-largest phylum of the 23; contains 1300+ species; includes: Class: Alphaproteobacteria Environmentally important class—some bacteria like Rhizobium and Bradyrhizobium have symbiotic relationships with plants by supplying usable nitrogen to the plant Class: Betaproteobacteria Bordetella B. pertussis-causes whooping cough Neisseria N. meningitides-causes meningitis N gonorrhea- causes gonorrhea Class: Gammaproteobacteria-there are 13 orders in this class and include: Enterobacterials Salmonella typhi Shigella spp.(multiple species) Yersinia pestis-causes “the plague” Escherichia coli Vibrionales-curved rods Vibrio cholera-produces cholera Pseudomonales Pseudomonas aeruginosa-produces skin infections Class: Epsilonproteobacteria Campylobacter C. jejuni-diarrheal illness Helicobacter H. pylori-gastric ulcers B13 Firmicutes-this pylum includes gram-positive bacilli and gram-positive cocci Clostridia-spore-forming rods that are gram-positive and strict anaerobes C. botulinum-botulism C. tetani-tetanus C. perfringens-gas gangrene and food poisoning Bacilli-spore-forming rods that are gram-positive and facultative (meaning they can live with or without oxygen) B. anthracis-anthrax Gram-positive cocci Staphylcoccus-facultative anaerobes Streptococcus-produce lactic acid B14 Actinobacteria-oddly shaped bacteria Bifidobacterium genus-irregularly shaped cells Corynebacterium diptheriae-diptheria Mycobacterium genus-acid fast Causes tuberculosis and Hansen’s disease (leprosy) B16 Chlamydiae-obligate intracellular parasites (require hosts for growth) Complicated reproductive cycle Elementary body enters host cell Elementary bodies change into reticulate bodies Reticulate bodies multiply Reticulate bodies change back into elementary bodies Host cell lyses releasing elementary bodies-Chlamydiospore-spreads infection Chlamydia trachomatis-causes chlamydia B17 Spirochaetes-corkscrew motility, causes of human diseases like: Treponema pallidum-syphilis Borrelia burgdorferi-Lyme’s disease B20 Bacteroidetes-purple nonsulfur bacteria Common in the mouth and intestinal tract Involved in intraabdominal abscesses

Chapter 5 The Eukaryotes Cell Structure of Eukaryotic cells Appendages Flagella-made up of 9 pair of microtubules surrounding a single central pair For motility Wave-like motion (not propeller) Cilia-similar function as flagella Shorter and more numerous Glycocalyx-complex outer layer Made up of polysaccharides and appears as a network of fibers, a slime layer, or a capsule much like the glycocalyx of prokaryotes Contributes to protection, adherence of cells to surfaces, and reception of signals from other cells Cell wall-animal cells don’t have a cell wall Fungi and algae have cell walls Composition varies-chitin, mixed glycans, cellulose Offers rigidity and provides structural support and shape Cell membrane-bilayer of phospholipids in which protein molecules are embedded Also contain sterols (like cholesterol) to strengthen which is important because generally there is no cell wall Selectively semipermeable Cytoplasmic streaming-means for which nutrients move throughout the cell; streaming allows amoebae and slime molds (fungus) to move by psuedopods or “false feet” Membrane Transport Endocytosis-brings stuff into the cell Phagocytosis-engulfing cells Pinocytosis-cell drinking Exocytosis-exports stuff out of cell Nucleus-contains the DNA Nuclear membrane Lipid bilayer surrounding nucleus Nuclear pores-for passage of materials Nucleoplasm-gelatinous matrix of nucleus Nucleolus-dense masses of RNA and proteins Endoplasmic reticulum (ER)-Assembly Factory Rough ER-has ribosomes ; for protein synthesis Smooth ER-no ribosomes; for lipid synthesis Golgi Apparatus-UPS Stacks of flattened membrane sacs where molecules are modified (packaged) into: Vesicles-transport from ER to Golgi; from Golgi to final destination (in and out of cell) Mitochondria-powerhouses Double membrane system Outer membrane-separate from rest of cell Inner membrane-highly folded called cristae-holds enzymes and electron carriers of aerobic respiration Contains circular strands of DNA, divide independently of the cell Fungi General characteristics Heterotrophic-fungi use organic compounds as carbon source Nonphototrophic-does not use light as energy Absorptive-take up nutrients in a solution Saprophytic (most fungi)-decompose organic matter to obtain nutrients Ecology-where do fungi hang out? Acidic environments Where there are high concentrations of salt or sugar Can grow at temperatures below freezing Can grow with miniscule amounts of nutrients Aerobic (most) Morphology-two basic morphological types: yeasts and hyphae Yeast-round or oval shape, single cells Grows swellings on its surface called buds, which then becomes a separate cell Grows at body temperature Numerous yeasts are pathogenic –Ex. Candida albicans Dimorphism-means two shapes; switch between growing as a yeast or a mold-yeast grows at body temperature, mold at room temperature Ex.-Histoplasma capsulatum-causes histoplamosis Hyphae-individual filaments; Mycelium-connected hyphae=molds Lower fungi- if walls are undivided (coenocytic) Higher fungi-if mycelia appear to be divided by a septa-incomplete divisions Can also have a fleshy body (thallus)-fruiting structures, mushrooms Reproduction-perfect fungi produce sexual and asexual spores, imperfect fungi produce only asexual spores Asexual Occurs by elongation and fragmentation of hyphae if a mold Occurs by budding or division of cells if a yeast 2 types of asexual spores-Sporangiospores-produced within spores then released & Conidiospores-borne naked, free spores Sexual-sexual fusion of gametes Perfect Fungi-sub Kingdom Amastigomycota-4 divisions (3 listed) Zygomycota (usually hyphae-not divided by septa-thus a lower fungi) Terrestrial molds Includes Rhizopus nigricans-black mold on stale bread Causes zygomycoses Ascomycota (divided by septa-thus a higher mold) Ascospores-sexually produced spores Ex. Histoplasma, Penicillium, Saccharomyces (produces the alcohol in beer) Basidiomycota (incomplete septa-thus a higher mold) Basidiospores-sexual spores Conidia-asexual spores Mushrooms Cryptococcus neoformans Imperfect fungi Deuteromycetes “imperfect” fungi-lack sexual stage No sexual spores, but conidiospores Ex. Aspergillus, Stachybotrys (black molds that covers walls), Candida Human disease with fungus Mycoses Superficial mycoses Cutaneous mycoses Subcutaneous mycoses Systemic mycoses Some produce antimicrobial agents Penicillium Some produce toxins Aflatoxin-Aspergillus spp. Black mold toxin (sick building syndrome)-Stachybotrys chartaum Protists-single-celled or colonial eukaryotes that are not plant, animal, or fungi Algae There are two associated with human pathogologies Overgrowth of a certain algae imparts a brilliant red color to the water which is referred to as “red tide”. When the intertidal animals feed, their bodies accumulate toxins. When humans eat these shellfish they become sick-marked by severe neurological symptoms which can be fatal Prototheca-rare cause of wound infections; associated with bursitis Slime molds Protozoa-four groups-based on motility The Mastigophora (Flagellates)-has flagella Trypanosoma brucei-causes sleeping sickness Giardia lamblia-causes diarrhea The Sarcodina (Amoebas)-have pseudopods which are organelles of locomotion and feeding (Clumpy feet) Entamoeba histolytica-amoebic dysentery Naegleria fowleri-amoebic encephalitis Sporozoa-nonmotile; all are parasitic; can be sexual or asexual reproducers Plasmodium spp. –causes Malaria; has three forms 1) Trophozoite-multiply form; 2)Sporozoite-infectious form; 3) merozoite-infects RBCs Toxoplasma gondii-causes toxoplasmosis Ciliates-are ciliated-have 2 nuclei The bigger nuclei (macro) is for growth and cell division The smaller nuclei (micro) is for sexual reproduction Helminths Flatworms Tapeworms-made up of the scolex (the head of sorts with suckers on it for attachment), proglottids (body segments), and the germinal center (where new segments are made) Flukes-have flat ovoid bodies Roundworms-have an elongate, cylindrical, unsegmented body Trichinella spiralis-causes trichinosis Arthropod Vectors-critters that transmit disease Mechanical vector-external transmission—like when a fly lands on your picnic chicken and poops on it Biological vector-internal transmission—part of the microorganism’s life cycle Ticks-carry bacterium that causes Rocky Mountain Spotted Fever Lice-transmit disease and cause infestation Reduviid bug-causes Chagas’ disease Mosquito-transmits Malaria Flies-cause gastric ulcers by transmitting H. pylori Flea-can carry Bubonic plague