MICROBIOLOGY AND PARASITOLOGY By: Evelyn R. Perez CHAPTER 1 INTRODUCTION TO MICROBIOLOGY CHAPTER 1: INTRODUCTION TO MICROBIOLOGY MICROBIOLOGY Study of living minute organisms invisible to naked eye MICRO ORGANISMS BACTERIA(Bacteriology) FUNGI(Mycology) MOLDS(Mycology) YEAST(Mycology) ALGAE(PHYTOPLANKTON (Phycology/Algology) VIRUS(Virology) PROTOZOAN(Protozoology) by Anton Van Leeuwenhoek /Netherlands ,17th century inventor of microscope METAZOAN(HELMINTHS) BRANCHES OF MICROBIOLOGY DAIRY MICROBIOLOGY(curd, yogurt, cheese) FOOD MICROBIOLOGY(pickles,sauerkraut,olives,soy sauce) INDUSTRIAL MICROBIOLOGY(drugs,chemicals,fuels,electricity AGRICULTURAL MICROBIOLOGY(increased soil fertility,prebiotic and probiotics, actinomycetes) SANITARY MICROBIOLOGY(to inactivate microorganisms) MEDICAL MICROBIOLOGY(diagnose, treat and prevent infection) USES OF MICROORGANISMS VITAMINS,AMINO ACIDS,ENZYMES,GROWTH SUPPLEMENT FERMENTED DAIRY PRODUCTS:SOUR CREAM,YOGURT,BUTTERMILK,PICK LES,SAUERKRAUT,BREADS,ALCOHO LIC BEVERAGES BIOTECHNOLOGY:HUMAN HORMONE INSULIN,ANTIVIRAL SUBSTANCE INTERFERON,BLOOD COLORING FACTORS,CLOT DISSOLVING ENZYMES,VACCINES HISTORICAL DEVELOPMENT OF MICROBIOLOGY 1. 2. 3. 4. 5. 6. 7. 1. 2. 3. 4. LEEUWENHOEK -”ANIMALCULES” • ABIOGENESIS/SPONTANEOUS GENERATION Life Comes from Non life” VAN HELMONTH (+)Mice in hay infusion +wheat grain+ soiled linen+cheese FRANCISCO REDI (+)Maggots if flies eggs deposited uncovered on meat and fish LOUIS GOBLET (-)animalcules) baked , autoclaved hay infusion + H2o JOHN NEEDHAM +animalcules) even baked and autoclaved due to spores SPALLANZANI/ LAZZARO (-animalcules) if proper storage no dust and air PASTEUR LOUIS -Fermentation result of yeast multiplication Pasteurization: alcohol is produced from sugar by yeast ROBERT HOOKE ROBERT KOCH KITASATO D. IVANSKI - Organisms are made up of cell basic unit of life -Germ Theory, organisms cause disease and infection -18th century discovered cause of bubonic plague, Yersinia pestis -infected plant sap can infect other plants, discover virus GOLDEN AGE OF MICROBIOLOGY (advancement and discoveries) ANTIBIOTIC BACTERIAL DISEASES VACCINES - VIRAL DISEASES PHARMACEUTICAL PRODUCTS QUALITY CONTROL PRODUCTS HISTORY OF THE CLASSIFICATION OF MICRO ORGANISMS TAXONOMY(systemic classification of organisms) TAXONOMIST ARISTOTLE: classified living things as plants and animals (Taxonomy) CARL LINNAEUS: introduced systemic method Taxonomic Nomenclature ( Genus .. Species) ERNST HENRICH HAECKEL -THREE(3) KINGDOM SYSTEM A. PROTISTA B. ANIMALEAE C. PLANTAE MODERN CLASSIFICATION SYSTEM ROBERT WHITTAKER • FIVE(5) KINGDOM CLASSIFICATION A. ANIMALIA B. PLANTAE C.PROTISTA: single celled eukaryotes algae,amoeba,slime moulds,plasmodium.protozoans D. FUNGI: fungus-like and related eukaryotic organisms. Yeast, molds, mushrooms E.MONERA(Prokaryotes) CARL WOESE • THREE(3) PRIMARY KINGGDOMS FOR LIVING THINGS A. ARCHAEBACTERIA B. EUBACTERIA C. EUKARYOTES PROTISTA FUNGI ANIMALIA PLANTAE CHAPTER 2: THE FIVE (5)BASIC GROUPS OF MICRO ORGANISMS I.BACTERIUM (PROKARYOTE) II.FUNGUS,MOLDS,YEAST (EUKARYOTE) ALGAE (EUKARYOTE) III.VIRUS IV.PROTOZOAN PARASITES V.METAZOAN (HELMINTHS) Five (5) Basic Groups of Microbes 1.BACTERIUM (Prokaryote) 2.EUKARYOTIC Group FUNGUS MOLDS YEAST ALGAE 3.VIRUS 4.PROTOZOAN (Parasite) SARCODINA MASTIGOPHORA SPOROZOA CILIATA 5. METAZOAN (Helminths) PLATYHELMINTHES CESTODES TREMATODES NEMATHELMINTHES NEMATODES CELLULAR ORGANIZATION POINT OF COMPARIS ON PROKARYOTIC (BACTERIUM) EUKARYOTIC (FUNGUS, MOLDS, YEAST, ALGAE,ANIMAL & PLANT CELL) 1.NUCLEUS (-)Nucleus or nuclear membrane and nucleoli only NUCLEOID (+)Nucleus consisting nuclear membrane and nucleoli 2.MEMBRANE ENCLOSED (-) (+)Examples includes: (Lysosomes, Golgi Complex, endoplasmic reticulum, mitochondria, choloroplasts) 3.CELL WALL USUALLY PRESENT: chemically complex (typical bacterial cell wall includes peptidoglycan) WHEN PRESENT: chemically simple 4.PLASMA MEMBRANE NO CARBOHYDRATES, (and generally LACKS STEROLS(essential in cell structure) (+)Sterols & carbohydrates that serves as receptors ORGANELLES CELLULAR ORGANIZATION POINT OF COMPARISON PROKARYOTIC CELL (BACTERIUM) EUKARYOTIC CELL (FUNGUS,MOLDS, YEAST, ALGAE,ANIMAL, PLANT CELL) 5.CYTOPLASM (-)No cytoskeleton and cytoplasmic streamig (+)Cytoskeleton and cytoplasmic streaming 6.RIBOSOMES Smaller in size Facilitate binding of mRNA and tRNA Larger in size Gets the orders for protein synthesis 7.CELL DIVISION BINARY FISSION (Asexual separation of body into 2 new bodies) MITOSIS cell replicates producing 2 identical daughter cells 8.CHROMOSOMES SINGLE circular chromosomes; lacks HISTONES MULTIPLE: linear chromosomes; with HISTONES (proteins that attach to DNA ,form chrosomes and regulate gene activity 9.SEXUAL REPRODUCTION No MEIOSIS: transfer of DNA fragments only (CONJUGATION)DNA transfer through direct contact Involves MEIOSIS, process by which gametes are produced CELLULAR ORGANIZATION POINT OF COMPARISON PROKARYOTIC (BACTERIUM) EUKARYOTIC (FUNGUS,MOLDS, YEAST,ALGAE, ANIMAL,PLANT CELL) 10.SIZE 0.2 -2.0 microns in diameter 10 -100microns in diameter 11.FLAGELLA Mobility/loco motory organ Mobility/multiple microtubules 12.GLYCOCALYX (+)as a capsule or slime layer/,regulate s permeability of nutrients Compose of sugar . Strenghten cell surface Chitin cellulose Chapter 2: Basic Five (5) Groups of Microbes BACTERIA (PROKARYOTIC CELL) E.COLI The Prokaryotic Cell: Bacterium General Characteristics Large group of mostly microscopic ,unicellular organisms Lacks distinct nucleus usually reproduce by cell division Tiny and variable in the ways they obtain energy and nourishment Can be found in all environments: • Air, soil, ice /hot springs • Hydrothermal vents (heat loving thermophiles) • Deep ocean floor (home of the sulfur metabolizing bacteria) • All food products The Prokaryotic Cell: Bacterium Classifying Bacteria: Criteria Used MORPHOLOGY (forms) 2. MODE OF NUTRITION 3. LOCOMOTORY STRUCTURES 4. GROWTH CHARACTERISTICS 5. METABOLISM (chemical changes) 6. ENDOSPORE(asexual spore inside bacterial cell) 7. STAINING CHARACTERISTICS 8. COLONY CHARACTERISTICS 9. GENETIC CHARACTERISTICS 1. MORPHOLOGY SIZE/SHAPE COCCI (spherical) BACILLUS (rod) COCCOBACILLI (no perfectly round/oval) SPIRILLUM (spiral curved bodies) SPIROCHETES- (spiral but more flexible ARRANGEMENT (GROUPINGS) COCCI GROUPING Diplococci Streptococci Staphylococci Tetrads Sarcinus -pairs of cocci -chains of cocci -clusters or geometrically arranged cocci -packets of four(4) cells -packets of eight(8) cells BACILLI GROUPING Diplobacilli Streptobacilli Palisade Mode of Nutrition Autotrophic organisms synthesize their own food Photoautotrophs (photosynthesis) Chemoautotrophs (chemosynthesis) Heterotrophic depend on other organisms for their food Saprophytic(absorbing dissolved organic materials) Holozoic(digestion, absorption, assimilation of the food, egestion) Symbiotic (share nourishment) Parasitic( gets nourishment from a host Locomotory Structures Protozoan Pseudopodia (sarcodina/amoeba) Cilia (ciliata/ciliates) Flagella (mastigophora/flagellates) Bacilli Has locomotory structure B cereus, B anthrasis Cocci No locomotory structures Characteristic of Flagellation Monotrichous-single flagellum Peritrichous -all around Amphitrichous-both sides Lophotrichous -tuft of many flagella at one end or both ends. Growth Characteristics Oxygen (O2) Requirement Aerobic: oxygenated environment (S .aureaus) Anaerobic: without oxygen requirement(E.coli) Temperature Requirement Heat Lover: “thermophile (Clostridium , Bacillus because of its spores) Cold Lover:”psychrophilic(Listeria monocytogenes Metabolism Characteristics Biochemical & Physiological depending on enzymes they produce and use. Lipolitic -Lipase & fats Saccharolytic -Carbohydrates Proteolytic - Proteins Endospore Definition: -a spore or seed like form, non reproductive structure Function: -ensure the survival of a bacterium through periods of environmental stress. These are resistant to: • • • • • • UV and Gamma Radiation Dessication Lysosome Temperature Starvation Chemical disinfectants Staining Characteristics: Gram (+)Positive Organism Principle: The cell membrane is made up of 80% of thick layer of a particular substance(PEPTIDOGLYCAN) consisting of TECHOIC and LIPOTEICHOIC ACID Complexes)which is INSOLUBLE to Alcohol Decolorizer,the CV Complex remains INTACT,therefore the organism stains the color of the initial stain-CV blue-violet) Examples of the organisms are: Staphylococci Streptococci Pneumococci Corynebacterium diphtheriae Bacillus anthracis(Anthrax) Gram (-) Negative Organism Principle:The cell wall is composed of thin layer of a particular substance(PEPTIDOGLYCAN) covered by an outer membrane of LIPOPROTEIN and LIPOPOLYSACCHARIDE containing ENDOTOXIN), which is SOLUBLE to Acid Decolorizer,it losses the CV Complex (pink – red). Examples of the organisms are: GIT Bacteria-E.coli Neisseria Species Staining Characteristics Gram Stain Principle: A Differential Stain that distinguish between Gram (+) Positive and Gram (-) Negative Organism, base on whether takes up and retain the CV stain or not. Reagents: Crystal (Gentian) Violet- Initial Stain Iodine -Mordant (strengthen the affinity of bacteria with CV, if they have strong affinity with initial stain. Acid Alcohol -Decolorizer Safranin -Counter Stain Procedure: A. Preparation of Bacterial Smear 1. Fish out loop of inoculum. . 2. Emulsify if solid ,with distilled water/NSS. 3. Spread evenly/thinly on clean glass slide. 4. Air dry. Fix by passing slide above the flame to let organism adhere to glass slide. B. Staining 1. Flood bacterial smear with initial stain (CV) for 1 min., Rinse with water. 2. Flood with Iodine (mordant), Alcohol Acetone (decolorizer), till no more shall come out. Rinse with water. 3. Flood with Safranin (counter stain) or Bismarck Brown Staining Characteristics Acid-Fast Organism : Characterized by wax like nearly IMPERMEABLE cell walls, they contain MYCOLIC ACID and large amount of FATTY ACIDS WAXES and COMPLEX LIPIDS. Acid Fast organisms are highly resistant to disinfectants and dry conditions. Because the cell wall is so resistant to most compounds, these requires a special staining technique. Principle: Carbol Fuchsin (Primary Stain) is a LIPID SOLUBLE and contains Phenol, which helps the stain penetrate the cell wall. This is farther assisted by addition of HEAT. The smear is then rinsed with a very strong de colorizer, which strips the stain from all non acid fast cells but does not permeate the cell wall of acid-fast organism. The non acid fast cells then take up the counter stain, Methylene Blue or Brilliant Green . Examples of Organisms are: Mycobacterium Species Staining Characteristics Acid-Fast Stain: A Differential Stain used to identify acid fast organisms such as members of the genus MYCOBACTERIUM. Principle: Depends on the relative solubility of substance. The nature of Carbol Fuchsin ; a. phenol is more soluble in lipid substance than in ACID ALCOHOL b. fuchsin dye or more soluble in Phenol than in water, as a result, the fuchsin (pink- red) has a greater affinity with the bacterial cell and so retain the color of Carbol Fuchsin (pink- red) . Reagents: Carbol Fuchsin -Initial Stain Phenol (carbol fuchsin mixture) -Mordant Alcohol( 90 -95% w/ HCL 3-5 % -Decolorizer Methylen Blue, Brilliant Green -Counterstain Procedure: 1. Apply the smear with initial stain(carbol fuchsin) w/in 4-5 mins. 2.Steam heat w/in 4-5 mins(because difficult to stain,to allow stain to penetrate deeper to bacterial smear because the cell wall is made up of MYCOLIC ACID,lipids, fatty substances),these leaves with water. 3. Apply decolorizer alcohol 90-95%w/HCl,3 -5%) 4. Apply counterstain (Methylene Blue, Brilliant Green. Colony Characteristics Colony: VISIBLE mass of microorganisms all originating from a single mother cell, therefore constitute a clone of bacteria all genetically alike. Colonial Morphology: Bacteria growing on a solid surface which present cultural characteristics. Description of Colonial Morphology: 1. Shape -Round Irregular, Filamentous, Curled 2. Edge /Margin-edge view, shape entire - Filamentous, Undulate, Lobate 3. Elevation -side view, - Raised,Flat,Convex,Umbonate, 4. Opacity - Transpaent,Transluscent, Opaque , Iridiscent 5. Surface -Smooth, Glistening, Rough, Dull, Wrinkled 6. Consistency - Mucoid, Viscous, Brittle, Dry Anatomy of Bacterial Cells Structures Outside the Cell Wall Flagella Capsule Pili/Fimbriae Structures within cytoplasm Cytoplasm/Protoplasm Nucleoid Ribosomes Endospore Inclusion Granules Cytoplasmic Membrane Structures outside the cell wall: Flagella Definition: Long, filamentous structures originating from the basal granules of cell membranes. Appear as waxy filament under stained preparation and cylindrical helix in living cells. Functions/Uses: (Locomotory ) • Move toward nutrients • Move away from toxic chemical • Move toward the light like photosynthetic organo bacteria Three(3) Major Domains of Bacterial Flagellum consist of: • Ion driven motor(provide a torque to any direction) • Hook(universal joint transmit motor torque even if it is curved • Filament(very long structure)which acts as a propeller Flagellar Arrangement: • • • • Atrichous Monotrichous Lipotrichous Amphitrichous • Peritrichous -non- motile, all cocci (Staph, Strep,Diplococcus) -has single flagellum in oneend, all (Campylobacter and Vibrio Species) -tuft of flagella in one end,(Spirillum undula spirilluminus) - tuft on flagella on both ends, or single flagellum in both ends,(P aeruginosa - cell surrounded with flagella(P.vulgaris,S.typhosa) Structures outside the cell wall: Capsule Definition/Description: viscous hollow shaped structure enclosing the pathogenic bacterial cell. Some species of bacteria have a third protective covering. Made up of Polysaccharide (complex carbohydrates).The capsule are chamically diverse but the majprity of them are Polysaccharide in nature. Some may contain HAc, Pyruvic Acid and /or the methyl esters or hexoses. Maybe weakly antigenic to strongly antigenic. Functions: • Keep the bacteria from drying out • Protect it from phagocytosis (engulfing) by larger microorganisms. • Detemine the virulence factor of organisms Major Disease –causing organisms • Strep .pneumoniae -capsulated • E.coli -non capsulated (avirulent, depends on quantity) Pathogenic Organisms producing protein capsule • B.anthracis -capsule of pure D-glutamic acid • Y. pestis - capsules of mixed amino acids Other Species with capsules • Klebsiella pneumoniae • M.t.b • C.perfringens • D.pneumoniae Structures outside the cell wall: Pili/Fimbriae Definition/Description: • resembles flagella but not for locomotory purposes, shorter and more numerous. • thin protein tubes originating from the cytoplasmic membrane, found in all gram(-)negative bacteria, but not in many Gram(+) positive bacteria. Functions: • for attachment specially during conjugation Structures within cytoplasm: Cytoplasm/Protoplasm: • where the function of CELL GROWTH, METABOLISM, & REPLICATION are carried out. • gel like matrix composed of water, enzymes, wastes, gases and cell structures such as ribosomes, chromosomes, and plasmids. • The cell envelope encases the cytoplasm and all its component. Unlike a Eukaryotic(true cell) bacteria do not have a membrane enclosed nucleus. • The chromosome ,a single continuous strand of DNA )is localized but NOT CONTAINED)),in a region of the cell called the Nucleoid. All other cellular components are scattered throughout the cytoplasm. Nucleoid • localized are of the chromosome,DNA) not enclosed or contained. • The region of cytoplasm where the chromosomal DNA is located. It is not a membrane bound nucleus. • Host bacteria have a single, circular chromosome that is responsible for replication, although a few species have 2 or more. • PLASMIDS: smaller circular auxillary DNA strands are also found in the cytoplasm. Ribosomes • Microsopic “FACTORIES” found in all cells, including bacteria. • Translate the genetic code from the molecular language of Nucleic Acid to that of amino acids- the building blocks of proteins. PROTEINS are the molecules that perform all the functions of cells and living organisms. • Bacterial ribosomes are similar to those of eukaryotes, but SMALLER, and HAVE A SLIGHT different composition and molecular structures. And are never bound to other organelles as they sometimes are (bound to E R) in eukaryotes ,but are FREE STANDING structures distributed throughout the cytoplasm. • DIFFERENCE: BACTERIAL RIBOSOME -some antibiotic inhibits its function, thus killing the bacteria EUKARYOTE RIBOSOME - antibiotic will not inhibit its function not kill the eukaryotic organism Endospore: • Is NOT A REPRODUCTIVE structure but rather s RESISTANT DORMANT SURVIVAL form of the organism. Resistant to: a. high temperature (including boiling) b. most disinfectants c. low energy radiation d. drying • It can survive possibly thousand of years until a variety of environmental stimuli trigger GERMINATION, allowing outgrowth of a single vegetative bacterium. e. resistant to antibiotics • The impermeability of the SPORE COAT is thought to be responsible for the endospore resistance to chemicals. • The heat resistant endospore is due to variety of factors: a. CALCIUM DIPICOLINATE b. SPECIALIALIZED DNA (survive without nutrient) c. The CORTEX, may osmotically remove water from the interior of the andospore and the DEHYDRATION that results is thought to be very important in the endospores resistance to heat and radiation. d. The DNA repair enzymes contained w/in the endospore are able to repair damaged DNA during germination. Inclusion/Granules Metachromatic Granules Ernst Bodies Store nutrients such as : a. fat b. poly meta phosphate of VOLUTIN serves as source of food. c. glycogen deposited in dense crystals or particles that can be tapped when needed. CYTOPLASMIC MEMBRANE/PLASMA MEMBRANE COMPOSED OF: PHOSPHOLIPIDS/PROTEIN MOLECULES FLUID PHOSPHOLIPID BILAYER embedded with protein. MYCOPLASMA PROKARYOTIC Membrane FUNCTIONS: I. It is a relatively permeable membrane that DETERMINES what goes in and out of the organism. • • • • • II. Water- dissolves gases such as CO2 & O2 Lipid Soluble Molecules, simply diffuse across the phospho lipid bilayer H2O soluble ions pass through small pores in the membrane. All other molecules require CARRIER MOLECULES to transport them through the ,membranes. Materials move across the bacterial cytoplasmic membrane by: A. PASSIVE DIFFUSION B. ACTIVE DIFFUSION C. CYTOLYSIS FUNCTIONS associated with the bacterial cytoplamic membrane & DIVISOME I. FUNCTION A. PASSIVE DIFFUSION movement of gas ( N2,O2,CO2) or small polar molecules ( ethanol, H2) ,Urea) across a phospholipid bilayer membrane from an area of higher concentration to an area of a lower concentration. Powered by the potential energy of a concentration gradient and does not require the expenditure of metabolic energy. OSMOSIS ISOTONIC HYPERTONIC HYPOTONIC FACILITATED DIFFUSION(through transport proteins) UNIPORTER transport single specie of substrate molecule CHANNEL PROTEINS(AQUAPORINS); allow water diffuse through at very fast rate WATER CHANNELS In diffusion, particles move from an area of higher concentration to one of lower concentration until equilibrium is reached In osmosis, a semi permeable membrane is present, so only the solvent molecules are free to move to equalize concentration. In facilitated diffusion, molecules diffuse across the plasma membrane with assistance from membrane proteins, such as channels and carriers. A concentration gradient exists for these molecules, so they have the potential to diffuse into (or out of) the cell by moving down it. B. ACTIVE TRANSPORT TRANSPORT PROTEINS Transport Proteins (Carrier Proteins) Anti Porters(membrane protein transport2 2 molecules at same time in opposite direction Symporters(s molecules in same direction) Proteins for the ATP-binding casette(ABC) System(translocate wide variety of substrates) Proteins involved in group TRANSLOCATION It converts the energy gained from ATP hydrolysis into trans-bilateral movement of substrate either into the cytoplasm (import) or out of the cytoplasm (export C. CYTOLYSIS Allows substances to move into and out of cells without passing through the hydrophobic internal portion of the plasma membrane. Vesicle/phagosome: is a membrane bound sphere formed when plasma membrane wraps around a substance ,engulfs that substance. TYPES OF CYTOLYSIS ENDOCYTOSIS: Cells absorbs material from outside by engulfing it. • PHAGOCYTOSIS:invaginate around large macromolecules (proteins ,virus) that unable o diffuse into the cell,”cell eating” • PINOCYTOSIS uptake of extracellular fluids and small molecules,”cell drinking” • RECEPTOR MEDIATED;capture a specific target molecule EXOCYTOSIS: cells directs secretory vesicles out of the cell membrane • Move materials from within cell into extracellular fluid when vesicle fuses with plasma membrane Cytolysis, or osmotic lysis, occurs when a cell bursts due to an osmotic imbalance that has caused excess water to diffuse into the cell. Endocytosis involves cells taking in substances from outside the cell by engulfing them from the cell in a vesicle derived membrane. Exocytosis is where cells shift materials, such as waste products, from inside the cell to the extracellular space II. FUNCTION Associated with the bacterial cytoplasmic membrane and “DIVISOME” “DIVISOME”- cell divisome machinery Energy Production Contain BASES of bacterial flagella used in motility Waste removal Formation of endospore The divisome is a membrane protein complex with proteins on both sides of the cytoplasmic membrane. The divisome is a protein complex in bacteria that is responsible for cell division, constriction of inner and outer membranes during division, and peptidoglycan (PG) synthesis at the division site. ANTIBIOTICS kill bacteria Making bacteria difficult to grow ad multiply Penicillin,tetracyclinecephalosporin DISINFECTANTS kills germs on surface of non living objects Alcohol, bleach solution,hand sanitizers with 60%alcohol ANTISEPTICS Applied to reduce possibility of infection,sepsis Povidone,iodine, hydrogen peroxide Action of ANTIBIOTIC to PEPTIDOGLYCAN WORK BY INHIBITING NORMAL SYNTHESIS OF PEPTIDOGLYCAN IN BACTERIA CAUSING THEM TO BURST AS A RESULT OF osmotic LYSIS. Chapter 1 Chapter 2 Done! Thank you for your attention!