PHC412 Lec1 Microbiology Classification of Microorganisms PDF

PHARMACEUTICALS MICROBIOLOGY PHC 412 Classification of Microorganisms LEARNING OUTCOME: Students should be able to: 1. Identify the basic shapes of bacteria. 2. Describe the main feature that distinguishes prokaryotes from eukaryotes. 3. Describe the overall cell structure and function of p...

PHARMACEUTICALS MICROBIOLOGY PHC 412 Classification of Microorganisms LEARNING OUTCOME: Students should be able to: 1. Identify the basic shapes of bacteria. 2. Describe the main feature that distinguishes prokaryotes from eukaryotes. 3. Describe the overall cell structure and function of prokaryotes and eukaryotes Basic Cell Types Prokaryotic - pro (before) and karyon (nucleus) - structurally simpler and smaller than eukaryotes. - include bacteria and archaea - no nucleus or other membrane-bound Eukaryotic - eu (true) and karyon (nucleus) - typically larger and structurally more complex than the prokaryotic cell. - include algae, protozoa, fungi, plants and animals. The Structure of a Prokaryoti c Cell  Comparing Prokaryotic and Eukaryotic Cells: (https://youtu.be/zZtcMBTQaS4) Characteristic Prokaryotic cells Eukaryotic cells Genetic Structures Intracellular Structures Extracellular Structures Reproductive Process Comparing Prokaryotic and Eukaryotic Cells: (https://youtu.be/zZtcMBTQaS4) The Prokaryotic Cell Size Prokaryotes are among the smallest of all organisms. Most bacteria range from 0.2 - 2.0 μm in diameter and from 2 - 8 μm in length. Shape Three basic shapes: Coccus (plural: cocci) – spherical Bacillus (plural: bacilli) – rodlike Coccobacilli Spirillum (plural: spirilla) – curved shapes, twists, never straight. Vibrio - comma-shaped bacterium Spirochete – corkscrew-shaped Other shapes: Monomorphic - maintain a single shape. - star-shaped cells Pleomorphic - can have many shapes (such as Rhizobium, - rectangular, flat cells Corynebacterium) - triangular cells Common Bacterial Shapes Arrangement of Cocci Arrangement of Bacili External Structures Appendages - Two major groups of appendages: i. Motility - Flagella and Axial filaments ii. Attachment or channels - Fimbriae and Pili Flagella (singular; flagellum) - Long filamentous appendages that propel bacteria. - made up of protein subunit called 'flagellin' - highly antigenic (H antigens) and some of the immune responses to infection are directed against these proteins. - Atrichous - bacteria that lack flagella. - Has three basic parts: i Filament - long, thin, helical structure composed of protein flagellin. ii.Hook - curve sheath iii.Basal body - anchors the flagellum to the cell wall and plasma membrane. bears a set of rings; one pair in gram +ve bacteria and 2 pairs in gram -ve. Arrangement of flagella Monotrichous – single flagellum at one end. Ex: Vibrio cholerae. Lophotrichous – small bunches emerging from the same site.(Bartonella bacilliformis) Amphitrichous – flagella at both ends of the cell. (Spirillum serpens) Peritrichous – distributed over the entire cell.(E.coli) Flagellar Responses Rotates 360o Capable of various pattern of motility. Advantage of motility: enables a bacterium to move toward a favorable environment or away from an adverse one. 'Runs' or 'swim'- bacterium moves in one direction for a length of time. 'Tumbles' - random changes in direction. Flagellar Responses  Taxis - movement of bacterium toward or away from a particular stimulus.  Chemotaxis - chemical stimuli. (positive and negative)  Phototaxis - light stimuli. (positive and negative)  In response to stimuli, information is passed to the flagella. If the chemotactic signal is positive (attractant), - bacteria move towards the stimulus - many runs and few tumbles. If the chemotactic signal is negative (repellent), - frequency of tumbles increased as the bacteria move away from the stimulus. Ex: Helicobacter pylori (agent of gastric ulcer) – bores through the stomach lining. Vibrio cholerae (cause of cholera) - penetrates the small intestine with the help of its flagellum. Periplasmic Flagella / Axial Filaments  Spirochetes - corkscrew-shaped bacteria that have unique structure and motility.  Internal flagellum - enclosed in the space between the outer sheath and cell wall peptidoglycan.  Treponema pallidum - best known spirochetes; causative agent of syphilis. Spirochetes move by The rotation of the means of axial filament, filaments produces a or endoflagella (bundles movement of the outer of fibrils that arise at the sheath that propels the end of the cell beneath spirochetes in a spiral an outer sheath and motion - corkscrew spiral around the cell). move. Nonflagellar Appendages: Fimbriae & Pili Fimbriae Fine, proteinaceous, hairlike bristles emerging from the cell surface. shorter and finer than flagella. Function: - tendency to adhere to each other - involved in forming biofilms and other aggregations on the surface of the liquids, glass and rocks. - help bacteria adhere to epithelial surfaces in the body. (fimbriae on Neisseria gonorrhoeae (gonorrhoeae) - help microbe to colonize mucous membrane and cause disease). - contribute to the pathogenicity of certain bacteria Pili (singular; pilus) Usually longer than fimbriae. Composed of pilin protein. Involved in motility and DNA transfer. Function to join bacterial cells for partial DNA transfer - conjugation. Pili of different bacteria are antigenically distinct and elicit the formation of antibodies by the host. Type IV – found only in gram –ve bacteria. Neisseria gonorrhoeae – gonorrhea – binding to the epithelial cells of the reproductive tract. Glycocalyx Polysaccharide coating that is secreted by many bacteria. composed of polysaccharide, polypeptide or both. it is viscous(sticky) gelatinous polymer. It covers surfaces like a film - allows the bacteria to adhere firmly to various structures (skin, heart valves, and catheters). Two types: Capsule - condensed, highly organized layer closely surrounding the cell, bound more tightly to the cell. Slime layer - unorganized and loosely attached  Function of the glycocalyx:  Protect cells from dehydration and nutrient loss.  Contributing to bacterial virulence - protect pathogenic bacteria from phagocytosis by the cells of the host. (Ex: Streptococcus pneumoniae causes pneumoniae - cells are protected by a capsule - prevent it from being destroyed by phagocytosis).  Important component of biofilms - helps cells in a biofilm attach to their target environment (plants, human teeth, medical implants, water pipes) and to each other (extracellular polymeric substance, EPS).(Ex: Streptococcus mutans, cause of dental caries, attaches itself to the surface of teeth by glycocalyx). Cell Walls  complex and semirigid structure.  Composed of an inner layer of peptidoglycan and an outer membrane that varies in thickness and chemical composition depending upon the bacterial type.  Major functions: i. maintain the shape of the bacterium. ii. prevent the cell from bursting when the water pressure inside the cell is greater than that outside the cell. iii. Provides strong structural support - keep bacterium intact despite changes in environmental conditions.  The peptidoglycan layer  also known as murein, mucopeptide.  It is found only in bacterial cell wall (not in human cells, it is a good target for antibacterial drugs).  Provides rigid support for the cell.  Important in maintaining the characteristic shape of the cell.  Allows the cells to withstand media of low osmotic pressure, such as water.  Peptidoglycan is a complex polymer consisting of 3 parts: - a backbone: alternating monosaccharides, N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM). - a set of identical tetrapeptide side chains attached to NAM. - a set of identical peptide cross-bridges.  Penicillin interferes with the final linking of the peptidoglycan rows by peptide cross-bridges. As a result, the cell wall is greatly weakened and the cell undergoes lysis. Structures of Gram-Positive and Gram-Negative Cell Walls Gram (+) Gram (-) Structures of Gram-Positive Cell Wall Structures of Gram-Negative Cell Wall Comparison of Gram-Positive and Gram-Negative Cell Walls The Gram Stain  Differential stain that distinguishes cells with a gram-positive cell wall from those with a gram- negative cell wall. Gram-positive - retain crystal violet and stain purple. Gram-negative - lose crystal violet and stain red from safranin counterstain. Copyright © McGraw-Hill Education. Permission required for reproduction or display. Chemical Reaction in Cell Microscopic Appearance of Cell (very magnified view) Gram (+) Gram (–) Gram (+) Gram (–) Step 1 Crystal Violet (primary dye) Both cell walls stain with the dye. 2 Gram’ siodine (mordant) Dye crystals No trapped in cell effect of iodine 3 Alcohol (decolorizer) Crystals remain Outer wall is in cell. weakened; cell loses dye. 4 Safranin (red dye counterstain) Red dye Red dye stains has no effect. the colorless cell. Nontypical Cell Walls  Tubercle bacillus (Mycobacterium tuberculosis) - unusual cell wall – contain peptidoglycan and stain gram-positive.  Cell wall composed high concentration of lipids - mycolic acid.  Mycolic acid – thick, waxy - contributes to the pathogenicity. - resistance to certain chemicals and dyes.  ‘Acid fast stain’ - used to diagnosed tuberculosis and leprosy. - Acid-fast bacteria can be stained with hot carbolfuchsin dyes - heating enhances penetration of the stain. - Carbolfuchsin penetrates the cell wall - binds to cytoplasm and resist removal by washing with acid-alcohol. Mycoplasmas and Other Cell Wall – Deficient Bacteria Mycoplasmas  lack a cell wall  its cell membrane contains sterol – resistant to lysis. L-forms  wall-deficient forms  due to mutation in the wall forming genes.  can be induced artificially by treatment with a chemical (lysozyme or penicillin) that disrupts the cell wall. Protoplast  a fragile cell bounded only by a membrane.  gram-positive cell loses it cell wall completely.  highly susceptible to lysis. Spheroplast  gram-negative cell that lose the peptidoglycan layer of its cell wall but retains its outer membrane.  less fragile but weakend spheroplast. Cell membrane  thin (5 – 10 nm) structure lying inside the cell wall and enclosing the cytoplasm of the cell.  phospholipid bilayer with embedded protein (fluid-mosaic model).  Eukaryotic plasma membrane - also contain carbohydrates and sterols (such as cholesterol).  Prokaryotes - lack of sterols - plasma membranes are less rigid.  Each phospholipid molecule contains: Polar head – oriented towards the outside Nonpolar tails – towards the center of the membrane  Contains primarily phospholipids (30 – 40% of membrane mass) and proteins (60 – 70%).  Glycoproteins - proteins attached to carbohydrates.  Glycolipids - lipids attached to carbohydrates. Functions of the cell membrane  Barrier between the inside and outside of the cell – regulating transport.  Secretion or the release of metabolic products into the extracellular environment.  Important site for a number of metabolic activities.. Bacterial Internal Structures Cytoplasm (cytoplasmic matrix)  structure of the cell inside the cell membrane.  is about 80% water – serves as a solvent for a complex mixture of nutrients (sugars, amino-acids, organic molecules, salts).  Chromosomes, ribosomes, granules and actin strands. Bacterial chromosomes and Plasmids  Bacteria do not have true nucleus.  Prokaryotes DNA ; single, circular molecule - contains about 2000 genes (human DNA has ~100000 genes).  Nucleoid – area in the cytoplasm in which DNA in located.  cell's genetic information - carries all the information required for the cell's structures and functions.  Plasmids – additional genetic elements – carry genes that confer favorable traits on the bacterial cell. Ribosomes made of ribosomal RNA, rRNA (60%) and protein (40%). consist of 2 subunits: large subunit (50S) + small subunit (30S). prokaryotic ribosomes are called '70S' ribosomes. eukaryotic cells are known as '80S' ribosomes. S - refer to Svedberg units (indicate the relative rate of sedimentation during ultra high-speed centrifugation). Sedimentation rates - indicate size, weight and shape of a particle. F(x): site for protein synthesis. Some antibiotics - inhibit protein synthesis on prokaryotic ribosomes. Streptomycin & Gentamicin - attach to the 30S subunit - interfere protein synthesis. Inclusions Compartment within the cytoplasm. serve as storage areas for nutrients - use them when the environment is deficient. Varying size, number and content. Gas vesicles – found in some aquatic bacteria – provide buoyancy and flotation. Granules – contain crystal of inorganic compounds. Metachromatic granules - large granules, reserve of inorganic phosphate that can be used in the synthesis of ATP, found normally in algae, fungi, protozoa as well as in bacteria. Microcompartments – polyhedral (many sided) packets formed by proteins bound together in compact units. Magnetosomes – inclusion of iron oxide that have magnetic properties. - found in bacteria living in oceans and swamps. - f(x): to orient the cells in the earth’s magnetic field.  Bacterial endospores  formed by the genus Bacillus and Clostridium  when essential nutrients are depleted (carbon, nitrogen, phosphorous).  2-phase life-cycle: i) Vegetative cell - metabolically active and growing. ii) Endospore  formed when exposed to adverse environmental conditions (sporulation), capable of high resistance & and very long-term survival.  formed internal to the bacterial cell membrane.  Pressurized steam at 120oC for 20-30 minutes will destroy.  The primary function - to ensure a bacterium’s survival through periods of environmental stress.  They are resistant to: - UV and gamma radiation. - desiccation. - lysozyme. - temperature. - starvation. - chemical disinfectants.  Variations in endospore morphology (1,4): central endospore; (2,3,5): terminal endospore; (6): lateral endospore  Important features of spores and their medical implications. Features Medical implication Highly resistant to heating; spore are not killed by boiling (100°C), Medical supplies must be heated to 121°C for at least 15 min but are killed at 121°C. to be sterilized. Highly resistant to many chemicals, including many disinfectants. Only solutions designated as sporicidal will kill spores. They can survive for many years, especially in the soil. Wound contaminated with soil can be infected with spores and cause diseases such as tetanus and gas gangrene. They exhibit no measurable metabolic activity. Antibiotics are ineffective against spores because antibiotics act by inhibiting certain metabolic pathways of bacteria. Spore coat is also impermeable to antibiotics. Spores form when nutrients are insufficient but then germinate to Spores are not often found at the site of infections because form bacteria when nutrients become available. nutrients are not limiting. Bacteria rather than spores are usually seen in gram-stained smears. Spores are produced by members of only two genera, Bacillus and Infections transmitted by spores are caused by species of Clostridium, both are gram-positive rods either Bacillus or Clostridium.  The Eukaryotic Cell Appendages External Flagella organelles and Cilia other structures Glycocalyx Capsules Slimes Eukaryotic cell Boundary of cell Cell wall Cell/cytoplasmic membrane Cytoplasmic matrix Nuclear envelope Nucleus Nucleolus Chromosomes Internal Endoplasmic reticulum organelles and Organelles Golgi complex other contents Mitochondria Ribosomes Chloroplasts Microtubules Cytoskeleton Microfilaments The Structure of a Eukaryotic Cell Cilia and Flagella Cilia  Found only in certain protozoa and animal cells.  Very similar to flagella - but they are shorter and more numerous.  Provide rapid motility.  Also as feeding and filtering structures. Flagella  Eukaryotic flagellum is thicker (by a factor of 10).  Long, sheathed cylinder, containing microtubules (9 + 2 arrangement) – permit microtubules to ‘walk’ by sliding past each other, whipping the flagellum back and forth. Eukaryotic Cell: Internal Structures Nucleus the largest structure in the cell. contains DNA. surrounded by a double membrane called the 'nuclear envelope'. Tiny channels in the membrane called 'nuclear pores' allow the nucleus to communicate with the cytoplasm. Nucleoli (nucleolus) - spherical bodies within the nuclear envelope - condensed region of chromosoms where ribosomal RNA is being synthesized. Contain chromosomes.  Simple staining Special staining Staining  Eg: methylene blue,  Negative stain - use to carbolfuchsin, crystal violet, demonstrate the presence safranin. of capsules.  used to highlight microorganims  Endospore staining - used to determine cellular shapes and arrangements. to detect the presence of endospores in bacteria.  Aqueous or alcohol solution of a single basic dye stains cells.  Flagella staining - used to demonstrate the presence of flagella. A mordant is Differential staining used to build up the  Gram stain - to distinguish diameters of flagella until different kinds of bacteria. they become visible microscopically when  Acid fast stain - used to stained with calbolfuchsin. distinguish Mycobacterium species and some species of Nocardia.