Microbiology: Binomial Nomenclature & Microbes

• Study notes derived from flashcards on microbiology topics

Binomial Nomenclature

• Classification system identifies organisms by genus and species.
• Order: Genus species.
• Genus is capitalized, species is not; can be shortened to G. species after first use.
• Underline or italicize the name.
• Established by Carolus Linnaeus.

Characteristics of Microbes

• Bacteria: Prokaryotic, single-celled, peptidoglycan walls, divide via binary fission, nutrition from inorganic/organic chemicals or photosynthesis, mobility via flagella.
• Fungi: Eukaryotic, chitin cell walls, nutrition from organic chemicals. Yeasts are unicellular, molds and mushrooms are multicellular.
• Mold: Consists of masses of mycelia composed of filaments called hyphae.
• Algae: Eukaryotic, cellulose cell walls, found in soil, freshwater, and saltwater, nutrition via photosynthesis, reproduction sexually or asexually.
• Protozoa: Eukaryotic, nutrition from organic chemicals, mobility via flagella, pseudopods, or cilia. Can be free-living or parasitic, some are photosynthetic, reproduce sexually or asexually, unicellular (helminth).
• Viruses: Acellular, DNA or RNA core with a protein coat (may have a lipid envelope), replicate only within a living host cell.

Cell Theory and Spontaneous Generation

• Biogenesis: Living cells arise only from preexisting living cells.
• Spontaneous Generation: Life arises from nonliving matter; requires a "vital force."
• Robert Hooke: Reported that living things are made of cells, marking the beginning of cell theory.
• Antonie van Leeuwenhoek: Discovered protists and bacteria, called them "animalcules."
• Francesco Redi: Experiment with decaying meat in jars disproved spontaneous generation.
• John Needham: Boiled nutrient broth in covered flasks, microbial growth occurred.
• Lazzaro Spallanzani: Boiled nutrient solutions in sealed flasks, no microbial growth.
• Rudolf Virchow: Proposed new cells are formed only from existing cells.
• Louis Pasteur: Microorganisms are present in the air; S-shaped flasks kept microorganisms out but allowed air in; disproved spontaneous generation; microorganisms responsible for fermentation.
• Pasteurization: Application of high heat for a short time to kill harmful bacteria in beverages.

Koch's Postulates

• The microorganism should be abundant in diseased organisms but not in healthy ones.
• The microorganism should be isolated from a diseased organism and grown in pure culture.
• The cultured microorganism should cause disease when introduced into a healthy organism.
• The microorganism should be isolated from the experimentally infected host.
• Used to prove a specific bacterium causes a specific disease.
• Robert Koch discovered that bacterium causes anthrax and established Koch's Postulates.
• Ignaz Semmelweis advocated handwashing to prevent the spread of puerperal fever.
• Joseph Lister used a chemical antiseptic (phenol) to prevent surgical wound infections.
• Edward Jenner discovered the smallpox vaccine by inoculating with cowpox virus.
• Paul Ehrlich speculated about a "magic bullet" to destroy pathogens without harming the host.
• Alexander Fleming discovered penicillin, an antibiotic made by Penicillium fungus, that killed S. aureus.

Fields of Microbiology

• Bacteriology: Study of bacteria.
• Mycology: Study of fungi.
• Parasitology: Study of parasites and protozoa.
• Virology: Study of viruses.
• Microbial Genetics: Study of how microbes inherit traits.
• Genomics: Study of an organism's genes; provides new tools for classifying microorganisms.
• Molecular Biology: Study of how DNA directs protein synthesis.
• Recombinant DNA: DNA made from two different sources.
• Recombinant Technology: Combines genes from different sources into a single DNA molecule.
• Immunology: Study of the immune system.
• Rebecca Lancefield classified streptococci based on their cell wall components.
• George Beadle and Edward Tatum showed that genes encode a cell's enzymes.
• Oswald Avery, Colin MacLeod, and Maclyn McCarty showed DNA is the hereditary material.
• James Watson and Francis Crick proposed a model of DNA structure.

Conversions

• 1 mL = 0.001 L
• 1 L = 1,000,000 uL
• 1 mL = 1000 uL
• 1 uL = 10^-6 L
• 1 L = 1000 mL
• 1 uL = 0.001 mL

Microscopy

• Total Magnification: Objective lens (4X, 10X, 40X, 100X) multiplied by ocular lens (10X).
• Resolution: Ability of lenses to distinguish two points; shorter wavelengths of light provide greater resolution.
• Immersion Oil: Used to prevent light refraction.
• Bright-field Microscope: Produces a dark image against a brighter background; reflected light from the specimen doesn't enter the objective lens.
• Dark-field Microscope: Light objects are visible against a dark background; only light reflected off the specimen enters the objective lens.
• Phase Contrast Microscope: Allows examination of living organisms and internal cell structures; brings together direct and diffracted light rays to form an image.
• Differential Interference Contrast Microscope: Uses two light beams and prisms to split light beams, giving more contrast and color to the specimen (similar to phase contrast).
• Transmission Electron Microscope: Beam of electrons passes through ultrathin sections, then through an electromagnetic lens, and focused on a projector lens. Specimens may be stained with heavy-metal salts for contrast. Magnifies objects 10,000 to 10,000,000x; highest resolution and magnification.

Staining Techniques

• Acid-Fast Stain: Binds only to bacteria with waxy material in their cell walls.
  • Primary Stain: Carbolfuchsin (both acid-fast and non-acid-fast are red).
  • Decolorizing Agent: Acid-Alcohol (acid-fast remains red, non-acid-fast becomes colorless).
  • Counterstain: Methylene Blue (acid-fast remains red, non-acid-fast turns blue).
• Endospore Stain: Used to stain endospores, resistant dormant structures.
  • Primary stain: malachite green, usually with heat
  • Decolorize cells: water
  • Counterstain: safranin. Spores appear green within red or pink cells
• Gram Stain: Classifies bacteria into gram-positive or gram-negative.
  • Gram-positive: Thick peptidoglycan cell walls; appear purple.
  • Gram-negative: Thin peptidoglycan cell walls and a layer of lipopolysaccharides; turn pink/red after safranin is added.
• Negative Stain: Colors the background, making capsules more visible.
• Air Dry and Heat Fix: Air dry ensures bacteria stay in place; heat fix prevents contamination.

Cell Structure

• Eukaryotic Microbes: Fungi, protozoa, algae, multicellular animal parasites
• Light from the Condenser: Passes through the objective lens.
• Prokaryotic Cell: One circular chromosome, not in a membrane; no histones; no organelles; bacteria have peptidoglycan cell walls; archaea have pseudomurein cell walls; divides by binary fission
• Eukaryotic Cell: Paired chromosomes in nuclear membrane; histones; organelles; polysaccharide cell walls; divides by mitosis
• Main Feature Distinguishing Prokaryotes from Eukaryotes: Lack of nucleus in prokaryotes.
• Size of Bacterial Cells: 0.2 to 2.0 μm diameter × 2 to 8 μm length.
• Monomorphic: Single-shaped.
• Pleomorphic: Many shapes.

Bacterial Morphology

• Bacterial Shapes: Coccus, bacillus, spirillum, vibrio, spirochete, star-shaped, rectangular.
• Streptococci: Identified by chain-like patterns under a microscope.
• Bacillus: Rod-shaped bacteria.
• Coccus: Spherical bacteria.
• Pairs of Bacteria: Diplococci, diplobacilli.
• Clusters of Bacteria: Staphylococci.
• Chains of Bacteria: Streptococci, streptobacilli.
• Groups of Four: Tetrads.
• Cube-like Groups of Eight: Sarcinae.

External Structures

• Pili: Hair-like structures for bacterial adhesion and colonization; involved in movement.
• Capsule: Polysaccharide layer outside the cell envelope; prevents phagocytosis; neatly organized and firmly attached.
• Glycocalyx: External to the cell wall; made of polysaccharide and/or polypeptide; dense, gel-like meshwork that surrounds the cell, constituting a physical barrier for any object to enter the cell; modulates adhesion between cells.
• Flagella: Filamentous appendages for bacterial propulsion; made of flagellin protein. Three parts:
  • Filament: outermost region
  • Hook: attaches to filament
  • Basal Body: Anchors flagellum to cell wall and membrane; consists of rod and pairs of rings.
• Cilia: Small hair-like protuberances used for locomotion and sensory functions in eukaryotic cells.
• Fimbriae: Hair-like appendages that allow for attachment; enable the bacteria to bind to specific receptor structures and thereby to colonize specific surfaces

Cell Wall Composition

• Gram-Positive Cell Wall: Thick peptidoglycan wall; teichoic acids which contribute to bacterial cell surface charge and hydrophobicity, which in turn affects binding of extracellular molecules; polysaccharides and teichoic acids provide antigenic specificity.
• Gram-Negative Cell Wall: Thin peptidoglycan wall; outer membrane; periplasmic space (between inner and outer membranes) containing peptidoglycan; protects from phagocytes and antibiotics, made of lipopolysaccharide (LPS); Lipid A (endotoxin) in top layer; porins (proteins) form channels through the membrane.
• Gram-Positive Appearance: Purple.
• Gram-Negative Appearance: Red/Pink.
• NAM: N-acetylmuramic acid.
• NAG: N-acetylglucosamine.

Gram Staining Steps

• Crystal Violet: Primary stain, adheres to cell membranes of both gram-positive and gram-negative cells.
• Gram's Iodine: Mordant; increases stain affinity by binding to crystal violet, forming an insoluble complex trapped in the cell wall.
• Ethanol/Acetone: Decolorizes; dehydrates peptidoglycan layer, shrinking and tightening it.
• Safranin: Counterstain; directly stains decolorized bacteria, distinguishing gram-negative from gram-positive.

Study notes on the binomial nomenclature system, established by Carolus Linnaeus, which classifies organisms by genus and species. Also describes the characteristics of microbes. Covers bacteria, fungi, mold, algae and protozoa.