Introduction and Classification of Microorganisms

Major Historical Figures and Accomplishments

• Antonie van Leeuwenhoek: First to observe living microorganisms using a microscope.

• Louis Pasteur: Disproved spontaneous generation; developed pasteurization; contributed to germ theory.

• Robert Koch: Established Koch's postulates; identified causative agents of tuberculosis and cholera.

• Carl Woese: Proposed the three-domain system based on rRNA sequencing.

Prokaryote vs. Eukaryote Distinctions

• Prokaryotes: Lack a nucleus and membrane-bound organelles; include Bacteria and Archaea.

• Eukaryotes: Have a true nucleus and membrane-bound organelles; include Fungi, Protozoa, Algae, and Helminths.

Taxonomy: Domains, Kingdoms, and Nomenclature

• Three Domains: Bacteria, Archaea, Eukarya.

• Five Kingdoms: Monera, Protista, Fungi, Plantae, Animalia.

• Taxonomic Hierarchy: Domain > Kingdom > Phylum > Class > Order > Family > Genus > Species.

• Binomial Nomenclature: Scientific naming using Genus species (e.g., Escherichia coli).

Microscopy

Principles of Microscopy

• Total Magnification: Product of the magnification of the objective and ocular lenses.

• Resolution: Ability to distinguish two points as separate; higher resolution reveals more detail.

• Oil Immersion Lens: Increases resolution by reducing light refraction.

Types of Microscopy

• Transmission Electron Microscope (TEM): Visualizes internal structures at high resolution.

• Scanning Electron Microscope (SEM): Provides 3D images of specimen surfaces.

Staining Techniques

• Purpose: Enhances contrast to visualize cells and structures.

• Gram Stain: Differentiates bacteria into Gram-positive (purple) and Gram-negative (pink).

• Capsule Stain: Visualizes extracellular capsules.

• Acid-Fast Stain: Identifies Mycobacterium species.

• Endospore Stain: Detects bacterial endospores.

Bacteria and Archaea

Shapes and Arrangements

• Shapes: Cocci (spherical), Bacilli (rod-shaped), Spirilla (spiral).

• Arrangements: Chains (strepto-), clusters (staphylo-), pairs (diplo-).

Flagella and Motility

• Flagella Arrangements: Monotrichous (single), Lophotrichous (tuft), Amphitrichous (both ends), Peritrichous (all over).

Cell Wall Structure

• Gram-Positive: Thick peptidoglycan, teichoic acids.

• Gram-Negative: Thin peptidoglycan, outer membrane with lipopolysaccharide (LPS).

• Atypical Cell Walls: Mycobacterium (waxy mycolic acids), Mycoplasma (no cell wall), Archaea (pseudopeptidoglycan or S-layer).

Internal Structures

• Cytoplasm: Contains ribosomes, DNA, inclusions.

• Endospores: Dormant, resistant structures for survival.

• Inclusions: Storage granules for nutrients.

Microbial Metabolism

Enzymes and Their Function

• Enzyme: Biological catalyst that speeds up reactions.

• Substrate: Molecule upon which an enzyme acts.

• Active Site: Region where substrate binds.

• Allosteric Site: Site for regulatory molecule binding.

• Coenzyme/Cofactor: Non-protein helpers (e.g., vitamins, metal ions).

• Inhibition: Competitive (blocks active site), Non-competitive (binds elsewhere).

Catabolic Pathways

• Glycolysis

• Krebs Cycle (Citric Acid Cycle)

• Electron Transport Chain

Fermentation vs. Respiration

• Fermentation: Anaerobic; produces less ATP; end products include acids, alcohols, gases.

• Respiration: Aerobic or anaerobic; involves electron transport chain; more ATP produced.

• ATP Yield (Aerobic Respiration): Up to 38 ATP per glucose in prokaryotes.

Microbial Nutrition and Growth

Types of Microbial Nutrition

• Photoautotrophs: Use light and CO2 as carbon source.

• Photoheterotrophs: Use light and organic compounds.

• Chemoautotrophs: Use inorganic chemicals and CO2.

• Chemoheterotrophs: Use organic compounds for energy and carbon.

Transport Mechanisms

• Passive Transport: No energy required (diffusion, osmosis).

• Active Transport: Requires energy (ATP); moves substances against gradient.

Osmotic Effects

• Isotonic: No net water movement.

• Hypotonic: Water enters cell; may cause lysis.

• Hypertonic: Water leaves cell; causes plasmolysis.

Microbial Growth

• Generation Time: Time for population to double.

• Binary Fission: Main method of prokaryotic cell division.

• Growth Curve Phases: Lag, Log (Exponential), Stationary, Death.

Measuring Growth

• Direct counts (microscopy, plate counts)

• Indirect methods (turbidity, metabolic activity)

Culture Media Types

• Physical States: Liquid, semisolid, solid.

• Selective Media: Inhibits some, allows others to grow.

• Differential Media: Distinguishes organisms by biochemical reactions.

• Enriched Media: Contains nutrients for fastidious organisms.

• Defined vs. Complex Media: Known vs. unknown composition.

Physical and Chemical Control of Microbes

Definitions

• Sterilization: Destroys all forms of microbial life.

• Disinfection: Destroys most pathogens on inanimate objects.

• Antisepsis: Destroys pathogens on living tissue.

Physical Methods

• Heat: Moist (autoclave), dry (oven).

• Filtration: Removes microbes from liquids/air.

• Radiation: Damages DNA (UV, ionizing).

Chemical Methods

• Disinfectants: Used on surfaces (e.g., bleach).

• Antiseptics: Used on skin (e.g., alcohol).

• Chlorine: Oxidizing agent.

• Heavy Metals: Denature proteins (e.g., silver).

• Alcohols: Denature proteins, disrupt membranes.

• Gaseous Sterilants: Ethylene oxide.

Measuring Effectiveness

• Bacteriostatic: Inhibits growth.

• Bactericidal: Kills bacteria.

• MIC (Minimum Inhibitory Concentration): Lowest concentration of drug that inhibits growth.

• Zone of Inhibition: Area around antibiotic disk where bacteria do not grow.

Antimicrobial Drugs

Key Concepts

• Selective Toxicity: Drug harms microbe, not host.

• Spectrum: Broad (many types) vs. narrow (few types).

• Resistance: Microbes evolve to withstand drugs.

Beta-Lactam Antibiotics

• Penicillin: Inhibits cell wall synthesis.

Testing Antimicrobial Activity

• Disk Diffusion: Measures zone of inhibition.

• Broth Dilution: Determines MIC.

Microbial Genetics

DNA Structure and Replication

• DNA: Double helix; composed of nucleotides (A, T, G, C).

• DNA Polymerase: Synthesizes new DNA strands.

• Replication Fork: Site where DNA is unwound.

• Leading/Lagging Strands: Continuous vs. discontinuous synthesis.

Gene Expression

• Transcription: DNA to RNA; RNA polymerase binds promoter.

• Translation: mRNA to protein; involves ribosomes, tRNA, genetic code.

• Start Codon: AUG; Stop Codons: UAA, UAG, UGA.

Genetic Exchange

• Transformation: Uptake of naked DNA.

• Transduction: DNA transfer via bacteriophage (generalized/specialized).

• Conjugation: DNA transfer via pilus; F plasmids; Hfr (high frequency recombination).

Mutations

• Auxotroph: Mutant requiring a growth factor.

• Induced vs. Spontaneous Mutations: Caused by mutagens vs. natural errors.

• Ames Test: Detects mutagenic potential of chemicals.

Viruses, Viroids, and Prions

Structure and Classification

• Capsid: Protein coat; made of capsomeres.

• Nucleocapsid: Capsid plus nucleic acid.

• Shapes: Spherical, rod, complex.

• Enveloped vs. Naked: With or without lipid envelope.

• Surface Proteins (Spikes): Attachment to host cells.

Viral Cultivation and Replication

• Cultivation: In living cells, eggs, or cell cultures.

• Plaques: Clear zones indicating viral lysis.

• Lytic Cycle: Virus replicates and lyses host.

• Lysogenic Cycle: Viral DNA integrates into host genome.

• Cytopathic Effects (CPE): Visible changes in host cells due to viral infection.

Viroids and Prions

• Viroids: Infectious RNA molecules (plants).

• Prions: Infectious proteins (e.g., mad cow disease).

Epidemiology

Symbiotic Relationships

• Commensalism: One benefits, other unaffected.

• Mutualism: Both benefit.

• Parasitism: One benefits, other harmed.

Disease Classification

• Communicable: Spread from host to host.

• Noncommunicable: Not spread between hosts.

• Frequency: Sporadic, endemic, epidemic, pandemic.

• Severity: Acute, chronic, subacute, latent.

Incidence vs. Prevalence

• Incidence: New cases in a time period.

• Prevalence: Total cases at a given time.

Healthcare-Associated Infections (HAIs)

• Infections acquired in healthcare settings.

Epidemiology Definition

• Study of disease occurrence, distribution, and control.

Mechanisms of Pathogenicity

Virulence Factors

• Capsules: Prevent phagocytosis.

• Enzymes: Aid invasion (e.g., hyaluronidase, coagulase).

• Exotoxins: Secreted proteins; specific effects.

• Endotoxins: Lipid A of LPS in Gram-negative bacteria; cause fever, shock.

• Cytopathic Effects: Damage to host cells by viruses.

Innate Immunity: Nonspecific Defenses

First and Second Lines of Defense

• First Line: Skin, mucous membranes, secretions.

• Second Line: Phagocytes, natural killer cells, inflammation, fever, complement system.

Phagocytosis

• Engulfment and digestion of microbes by phagocytes.

Inflammatory Response

• Redness, heat, swelling, pain; steps include vasodilation, migration of phagocytes, tissue repair.

Fever

• Systemic response; inhibits pathogens, enhances immune response.

Complement System

• Proteins that enhance phagocytosis (opsonization), lyse microbes, and trigger inflammation.

Adaptive Immunity: Specific Immune Response

Cell-Mediated Immunity

• Cytotoxic T Cells (CD8+): Destroy infected or abnormal cells.

Humoral Immunity

• B Cells: Produce antibodies.

• Helper T Cells (Th2): Stimulate B cells.

• Memory B Cells: Provide long-term immunity.

Immunoglobulin (Ig) Classes

• IgG, IgM, IgA, IgD, IgE; each with specific roles.

Primary vs. Secondary Immune Response

• Primary: First exposure; slower, less antibody.

• Secondary: Faster, stronger due to memory cells.

Types of Immunity

• Natural vs. Artificial: Acquired through infection vs. vaccination.

• Active vs. Passive: Own immune response vs. receiving antibodies.

Vaccines

• Stimulate active immunity without causing disease.

Applications in Immunology

Agglutination and Precipitation

• Agglutination: Clumping of cells/particles by antibodies.

• Precipitation: Formation of insoluble complexes between antigens and antibodies.

Immune Disorders

Hypersensitivity Reactions

• Type I: Immediate (allergy; IgE-mediated).

• Type II: Cytotoxic (antibody-mediated cell destruction).

• Type III: Immune complex-mediated.

• Type IV: Delayed (cell-mediated; e.g., contact dermatitis).

Microbial Diseases by Body System

Skin and Eye Diseases

• Impetigo: Bacterial skin infection.

• Chickenpox/Shingles: Varicella-zoster virus; latent infection can reactivate as shingles.

• Measles: Viral; causes rash, fever, complications.

Nervous System Diseases

• Meningitis: Inflammation of meninges; bacterial or viral.

• Tetanus: Caused by Clostridium tetani; neurotoxin causes muscle spasms.

• Botulism: Clostridium botulinum toxin; flaccid paralysis.

• Leprosy: Chronic infection by Mycobacterium leprae.

Cardiovascular and Lymphatic Diseases

• Lyme Disease: Caused by Borrelia burgdorferi; transmitted by ticks.

Respiratory Diseases

• Strep Throat: Streptococcus pyogenes.

• Diphtheria: Corynebacterium diphtheriae; pseudomembrane in throat.

• Whooping Cough: Bordetella pertussis; severe coughing fits.