1. A Brief History of Microbiology

Six Groups of Microorganisms

Microorganisms are classified into six major groups based on cell type and key characteristics. Understanding these groups is foundational for microbiology.

• Bacteria: Prokaryotic; cell walls with peptidoglycan; reproduce asexually; require moisture; some are pathogenic.

• Archaea: Prokaryotic; cell walls lack peptidoglycan; asexual; inhabit extreme environments; not known to cause human disease.

• Fungi: Eukaryotic; obtain nutrients from other organisms; have cell walls; include multicellular molds and unicellular yeasts.

• Protozoa: Eukaryotic; single-celled; live in water or animal hosts; motile via pseudopods, cilia, or flagella.

• Algae: Eukaryotic; uni- or multicellular; photosynthetic; classified by pigmentation and cell wall composition.

• Parasites/Small Animals: Range from microscopic to 10 m; most adult worms are not microscopic but can cause disease.

• Viruses: Acellular; obligate intracellular parasites; composed of DNA or RNA and a protein coat; visible only with electron microscopy.

Prokaryotic vs. Eukaryotic Cells

• Prokaryotic: Lack a true nucleus and membrane-bound organelles; typically <1.0 µm; includes Bacteria and Archaea.

• Eukaryotic: Have a true nucleus and membrane-bound organelles; typically 10–100 µm; includes Algae, Protozoa, Fungi, Animals, and Plants.

The Golden Age of Microbiology (1800–1900): Key Questions

• Is spontaneous generation possible?

• What causes fermentation?

• What causes disease?

• How can infection be prevented?

Spontaneous Generation: Scientists & Experiments

Koch's Postulates: Proving Disease Causation

1. Suspected agent must be present in every case of the disease and absent from healthy hosts.

2. Agent must be isolated and grown in pure culture.

3. Agent must cause disease when introduced into a healthy host.

4. Same agent must be re-isolated from the diseased experimental host.

Major Scientists & Their Contributions

2. The Chemistry of Microbiology

Matter, Atoms, and Atomic Structure

• Matter: Anything with mass and volume.

• Atom: Smallest unit of matter; consists of protons, neutrons, and electrons.

• Element: Substance composed of one type of atom.

• Atomic Number: Number of protons in the nucleus.

• Atomic Mass: Sum of protons, neutrons, and electrons.

• Isotopes: Atoms of the same element with different numbers of neutrons (e.g., C-12, C-14).

Electron Shells & Valence Electrons

• Electrons occupy shells around the nucleus; first shell holds 2, second and third hold 8 each.

• Valence electrons (outermost shell) determine chemical reactivity.

• Atoms are most stable with 8 valence electrons (Octet Rule).

Chemical Bonds

Chemical Reactions

• Synthesis (Anabolism): Building larger molecules from smaller ones; endothermic. Example: protein synthesis.

• Decomposition (Catabolism): Breaking down molecules; exothermic. Example: digestion.

• Exchange: Atoms are exchanged between molecules; both endo- and exothermic steps.

• Metabolism: Sum of all chemical reactions in an organism.

Water: Five Vital Qualities

1. Cohesion/surface tension

2. Excellent solvent

3. Remains liquid over a wide temperature range

4. High heat capacity

5. Participates in chemical reactions

Acids, Bases, Salts, and Buffers

Note: Most microbes grow best between pH 6.5 and 8.5.

Organic Macromolecules

• Lipids: Hydrophobic molecules; types include triglycerides (energy storage), phospholipids (membranes), waxes (waterproofing), and steroids (membranes, hormones).

• Carbohydrates: (CH2O)n; energy storage, structural roles, cell recognition. Types: monosaccharides, disaccharides, polysaccharides.

• Proteins: Polymers of amino acids; functions include structure, enzymes, regulation, transport, and defense. Structure levels: primary, secondary, tertiary, quaternary.

• Nucleic Acids: DNA and RNA; composed of nucleotides (phosphate, sugar, nitrogenous base). DNA is double-stranded, RNA usually single-stranded.

• ATP: Adenosine triphosphate; main short-term energy carrier in cells.

3. Cell Structure and Function

Major Processes of Living Cells

• Growth: Increase in size.

• Reproduction: Increase in number; can be sexual or asexual.

• Responsiveness: Ability to respond to environmental stimuli (e.g., taxis).

External Structures

• Glycocalyx: Protective outer layer; capsule (organized, firmly attached) or slime layer (loose, sticky).

• Flagella: Motility structures; arrangements include monotrichous, lophotrichous, amphitrichous, peritrichous, polar, and endoflagella (spirochetes).

• Fimbriae: Short, bristle-like projections for adhesion and biofilm formation.

• Pili (Sex Pili): Longer than fimbriae; used for DNA transfer (conjugation).

Bacterial Shapes and Arrangements

• Cocci: Spherical; arrangements include single, diplo, strepto (chains), staphylo (clusters), tetrads, sarcinae.

• Bacilli: Rod-shaped; single, diplo, strepto, angular/branching.

• Spirilla/Spirochetes: Spiral or curved; includes vibrio, spirillum, spirochete.

Bacterial Cell Walls: Peptidoglycan & Gram Staining

Cytoplasmic Membrane: Fluid Mosaic Model

• Phospholipid bilayer with embedded proteins; selectively permeable.

• Integral proteins span the membrane; peripheral proteins are attached to the surface.

• Impermeable to large, charged, or hydrophilic molecules without transport proteins.

Movement Across Membranes

Osmotic Conditions

• Isotonic: Equal solute concentration; no net water movement.

• Hypertonic: Higher solute outside; water leaves cell (plasmolysis).

• Hypotonic: Lower solute outside; water enters cell (cell swells or bursts).

Bacterial Cytoplasm

• Cytoplasm: Gel-like interior; contains cytosol, nucleoid (DNA region), plasmids, inclusions (storage granules).

• Endospores: Resistant structures formed by Bacillus and Clostridium during harsh conditions; highly durable.

• Ribosomes: Sites of protein synthesis; 70S in prokaryotes, 80S in eukaryotes.

• Cytoskeleton: Protein fibers that maintain cell shape.

Endosymbiotic Theory

• Eukaryotes evolved from prokaryotes via engulfment of smaller cells (mitochondria, chloroplasts).

• Evidence: organelles have circular DNA, double membranes, and 70S ribosomes.

4. Microscopy, Staining, and Classification

Metric Units of Length

• Meter (m), Centimeter (cm, 10-2), Millimeter (mm, 10-3), Micrometer (µm, 10-6), Nanometer (nm, 10-9).

• Bacteria: 0.1–10 µm; Viruses: measured in nm.

Types of Microscopy

Staining Techniques

Taxonomy: Purposes and Hierarchy

• Provides universal naming and classification system.

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

• Binomial nomenclature: Genus species (e.g., Staphylococcus aureus).

Three Domains (Woese and Fox)

Procedures for Identifying and Classifying Microorganisms

1. Morphological Characteristics: Shape, size, arrangement, staining, motility.

2. Differential Staining: Gram, acid-fast stains.

3. Biochemical Testing: Metabolic capabilities.

4. Serology: Antibody-antigen reactions.

5. Nucleic Acid Analysis: rRNA/DNA sequencing; most accurate.

Modifications of the Linnaean System

• Molecular phylogenetics: DNA/rRNA sequences for evolutionary relationships.

• Three-domain system: Domain added above Kingdom.

• Numerical taxonomy: Statistical comparison of many traits.

• Cladistics: Groups by shared derived characteristics from common ancestors.