Introduction to Microbiology

Definition and Scope

• Microbiology is the scientific study of microorganisms, including bacteria, archaea, viruses, fungi, protists, and non-living infectious agents such as prions.

• Microbes are organisms too small to be seen with the naked eye.

• Pathogens are microbes that cause disease; however, less than 1% of all microbes are pathogenic.

Historical Figures and Theories

• Robert Hooke (1665): First to publish descriptions of cells.

• Antonie van Leeuwenhoek (1632–1723): Improved microscopes and first observed bacteria.

• Spontaneous Generation: The disproven idea that life arises from nonliving matter.

• Biogenesis: Life arises from pre-existing life (supported by Redi, Spallanzani, Pasteur).

• Louis Pasteur: Disproved spontaneous generation, developed pasteurization, and contributed to the germ theory of disease.

• Robert Koch: Developed Koch's postulates to link specific microbes to specific diseases.

Koch’s Postulates

1. The same microbe must be present in every case of the disease.

2. The organism must be isolated and grown in pure culture.

3. The isolated organism should cause the same disease when introduced into a healthy host.

4. The organism must be re-isolated from the experimentally infected host.

Limitations: Not all microbes can be cultured; ethical concerns limit testing in humans; not all hosts are susceptible.

Cell Theory and Taxonomy

• Cell Theory: All living organisms are composed of cells, which arise from preexisting cells.

• Taxonomy: The science of classifying, naming, and identifying organisms (Carl Linnaeus).

• Binomial Nomenclature: Two-part scientific naming system: Genus species (e.g., Escherichia coli).

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

Biochemistry Basics

Atoms, Elements, and Bonds

• Atoms are the smallest units of elements, composed of protons, neutrons, and electrons.

• Atomic number: Number of protons; Atomic mass: Protons + neutrons.

• Isotopes: Atoms of the same element with different numbers of neutrons.

• Valence electrons: Electrons in the outermost shell, determine chemical reactivity.

• Chemical bonds: Covalent (sharing electrons), ionic (transfer of electrons), hydrogen bonds, van der Waals interactions.

Acids, Bases, and pH

• Acids: Donate H+ ions; Bases: Accept H+ ions.

• pH scale: Measures acidity/basicity (0–14); pH = 7 is neutral.

• Formula:

Organic Molecules and Functional Groups

• Organic molecules: Contain carbon and hydrogen.

• Functional groups: Specific groups of atoms (e.g., methyl, hydroxyl, carboxyl, amino, phosphate, sulfhydryl) that determine chemical properties.

Macromolecules

• Carbohydrates: Monosaccharides, disaccharides, polysaccharides; energy sources and structural components (e.g., cellulose, chitin, peptidoglycan).

• Lipids: Hydrophobic molecules including fats, oils, steroids, waxes, phospholipids; major components of cell membranes.

• Nucleic Acids: DNA and RNA; polymers of nucleotides (phosphate, pentose sugar, nitrogenous base).

• Proteins: Polymers of amino acids; structure, enzymes, transport, signaling.

Introduction to Prokaryotic Cells

Characteristics of Prokaryotes

• Prokaryotes: Unicellular organisms lacking a nucleus and membrane-bound organelles; include Bacteria and Archaea.

• Size: 0.2–750 μm (most 0.5–2.0 μm).

• Shapes: Cocci (spherical), bacilli (rod-shaped), spirilla (spiral), vibrio (comma-shaped), stella (star-shaped).

• Arrangements: Diplococci, streptococci, staphylococci, diplobacilli, streptobacilli, palisade.

Binary Fission

1. DNA is copied.

2. Cell grows; chromosomes move to opposite ends.

3. Septum forms at the midpoint.

4. Septum completes, dividing the cell.

5. Two daughter cells separate.

Prokaryotic Cell Structures

• Plasma membrane: Phospholipid bilayer; selective permeability; fluid-mosaic model.

• Cell wall: Bacteria (peptidoglycan), Archaea (pseudopeptidoglycan or other polymers).

• External structures: Flagella (motility), fimbriae (adhesion), pili (gene transfer), glycocalyx (protection, biofilm formation).

• Cytoplasm: Site of biochemical reactions; contains ribosomes, nucleoid (DNA), inclusion bodies.

• Endospores: Dormant, highly resistant structures (e.g., Bacillus, Clostridium).

Cell Wall Types

Transport Mechanisms

• Passive transport: Diffusion, facilitated diffusion, osmosis (no energy required).

• Active transport: Requires energy (ATP); moves substances against concentration gradients.

• Group translocation: Substance is chemically modified during transport.

Introduction to Eukaryotic Cells

Characteristics of Eukaryotes

• Eukaryotes: Organisms with a true nucleus and membrane-bound organelles; include animals, plants, fungi, and protists.

• Size: 10–100 μm.

• Cell division: Mitosis (asexual), meiosis (sexual).

Key Organelles and Structures

• Nucleus: Contains DNA; site of transcription.

• Endoplasmic reticulum (ER): Rough ER (protein synthesis), smooth ER (lipid synthesis, detoxification).

• Golgi apparatus: Modifies, sorts, and packages proteins and lipids.

• Mitochondria: ATP production; double membrane; contains 70S ribosomes and circular DNA (supports endosymbiotic theory).

• Chloroplasts: Photosynthesis in plants and algae; similar evolutionary origin as mitochondria.

• Cytoskeleton: Microtubules, intermediate filaments, microfilaments; structure, movement, division.

• Plasma membrane: Phospholipid bilayer with sterols (cholesterol in animals, phytosterols in plants).

• Cell wall: Present in plants, fungi, some protists (not in animals); made of cellulose (plants), chitin (fungi).

• Glycocalyx: Carbohydrate-rich layer for adhesion and communication.

Endosymbiotic Theory

• Mitochondria and chloroplasts originated from engulfed prokaryotes.

• Evidence: Circular DNA, 70S ribosomes, binary fission, similar size to bacteria.

Types of Eukaryotes

• Animals: Multicellular, heterotrophic, include helminths (parasitic worms).

• Plants: Multicellular, photosynthetic, contain chloroplasts.

• Fungi: Unicellular (yeasts) or multicellular (molds); cell walls of chitin; reproduce via spores.

• Protists: Diverse group; unicellular or multicellular; include protozoa (animal-like), algae (plant-like), and slime molds.

Viruses and Prions

Characteristics of Viruses

• Viruses: Acellular, obligate intracellular pathogens; extremely small (20–400 nm).

• Composed of a protein capsid (made of capsomeres) and genetic material (DNA or RNA).

• Some viruses have a lipid envelope derived from the host cell membrane; others are naked.

• Spikes (peplomers) are glycoproteins that aid in host cell attachment.

Viral Genomes

• Can be DNA or RNA, single- or double-stranded, linear or circular, segmented or non-segmented.

• RNA viruses mutate more rapidly due to lack of proofreading by RNA polymerases.

• Retroviruses use reverse transcriptase to convert RNA to DNA (e.g., HIV).

Viral Replication Cycles

Bacteriophage Lytic Cycle

1. Attachment

2. Penetration

3. Replication

4. Assembly

5. Release (lysis of host cell)

Lysogenic Cycle

• Phage genome integrates into host DNA as a prophage.

• Prophage is replicated with host genome; can later enter lytic cycle.

Animal Virus Replication

1. Attachment

2. Penetration (endocytosis or membrane fusion)

3. Uncoating

4. Replication

5. Assembly

6. Release (budding for enveloped viruses, lysis for naked viruses)

Viral Pathogenesis and Evolution

• Viruses can cause acute, chronic, or latent infections.

• Antigenic drift: Minor changes due to mutations (e.g., influenza).

• Antigenic shift: Major changes due to reassortment of genome segments.

• Oncogenic viruses can cause cancer (e.g., HPV).

Prions

• Infectious proteins; lack nucleic acids.

• Cause transmissible spongiform encephalopathies (TSEs) such as Creutzfeldt-Jakob disease.

Microbial Growth and Laboratory Techniques

Growth Media and Culturing

• Growth media: Nutrient mixtures for culturing microbes (agar plates, broths, slants).

• Aseptic techniques: Prevent contamination during culturing.

• Streak plate technique: Isolates pure colonies from mixed cultures.

Staining Techniques

• Simple stains: Use one dye to increase contrast.

• Differential stains: Use multiple dyes to distinguish cell types (e.g., Gram stain, acid-fast stain).

• Special stains: Highlight specific structures (e.g., capsule, endospore, flagella).

Microscopy

• Compound light microscope: Uses visible light; magnification up to 1000x.

• Fluorescence microscopy: Uses UV light and fluorescent dyes.

• Electron microscopy: Uses electron beams for high-resolution imaging (TEM for internal structures, SEM for surfaces).

Symbiosis and Microbiota

Types of Symbiotic Relationships

Normal Microbiota

• Resident microbiota: Long-term inhabitants of the body.

• Transient microbiota: Temporary residents, removed by hygiene.

• Functions: Train immune system, aid digestion, produce vitamins, protect against pathogens.

• Disruption (e.g., antibiotics) can lead to opportunistic infections.

Biofilms

• Structured communities of microbes attached to surfaces and embedded in a self-produced matrix.

• Form on teeth, medical devices, water systems; highly resistant to antibiotics and immune responses.

Summary Table: Prokaryotes vs. Eukaryotes

Additional info:

• Many details on microbial metabolism, genetics, and host-microbe interactions are foundational for later chapters.

• Laboratory techniques such as PCR, ELISA, and plaque assays are essential for diagnostics and research.