Introduction to Microbiology

What is Microbiology?

Microbiology is the study of organisms too small to be seen with the naked eye, requiring a microscope for observation. The cell is the smallest unit of life and serves as the basic unit of structure and function in all living things.

• Importance: Microorganisms are crucial for planetary survival, involved in essential cycles, and are ubiquitous.

• Roles: Beneficial (e.g., nitrogen fixation, fermentation, genetic engineering) and harmful (e.g., pathogens causing diseases like COVID-19, HIV, anthrax).

Scientific Nomenclature

• Binomial Nomenclature: Developed by Carolus Linnaeus; each organism has a Genus (capitalized) and species (lowercase) name, both italicized (e.g., Escherichia coli).

• Bacterial Species: Group of cells with similar characteristics; strains are derived from a single cell.

Types of Microorganisms

• Prokaryotes: No nuclear membrane (e.g., Bacteria, Archaea).

• Eukaryotes: Have a nuclear membrane and organelles (e.g., Fungi, Protozoa, Algae).

• Viruses: Acellular, contain DNA or RNA, obligate intracellular parasites.

• Multicellular Animal Parasites: E.g., helminths.

History of Microbiology

Key Discoveries

• Microscopy: Robert Hooke (1665) observed "cells" in cork; Anton van Leeuwenhoek (1673–1723) observed living microorganisms.

• Cell Theory: All living things are made of cells (Schleiden & Schwann).

• Louis Pasteur: Disproved spontaneous generation, developed pasteurization, linked microbes to fermentation and disease, developed rabies vaccine.

• Robert Koch: Identified causative agents of disease (e.g., anthrax), developed pure culture techniques, and formulated Koch's postulates.

Koch's Postulates

1. The same specific causative agent must be found in every case of the disease.

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

3. The cultured organism must cause the disease when introduced into a healthy host.

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

Spontaneous Generation vs. Biogenesis

• Spontaneous Generation: Life arises from nonliving matter (disproved by Pasteur's swan-neck flask experiment).

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

Germ Theory of Disease

• Semmelweis: Advocated handwashing to reduce childbirth deaths.

• Lister: Introduced antiseptic surgery using phenol.

Vaccination and Chemotherapy

• Vaccination: Jenner (smallpox), Pasteur (rabies, attenuation).

• Chemotherapy: Ehrlich's "magic bullet" (Salvarsan for syphilis), Fleming's discovery of penicillin, Waksman's discovery of streptomycin.

Classification of Microorganisms

Taxonomy and Classification Systems

• Taxonomy: Science of classifying organisms to depict relationships and aid identification.

• Historical Systems: Two-kingdom (plants/animals), five-kingdom (Monera, Protista, Fungi, Plantae, Animalia), three-domain (Bacteria, Archaea, Eukarya).

• Three-Domain System: Based on rRNA differences (Woese, 1978):

  • Bacteria: True bacteria, peptidoglycan cell walls.

  • Archaea: Extremophiles, no peptidoglycan.

  • Eukarya: Protists, fungi, plants, animals.

• Endosymbiotic Theory: Eukaryotes evolved from prokaryotes living inside one another (mitochondria, chloroplasts).

Taxonomic Hierarchy

• Domain > Kingdom > Phylum > Class > Order > Family > Genus > Species

Viruses

• Not classified in the three-domain or five-kingdom systems; acellular, require host cells for replication.

• Classified by nucleic acid type, capsid shape, and envelope presence.

Bergey’s Manual

• Identification of bacteria based on morphology, staining, biochemical tests, and molecular techniques.

Chemical Principles

Macromolecules

• Carbohydrates: Sugars and starches; (CH2O)n; energy source, structural roles.

• Lipids: Nonpolar, energy storage, membrane structure (phospholipids, steroids).

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

• Nucleic Acids: DNA (heredity), RNA (protein synthesis); made of nucleotides (base, sugar, phosphate).

• ATP: Main energy currency; hydrolysis releases energy:

Carbohydrates

• Monosaccharides: Simple sugars (glucose, fructose, ribose).

• Disaccharides: Two monosaccharides joined by glycosidic bond (e.g., sucrose, lactose).

• Polysaccharides: Many monosaccharides (e.g., glycogen, cellulose).

Lipids

• Simple Lipids: Fats/triglycerides (glycerol + fatty acids, ester bonds).

• Complex Lipids: Contain P, N, or S (e.g., phospholipids in membranes).

• Steroids: Fused ring structures (e.g., cholesterol).

Proteins

• Structure: Primary (sequence), secondary (α-helix, β-sheet), tertiary (3D folding), quaternary (multiple polypeptides).

• Denaturation: Loss of structure/function due to heat, pH, chemicals.

Nucleic Acids

• DNA: Double-stranded, deoxyribose sugar, A-T and C-G base pairing.

• RNA: Single-stranded, ribose sugar, A-U and C-G base pairing; types: mRNA, tRNA, rRNA.

Prokaryotic and Eukaryotic Cells

Prokaryotes vs. Eukaryotes

• Prokaryotes: Unicellular, no nuclear membrane, no organelles, circular DNA, divide by binary fission.

• Eukaryotes: True nucleus, organelles, linear chromosomes, divide by mitosis/meiosis.

Prokaryotic Cell Structures

• Glycocalyx: Polysaccharide/polypeptide layer; capsule (organized) or slime layer (loose); aids in attachment and protection.

• Biofilms: Communities of microbes in a matrix (EPS); resistant to antibiotics; important in disease.

• Flagella: Motility; arrangements: monotrichous, amphitrichous, lophotrichous, peritrichous; composed of filament, hook, basal body.

• Fimbriae: Short, numerous; attachment to surfaces.

• Pili: Longer, few; DNA transfer (conjugation).

• Cell Wall: Peptidoglycan (bacteria), pseudomurein (archaea); provides shape and protection.

• Gram-Positive: Thick peptidoglycan, teichoic acids.

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

• Cell Wall Alternatives: Mycoplasma (no wall), Mycobacteria (acid-fast), Archaea (pseudomurein).

• Plasma Membrane: Phospholipid bilayer, proteins; selective barrier, site of ATP production.

• Cytoplasm: 80% water, contains DNA, ribosomes, inclusions.

• Nucleoid: Region with circular DNA; may have plasmids.

• Ribosomes: 70S (30S + 50S); protein synthesis.

• Inclusions: Storage granules (e.g., phosphate, glycogen).

• Endospores: Dormant, resistant structures (e.g., Bacillus, Clostridium); survive harsh conditions.

Eukaryotic Cell Structures

• Nucleus: Double membrane, contains DNA (chromatin), nucleolus (rRNA synthesis).

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

• Golgi Apparatus: Modifies, sorts, and packages proteins/lipids.

• Mitochondria: ATP production, double membrane, own DNA and 70S ribosomes.

• Chloroplasts: Photosynthesis (plants, algae).

• Other Organelles: Lysosomes (digestion), vacuoles (storage), centrioles (cell division).

• Flagella/Cilia: 9+2 microtubule arrangement; movement.

• Cell Wall: Plants (cellulose), fungi (chitin), no peptidoglycan.

• Glycocalyx: Cell recognition, adhesion.

• Plasma Membrane: Contains sterols, glycoproteins; endocytosis (phagocytosis, pinocytosis).

• Ribosomes: 80S (60S + 40S) in cytoplasm; 70S in mitochondria/chloroplasts.

Microbial Metabolism

Metabolism Overview

• Catabolism: Breakdown of molecules, releases energy (exergonic), coupled to ATP synthesis.

• Anabolism: Synthesis of molecules, requires energy (endergonic), coupled to ATP breakdown.

Enzymes

• Biological Catalysts: Proteins (sometimes RNA/ribozymes) that speed up reactions by lowering activation energy.

• Specificity: Each enzyme acts on a specific substrate (lock-and-key model).

• Structure: Holoenzyme = apoenzyme (protein) + cofactor (non-protein, e.g., metal ion or coenzyme).

• Coenzymes: NAD+, NADP+, FAD, CoA (electron carriers).

• Factors Affecting Activity: Temperature, pH, substrate concentration.

Oxidation-Reduction (Redox) Reactions

• Oxidation: Loss of electrons.

• Reduction: Gain of electrons.

• Always coupled; electron carriers (e.g., NAD+) facilitate transfer.

ATP Generation

• Substrate-Level Phosphorylation: Direct transfer of phosphate to ADP.

• Oxidative Phosphorylation: Electron transport chain (ETC) and chemiosmosis; final electron acceptor is O2 (aerobic) or another molecule (anaerobic).

• Photophosphorylation: Light energy used to generate ATP (photosynthetic organisms).

Carbohydrate Catabolism

• Glycolysis: Glucose (6C) → 2 pyruvate (3C), net 2 ATP, 2 NADH; occurs in cytoplasm, no O2 required.

• Prep Step: Pyruvate → Acetyl CoA + CO2 + NADH.

• Krebs Cycle: Acetyl CoA oxidized; produces NADH, FADH2, ATP, CO2.

• ETC: Electrons from NADH/FADH2 passed through carriers; O2 is final acceptor (aerobic); generates proton motive force for ATP synthesis.

• Anaerobic Respiration: Final electron acceptor is not O2 (e.g., NO3-, SO42-); less ATP produced.

• Fermentation: Organic molecule is final electron acceptor; produces lactic acid, ethanol, or mixed acids; regenerates NAD+.

Lipid and Protein Catabolism

• Lipids: Broken down by lipases; fatty acids enter via β-oxidation as Acetyl CoA.

• Proteins: Broken down by proteases; amino acids deaminated, enter Krebs cycle.

Nutritional Patterns

• Energy Source: Light (phototroph), chemical (chemotroph).

• Carbon Source: CO2 (autotroph), organic compounds (heterotroph).

• Chemoheterotroph: Uses organic compounds for both energy and carbon.

Microbial Growth

Growth and Division

• Growth: Increase in cell number (not size); binary fission is main method.

• Colony: Clump of genetically identical cells (clone).

• Binary Fission Steps:

  1. Cell elongation and DNA replication

  2. Cell wall and membrane invagination

  3. Cross-wall formation

  4. Cell separation

• Generation Time: Time for population to double; varies by species and conditions.

• Growth Curve Phases:

  1. Lag: Metabolic activity, no division

  2. Log (Exponential): Rapid division, maximal growth

  3. Stationary: Growth rate = death rate; nutrients deplete, waste accumulates

  4. Death: Cells die exponentially

• Mathematical Expression: Where = final number of bacteria, = initial number, = number of generations.

Growth Requirements

• Physical: pH (most bacteria: 6.5–7.5), temperature (psychrophiles, mesophiles, thermophiles), osmotic pressure (halophiles).

• Chemical: Carbon, nitrogen, sulfur, phosphorus, trace elements, vitamins, oxygen.

• Oxygen Requirements:

  • Obligate aerobes: Require O2

  • Facultative anaerobes: Can use O2 but not required

  • Obligate anaerobes: Cannot use O2

  • Aerotolerant anaerobes: Tolerate O2

  • Microaerophiles: Require low O2, high CO2

• Toxic Oxygen Species: Singlet oxygen, superoxide radicals, peroxide anion, hydroxyl radical; detoxified by SOD, catalase, peroxidase.

Biofilms

• Communities of microbes in a self-produced matrix (polysaccharides, proteins, DNA).

• Quorum sensing enables coordinated behavior.

• Biofilms are highly resistant to antibiotics and immune responses; major cause of nosocomial infections.

• Prevention strategies: surface antibiotics, quorum sensing inhibitors, lactoferrin.

Table: Comparison of Prokaryotic and Eukaryotic Cells

Table: Oxygen Requirements of Microorganisms

Example: Glycolysis Net Reaction

Glucose + 2 NAD+ + 2 ADP + 2 Pi → 2 Pyruvate + 2 NADH + 2 ATP + 2 H2O

Example: Bacterial Growth Calculation

If a culture starts with 100 bacteria and has a generation time of 30 minutes, how many bacteria will there be after 3 hours?

• Number of generations:

• Final number:

Additional info: Some explanations and examples have been expanded for clarity and completeness, including the tables and calculation examples.