Foundations of Microbiology: Cell Structure, Diversity, and Metabolism

Introduction to Microbiology

This study guide covers foundational concepts in microbiology, including cell structure, microbial diversity, microscopy, cell walls, and basic metabolism. It is designed to help students prepare for exams by summarizing key topics and providing academic context.

Prokaryotic vs. Eukaryotic Cells

Cellular Structures and Genomes

• Prokaryotic cells lack a membrane-bound nucleus and organelles; their DNA is typically a single, circular chromosome located in the nucleoid region.

• Eukaryotic cells possess a true nucleus surrounded by a nuclear envelope and contain membrane-bound organelles (e.g., mitochondria, endoplasmic reticulum).

• Prokaryotes generally have smaller genomes and simpler internal structures compared to eukaryotes.

• Cell division in prokaryotes occurs via binary fission, while eukaryotes use mitosis and meiosis.

Distribution and Beneficial Aspects of Microorganisms

Where Are Most Microbial Cells Found?

• Most microbial cells are found in the subsoil, which harbors vast microbial diversity and biomass.

Beneficial Aspects of Microorganisms

• Decomposition: Microbes recycle nutrients by breaking down organic matter.

• Biotechnology: Used in the production of antibiotics, enzymes, and biofuels.

• Food Production: Fermentation processes (e.g., yogurt, cheese, bread).

• Symbiosis: Nitrogen-fixing bacteria in plant roots, gut microbiota in animals.

• Bioremediation: Degradation of pollutants and waste treatment.

History of Microbiology

Pioneers and Their Contributions

• Robert Hooke: First to describe cells using a microscope.

• Antoni van Leeuwenhoek: First to observe and describe single-celled microorganisms.

• Edward Jenner: Developed the first vaccine (smallpox).

• Louis Pasteur: Disproved spontaneous generation; developed pasteurization and vaccines.

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

• Ignaz Semmelweis: Advocated handwashing to prevent puerperal fever.

• Joseph Lister: Introduced antiseptic surgery.

• Florence Nightingale: Pioneered modern nursing and hospital sanitation.

• Paul Ehrlich: Developed the concept of selective toxicity; discovered Salvarsan for syphilis.

• Alexander Fleming: Discovered penicillin.

• Martinus Beijerinck: Developed enrichment culture techniques; discovered viruses.

• Sergei Winogradsky: Discovered chemolithotrophy and nitrogen fixation.

• Carl Woese: Defined the Archaea domain using 16S rRNA sequencing.

Taxonomy and Phylogeny

Three Domains of Life

• Bacteria: Prokaryotic, peptidoglycan cell walls, diverse metabolism.

• Archaea: Prokaryotic, unique membrane lipids (ether bonds), often extremophiles.

• Eukarya: Eukaryotic, membrane-bound organelles, includes plants, animals, fungi, and protists.

SSU rRNA Genes in Phylogeny

• Highly conserved sequences allow for evolutionary comparisons.

• Present in all cellular organisms (16S in prokaryotes, 18S in eukaryotes).

• Slow mutation rate provides reliable phylogenetic markers.

Relationship Between Eukarya and Archaea

• Both lack sensitivity to many antibiotics that affect Bacteria.

• Share similarities in RNA polymerase and ribosomal proteins.

Prokaryotic Species and 16S rRNA Threshold

• A prokaryotic species is a group of strains with high genetic similarity.

• Species threshold: >97% similarity in 16S rRNA gene sequence.

Bergey’s Manual of Determinative Bacteriology

• Comprehensive reference for bacterial identification and classification based on phenotypic characteristics.

Bacterial Diversity

Unique Features of Selected Bacteria

• Rickettsia: Obligate intracellular parasites.

• Agrobacterium: Plant pathogen causing crown gall disease.

• E. coli / Salmonella: Mixed acid fermenters.

• Enterobacter / Klebsiella: Butanediol fermenters.

• Proteus: Exhibits swarming motility.

• Bdellovibrio: Bacterial predator.

• Mycoplasma: Wall-less bacteria.

• Streptomyces: Produces antibiotics.

Microscopy

Magnification vs. Resolution

• Magnification: Enlargement of an image.

• Resolution: Ability to distinguish two close objects as separate; depends on wavelength and numerical aperture (NA).

Resolution Formula

• Resolving power (RP): $RP = \frac{0.5 \times \text{wavelength}}{NA}$

Factors Affecting Resolution

• Shorter wavelength increases resolution.

• Higher NA increases resolution.

• Immersion oil increases NA by reducing light refraction.

Types of Light Microscopy

• Bright field: Standard illumination; best for stained specimens.

• Phase-contrast: Enhances contrast in unstained cells.

• Dark-field: Highlights specimens against a dark background.

• Fluorescence: Uses fluorochromes to visualize specific structures.

Electron and Scanning Tunneling Microscopes

• Electron microscopes: Use electron beams for much higher resolution than light microscopes.

• Scanning tunneling microscopes: Visualize surfaces at the atomic level using quantum tunneling.

Staining Techniques

• Basic dyes: Positively charged; bind to negatively charged cell components (e.g., crystal violet, methylene blue).

• Acidic dyes: Negatively charged; stain background (e.g., eosin, nigrosin).

• Simple stains: Use one dye to color all cells.

• Differential stains: Distinguish cell types (e.g., Gram stain, Acid-fast stain).

Gram and Acid-Fast Staining

• Gram stain: Differentiates bacteria into Gram-positive (purple) and Gram-negative (pink) based on cell wall structure.

• Acid-fast stain: Identifies Mycobacterium species with waxy cell walls (e.g., M. tuberculosis).

Bacterial Cell Structures

Shapes and Arrangements

• Cocci: Spherical

• Bacilli: Rod-shaped

• Spirilla: Spiral-shaped

• Arrangements: single, pairs (diplo-), chains (strepto-), clusters (staphylo-)

Significance of Small Size

• High surface area-to-volume (SA/V) ratio allows efficient nutrient uptake and waste removal.

Plasma Membrane Structure

• Bacterial membranes: Phospholipid bilayer with embedded proteins; ester linkages.

• Eukaryotic membranes: Similar structure but may contain sterols (e.g., cholesterol).

Archaeal vs. Bacterial Membranes

• Archaea: Ether linkages, isoprene units, can form monolayers (for stability in extreme environments).

• Bacteria: Ester linkages, fatty acids, always bilayers.

• Hopanoids: Sterol-like molecules in bacterial membranes for stability.

• Phytanyls: Branched isoprene chains in archaeal membranes.

Nutrient Transport Mechanisms

• Simple transport: Driven by proton motive force.

• Group translocation: Substance chemically modified during transport (e.g., phosphotransferase system).

• ABC system: ATP-binding cassette transporters use ATP hydrolysis for transport.

• All require energy input.

Peptidoglycan Structure

• Composed of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) with tetrapeptide side chains and peptide cross-bridges.

• Lysozyme: Cleaves glycosidic bonds in peptidoglycan.

• Penicillin: Inhibits cross-linking of peptidoglycan.

Gram-Positive vs. Gram-Negative Cell Walls

• Gram-positive: Thick peptidoglycan, teichoic acids, more susceptible to lysozyme.

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

Functions of the Bacterial Cell Wall

• Maintains cell shape

• Prevents osmotic lysis

• Anchors flagella

• Contributes to pathogenicity

• Prokaryotes lacking cell walls: Mycoplasma, Thermoplasma

Outer Layer of Gram-Negative Bacteria

• Contains LPS, porins, and proteins; acts as a barrier to certain antibiotics and detergents.

Archaeal Cell Walls and S-Layer

• May lack peptidoglycan; often have S-layer (protein or glycoprotein lattice) for protection and structure.

Capsules and Slime Layers

• Polysaccharide or polypeptide layers outside the cell wall.

• Functions: protection from desiccation, phagocytosis, and aids in attachment.

Fimbriae and Pili

• Fimbriae: Short, numerous; attachment to surfaces.

• Pili: Longer, fewer; involved in conjugation and motility.

Cell Inclusions

• Storage granules (e.g., polyphosphate, sulfur, glycogen), gas vesicles, magnetosomes.

Endospores

• Dormant, resistant structures formed by Bacillus and Clostridium.

• Resistant to heat, desiccation, chemicals, and radiation.

• Formed via sporulation under nutrient limitation.

Flagella and Motility

• Arrangements: polar (one or both ends), peritrichous (all over), lophotrichous (tuft at one end).

• Flagella rotate for movement; different from eukaryotic wave-like motion.

• Axial filaments (endoflagella) in spirochetes enable corkscrew motion.

Microbial Metabolism (Part 1)

Types of Microbial Nutrition

• Chemoorganotrophs: Use organic compounds for energy.

• Chemolithotrophs: Use inorganic compounds for energy.

• Photoautotrophs: Use light for energy and CO2 as carbon source.

• Photoheterotrophs: Use light for energy and organic compounds for carbon.

Free Energy and Reaction Types

• Free energy (G): Energy available to do work.

• Exergonic reactions: Release energy ($\Delta G < 0$).

• Endergonic reactions: Require energy input ($\Delta G > 0$).

Enzymes

• Biological catalysts; lower activation energy of reactions.

• Highly specific for substrates.

• Classified by reaction type (e.g., oxidoreductases, transferases).

Prosthetic Groups and Coenzymes

• Prosthetic groups: Tightly bound, permanent (e.g., heme in cytochromes).

• Coenzymes: Loosely bound, transient (e.g., NAD+, FAD).

Factors Affecting Enzyme Activity

• Temperature, pH, substrate concentration, inhibitors.

• Allosteric inhibition: Regulator binds to site other than active site, changing enzyme shape and activity.

Oxidation and Reduction

• Oxidation: Loss of electrons.

• Reduction: Gain of electrons.

• Oxidizing agent: Accepts electrons.

• Reducing agent: Donates electrons.

Redox Tower

• Ranks substances by reduction potential (E').

• Greater difference between donor and acceptor = more energy released.

Glycolysis Overview

• Central pathway for glucose catabolism.

• Stage I: Energy investment (2 ATP used).

• Stage II: Energy payoff (4 ATP produced, net gain 2 ATP).

• End products: 2 pyruvate, 2 ATP (net), 2 NADH per glucose.

• Key enzymes: hexokinase, aldolase, pyruvate kinase, glyceraldehyde-3-phosphate dehydrogenase.

Appendix: Table - Comparison of Cell Wall Types

Feature	Gram-Positive	Gram-Negative	Archaea
Peptidoglycan Thickness	Thick	Thin	Absent (usually)
Outer Membrane	Absent	Present (LPS)	Absent
Sensitivity to Lysozyme	High	Low	Variable
Unique Features	Teichoic acids	LPS, porins	S-layer, pseudomurein

Additional info: Some explanations and examples were expanded for clarity and completeness based on standard microbiology textbooks.