Microbiology: Foundations, Cell Structure, and Metabolism Study Guide

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Microbiology and Its Historical Foundations

History of Microbiology

Microbiology has shaped human history through its impact on health, science, and technology. Understanding its origins provides context for modern advances.

Smallpox Epidemic (1837) and the Mandan Nation: The devastating effects of infectious diseases on populations, such as the Mandan nation, highlight the importance of microbiology in public health.
Louis Pasteur: Developed the germ theory of disease, disproved spontaneous generation, and pioneered vaccination and pasteurization.
Robert Koch: Established Koch's postulates, identified causative agents of tuberculosis and anthrax, and advanced laboratory techniques.
Areas of Agreement: Both emphasized the microbial cause of disease.
Areas of Disagreement: Differences in experimental approaches and interpretation of results.
Origin of Aseptic Surgery: Introduction of sterile techniques in surgery to prevent infection.
Antimicrobial Drug Therapy: Development of antibiotics and chemotherapeutic agents to treat microbial infections.
21st Century Health Challenges: Emerging infectious diseases, antibiotic resistance, and global pandemics.

Three Domains of Life

The classification of life into three domains reflects fundamental differences in cellular structure and genetics.

Bacteria: Prokaryotic, peptidoglycan cell wall, no nucleus.
Archaea: Prokaryotic, unique membrane lipids, cell wall without peptidoglycan.
Eukarya: Eukaryotic, membrane-bound organelles, nucleus, linear chromosomes.

Domain	Cell Type	Cell Wall	Membrane Lipids	Genetic Material
Bacteria	Prokaryotic	Peptidoglycan	Ester-linked	Circular, no histones
Archaea	Prokaryotic	Pseudomurein/S-layer	Ether-linked	Circular, +/- histones
Eukarya	Eukaryotic	Varied	Ester-linked	Linear, histones

Microscopy and Cell Visualization

Types of Microscopy

Microscopy is essential for visualizing microbial cells and their structures. Each type offers unique advantages for studying different cell features.

Brightfield Light Microscopy: Uses visible light; specimens often stained for contrast. Best for general cell morphology.
Gram Stain: Differentiates bacteria by cell wall structure (Gram-positive vs. Gram-negative).
Negative Stain: Highlights cell capsules by staining the background.
Endospore Stain: Identifies bacterial endospores.
Phase Contrast Microscopy: Enhances contrast in unstained cells; ideal for live specimens.
Darkfield Microscopy: Illuminates specimens against a dark background; useful for motile bacteria.
Fluorescence Microscopy: Uses fluorescent dyes or proteins; includes immunofluorescence and FISH (fluorescence in-situ hybridization).
Transmission Electron Microscopy (TEM): High resolution; thin sectioning, negative staining, cryo-TEM for internal structures.
Scanning Electron Microscopy (SEM): Surface visualization in 3D.
X-ray Crystallography: Determines atomic structure of macromolecules.

Microscopy Type	Resolution	Best Visualized Structures
Brightfield	~0.2 µm	Cell shape, stained cells
Phase Contrast	~0.2 µm	Live cells, internal structures
Darkfield	~0.2 µm	Motile cells
Fluorescence	~0.2 µm	Specific molecules, tagged cells
TEM	~0.2 nm	Internal ultrastructure
SEM	~1-10 nm	Surface topology
X-ray Crystallography	~0.1 nm	Macromolecular structure

Prokaryotic Cell Structure

Bacterial Cell Envelope

Bacterial cell envelopes are critical for protection, nutrient transport, and interaction with the environment.

Plasma Membrane: Composed of phospholipids and proteins; selective barrier.
Peptidoglycan: Carbohydrate strands (N-acetylglucosamine and N-acetylmuramic acid) cross-linked by peptides; provides rigidity.
Gram-Positive Envelope: Thick peptidoglycan layer, lipoteichoic acids.
Gram-Negative Envelope: Thin peptidoglycan, periplasmic space, outer membrane with phospholipids, lipopolysaccharides (LPS), and porins.
LPS Structure: Lipid A (endotoxin), core polysaccharide, O-antigen; important in immune response.

Bacterial Motility

Flagella: Helical filaments powered by proton motive force; enable swimming.
Periplasmic Flagella (Spirochetes): Bundles within periplasm; cause corkscrew motion.
Gliding and Twitching Motility: Surface movement via pili or secreted slime.

Bacterial Genetics and Internal Structures

Chromosome Topology: Circular chromosomes, high gene density, lack histones.
Plasmids: Small, circular DNA molecules; often carry antibiotic resistance genes.
Ribosomes: 70S (smaller than eukaryotic 80S); similar to Archaea but differ in protein and rRNA sequence.
Inclusions: Storage granules (hydroxybutyrate, phosphate, sulfur, magnetite).
Thylakoids: Membrane structures in cyanobacteria for photosynthesis.

Archaeal Cell Structure

Membrane Lipids: Glycerol phosphate diether phytanyl bilayer or tetraether monolayer; ether-linked for stability.
Cell Wall: Pseudomurein or S-layer (protein lattice).
Chromosomes: Circular, may have histones.
Archaella: Similar to flagella; powered by ATP.

Eukaryotic Cell Structure

Nuclear Envelope: Surrounds linear chromosomes; histones present.
Endomembrane System: Includes rough ER, Golgi apparatus, transport vesicles; involved in protein secretion.
Organelles: Mitochondria (energy), lysosomes (digestion), chloroplasts (photosynthesis).
Cytoskeleton: Microtubules, microfilaments, intermediate filaments; structural support and movement.
Cilia and Flagella: Complex structures for motility; powered by ATP.

Microbial Metabolism and Energy

Energy, Enzymes, and Thermodynamics

Microbial metabolism is governed by the principles of energy transformation and enzyme catalysis.

Work: Energy transfer for movement, synthesis, or transport.
First Law of Thermodynamics: Energy cannot be created or destroyed.
Second Law of Thermodynamics: Entropy (disorder) increases in spontaneous processes.
Enthalpy (H): Total heat content.
Endothermic: Absorbs heat; Exothermic: Releases heat.
Entropy (S): Measure of disorder.
Free Energy (G): Energy available to do work.
Exergonic Reaction: Releases energy; spontaneous.
Endergonic Reaction: Requires energy input; non-spontaneous.
Activation Energy: Energy required to initiate a reaction.
Catalyst: Substance that increases reaction rate without being consumed.
Enzyme: Biological catalyst; highly specific and efficient.
Effect of pH and Temperature: Enzyme activity is optimal at specific pH and temperature; extremes can denature enzymes.
Metabolic Pathway: Series of enzyme-catalyzed reactions.

Chemoheterotrophic Metabolism

Chemoheterotrophs obtain energy and carbon from organic compounds through respiration and fermentation.

Respiration: Oxidation of organic molecules to generate ATP.
Oxidation-Reduction Reaction: Transfer of electrons between molecules.
Standard Reduction Potential (E0): Used to calculate free energy change ().
NAD+/NADH and FAD+/FADH2: Electron carriers in respiration.
Ultimate Fate of NADH: Oxidized in electron transport chain to regenerate NAD+.
Glycolysis: Occurs in cytoplasm; converts glucose to pyruvate, produces ATP and NADH.
Krebs Cycle: Occurs in cytoplasm (prokaryotes) or mitochondria (eukaryotes); oxidizes acetyl-CoA, produces NADH, FADH2, CO2.
Electron Transport Chain: Located in plasma membrane (prokaryotes) or mitochondrial inner membrane (eukaryotes); requires oxygen for aerobic respiration.
Substrate-Level Phosphorylation: Direct transfer of phosphate to ADP to form ATP.
Fermentation: Allows glycolysis to continue without oxygen; produces lactic acid (muscle), ethanol (yeast), etc.
Citric Acid Cycle: Starting materials: Acetyl-CoA; products: CO2, NADH, FADH2, ATP.
Role of Coenzyme A: Carries acetyl group into Krebs cycle.
Electron Transport Chain Components: NADH dehydrogenase, cytochromes, cytochrome oxidase, ATP synthase; protons translocated to create gradient.
ATP Synthase: Uses proton gradient to synthesize ATP ().

Pathway	Location	Requires Oxygen?	Products
Glycolysis	Cytoplasm	No	Pyruvate, ATP, NADH
Krebs Cycle	Cytoplasm/Mitochondria	No	CO2, NADH, FADH2, ATP
Electron Transport Chain	Membrane	Yes (aerobic)	ATP, H2O

Microbial Diversity in Energy and Carbon Acquisition

Chemoheterotrophs: Use organic compounds for energy and carbon.
Chemoautotrophs: Use inorganic compounds for energy, CO2 for carbon.
Photoautotrophs: Use light for energy, CO2 for carbon.
Photoheterotrophs: Use light for energy, organic compounds for carbon.

Acquisition of CHONPS Elements

Carbon: Organic or inorganic sources.
Hydrogen: Water, organic compounds.
Oxygen: Water, O2 gas.
Nitrogen: Ammonia, nitrate, atmospheric N2.
Phosphorus: Inorganic phosphate.
Sulfur: Sulfate, sulfide.
Selective Media: Designed based on nutrient requirements to grow specific microbes.

Anaerobic Respiration and Chemolithotrophy

Anaerobic Respiration

Some microbes use alternative electron acceptors in the absence of oxygen.

Denitrification: Reduction of nitrate to dinitrogen gas; intermediates include nitrite, nitric oxide, nitrous oxide.
Microbes: Paracoccus can perform complete denitrification; others only reduce nitrate to nitrite.
Sulfate Respiration: Used by sulfate-reducing bacteria in anaerobic environments; product is hydrogen sulfide (H2S).

Chemolithotrophy

Electron Donors: Ammonia, hydrogen, iron, sulfur compounds.
Products: Nitrate, water, ferric iron, sulfate.
Free Energy Calculation:
Ammonia Oxidation (Nitrosomonas): Ammonia oxidized to nitrite; electron transport chain similar to mitochondria but uses different electron donors.

Phototrophy and Autotrophy

Phototrophy

Microbes harness light energy to drive electron transport and ATP synthesis.

Oxygenic Photosynthesis: Electrons from water; produces O2; proton gradient generated across thylakoid membrane.
Anoxygenic Photosynthesis: Electrons from H2S or other donors; no O2 produced.
Electron Flow: Electrons enter at photosystem, leave via NADP+ reduction.

Autotrophy and Carbon Fixation

Calvin Cycle: Fixes CO2 into organic molecules; key intermediates include ribulose-1,5-bisphosphate, 3-phosphoglycerate.
Enzymes: Rubisco catalyzes CO2 fixation.
Similarity to Other Pathways: Some steps resemble glycolysis and pentose phosphate pathway.
Reductive Citric Acid Cycle: Fixes CO2 using reverse steps of Krebs cycle; starting materials: CO2, products: acetyl-CoA, organic acids.