Foundations of Microbiology: Cell Structure, Function, and Bioenergetics

Microbiology: Introduction and Importance

Definition and Scope

Microbiology is the study of organisms that are too small to be seen with the naked eye, such as bacteria, viruses, fungi, and protozoa. These organisms require a microscope for observation and play essential roles in ecosystems and human health.

• Microorganisms: Include bacteria, archaea, viruses, fungi, and protozoa.

• They are among the oldest forms of life and are crucial for nutrient cycling and biotechnology.

Historical Contributions

• Louis Pasteur: Disproved spontaneous generation; demonstrated that microorganisms cause fermentation and disease.

• Robert Koch: Initiated pure bacterial culture techniques; established Koch's postulates for linking microbes to diseases.

• Beijerinck: Isolated pure bacterial cultures; first to identify viruses (tobacco mosaic virus).

• Winogradsky: Discovered nitrogen cycling in soil and the atmosphere; identified chemolithotrophy.

Laboratory Microscopes

Brightfield Microscopes

Brightfield microscopes are commonly used in microbiology labs to observe stained specimens.

• Magnification: Total magnification = ocular lens magnification × objective lens magnification. Typical objectives: 4X, 10X, 40X, 100X (oil immersion). Maximum magnification is usually 1000X.

• Resolution: The ability to distinguish two points as separate. Calculated as $R = 0.5 \lambda / \text{NA}$, where $\lambda$ is the wavelength of light and NA is the numerical aperture.

Increasing Contrast with Staining

• Simple Stain: Uses one dye.

• Differential Stain: Uses two or more dyes (e.g., Gram stain).

• Dyes: Acidic dyes bind to positive charges; basic dyes bind to negative charges.

• Gram Stain Results: Gram-positive cells appear purple; Gram-negative cells appear pink.

Electron Microscopes

Electron microscopes use electrons instead of light, providing much higher resolution (up to 0.2 nm, 100,000X greater than light microscopes).

Cell Morphology and Arrangement

Shapes and Arrangements

• Cocci: Spherical shape. Arrangements include diplococci (pairs), streptococci (chains), staphylococci (clusters), tetrads (groups of four), and sarcina (groups of eight).

• Bacilli: Rod shape. Arrangements include diplobacilli (pairs), streptobacilli (chains), corynebacterium, and palisades.

• Spirochete: Thin, helical, or spiral shape.

• Spirillum: Spiral shape.

• Vibrio: Curved rod shape.

• Pleomorphic: Variable shapes.

• Coccobacillus: Shape between cocci and bacilli.

• Aggregate: Cells that bind to each other.

Surface Area to Volume Ratio

A high surface area to volume ratio (S/V) allows for efficient nutrient exchange and faster growth. The surface area (S) of a sphere is $4\pi r^2$, and the volume (V) is $\frac{4}{3}\pi r^3$. Thus, $S/V = 3/r$.

• Smaller cells have a larger S/V ratio, which is ideal for fast growth.

• Example: E. coli S/V = 4.5; Mycoplasma S/V = 22.

Cell Membranes

Phospholipid Bilayer

The cell membrane is composed of a phospholipid bilayer with hydrophilic heads and hydrophobic tails.

Archaea vs. Bacteria/Eukaryotic Membranes

• Linkage: Archaeal membranes have ether linkages; bacteria/eukaryotes have ester linkages.

• Carbon Chains: Archaeal membranes have branched isoprenoid chains; bacteria/eukaryotes have fatty acids.

• Structure: Archaeal membranes can form monolayers or bilayers.

• Lipids: Archaeal membranes have more unsaturated lipids.

Membrane Transport

• Selective Permeability: Only certain molecules can cross the membrane.

• Passive Transport: No energy required; moves chemicals down a concentration gradient.

• Diffusion: Passive movement of molecules.

• Osmosis: Diffusion of water across the membrane.

• Active Transport: Requires ATP to move chemicals against a concentration gradient.

Solutions and Cell Lysis

• Isotonic: Equal solute concentration inside and outside the cell.

• Hypotonic: Lower solute concentration outside; water enters cell, may cause lysis.

• Hypertonic: Higher solute concentration outside; water leaves cell, may cause shrinkage.

Eukaryotic Cell Membranes

• Contain sterols (e.g., cholesterol) for stabilization.

• Can perform endocytosis and exocytosis.

Cell Walls

Gram-Positive vs. Gram-Negative Cell Walls

• Gram-Positive: Thick peptidoglycan layer (20-30 layers), contains teichoic acids and proteins.

• Gram-Negative: Outer membrane, thin peptidoglycan, periplasmic space, lipopolysaccharide (LPS).

• Archaea: No peptidoglycan; may have S-layer or pseudopeptidoglycan.

Gram-Negative LPS Structure

Component	Description
Lipid A	Fatty acids inserted into outer membrane; acts as endotoxin.
Core Polysaccharide	Conserved chain of sugars attached to Lipid A.
O-side chain	Variable chain of sugars; defines bacterial strain (e.g., E. coli O157:H7).

Biofilms, Endospores, and Motility

• Biofilm: Community of microorganisms adhering to surfaces; increases resistance to chemicals and antibiotics.

• Capsule/Slime Layer: Polysaccharide layer for protection and adherence.

• Bacterial Endospores: Dormant, non-reproductive structures for survival under harsh conditions.

• Motility: Individual cell movement (e.g., flagella).

• Swarming: Group movement of cells.

Prokaryotic vs. Eukaryotic Cells

• Prokaryotes: No nucleus, single circular DNA, 70S ribosomes, divide by binary fission.

• Eukaryotes: Nucleus, multiple linear chromosomes, 80S ribosomes, divide by mitosis/meiosis.

• Endosymbiotic Theory: Mitochondria and chloroplasts originated from prokaryotic cells; both have double membranes, their own DNA, and divide by binary fission.

Bioenergetics and Metabolism

Energy in Cells

• Exergonic Reactions: Release free energy ($\Delta G$ is negative).

• Endergonic Reactions: Require free energy ($\Delta G$ is positive).

• Redox Reactions: Involve transfer of electrons. OIL RIG: Oxidation Is Loss, Reduction Is Gain (of electrons).

• Electron Carriers: NAD+, NADP+, FAD (oxidized forms); NADH, NADPH, FADH2 (reduced forms).

Metabolic Strategies

• Aerobic: Final electron acceptor is oxygen.

• Anaerobic: Final electron acceptor is not oxygen (e.g., Fe, NO3-, SO42-).

Cellular Respiration

1. Glycolysis: Breaks down glucose (6C) into two pyruvate (3C), net gain of 2 ATP and 2 NADH per glucose.

2. Citric Acid Cycle (CAC): Pyruvate converted to acetyl-CoA, enters CAC, produces CO2, NADH, FADH2, and GTP/ATP.

3. Electron Transport Chain (ETC): Series of protein carriers in membrane; electrons transferred from NADH/FADH2 to oxygen (aerobic) or other acceptors (anaerobic), generating ATP.

• ATP Yield: Prokaryotes: 36 ATP/glucose; Eukaryotes: 38 ATP/glucose.

• ETC produces most ATP: 30 from NADH, 4 from FADH2, plus 4 from glycolysis and CAC.

Catabolism

Catabolism is the breakdown of molecules to produce ATP. Main pathways: glycolysis and citric acid cycle.

Summary Table: Gram-Positive vs. Gram-Negative Cell Walls

Feature	Gram-Positive	Gram-Negative
Peptidoglycan	Thick (20-30 layers)	Thin (1-2 layers)
Teichoic Acids	Present	Absent
Outer Membrane	Absent	Present (contains LPS)
Periplasmic Space	Small or absent	Large
Stain Color	Purple	Pink

Additional info:

• Some context and explanations have been expanded for clarity and completeness.

• Tables have been reconstructed and summarized for key comparisons.