Foundations of Microbiology: Cell Structure, Metabolism, and Microbial Diversity

Introduction to Microbiology

What is Microbiology?

Microbiology is the study of all living organisms that are too small to be visible with the naked eye. This includes bacteria, archaea, viruses, fungi, protozoa, and algae, collectively known as microbes.

• Microbes play essential roles in ecosystems, health, and industry.

• They are found in diverse environments, from soil and water to extreme habitats.

Main Similarities and Differences: Prokaryotes vs. Eukaryotes

Microbial cells are classified as either prokaryotic or eukaryotic based on their cellular structure.

• Prokaryotes: Bacteria and archaea; lack a nucleus, have small, circular DNA, single-celled, binary fission.

• Eukaryotes: Fungi, protists, plants, animals; nucleus, larger, linear chromosomal DNA, unicellular or multicellular, mitosis or meiosis.

• Both types have DNA, surrounded by cell membrane, contain cytoplasm, ribosomes.

Abundance and Diversity of Microbes

Microbes are highly abundant and diverse, making up a significant portion of Earth's biomass.

• Microbes make up 17% of Earth's biomass.

• They play critical roles in nutrient cycling, decomposition, and supporting life.

• Example: In one spill, microbes cleaned up about 50% of spilled oil by deepwater horizon.

Harmful vs. Beneficial Microbes

Most microbes are harmless or beneficial, but some can cause disease.

• Less than 1% of microbes are harmful.

• Many microbes are essential for health, nutrient cycling, and biotechnology.

Microbial Abundance in the Human Body

The human microbiome contains about 40 trillion bacterial cells and 60,000 genes, which perform functions that our body cannot do on its own.

• Microbiome functions: breakdown nutrients, synthesize vitamins, pathogen resistance, immune modulation.

Historical Perspective of Microbiology

Early Discoveries

• Robert Hooke: Used microscopes to view mold and individual "cells" in 1665; first to describe microorganisms.

• Antony van Leeuwenhoek: Discovered bacteria through microscopy in 1676; 200-300x magnification.

Louis Pasteur and His Contributions

• Discovered the microbial basis of fermentation.

• Studied crystals that formed in alcohol production.

• Observed two types with minor image structures.

Pasteurization

• Use of heat to control microbial growth.

• Boiled yeast extract/fruit juice: no fermentation.

• Added yeast: fermentation begins.

• Added bacteria: solutions spoil.

• Boil solution: wine does not spoil.

The Germ Theory of Disease

• Pasteur added scientists to the understanding that microbes cause disease.

• Robert Koch: Linked specific microbes to specific diseases (e.g., anthrax).

• Koch's Postulates: Associate a specific microbe with a specific disease.

Swan Neck Flasks and Spontaneous Generation

• Organisms only appear in broth after exposure to air; microbes can be transmitted through the air.

• Disproved spontaneous generation: life does not arise from nonliving matter.

Microbial Cell Structure and Function

Structural Differences: Prokaryotes vs. Eukaryotes

• Eukaryotes: Membrane-enclosed cell nucleus, genetic functions (DNA), many internal structures.

• Prokaryotes: Lack a cell nucleus, fewer organelles.

Common Bacterial Cell Morphologies

• Cocci: Spherical cells, diplo- (pairs), strepto- (chains), staphylo- (clusters).

• Bacilli: Rod-shaped.

• Spirilla, spirochetes: Spiral-shaped.

Macromolecules of the Cell

• Nucleic acids: Store genetic info (DNA, RNA).

• Proteins: Cell structure, catalysis, replication.

• Carbohydrates: Cell structure, energy storage.

• Lipids: Cell structure, energy storage.

Bacterial Cell Structures (Internal and External)

• Surface structures: Flagella (movement), pili/fimbriae (attachment).

• Cytoplasmic structures: Cytoplasm, ribosomes, inclusion bodies.

Cell Membrane: Composition and Function

• Made of lipids and proteins.

• Keeps inside in and outside out; controls passage of materials.

Cell Wall: Composition and Function

• Made of polysaccharides and carbohydrates.

• Provides structural support and protection.

Peptidoglycan and Protein Cross-links

• Gram-positive: Thick peptidoglycan, one cell membrane.

• Gram-negative: Thin peptidoglycan, inner and outer cell membrane, lipopolysaccharides (LPS).

• Penicillin: Disrupts peptidoglycan synthesis.

Structure of Prokaryotic Chromosome (Circular)

• Single, circular DNA molecule.

• Plasmids: small DNA molecules that replicate independently.

Motility and Surface Structures

• Flagella: Movement.

• Pili/fimbriae: Attachment.

• Slime secretion: Glides over surfaces.

Capsules and Slime Layer (Environmental Importance)

• Capsule: Carbohydrate "snot"; protects cell from drying out, chemicals, and environmental stress.

Microbial Metabolism and Energy

Enzymes and Metabolism

Enzymes are proteins that catalyze metabolic reactions, increasing the rate and specificity of chemical processes in cells.

• Highly specific, reusable, required in small amounts.

• Run on ATP (adenosine triphosphate).

Catabolic and Anabolic Reactions

• Catabolic: Decomposition, makes energy, breaks down molecules.

• Anabolic: Synthesis, uses energy, builds molecules.

Redox Reactions and Electron Transfer

• Oxidation: Loss of electrons.

• Reduction: Gain of electrons.

• Carried by molecules like NAD/NADH or FAD/FADH2.

Energy Coupling and ATP

• Catabolic reactions release energy, stored in ATP.

• Anabolic reactions use ATP for biosynthesis.

ATP Hydrolysis Equation:

$\text{ATP} \rightarrow \text{ADP} + \text{P}_i$

Classification of Microbes by Energy and Carbon Source

• Chemotrophs: Carbon-organic, energy-organic compound.

• Phototrophs: Carbon-CO2, energy-light.

• Chemoautotrophs: Carbon-CO2, energy-inorganic compounds.

Respiration and Utilization of Glucose

• Aerobic respiration: Uses oxygen as terminal electron acceptor.

• Anaerobic respiration: Uses non-oxygen electron acceptors (nitrate, sulfate, etc.).

• Fermentation: Energy from substrate-level phosphorylation, no ETC.

Function of Terminal Electron Acceptors

• Remove electrons from ETC, prevent backup, allow continuous ATP production.

Function of NAD and NADH

• NAD+: Electron acceptor, accepts electrons and a proton during metabolism.

• NADH: Electron donor in electron transport chain (oxidative phosphorylation).

Aerobic Respiration: Glycolysis and TCA Cycle

• Glycolysis: 2 ATP, 2 NADH produced per glucose.

• Pyruvate oxidation: 2 NADH produced per glucose.

• Krebs cycle: 2 ATP, 2 FADH2, 4 NADH produced per glucose.

Fermentation (Industrial and Environmental Importance)

• Energy from substrate-level phosphorylation in absence of oxygen.

• Produces alcohol, lactic acid, and other products.

Differences Between Types of Microbial Metabolism

Type	Electron Acceptor	Electron Donor	Products
Aerobic Respiration	O2	Glucose, fatty acids	CO2, H2O, ATP
Anaerobic Respiration	Nitrate (NO3-), Sulfate (SO42-), etc.	Glucose, fatty acids	CO2, ATP, reduced acceptors
Fermentation	Organic molecules	Glucose	Alcohol, lactic acid, ATP

Industrial Applications of Microbes

Microbes in Industry

• Microbes are used for production of antibiotics, enzymes, alcohol, and other chemicals.

• They play roles in bioremediation, waste treatment, and food production.

Microbes and Disease

• Microbes cause infectious diseases, but also contribute to health (e.g., gut microbiome).

• Disease outbreaks are increasing due to travel, urbanization, and poverty.

Additional info:

• Binomial nomenclature is the formal system of naming species using Latinized names: genus and species.

• Microbial cell wall composition is critical for antibiotic targeting.

• Environmental factors can affect microbial cell shape and arrangement.