Foundations of Microbiology: History, Chemistry, Cell Structure, and Metabolism

Chapter 1: A Brief History of Microbiology

Key Historical Figures and Discoveries

• Joseph Lister: Developed the aseptic technique, using carbolic acid to spray wounds and surgical tools, reducing infection rates.

• Florence Nightingale: Introduced cleanliness and other aseptic practices in nursing, significantly improving patient outcomes.

• Edward Jenner & Smallpox: Invented vaccination using cowpox to protect against smallpox.

• Carl Linnaeus: Developed the binomial naming system for organisms.

• Louis Pasteur: Father of microbiology; disproved spontaneous generation, developed pasteurization, and contributed to vaccine development.

• Francesco Redi & Spontaneous Generation: Disproved the idea that life could arise spontaneously from non-living matter.

Contributions of Microbes

• Fermentation

• Vitamins

• Decomposition

• Antibiotics

• Molecular Biology

Classification of Microorganisms

• Bacteria and Archaea: Prokaryotic, lack a nucleus, much smaller than eukaryotes.

• Eukaryotes: Have a nucleus, typically multicellular, include fungi, protozoa, algae, and animals.

• Viruses: Acellular, require a host to replicate.

• Algae: Photosynthetic eukaryotes.

• Fungi: Non-photosynthetic eukaryotes.

Germ Theory and Koch's Postulates

• Germ Theory (Pasteur): Microbes cause fermentation and disease.

• Koch's Postulates:

  1. Suspected agent is present in every diseased and absent in healthy organisms.

  2. Agent is isolated and grown outside the host.

  3. Agent causes disease in a healthy, susceptible host.

  4. Agent is found in newly diseased host.

Chapter 2: The Chemistry of Microbiology

Atomic Structure

• Protons and Neutrons: Located in the nucleus; atomic mass is the sum of protons and neutrons.

• Electrons: Orbit the nucleus; number of protons equals number of electrons in a neutral atom.

• Isotopes: Atoms of the same element with different numbers of neutrons.

Water and Chemical Bonds

• Polar Molecules: Water is polar because oxygen is more electronegative than hydrogen.

• Hydrogen Bonds: Weak attractions between polar molecules, important in DNA and protein structure.

• Ionic Bonds: Electrons are donated from one atom to another, forming charged ions (e.g., NaCl).

• Covalent Bonds: Electrons are shared between atoms.

Macromolecules

• Carbohydrates: Monosaccharides (simple sugars), disaccharides, polysaccharides; energy source and structural role.

• Lipids: Fats (triglycerides), phospholipids (major component of cell membranes), steroids (cholesterol).

• Proteins: Polymers of amino acids; structure determined by sequence and folding; functions include enzymes, transport, and signaling.

• Nucleic Acids: DNA and RNA; store and transmit genetic information; composed of nucleotides (sugar, phosphate, nitrogenous base).

Protein Structure

• Primary: Sequence of amino acids.

• Secondary: Alpha helices and beta sheets (hydrogen bonding).

• Tertiary: 3D folding due to side chain interactions.

• Quaternary: Multiple polypeptide chains.

Important Functional Groups

• Carboxyl, amino, hydroxyl, phosphate, methyl, R group: Determine properties and reactivity of molecules.

Chapter 3: Cell Structure and Function

Characteristics of Life

• Reproduction, growth, response to environment, metabolism.

Prokaryotes vs. Eukaryotes

Feature	Prokaryotes	Eukaryotes
Nucleus	No	Yes
Organelles	No	Yes
Cell Wall	Peptidoglycan (bacteria)	Cellulose/chitin (some)
Size	Small	Larger

Prokaryotic Cell Structure

• Cell Membrane: Phospholipid bilayer, fluid mosaic model.

• Cell Wall: Made of peptidoglycan (bacteria); Gram-positive (thick), Gram-negative (thin, outer membrane).

• Special Structures: Glycocalyx (capsule/slime layer), flagella, pili, fimbriae.

Eukaryotic Cell Structure

• Organelles: Nucleus, mitochondria, ER, Golgi, lysosomes, etc.

• Cell Wall: Present in plants, fungi (not in animals).

Chapter 4: Microbial Metabolism

Energy in Cells

• Cells need energy, usually obtained from oxidation of carbohydrates, lipids, or proteins.

Redox Reactions

• Oxidation: Loss of electrons.

• Reduction: Gain of electrons.

• Mnemonic: OIL RIG (Oxidation Is Loss, Reduction Is Gain).

Electron Carriers

• NAD+ and FAD carry electrons and hydrogen atoms during metabolism.

• Reduced forms: NADH, FADH2.

ATP Production

• ATP is produced by substrate-level phosphorylation, oxidative phosphorylation, and photophosphorylation.

Glucose Metabolism

• Glycolysis: Oxidizes glucose to pyruvate, produces ATP and NADH.

• Citric Acid Cycle: Pyruvate is converted to acetyl-CoA, enters the cycle, produces NADH, FADH2, CO2, and ATP.

• Electron Transport Chain: Uses electrons from NADH/FADH2 to generate ATP via a proton gradient.

Fates of Pyruvate

• Aerobic Respiration: Pyruvate → Acetyl-CoA → Citric Acid Cycle → Electron Transport Chain (final electron acceptor is O2).

• Anaerobic Respiration: Final electron acceptor is not O2 (e.g., nitrate, sulfate).

• Fermentation: Pyruvate is converted to lactic acid or ethanol; regenerates NAD+ for glycolysis.

ATP Yield

• Aerobic Respiration: Up to 38 ATP per glucose (in prokaryotes).

• Fermentation: Only 2 ATP per glucose.

Key Equations

• Glycolysis: $\text{Glucose} + 2\,\text{NAD}^+ + 2\,\text{ADP} + 2\,\text{P}_i \rightarrow 2\,\text{Pyruvate} + 2\,\text{NADH} + 2\,\text{ATP} + 2\,\text{H}_2\text{O}$

• Aerobic Respiration (overall): $\text{C}_6\text{H}_{12}\text{O}_6 + 6\,\text{O}_2 \rightarrow 6\,\text{CO}_2 + 6\,\text{H}_2\text{O} + \text{energy (ATP)}$