Classification and Evolution in Microbiology

Major Groups of Organisms

Microbiology studies a variety of organisms, including bacteria, archaea, fungi, protozoa, algae, and viruses. Each group has distinct characteristics:

• Bacteria: Prokaryotic, unicellular, diverse metabolic capabilities.

• Archaea: Prokaryotic, often extremophiles, unique membrane lipids.

• Fungi: Eukaryotic, includes yeasts and molds, decomposers.

• Protozoa: Eukaryotic, unicellular, often motile.

• Algae: Eukaryotic, photosynthetic, aquatic.

• Viruses: Acellular, require host for replication.

Carolus Linnaeus and Modern Classification

Carolus Linnaeus grouped organisms based on visible characteristics, using a hierarchical system (Kingdom, Phylum, Class, Order, Family, Genus, Species). Today, classification relies on genetic similarities, especially ribosomal RNA sequences.

• Binomial Nomenclature: Each organism is named with a genus and species (e.g., Escherichia coli).

• Phylogenetic Trees: Visual representations of evolutionary relationships based on genetic data.

Archaea: Prokaryotic or Eukaryotic?

Archaea are prokaryotic (lack a nucleus), but genetically, they are more closely related to eukaryotes than to bacteria. This is determined by comparing ribosomal RNA and other molecular markers.

Biochemical Tests and Phylogenetic Trees

• Biochemical Tests: Used to identify microbes based on metabolic activities (e.g., fermentation, enzyme production).

• Phylogenetic Trees: Show evolutionary relationships; viruses are excluded because they lack conserved genes used in tree construction.

Evolutionary Principles

• Natural Selection: Process where organisms with advantageous traits survive and reproduce.

• Evolution: Change in genetic composition of populations over time.

Important Microbes and Microbiota

• Alcanivorax borkumensis: Bacteria important for oil degradation in marine environments.

• Resident Microbiota: Non-pathogenic bacteria in the gut aid digestion and protect against pathogens.

Cell Structure and Function

Prokaryotic vs. Eukaryotic Cells

• Prokaryotic: No nucleus, simple structure, includes bacteria and archaea.

• Eukaryotic: Nucleus, complex organelles, includes fungi, protozoa, algae.

• Acellular: Not composed of cells (e.g., viruses).

Cell Theory

States that all living things are composed of cells, cells are the basic unit of life, and all cells arise from pre-existing cells.

Endosymbiotic Theory

Explains the origin of mitochondria and chloroplasts in eukaryotes as formerly free-living prokaryotes engulfed by ancestral eukaryotic cells.

Germ Theory of Disease

Proposes that microorganisms cause disease. Key contributors include:

• Louis Pasteur: Swan neck flask experiment disproved spontaneous generation.

• Ignaz Semmelweis: Observed handwashing reduced puerperal fever.

• John Snow: Traced cholera outbreak to contaminated water.

• Joseph Lister: Demonstrated antiseptic techniques; Listerine named after him.

• Koch's Postulates: Criteria to link a microbe to a disease.

Cell Wall Composition

• Gram Positive: Thick peptidoglycan, teichoic acids.

• Gram Negative: Thin peptidoglycan, outer membrane with lipopolysaccharide.

• Mycolic Acid (Acid Fast): Waxy cell wall, e.g., Mycobacterium.

• Teichoic Acid: Associated with Gram-positive cell walls; important in MRSA resistance.

Cell Morphology and Arrangements

• Shapes: Cocci (spherical), bacilli (rod-shaped), spirilla (spiral).

• Arrangements: Chains, clusters, pairs.

Osmosis and Osmotic Pressure

• Osmosis: Movement of water across a membrane.

• Osmotic Pressure: Pressure exerted by solutes; cells manage it via cell walls or contractile vacuoles.

• Hypertonic: Cell loses water, shrinks.

• Isotonic: No net water movement.

• Hypotonic: Cell gains water, may burst.

Inclusions and Endospores

• Inclusions: Storage granules for nutrients.

• Endospores: Resistant structures formed by Bacillus and Clostridium species; survive harsh conditions.

• Vegetative Cell: Active, growing cell.

Membrane Transport

• Simple Diffusion: Movement of molecules from high to low concentration.

• Facilitated Diffusion: Uses transport proteins.

• Active Transport: Requires energy (ATP).

Ribosomes

• Prokaryotic Ribosomes: 70S (30S + 50S subunits).

• Eukaryotic Ribosomes: 80S (40S + 60S subunits).

• Clinical Importance: Antibiotics target prokaryotic ribosomes.

Endomembrane System

Includes the endoplasmic reticulum, Golgi apparatus, vesicles; responsible for protein and lipid trafficking.

Biomolecules and Chemical Bonds

Covalent, Ionic, and Hydrogen Bonds

• Covalent Bonds: Atoms share electrons.

• Polar Covalent Bonds: Unequal sharing, leads to partial charges.

• Ionic Bonds: Transfer of electrons, forms charged ions.

• Hydrogen Bonding: Weak attraction between polar molecules.

Functional Groups, Hydrophilic, Hydrophobic

• Functional Groups: Specific groups of atoms (e.g., hydroxyl, carboxyl) that determine chemical properties.

• Hydrophilic: Water-loving, polar.

• Hydrophobic: Water-fearing, nonpolar.

Recognizing Biomolecules

• Glucose: Monosaccharide, energy source.

• Starch vs. Glycogen vs. Cellulose: Polysaccharides; starch (plants), glycogen (animals), cellulose (structural).

• Triglyceride: Glycerol + 3 fatty acids.

• Fatty Acid: Long hydrocarbon chain with carboxyl group.

• Phospholipid: Glycerol, 2 fatty acids, phosphate group; forms bilayer.

• Amino Acids: Building blocks of proteins; peptide bond forms via dehydration reaction.

• Steroids: Four fused rings; cholesterol is a key example.

• HDL vs. LDL: High-density vs. low-density lipoproteins; statins lower LDL.

Protein Structure

• Primary: Sequence of amino acids.

• Secondary: Alpha helices, beta sheets.

• Tertiary: 3D folding.

• Quaternary: Multiple polypeptides.

• Cystic Fibrosis: Caused by misfolded protein.

Conjugated Proteins

Proteins combined with non-protein components (e.g., glycoproteins, lipoproteins).

Dehydration Reaction vs. Hydrolysis

• Dehydration: Forms bonds by removing water.

• Hydrolysis: Breaks bonds by adding water.

Macromolecule Functions

Deoxyribose vs. Ribose

• Deoxyribose: Sugar in DNA, lacks an oxygen atom.

• Ribose: Sugar in RNA.

Microbial Metabolism

Endergonic and Exergonic Reactions

• Endergonic: Require energy input.

• Exergonic: Release energy.

Reaction Pathway (Diagram)

Shows energy changes during a reaction; activation energy is required to start.

NAD+/NADH, FAD/FADH2

• NAD+ and FAD: Electron carriers in metabolism.

• NADH and FADH2: Reduced forms, donate electrons to electron transport chain.

ATP: Formation and Function

• ATP: Adenosine triphosphate, main energy currency.

• Formation: Substrate-level and oxidative phosphorylation.

• Function: Powers cellular reactions by transferring phosphate.

Enzymes

• Function: Catalyze reactions by lowering activation energy.

• Holoenzyme: Complete enzyme with cofactors.

• Apoenzyme: Protein part only.

• Competitive Inhibition: Inhibitor binds active site.

• Non-competitive Inhibition: Inhibitor binds elsewhere, changes enzyme shape.

Glycolysis, Krebs Cycle, Electron Transport Chain

• Glycolysis: Occurs in cytoplasm; breaks glucose into pyruvate.

• Krebs Cycle: Occurs in cytoplasm (prokaryotes) or mitochondria (eukaryotes).

• Electron Transport Chain: Plasma membrane (prokaryotes), mitochondrial membrane (eukaryotes).

Fermentation and Lactic Acid Formation

• Fermentation: Anaerobic process; regenerates NAD+.

• Lactic Acid Formation: Occurs in muscle cells and some bacteria.

Microbial Growth and Genetics

Biofilms and Quorum Sensing

• Biofilms: Communities of microbes attached to surfaces.

• Quorum Sensing: Cell-to-cell communication to coordinate behavior.

Binary Fission

Process by which bacteria reproduce; cell divides into two identical cells.

Genetics and DNA Structure

• Gregor Mendel: Father of genetics; studied inheritance.

• Chromosomal Theory of Inheritance: Genes are located on chromosomes.

• Hammerling Experiments: Showed nucleus controls heredity.

• Nucleotide Structure: Phosphate, sugar, base.

• Pyrimidine vs. Purine: Pyrimidines (C, T, U), Purines (A, G).

• DNA Structure: Double helix; bases held by hydrogen bonds.

• Chargaff's Rules: ,

• Denaturing DNA: Breaks hydrogen bonds, separates strands.

• DNA vs. RNA: DNA has deoxyribose, thymine; RNA has ribose, uracil.

• tRNA Structure: Cloverleaf shape; carries amino acids.

• Centromere: Region joining sister chromatids.

• Histone Proteins: Package DNA.

• Nucleosome: DNA wrapped around histones.

• Solenoid: Higher-order DNA structure.

• Plasmid DNA: Small, circular DNA in bacteria.

Bacterial Growth Calculation

Bacterial growth is exponential. The formula for population size after n generations:

• Where is the initial number of cells, is the number of generations.

Essay Topics Overview

• Cholesterol: Structure, function in membranes, health implications.

• Competitive vs. Non-competitive Inhibition: Mechanisms and effects on enzyme activity.

• ETC in Eukaryotes vs. Prokaryotes: Location and differences.

• Glycolysis and Krebs Cycle: Steps, products, significance.