Comprehensive Study Guide: Microbiology Core Concepts

Roles of Microbes Beyond Disease

Beneficial Functions of Microbes

Microbes play essential roles in ecosystems and human health, far beyond causing disease.

• Decomposition: Microbes break down organic matter, recycling nutrients.

• Symbiosis: Many microbes form beneficial relationships with plants and animals (e.g., nitrogen-fixing bacteria in legumes).

• Biotechnology: Used in food production (yogurt, cheese), pharmaceuticals, and bioremediation.

• Microbiome: The collection of microbes living in and on humans, crucial for digestion, immunity, and health.

Microbial Ubiquity

Where Are Microbes Found?

Microbes inhabit nearly every environment on Earth.

• Soil, water, air: Found in extreme environments (hot springs, deep sea vents, polar ice).

• Human body: Skin, gut, mouth, and other surfaces.

• Other organisms: Plants, animals, and insects.

Binomial Nomenclature and Taxonomy

Classification and Naming of Microbes

Microbes are classified using a hierarchical system and named using binomial nomenclature.

• Binomial nomenclature: Each organism has a two-part scientific name: Genus species (e.g., Escherichia coli).

• How to write: Genus capitalized, species lowercase, both italicized.

• Taxonomic hierarchy: Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species (DKPCOFGS).

• Three domains: Bacteria, Archaea, Eukarya.

Characteristics of Microbes

Major Groups of Microbes

Microbes include diverse groups with unique characteristics.

• Bacteria: Prokaryotic, cell walls with peptidoglycan, diverse shapes.

• Archaea: Prokaryotic, cell walls without peptidoglycan, often extremophiles.

• Fungi: Eukaryotic, cell walls with chitin, includes yeasts and molds.

• Viruses: Acellular, require host for replication, consist of nucleic acid and protein coat.

• Protists: Eukaryotic, diverse group including algae and protozoa.

• Multicellular parasites: Eukaryotic, includes helminths (worms).

Disproving Spontaneous Generation

Historical Experiments

Spontaneous generation was disproved by experiments showing life arises from existing life.

• Louis Pasteur: Swan-neck flask experiment demonstrated microbes come from the environment, not spontaneously.

Koch’s Postulates and Limitations

Establishing Disease Causation

Koch’s postulates are criteria to link a microbe to a disease.

• Postulates: Microbe must be found in diseased organisms, isolated and grown, cause disease in healthy host, and be re-isolated.

• Limitations: Not all microbes can be cultured; some diseases are multifactorial.

Hand Washing in Medical Settings

Historical Context

Hand washing was delayed in medical practice due to lack of understanding of germ theory and resistance to change.

• Ignaz Semmelweis: Advocated hand washing to prevent puerperal fever.

Prokaryotes vs Eukaryotes

Comparative Features

Prokaryotes and eukaryotes differ in cellular structure and complexity.

• Prokaryotes: No nucleus, simple organelles, smaller size.

• Eukaryotes: Nucleus, complex organelles, larger size.

Bacterial Shape and Morphology

Classification by Shape

Bacteria are classified by their shape and arrangement.

• Cocci: Spherical

• Bacilli: Rod-shaped

• Spirilla: Spiral-shaped

• Arrangements: Chains (strepto-), clusters (staphylo-), pairs (diplo-)

External Bacterial Structures

Surface Features and Functions

Bacteria possess various external structures that aid in survival and pathogenicity.

• Capsule, slime layer, glycocalyx: Protective, aids in adhesion, evades immune response.

• Fimbriae: Attachment to surfaces.

• Flagella: Motility; arrangements include monotrichous, lophotrichous, amphitrichous, peritrichous.

• Pili: Conjugation (sex pilus), attachment.

Bacterial Cell Envelope

Cell Wall Structure and Composition

The cell envelope protects bacteria and determines their response to antibiotics.

• Peptidoglycan: Structural polymer in cell walls.

• Gram-positive: Thick peptidoglycan, teichoic acids.

• Gram-negative: Thin peptidoglycan, outer membrane with lipopolysaccharide (LPS), lipid A (endotoxin).

• Acid-fast: Mycolic acids, resistant to staining.

• Penicillin: Inhibits peptidoglycan synthesis.

Cell Membrane

The cell membrane is a phospholipid bilayer with amphipathic lipids.

• Composition: Phospholipids, proteins.

• Amphipathic lipid: Contains hydrophilic head and hydrophobic tail.

Internal Bacterial Components

Cellular Machinery

Bacteria contain essential internal structures for survival and replication.

• Ribosomes: Protein synthesis.

• Chromosome: Genetic material, usually circular.

• Plasmids: Extra-chromosomal DNA, often carry antibiotic resistance genes.

Endospores

Formation and Significance

Endospores are highly resistant structures formed by certain bacteria.

• Genera: Bacillus, Clostridium.

• Formation: Sporulation under stress.

• Concern: Resistant to heat, chemicals, and desiccation; difficult to eradicate.

Microbiome

Definition and Importance

The microbiome is the community of microbes living in and on the human body.

• Functions: Digestion, immune modulation, protection against pathogens.

• Importance: Essential for health; disruptions linked to disease.

Germ-Free Mice

Used to study the role of the microbiome by comparing normal and microbe-free animals.

Prebiotic and Probiotic

• Prebiotic: Non-digestible food ingredients that promote beneficial microbes.

• Probiotic: Live microbes administered to confer health benefits.

Bacterial Metabolism

Metabolic Processes

Bacterial metabolism includes all chemical reactions for energy and growth.

• Metabolism: Sum of all biochemical reactions.

• Catabolism: Breakdown of molecules, releases energy.

• Anabolism: Synthesis of molecules, requires energy.

• Exergonic: Energy-releasing reactions.

• Endergonic: Energy-consuming reactions.

• ATP/ADP: Energy currency; ATP is generated and used in cellular processes.

• Collision theory: Explains how molecules interact to form products.

Enzymes

Function and Regulation

Enzymes are biological catalysts that speed up reactions.

• Phosphorylation: Addition of phosphate group; three types: substrate-level, oxidative, photophosphorylation.

Cellular Respiration

Aerobic and Anaerobic Pathways

Bacteria use various pathways to generate energy.

• Glycolysis: Breakdown of glucose to pyruvate.

• Pentose-phosphate pathway: Generates NADPH and pentoses.

• Entner-Doudoroff pathway: Alternative to glycolysis in some bacteria.

• Electron carriers: NADH, FADH2 transport electrons.

• Citric acid cycle: Oxidizes acetyl-CoA, produces energy carriers.

• Electron transport chain (ETC): Transfers electrons, generates ATP; terminal electron acceptor varies (O2 for aerobic, other molecules for anaerobic).

• Location: ETC occurs in bacterial cell membrane.

• Fermentation: Anaerobic process, produces organic acids, alcohols.

Evolution

Genetic Variation and Adaptation

Microbial evolution is driven by genetic changes and environmental pressures.

• Genes and alleles: Units of heredity; alleles are variants.

• Mutations: Changes in DNA sequence.

• Selective pressure: Environmental factors favoring certain traits.

• Evolution: Change in allele frequency over time.

Microbial Growth

Growth Patterns and Factors

Bacteria reproduce by binary fission and exhibit characteristic growth curves.

• Binary fission: Asexual reproduction.

• Growth curve: Lag, log, stationary, death phases; nutrient availability and waste accumulation affect each phase.

• Long-term stationary phase: Population adapts, undulations reflect survival strategies.

• Factors impacting growth: Oxygen utilization (aerobes, anaerobes, facultative), temperature, pH.

• Exploiting factors: Used to control microbial growth (e.g., refrigeration, acidity).

• Lab vs environment: Growth conditions differ; eutrophic (nutrient-rich) vs oligotrophic (nutrient-poor).

• Persisters: Cells that survive stress, contribute to chronic infections.

Biofilms

Structure and Impact

Biofilms are communities of microbes attached to surfaces, exhibiting emergent properties.

• Emergent properties: New behaviors arise from community interactions (e.g., increased resistance).

• Impact on health: Biofilms cause persistent infections, resist antibiotics.

• Quorum sensing: Cell-to-cell communication regulates gene expression based on population density.

• Control methods: Physical removal, antibiotics, quorum sensing inhibitors; physical removal is often most effective.

Bacterial Genetics

Central Dogma and Gene Transfer

Bacterial genetics involves DNA replication, transcription, translation, and gene transfer mechanisms.

• DNA vs RNA: DNA is genetic material; RNA is involved in protein synthesis.

• Replication: DNA polymerase copies DNA.

• Transcription: RNA polymerase synthesizes RNA from DNA.

• Translation: Ribosomes synthesize proteins from mRNA.

• Origin of replication: Starting point for DNA replication.

• Sigma factor: Initiates transcription in prokaryotes.

• Coupled transcription and translation: Occurs simultaneously in prokaryotes.

Gene Transfer

• Vertical gene transfer: Parent to offspring; contributes to diversity.

• DNA pol IV and V: Specialized polymerases involved in DNA repair and mutagenesis.

• Horizontal gene transfer: Transfer between organisms; includes conjugation, transformation, transduction.

• Conjugation: F plasmid, relaxasome, transferasome, donor/recipient.

• Transformation: Uptake of DNA; competency required; used in medicine (e.g., insulin production).

• Transduction: Bacteriophage-mediated; lysogenic conversion can alter bacterial traits.

• Antibiotic resistance: Both vertical and horizontal transfer contribute.

Mechanisms of Antibiotic Resistance

How Bacteria Resist Antibiotics

Bacteria employ multiple strategies to evade antibiotics.

• Biofilm formation: Physical barrier.

• Impermeability: Reduced uptake.

• Modification of target: Altered binding sites.

• Inactivating enzymes: Destroy antibiotics (e.g., beta-lactamases).

• Pumps: Efflux pumps remove drugs.

• R factors: Plasmids carrying resistance genes.

Ames Test

Detecting Mutagenicity

The Ames test assesses the mutagenic potential of compounds using bacteria.

• Principle: Measures rate of mutation in Salmonella strains.

Viruses

Structure and Life Cycles

Viruses are acellular entities with unique replication cycles.

• Structure: Nucleic acid (DNA or RNA), protein coat (capsid), sometimes envelope.

• Life cycles: Animal viruses and bacteriophages follow distinct steps: attachment, entry, replication, assembly, release.

• Influenza: Annual vaccine changes due to antigenic variation.

• Spike proteins: Mediate attachment to host cells.

• Antigenic shift: Major changes, new strains.

• Antigenic drift: Minor changes, gradual evolution.

Microbe Type	Cell Type	Cell Wall	Reproduction
Bacteria	Prokaryote	Peptidoglycan	Binary fission
Archaea	Prokaryote	Varied, no peptidoglycan	Binary fission
Fungi	Eukaryote	Chitin	Sexual/asexual
Viruses	Acellular	None	Host-dependent
Protists	Eukaryote	Varied	Sexual/asexual
Helminths	Eukaryote	None	Sexual

Example: Insulin Production via Transformation

Bacterial transformation is used to produce human insulin by inserting the human insulin gene into bacteria.

Key Equations

• ATP Hydrolysis:

• $\mathrm{ATP} + \mathrm{H}_2\mathrm{O} \rightarrow \mathrm{ADP} + \mathrm{P}_i + \text{energy}$

• Glycolysis (overall):

• $\mathrm{C}_6\mathrm{H}_{12}\mathrm{O}_6 + 2\mathrm{NAD}^+ + 2\mathrm{ADP} + 2\mathrm{P}_i \rightarrow 2\mathrm{C}_3\mathrm{H}_4\mathrm{O}_3 + 2\mathrm{NADH} + 2\mathrm{ATP} + 2\mathrm{H}_2\mathrm{O}$

Additional info: This guide expands on brief outline points to provide academic context and examples for each topic, ensuring completeness for exam preparation.