Microbiology Exam 1 Study Guide: Foundations, Cell Structure, and Metabolism

Study Guide - Smart Notes

Tailored notes based on your materials, expanded with key definitions, examples, and context.

History of Microbiology

Key Scientists and Their Contributions

The development of microbiology as a science was shaped by the discoveries and innovations of several key scientists. Their work laid the foundation for our understanding of microorganisms and their roles in health, disease, and the environment.

Louis Pasteur: Developed vaccines for tetanus, rabies, chicken cholera, and anthrax; invented pasteurization to prevent spoilage; used the swan neck flask to disprove spontaneous generation.
Robert Koch: Studied anthrax in cattle; established the link between specific microbes and diseases; discovered Mycobacterium tuberculosis; formulated Koch’s postulates.
Sergei Winogradsky: Identified prokaryotes that metabolize inorganic molecules; father of environmental microbiology; discovered chemoautotrophy (chemosynthesis).
Martinus Beijerinck: Discovered viruses; founded virology.
Antonie van Leeuwenhoek: Created the first microscope for visualizing bacteria.
John Needham: Supported spontaneous generation (heated broth, left open, observed growth).
Lazzaro Spallanzani: Disproved spontaneous generation (heated broth, sealed flask, no growth).
Christian Ehrenberg: Named "bacterium."
Ferdinand Julius Cohn: Systematically classified bacteria; described the first Bacillus spore.
Sir Alexander Fleming: Discovered penicillin from Penicillium notatum.
Alice Catherine Evans: Demonstrated that raw milk contained Bacillus abortus, causing brucellosis.

Debunking Spontaneous Generation

Needham (1745): Heated broth, left flask open, observed microbial growth.
Spallanzani (1765): Heated broth, sealed flask, no growth.
Pasteur (1861): Swan neck flask prevented airborne microbes from contaminating broth, disproving spontaneous generation.

Germ Theory of Disease

States that infectious diseases are caused by pathogenic microorganisms.
Koch (1876): Proved specific microbes cause specific diseases; developed Koch’s postulates.
Joseph Lister: Used antiseptic techniques in surgery, reducing wound infections.

Koch’s Postulates

Suspected pathogen must be present in all cases of disease and absent from healthy animals.
Pathogen must be grown in pure culture.
Cells from pure culture must cause disease in healthy animal.
Pathogen must be reisolated and shown to be the same as the original.

Cellular Organization: Prokaryotes vs. Eukaryotes

Structural and Genetic Differences

Prokaryotes (Bacteria/Archaea):
- No nucleus or membrane-bound organelles
- Divide by binary fission
- Small, haploid, single circular chromosome
- Genetic information in nucleoid region
Eukaryotes (Fungi, Protozoa, Algae, Helminths, Slime Molds):
- Have nucleus and membrane-bound organelles
- Divide by mitosis/meiosis
- Larger, diploid, multiple linear chromosomes
- Genetic information in nucleus

Viruses vs. Cells

Viruses: Lack cellular structure, require host for reproduction, no independent metabolism, no ribosomes, some have RNA genomes, evolve rapidly but differently from cells.
Cells: Have cellular structure, independent metabolism, contain ribosomes, DNA genomes.

Evolutionary Relationships and Microbial Diversity

Three Domains of Life and rRNA

Carl Woese: Used rRNA sequences to classify life into three domains: Bacteria, Archaea, Eukarya.
rRNA is ideal for phylogenetic studies due to ubiquity, functional constancy, slow evolutionary change, and resistance to horizontal gene transfer.

Microbial Metabolic Diversity

Chemoorganotrophs: Obtain energy by oxidizing organic molecules (e.g., sugars, fats, proteins).
Chemolithotrophs: Obtain energy by oxidizing inorganic molecules (e.g., H2, H2S, NH3, Fe2+).
Phototrophs: Use sunlight as energy source.

Bacterial Phyla Examples

Firmicutes, Actinobacteria, Cyanobacteria, Chlamydia, Planctomycetes, Spirochetes, Deinococcus

Microscopy

Types and Uses

Bright-field: Standard light microscopy for stained or naturally pigmented specimens.
Dark-field: Best for observing motility in live, unstained cells.
Phase Contrast: Enhances contrast in unstained, living cells; reveals internal structures.
DIC (Differential Interference Contrast): Produces 3D images and color in live, unstained specimens.
Fluorescence: Uses UV light to visualize fluorescently labeled cells or structures.
Confocal Scanning Laser: Combines laser and fluorescence for 3D, multi-plane imaging.
TEM (Transmission Electron Microscopy): 2D images of internal structures; requires heavy metal staining; nonliving specimens.
SEM (Scanning Electron Microscopy): 3D images of cell surfaces.

Bacterial Cell Morphology

Shapes and Arrangements

Cocci: Spherical; can form pairs (diplococci), chains (streptococci), tetrads, or clusters (staphylococci).
Rods (Bacilli): Cylindrical; may be single, paired, or form filaments.
Spirillum: Rigid, spiral-shaped rods; motile by polar flagella.
Spirochetes: Thin, flexible spirals with endoflagella; move in corkscrew motion.
Stalk and Hypha: Appendages for attachment or increased surface area; produced by budding.
Filamentous: Long rods forming chains or filaments.

Significance of Small Size: SAR11 Example

SAR11 clade: Represents up to 25% of marine microbial communities; highly abundant and ubiquitous.
Possess small, compact genomes; efficient metabolism; major impact on global carbon cycling.

Cell Membrane Structure and Function

Components and Functions

Phospholipid bilayer: Hydrophobic fatty acid tails and hydrophilic glycerophosphate heads.
Embedded proteins: Selective permeability, transport, and energy functions.
Membrane strengthening agents: Sterols (e.g., cholesterol in eukaryotes), hopanoids (in bacteria).

Archaeal Membrane Differences

Isoprenoid tails (built from isoprene units).
Ether linkages (not ester) between glycerol and isoprenoid chains.
Can form monolayers (tetraethers) or bilayers (diethers).

Transport Systems in Prokaryotes

Types of Transport

Simple Transport: Uses a single membrane-spanning protein; driven by proton motive force (PMF); includes symport, antiport, and uniport mechanisms.
Group Translocation: Only in bacteria; substance is chemically modified during transport (e.g., phosphotransferase system in E. coli uses PEP to phosphorylate glucose).
ABC Transporters: Consist of substrate-binding protein, membrane-spanning protein, and ATP-hydrolyzing protein; use ATP; important for uptake of nutrients and multidrug resistance.

Cell Wall Structure and Function

Peptidoglycan and Gram Stain Differences

Peptidoglycan: Provides strength via tetrapeptide cross-links; contains D-amino acids (rare in nature).
Gram Positive: Thick peptidoglycan layer (90% of wall); teichoic acids for rigidity; sensitive to lysozyme.
Gram Negative: Thin peptidoglycan; outer membrane with lipopolysaccharide (LPS); contains periplasmic space.
Lysozyme: Enzyme that cleaves β(1,4) glycosidic bonds in peptidoglycan, leading to cell lysis.
Prokaryotes without cell wall: Mycoplasma and Thermoplasma.

Outer Membrane and Periplasm

LPS (Lipopolysaccharide): Found in Gram-negative bacteria; core polysaccharide is conserved, O-polysaccharide is variable; Lipid A is an endotoxin.
Porins: Channels for small molecule transport; can be specific or non-specific.
Periplasm: Space between inner and outer membranes in Gram-negative bacteria; contains hydrolytic enzymes, binding proteins, chemoreceptors, and biosynthetic proteins.

Archaeal Cell Wall Differences

No peptidoglycan; some have pseudopeptidoglycan.
No outer membrane; S-layer (protein surface layer) is common.
Resistant to lysozyme and penicillin.

Bacterial Cell Surface Structures

Capsule and Pili

Capsule: Polysaccharide layer; aids in attachment, resists desiccation, and evades immune system.
Pili: Involved in motility, DNA transfer, adherence, and immune evasion.
- Type 1, Type 4, Curli (Gram-negative); Fibrils and pili (Gram-positive).
- Type 4 pili mediate twitching motility.

Inclusion Bodies and Gas Vesicles

Inclusion bodies: Aggregates of polymers for energy reserves (e.g., glycogen, sulfur globules, magnetosomes).
Gas vesicles: Protein-bound structures that confer buoyancy.

Endospores

Formation, Structure, and Function

Purpose: Survival under harsh conditions (nutrient depletion, heat, UV, chemicals, desiccation).
Vegetative Cell vs. Endospore:
- Vegetative: Less Ca2+, normal water, metabolically active, no SASPs.
- Endospore: More Ca2+, low water, metabolically inactive, contains SASPs and dipicolinic acid.
SASPs (Small Acid-Soluble Spore Proteins): Bind and protect DNA from UV; convert DNA from B-form to A-form.
Sporulation: Triggered by nutrient limitation; involves asymmetric division, forespore engulfment, cortex and coat formation, SASP production.
Germination: Triggered by nutrients; involves activation, germination (hydration, loss of resistance), and outgrowth (resumption of metabolism and division).

Bacterial Motility

Types of Motility

Twitching Motility: Type 4 pili extend, attach, and retract to pull cell forward; powered by ATP.
Gliding Motility: Surface movement using adhesion proteins and PMF.
Swimming Motility: Rotation of flagella (bacteria) or archaella (archaea) propels cell in liquid; "runs and tumbles" for direction changes.
Gas Vesicles: Provide buoyancy for vertical movement in aquatic environments.

Flagella Types and Structure

Polar: Single flagellum at one pole.
Lophotrichous: Tuft at one pole.
Amphitrichous: Flagella at both poles.
Peritrichous: Flagella distributed over entire cell.
Amphilophotrichous: Tufts at both ends.

Flagella Biosynthesis and Motor Function

Flagellum grows from tip; MS ring made first, followed by anchoring proteins, hook, cap, and filament.
Gram-negative basal body: L ring (outer membrane), P ring (peptidoglycan), MS ring (cytoplasmic membrane), C ring (cytoplasm).
Motor: Rotor (rings and rod) spins within stator (Mot proteins); proton flow via PMF drives rotation.
Fli proteins regulate motor function (act as a clutch).

How the Flagellar Motor Works

Proton flow through Mot proteins exerts force on rotor, causing rotation of MS ring, rod, hook, and filament.
Speed depends on proton flow rate.

Chemotaxis

Mechanism of Directed Movement

Movement in response to chemical gradients (toward attractants, away from repellents).
In E. coli, flagellar rotation is altered: CCW for runs (forward), CW for tumbles (direction change).
Longer runs when moving up attractant gradient; shorter runs when moving down.
Membrane chemoreceptors detect signals and modulate flagellar motor.

Bioenergetics and Metabolism

Aerobic vs. Anaerobic Respiration; Chemoorganotrophs vs. Chemolithotrophs

Aerobic respiration: Uses O2 as terminal electron acceptor.
Anaerobic respiration: Uses alternative electron acceptors (e.g., nitrate, sulfate).
Chemoorganotrophs: Organic molecules as electron donors.
Chemolithotrophs: Inorganic molecules as electron donors.

Enzymes and Energy

Endergonic reactions: Require energy input (ΔG > 0).
Exergonic reactions: Release energy (ΔG < 0).
Redox reactions: Oxidation coupled to reduction; electrons transferred from donor to acceptor.
Reduction potential (E0'): Indicates tendency to accept electrons; strongest electron acceptor is O2.
Redox tower: Visual representation of electron donors/acceptors and their potentials.
High-energy bonds: (e.g., ATP) store and transfer energy in metabolism.

Catabolism of Glucose: Respiration and Fermentation

Coenzymes (e.g., NAD+): Electron carriers in redox reactions.
Pathways: Glycolysis, TCA cycle, electron transport chain (ETC).
Fermentation: Anaerobic process; regenerates NAD+; produces organic end products (e.g., lactic acid, ethanol).
ATP synthase: Converts proton gradient energy into ATP (mechanical to chemical energy).
Alternative sugar catabolism: Pathways besides glycolysis exist (e.g., Entner-Doudoroff, pentose phosphate).

Key Equations

Gibbs Free Energy:
ATP Synthesis:

Laboratory Techniques

Aseptic Technique

Prevents contamination of cultures and environment by using sterile tools and procedures.

Staining Methods

Simple stain: Uses a single dye to color cells.
Negative stain: Stains background, leaving cells clear.
Gram stain: Differentiates Gram-positive (purple) and Gram-negative (pink) bacteria based on cell wall structure.

Diluting Bacteria (Streak Plate Method)

Used to isolate pure colonies by spreading bacteria over agar surface in a pattern that thins out the sample.

Additional info:

Some details (e.g., specific steps of glycolysis, TCA cycle, and electron transport) are not fully listed in the original notes but are essential for a complete understanding of microbial metabolism.
For a more comprehensive review, consult textbook chapters on microbial metabolism and laboratory techniques.