Comprehensive Study Notes: Microbial Cell Biology, Metabolism, and Growth (Based on Brock Biology of Microorganisms)

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Chapter 1: The Microbial World

1.1 Microorganisms: Tiny Rulers of the Earth

Microorganisms are the most abundant and diverse forms of life on Earth, playing essential roles in ecosystems and human health.

Pure culture: Population of cells grown from a single cell on a nutrient medium.
Medium: Nutrient solution used for microbial growth.
Growth: Increase in cell number due to cell division.
Colony: Visible mass of cells on a solid medium.

1.2 Structure and Activities of Microbial Cells

Microbial cells are structurally diverse but share common features such as cytoplasmic membranes, cytoplasm, and genetic material.

Cytoplasmic membrane: Selectively permeable barrier separating cytoplasm from the environment.
Cytoplasm: Aqueous mixture containing macromolecules and small molecules.
Ribosomes: Sites of protein synthesis.
Cell wall: Provides structural strength (present in most microbes).
Genome: Complete genetic content of an organism.
DNA replication: Duplication of the genome.
Metabolism: Uptake and transformation of nutrients into cellular material and energy.
Enzymes: Catalyze biochemical reactions.
Transcription: DNA to RNA.
Translation: RNA to protein.

1.3 Cell Size and Morphology

Microbial cells exhibit a variety of shapes and sizes, which influence their physiology and ecological roles.

Common shapes: Coccus (spherical), bacillus (rod-shaped), spirillum (spiral).
Arrangements: Chains (streptococci), clusters (staphylococci), pairs (diplococci).
Surface-to-volume ratio (S/V): Higher S/V ratios favor faster nutrient uptake and growth rates.

1.4 An Evolutionary Perspective

Microbial life is classified into three domains: Bacteria, Archaea, and Eukarya. Phylogenetic relationships are determined by molecular data, especially ribosomal RNA sequences.

Bacteria: Diverse group with many phyla.
Archaea: Includes extremophiles; distinct from bacteria.
Eukarya: Includes plants, animals, fungi, and protists.
LUCA: Last Universal Common Ancestor; root of the tree of life.

1.5 Microorganisms and the Biosphere

Microorganisms have shaped Earth's biosphere and are essential for biogeochemical cycles.

Phototrophs: Use light energy.
Chemoorganotrophs: Use organic chemicals.
Chemolithotrophs: Use inorganic chemicals.
Extremophiles: Thrive in extreme environments.

1.6 The Impact of Microorganisms on Human Society

Microorganisms are crucial in agriculture, industry, and health, with both beneficial and harmful effects.

Fermentation: Used in food production (e.g., yogurt, cheese).
Bioremediation: Use of microbes to degrade pollutants.
Pathogens: Cause infectious diseases.

1.8 Improving Contrast in Light Microscopy

Microscopy techniques enhance visualization of microbial cells and structures.

Bright-field microscopy: Standard light microscopy.
Phase-contrast microscopy: Enhances contrast in unstained cells.
Fluorescence microscopy: Uses fluorescent dyes or proteins to visualize specific structures.

1.15 Woese and the Tree of Life

Carl Woese revolutionized microbial phylogeny using ribosomal RNA sequencing, leading to the three-domain system.

Phylogeny: Evolutionary history of organisms.
Ribosomal RNA (rRNA): Highly conserved, ideal for evolutionary studies.

Chapter 2: Microbial Cell Structure and Function

2.1 The Cytoplasmic Membrane

The cytoplasmic membrane is a selectively permeable barrier composed of a phospholipid bilayer with embedded proteins.

Hydrophobic interior: Fatty acid chains.
Hydrophilic exterior: Glycerol-phosphate heads.
Integral proteins: Span the membrane.
Peripheral proteins: Loosely attached.

2.2 Transport Systems in the Cell

Microbes use various transport systems to import nutrients against concentration gradients.

Simple transport: Driven by proton motive force.
Group translocation: Chemical modification during transport (e.g., phosphotransferase system).
ABC transporters: Use ATP hydrolysis for transport.

2.3 The Cell Wall

The cell wall provides structural support and prevents osmotic lysis. Its composition varies between bacteria and archaea.

Peptidoglycan: Main component in bacteria; provides rigidity.
Gram-positive: Thick peptidoglycan layer.
Gram-negative: Thin peptidoglycan, outer membrane with lipopolysaccharide (LPS).
Archaeal cell walls: Lack peptidoglycan; may have S-layers or pseudomurein.

2.4 Outer Membrane Structure (Gram-negative Bacteria)

The outer membrane contains LPS, which contributes to pathogenicity and structural integrity.

Component	Function
Lipid A	Endotoxin activity
Core polysaccharide	Structural stability
O-polysaccharide	Antigenic variation

2.5 Cell Surface Structures

Microbes possess various external structures for protection, attachment, and motility.

Capsules and slime layers: Polysaccharide coatings for protection and adherence.
Pili and fimbriae: Protein appendages for attachment and genetic exchange.
Flagella: Helical structures for motility.

2.6 Cell Inclusions

Inclusions store nutrients or serve specialized functions.

Poly-β-hydroxybutyrate (PHB): Carbon storage.
Glycogen: Energy reserve.
Gas vesicles: Buoyancy in aquatic microbes.
Magnetosomes: Orientation along magnetic fields.

2.8 Endospores

Endospores are dormant, highly resistant cells formed by some bacteria for survival under harsh conditions.

Sporulation: Formation of endospores.
Germination: Return to vegetative state.
Small acid-soluble proteins (SASPs): Protect spore DNA.

2.9 Flagella, Archaella, and Swimming Motility

Flagella and archaella are rotary appendages that enable swimming motility in bacteria and archaea.

Peritrichous: Flagella distributed over the cell surface.
Polar: Flagella at one or both ends.
Flagellar motor: Powered by proton motive force.

2.10 Surface Motility

Some bacteria move across surfaces using gliding or twitching motility.

Twitching: Extension and retraction of pili.
Gliding: Movement along surfaces without flagella.

2.11 Chemotaxis

Chemotaxis is the directed movement of cells in response to chemical gradients.

Attractants: Cause movement toward the source.
Repellents: Cause movement away from the source.

Chapter 3: Microbial Metabolism

3.1 Defining the Requirements for Life

Microbial metabolism encompasses all biochemical reactions required for growth and maintenance.

Catabolism: Breakdown of molecules to release energy.
Anabolism: Synthesis of cellular components.

3.2 Electron Transfer Reactions

Redox reactions involve the transfer of electrons between molecules, driving energy generation.

Oxidation: Loss of electrons.
Reduction: Gain of electrons.
Electron carriers: NAD+/NADH, FAD/FADH2, quinones, cytochromes.

3.3 Calculating Changes in Free Energy

The change in free energy () determines whether a reaction is energetically favorable.

Equation:

n: Number of electrons transferred
F: Faraday constant
: Difference in reduction potential

3.4 Cellular Energy Conservation

ATP is the universal energy currency, generated by substrate-level phosphorylation and oxidative phosphorylation.

Substrate-level phosphorylation: Direct transfer of phosphate to ADP.
Oxidative phosphorylation: ATP synthesis via proton motive force and electron transport chain.

3.5 Catalysis and Enzymes

Enzymes are biological catalysts that accelerate metabolic reactions by lowering activation energy.

Active site: Region where substrate binds.
Cofactors: Non-protein components required for activity (e.g., metal ions, vitamins).

3.6 Glycolysis, the Citric Acid Cycle, and the Glyoxylate Cycle

Central metabolic pathways for energy generation and biosynthesis.

Glycolysis: Glucose to pyruvate, generating ATP and NADH.
Citric acid cycle: Oxidation of acetyl-CoA to CO2, producing NADH, FADH2, and ATP.
Glyoxylate cycle: Enables growth on C2 compounds (e.g., acetate).

3.7 Principles of Fermentation

Fermentation allows energy generation in the absence of external electron acceptors.

Substrate-level phosphorylation: Main mechanism for ATP generation.
End products: Organic acids, alcohols, gases.

3.8 Principles of Respiration (Electron Carriers)

Respiration involves electron transport chains and generation of a proton motive force for ATP synthesis.

NADH dehydrogenases: Transfer electrons from NADH to the chain.
Cytochromes: Contain heme groups; transfer electrons via redox reactions.
Quinones: Lipid-soluble electron carriers.

3.9 Principles of Respiration: Generating a Proton Motive Force

Electron transport chains create a proton gradient across the membrane, driving ATP synthesis via ATP synthase.

ATP synthase: Enzyme complex that synthesizes ATP from ADP and Pi using proton flow.

3.10 Anaerobic Respiration and Metabolic Diversity

Some microbes use alternative electron acceptors (e.g., nitrate, sulfate) in the absence of oxygen.

Denitrification: Reduction of nitrate to nitrogen gas.
Sulfate reduction: Reduction of sulfate to hydrogen sulfide.

3.11 Chemolithotrophy and Phototrophy

Microbes can obtain energy from inorganic compounds (chemolithotrophy) or light (phototrophy).

Phototrophs: Use light energy to drive ATP synthesis.
Oxygenic photosynthesis: Produces O2 (e.g., cyanobacteria).
Anoxygenic photosynthesis: Does not produce O2.

3.12 Autotrophy and Nitrogen Fixation

Autotrophs fix CO2 into organic carbon; some microbes fix atmospheric nitrogen into ammonia.

Calvin cycle: Main pathway for CO2 fixation.
Nitrogenase: Enzyme complex for nitrogen fixation.

Chapter 4: Microbial Growth and Its Control

4.1 Feeding the Microbe: Cell Nutrition

Microbes require macro- and micronutrients for growth, including carbon, nitrogen, phosphorus, sulfur, and trace elements.

Macronutrients: Required in large amounts (C, N, P, S, K, Mg, Ca, Fe).
Micronutrients: Trace elements and growth factors.

4.2 Growth Media and Laboratory Culture

Microbes are cultivated on defined or complex media, with solid media used for colony isolation.

Defined media: Exact chemical composition known.
Complex media: Contains extracts or digests of natural products.
Selective media: Inhibits growth of some organisms.
Differential media: Distinguishes between organisms based on metabolic traits.

4.3 Microscopic Counts of Microbial Cell Numbers

Direct counting methods use microscopy to estimate cell numbers, but cannot distinguish live from dead cells.

4.4 Viable Counting of Microbial Cell Numbers

Viable counts estimate the number of living cells by plating and counting colonies (CFUs).

4.5 Turbidimetric Measures of Microbial Cell Numbers

Cell density can be estimated by measuring the turbidity (optical density) of a culture.

4.6 Binary Fission and the Microbial Growth Cycle

Microbial populations grow by binary fission, resulting in exponential increases in cell number.

Generation time: Time required for the population to double.
Growth curve phases: Lag, exponential, stationary, death.

4.8 Continuous Culture

Chemostats maintain microbial cultures in a steady state by continuous nutrient supply and waste removal.

4.11 Temperature Classes of Microorganisms

Microbes are classified by their optimal growth temperatures.

Class	Temperature Range (°C)
Psychrophiles	0–20
Mesophiles	20–45
Thermophiles	45–80
Hyperthermophiles	>80

4.15 Osmolarity and Microbial Growth

Water activity and solute concentration affect microbial growth. Halophiles thrive in high-salt environments.

4.16 Oxygen and Microbial Growth

Microbes vary in their oxygen requirements.

Obligate aerobes: Require O2.
Obligate anaerobes: Killed by O2.
Facultative anaerobes: Can grow with or without O2.
Microaerophiles: Require low O2 levels.
Aerotolerant anaerobes: Indifferent to O2.

4.17 General Principles and Microbial Growth Control by Heat

Heat is commonly used to sterilize media and equipment, with autoclaving and pasteurization as standard methods.

4.18 Other Physical Control Methods: Radiation and Filtration

Microbial growth can be controlled by ionizing radiation and filtration through small-pore membranes.

4.19 Chemical Control of Microbial Growth

Antimicrobial agents include disinfectants, antiseptics, and antibiotics. Their effectiveness is measured by minimum inhibitory concentration (MIC).

Chapter 8: Molecular Aspects of Microbial Growth

8.11 Antibiotics and Microbial Growth

Antibiotics target essential cellular processes such as cell wall synthesis, protein synthesis, and DNA replication.

Resistance mechanisms: Enzymatic inactivation, target modification, efflux pumps.

8.12 Persistence and Dormancy

Some bacteria can enter dormant states (persisters) to survive antibiotic treatment and other stresses.

Persisters: Metabolically inactive cells tolerant to antibiotics.
Dormancy triggers: Starvation, stress, antibiotic exposure.

Additional info: These notes are based on a summary of 'Brock Biology of Microorganisms' and cover foundational topics in microbial cell biology, metabolism, and growth, suitable for college-level microbiology courses.