Microbiology Study Guide: Domains of Life, Bacterial Cell Structure, and Microbial Growth

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Overview of the Three Domains of Life

Characteristics of Archaea, Bacteria, and Eukarya

The three domains of life—Archaea, Bacteria, and Eukarya—represent the major evolutionary lineages of cellular organisms. Each domain is defined by unique molecular and cellular characteristics.

Archaea: Prokaryotic, unique membrane lipids (ether-linked), lack peptidoglycan in cell walls, often extremophiles (e.g., thermophiles, halophiles).
Bacteria: Prokaryotic, peptidoglycan cell walls, diverse metabolic pathways, found in nearly all environments.
Eukarya: Eukaryotic, membrane-bound organelles, linear chromosomes, includes animals, plants, fungi, and protists.

Organisms included:

Archaea: Halobacterium, Thermoproteus
Bacteria: Escherichia coli, Bacillus subtilis
Eukarya: Homo sapiens, Saccharomyces cerevisiae

Similarities between Domains:

Archaea & Bacteria: Both are prokaryotic, lack nucleus, reproduce by binary fission.
Archaea & Eukarya: Similarities in some genetic machinery (e.g., RNA polymerase, histones).
Bacteria & Eukarya: Both can perform glycolysis, have similar metabolic pathways.

Evidence for Evolution and Phylogenetic Relationships

rRNA alignment and signature sequences: Ribosomal RNA gene sequences are used to determine evolutionary relationships. Signature sequences are unique to each domain.
Ribosomal size: Prokaryotes have 70S ribosomes; eukaryotes have 80S ribosomes.
Compartmentalization: Eukaryotes have membrane-bound organelles; prokaryotes do not.
Genome: Bacteria and Archaea have circular chromosomes; Eukarya have linear chromosomes.
Plasmids: Common in Bacteria and Archaea; rare in Eukarya.
Biochemistry: Only Archaea perform methanogenesis; nitrogen fixation is found in some Bacteria and Archaea.
ATP synthase: Present in all domains, but with structural differences.
Cell wall: Bacteria (peptidoglycan), Archaea (pseudopeptidoglycan or S-layers), Eukarya (cellulose, chitin, or absent).
Membrane lipids: Bacteria/Eukarya (ester-linked), Archaea (ether-linked).
Chemolithotrophy: Found in Bacteria and Archaea.
Chlorophyll-based photosynthesis: Bacteria (cyanobacteria), Eukarya (algae, plants).

Horizontal Gene Transfer (HGT)

Definition: The movement of genetic material between organisms other than by vertical transmission (parent to offspring).

Mechanisms: Transformation, transduction, conjugation.
Conjugation: Direct transfer of DNA via cell-to-cell contact, often mediated by plasmids.

Impact: HGT contributes to genetic diversity and evolution, especially in prokaryotes.

Endosymbiotic Theory and Evolution of Eukaryotes

Endosymbiont theory: Eukaryotic organelles (mitochondria, chloroplasts) originated from free-living bacteria engulfed by ancestral eukaryotic cells.
Steps: Engulfment, symbiosis, gene transfer to host nucleus.
Nature of chloroplasts: Derived from cyanobacteria-like ancestors.

Key Historical Figures in Microbiology

Carl Woese: Defined Archaea as a separate domain using rRNA sequencing.
Jack Szostak: Research on the origin of life and RNA world hypothesis.
Antonie van Leeuwenhoek: First to observe microbes using a microscope.
Louis Pasteur: Disproved spontaneous generation, developed pasteurization.
Joseph Lister: Introduced antiseptic surgery.
Robert Koch: Developed Koch's postulates for linking microbes to disease.
Agostino Bassi, Miles Joseph Berkeley, Heinrich Anton de Bary, Emile Roux: Early contributors to germ theory and microbiology.

Early Life and Acellular Forms

Cyanobacteria: Photosynthetic bacteria, important in early oxygenation of Earth's atmosphere.
Stromatolites: Fossilized microbial mats, evidence of ancient life.
Viroids, Viruses, Prions: Acellular infectious agents. Viruses contain nucleic acid and protein coat; viroids are small RNA molecules; prions are infectious proteins.

Molecular Comparison of the Three Domains

Prokaryotic Cell Characteristics and Morphology

Cellular morphology: Study of cell shape and arrangement.
Common shapes: Cocci (spherical), bacilli (rod-shaped), spirilla (spiral), spirochetes (flexible spirals), vibrios (comma-shaped), coccobacilli (short rods).
Cell wall types: Gram-positive (thick peptidoglycan), Gram-negative (thin peptidoglycan, outer membrane).

Comparison of Bacterial, Plant, and Animal Cells

Bacterial cells: Prokaryotic, small (0.5–5 μm), peptidoglycan cell wall, no nucleus.
Plant cells: Eukaryotic, larger (10–100 μm), cellulose cell wall, chloroplasts.
Animal cells: Eukaryotic, no cell wall, various organelles.

Factors influencing bacterial size and shape: Nutrient uptake, motility, surface-to-volume ratio.

Bacterial Cell Walls and Structures

Gram-Positive vs. Gram-Negative Cell Walls

Peptidoglycan layer: Composed of N-acetylmuramic acid (NAM) and N-acetylglucosamine (NAG) linked by peptide interbridges.
Gram-positive: Thick peptidoglycan, teichoic acids, no outer membrane.
Gram-negative: Thin peptidoglycan, outer membrane with lipopolysaccharide (LPS), periplasmic space.

Feature	Gram-Positive	Gram-Negative
Peptidoglycan	Thick	Thin
Teichoic acids	Present	Absent
Outer membrane	Absent	Present
LPS	Absent	Present
Periplasmic space	Small	Large

Other components: Braun’s lipoprotein, porins, mycolic acid (in acid-fast bacteria).

Outer Coverings and Surface Structures

Capsules: Polysaccharide layer for protection and adhesion.
S-layers: Proteinaceous surface layers, structural support.
Slime layers: Loosely attached, aid in gliding motility.
Glycocalyx: General term for extracellular polysaccharide layers.

Flagella and Motility

Structure: Basal body (rings), hook, filament.
Differences: Gram-negative flagella have more rings than gram-positive.
MotA and MotB: Proteins involved in proton motive force-driven rotation.
Types of flagella placement: Monotrichous (single), peritrichous (many), lophotrichous (tufts).
Axial filaments: Found in spirochetes, enable corkscrew movement.

Fimbriae and Pili

Fimbriae: Short, numerous, for attachment.
Pili: Longer, fewer, involved in conjugation and twitching motility.

Movement Across Cell Membranes

Passive diffusion: Movement down concentration gradient.
Facilitated diffusion: Carrier proteins assist movement.
Active transport: Requires energy (ATP or ion gradients).
Primary active transport: ATP-binding cassette (ABC) transporters.
Secondary active transport: Major facilitator superfamily (MFS) transporters, use ion gradients.
Group translocation (PTS): Phosphotransferase system transfers phosphate to sugars during transport.

Chemotaxis and Bacterial Motility

Chemotaxis: Movement toward or away from chemical stimuli, mediated by flagellar rotation (counterclockwise = run, clockwise = tumble).
Other motility types: Twitching (pili), gliding (surface movement).

Bacterial Genome and Plasmids

Bacterial genome: Usually a single circular chromosome.
Plasmids: Small, extrachromosomal DNA, often carry antibiotic resistance genes.

Bacterial Growth and Reproduction

Reproductive Strategies

Binary fission: Most common, cell divides into two identical daughter cells.
Other methods: Budding, filamentous growth (in some bacteria).

Bacterial Cell Cycle vs. Eukaryotic Cell Cycle

Bacterial cell cycle: DNA replication, chromosome segregation, cytokinesis.
Eukaryotic cell cycle: G1, S, G2, M phases; more complex regulation.

DNA Replication in Bacteria

Leading strand: Synthesized continuously in 5'→3' direction.
Lagging strand: Synthesized discontinuously as Okazaki fragments.
Key enzymes: Helicase (unwinds DNA), topoisomerase (relieves supercoiling), DNA polymerase III (main synthesis), DNA polymerase I (removes primers), ligase (joins fragments).
Replication fork: Y-shaped region where DNA is being unwound and replicated.

Microbial Growth Curves

Phases: Lag, log (exponential), stationary, death.
Importance: Understanding growth phases aids in controlling infections and optimizing industrial processes.

Factors Influencing Microbial Growth

Osmosis: Water movement across membranes; mechanosensitive channels protect against osmotic shock.
Halophiles: Thrive in high salt (e.g., Halobacterium).
Acidophiles: Grow in low pH (e.g., Acidithiobacillus).
Neutrophiles: Prefer neutral pH.
Alkaliphiles: Grow in high pH (e.g., Bacillus alcalophilus).
Temperature adaptation: Psychrophiles (cold), mesophiles (moderate), thermophiles (hot), hyperthermophiles (very hot).
Starvation adaptation: Formation of spores, metabolic slowdown.

Biofilms and Quorum Sensing

Biofilm: Community of microbes attached to a surface, embedded in extracellular polymeric substance (EPS).
Formation: Attachment, microcolony formation, maturation, dispersal.
Importance: Biofilms are resistant to antibiotics and immune responses; significant in medical device infections.
Quorum sensing: Cell-to-cell communication using signaling molecules (e.g., N-acyl homoserine lactone, AHL) to coordinate group behavior.
Cross-species communication: Example: Rhizobium in plant root nodules.

Media Types

General purpose media: Supports growth of many microbes.
Selective media: Inhibits some microbes, allows others.
Differential media: Distinguishes microbes based on metabolic traits.

Key Terms and Definitions

Oligotrophic environment: Low nutrient availability.
Growth arrest: Cessation of cell division under stress.
Extracellular polymeric substance (EPS): Matrix in biofilms.
Persisters: Dormant cells tolerant to antibiotics.
Competent state: Ability to take up DNA from environment.

Example: Microbial Growth Curve Equation

The exponential phase of microbial growth can be described by:

Where: = final cell number = initial cell number = specific growth rate = time

Additional info: Some details, such as the full steps of the PTS system and specific examples of quorum sensing, were inferred based on standard microbiology curricula.