Lec 2:Three Domains of Life: Bacteria, Archaea, Eukarya

• There are three domains of life: Bacteria, Archaea, and Eukarya.

Domain Bacteria

• Usually single-celled organisms.
• Most have a cell wall containing peptidoglycan.
• Lack a membrane-bound nucleus.
• Play key roles in ecosystems and are mostly beneficial.
• Cyanobacteria produce significant oxygen.

Domain Archaea

• Distinguished from Bacteria by unique rRNA sequences.
• Cell walls lack peptidoglycan.
• Unique membrane lipids differentiate them from Bacteria and Eukarya.
• Exhibit unusual metabolic characteristics.
• Many live in extreme environments.
• No confirmed pathogenic species.

Domain Eukarya

• Larger and more complex than Bacteria and Archaea.
• Contain membrane-bound organelles like the nucleus and mitochondria.
• Major groups include protists, fungi, plants, and animals.
• Protists are diverse and mostly unicellular, including algae (photosynthetic), protozoa (motile "hunters"), slime molds (distinct life cycle stages), and water molds (cause plant diseases).
• Fungi can be unicellular (yeast) or multicellular (mold).

Origin of Eukaryotes: Endosymbiotic Hypothesis

• Mitochondria, chloroplasts, and hydrogenosomes originated as free-living bacteria that formed symbiotic relationships with early eukaryotic cells.
• Mitochondria are related to Rickettsia bacteria.
• Chloroplasts are related to Prochloron.
• Evidence includes reproduction by binary fission, double lipid membranes, circular DNA without histones, genomic sequences linking mitochondria to Rickettsia and chloroplasts to Prochloron, 70S ribosomes, bacterial-like enzymes and transport systems, similar size to bacteria, and susceptibility to mitoviruses.

Prokaryotes vs. Eukaryotes

• Prokaryotes differ from eukaryotes in size and simplicity.
• Most lack internal membrane systems and membrane-bound organelles.
• Prokaryotes are divided into Bacteria and Archaea domains.
• Bacteria can be classified by their Gram stain reaction: Gram-positive (thick peptidoglycan layer, purple stain) and Gram-negative (thin peptidoglycan layer, outer membrane, pink stain).

Multicellular-Like Behavior in Prokaryotes

• Example: Myxococcus xanthus behaves like a multicellular organism, exhibiting division of labor and forming fruiting bodies under stress.
• Characteristics of multicellular organisms include multiple cells working together, specialized functions, distinct tissues and organs, and division of labor.

Prokaryotic Shapes and Structures

• Cocci are spherical.
• Rods (Bacilli) are cylindrical.
• Spirochetes are spiral or corkscrew-shaped.
• Fruiting bodies are structures formed by some bacteria for survival and reproduction.

World’s Largest Bacterium: Candidatus Thiomargarita magnifica

• Found in red mangroves of the Lesser Antilles.
• 5,000 times larger than most bacteria, about 1 cm in length.
• Contains DNA and ribosomes in membrane-bound structures called pepins.
• Pepins hold up to 700,000 copies of the genome.

Size-Shape Relationship in Bacteria

• Nutrient uptake occurs through passive diffusion.
• Surface-to-volume ratio (S/V) is critical for efficient nutrient exchange.
• If a cell is too large, the S/V ratio becomes too small, making nutrient diffusion inefficient.
• As cell size increases, volume grows faster than surface area, which reduces the S/V ratio.

World’s Smallest Free-Living Bacterium: Mycoplasma genitalium

• Size: 200–300 nm.
• Genome: ~580 Kb.
• High surface-area-to-volume ratio enables survival in nutrient-poor environments.
• Causes urethritis, cervicitis, and pelvic inflammatory disease (PID), and linked to fertility issues.
• Lacks a cell wall, making it resistant to penicillin, with emerging concerns about drug-resistant strains.

World’s Smallest Archaea & Bacteria

World’s Smallest Archaeon: Nanoarchaeum equitans

• Genome: 490 Kb.
• Habitat: Hydrothermal vents up to 98ºC.
• Symbiotic/parasitic relationship with Ignicoccus.
• Dependent on host for nucleotides, amino acids, lipids, and cofactors.
• Encodes genes for DNA replication and repair but lacks biosynthetic pathways.

World’s Smallest Non-Free-Living Bacterium: Nasuia deltocephalinicola

• Genome: 112 Kb.
• Predicted genes: 137.
• Symbiotic relationship with leafhoppers, synthesizing 10 essential amino acids for the insect host.
• Highly reduced biosynthetic pathways, suggesting evolution toward a pre-organelle state.

Weirdest Archaeon: Haloquadratum walsbyi

• Extreme halophile thriving in 18% salt concentration at neutral pH.
• Unique square-shaped cells forming large, sheet-like structures.

Bacteria Cell Organization

Plasma Membrane

• Composed of a phospholipid bilayer, integral and peripheral proteins, oligosaccharides, and hopanoids.
• Provides fluidity and selective permeability.
• Proteins are involved in transport and signaling.
• Oligosaccharides aid in cell recognition.
• Transport systems can be passive or active.
• Electron Transport Chain (ETC) components enable ATP synthesis via oxidative phosphorylation.
• Types of Membrane Transport in Bacteria:
  • Carrier-Mediated Facilitated Diffusion: Utilizes carrier proteins, doesn't require energy, and is limited by protein availability.
  • Active Transport: Requires energy to move molecules against the concentration gradient.
• Siderophores – Iron Uptake System:
  • Bacteria produce siderophores to bind and solubilize iron, which is then transported into the cell.

Types of Bacterial Cell Walls

Gram-Positive Cell Wall

• Thick peptidoglycan layer (20–80 nm) that retains crystal violet stain, appearing purple.
• Contains teichoic acids and lipoteichoic acids for structural integrity and ion transport.
• No outer membrane, making it susceptible to lysozyme and penicillin.

Gram-Negative Cell Wall

• Thin peptidoglycan layer (2–7 nm) between two membranes.
• Does not retain crystal violet stain, appearing pink/red.
• Has an outer membrane with lipoproteins, porins, and lipopolysaccharides (LPS).
• More resistant to antibiotics due to the outer membrane.

Comparison of Gram-Positive and Gram-Negative Cell Walls

• Key differences include peptidoglycan layer thickness, presence of teichoic acids and outer membrane, staining properties, porins, lipoproteins, LPS, and antibiotic sensitivity.

Peptidoglycan Structure

• Composed of repeating disaccharide units of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM).
• Short peptide chains are attached to NAM with peptide cross-links for rigidity.
• Maintains cell shape, prevents osmotic lysis, allows diffusion of small molecules.
• Target for antibiotics like penicillin, which inhibits cross-linking.

LPS - Lipopolysaccharide

• Consists of Lipid A, core polysaccharide, and O side chain (O antigen).
• Contributes to negative charge, stabilizes the outer membrane, aids in attachment and biofilm formation, creates a permeability barrier, provides host defense, and acts as an endotoxin.

The Nucleoid

• Irregularly shaped region in bacteria and archaea containing the chromosome and associated proteins.
• Typically contains one circular, double-stranded DNA molecule folded via supercoiling and nucleoid proteins.

Ribosomes

• Complex structures of protein and RNA, which are the sites of protein synthesis.
• Bacterial and archaeal ribosome: 70S.
• Eukaryotic ribosome: 80S
• Ribosomal RNA Composition: 16S (small subunit) and 23S and 5S (large subunit).
• Archaea also have 5.8S, similar to eukaryotic ribosomes.
• Archaeal ribosomes are more similar to eukaryotic ribosomes than bacterial ribosomes.

Plasmids

• Small, circular DNA molecules that replicate independently of the chromosome.
• Contain non-essential genes that provide selective advantages, like drug resistance.
• Classified based on existence mode, spread, and function.
  • Fertility (F) Plasmids: Enable conjugation.
  • Resistance (R) Plasmids: Provide antibiotic resistance.
  • Col Plasmids: Code for bacteriocins.
  • Degradative Plasmids: Enable digestion of unusual substances.
  • Virulence Plasmids: Convert bacteria into pathogens.

The Cytoskeleton

• Bacteria have homologs of all three eukaryotic cytoskeletal elements.
• Archaea have two cytoskeletal homologs.
• Functions include cell division, protein localization, and cell shape determination.
• FtsZ forms a ring during septum formation, MreB maintains cell shape, and CreS maintains curved shape.

Inclusion Bodies

• Granules of organic or inorganic material stored for future use, sometimes enclosed by a single-layered membrane.
  • Glycogen Storage: Stores glucose polymers.
  • Carbon Storage: Poly-β-hydroxybutyrate (PHB).
  • Phosphate Storage: Polyphosphate granules.
  • Carboxysomes: Contain Rubisco for CO₂ fixation.
  • Gas Vacuoles: Provide buoyancy via gas vesicles, found in aquatic bacteria and archaea.
• Magnetosomes: Contain magnetite particles to orient bacteria in Earth’s magnetic field for aerotaxis.

Capsules, Slime Layers, and S-Layers

• Outer layers composed of polysaccharides, proteins, and glycoproteins.
• Functions include surface attachment, motility, protection from host defenses and harsh conditions.

Pili and Flagella

• Pili and Fimbriae: Short, thin appendages that mediate attachment to surfaces.
• Sex Pili: Longer, thicker, and less numerous, essential for conjugation.
• Flagella: Functions as a self-assembling rotary motor.

Mechanism of Flagellar Movement

• Motor System: Powered by proton motive force (PMF).
  • Stator (Mot A & Mot B Proteins): Forms a channel for proton flow, generating torque.
  • Rotor: C-ring and MS-ring rotate due to torque produced by PMF.