JC

Prokaryotic Cells and Their Internal/External Structures (Lecture Notes)

Prokaryotes: Comprehensive Study Notes

  • Source context: Transcript covers general characteristics, shapes/arrangements, external structures, cell wall structure and staining, transport across membranes, and internal cell components including DNA, ribosomes, inclusions, endospores, and related concepts.
  • Emphasis on terminology, structural features, functional significance, and laboratory techniques (Gram staining, acid-fast staining) as well as real-world relevance (antibiotic targets, conjugation, motility, and survival strategies).

1) General Characteristics of Prokaryotic Cells

  • Prokaryotes include Bacteria and Archaea.
  • No membrane-bound organelles.
  • No membrane-bound nucleus; DNA resides in a nuclear region called the nucleoid.
  • DNA is not contained within a membrane.
  • Generally smaller than eukaryotic cells.
  • Typical size references:
    • Diameter: 0.2 - 2\,\mu\mathrm{m}
    • Length: 2 - 8\,\mu\mathrm{m}
    • Note: 1\,\mu\mathrm{m}=10^{-6}\,\mathrm{m}
  • A single cell of ~5 mm length lined end-to-end would yield roughly 2000 cells per centimeter (illustrates their microscopic scale).
  • Major groups: Bacteria and Archaea.

2) Basic Shapes and Arrangements

  • Basic shapes:
    • Bacillus (rod)
    • Coccus (sphere)
    • Spiral (twisted forms)
  • Subtypes aid nomenclature:
    • Bacillus arrangements: single, diplobacillus (paired at poles after division), streptobacillus (chains), coccobacilli (oval-shaped, often single).
    • Coccus arrangements:
    • Single cocci
    • Diplococci (pairs)
    • Streptococci (chains)
    • Tetrads (groups of 4 in two planes)
    • Sarcinae (cubic groups of 8 in three planes)
    • Staphylococcus (grape-like clusters from multiple-plane division)
  • Spiral forms:
    • Vibrios: curved/bent rods (comma-shaped)
    • Spirilla: rigid, helical/corkscrew
    • Spirochetes: flexible helical; use axial filaments for movement
  • Spiral movement and morphology influence motility, attachment, and pathogenic potential.

3) Structures External to the Cell Wall (2.1)

  • Glycocalyx
    • A sticky covering of polysaccharides and proteins.
    • Types:
    • Capsule: thick, tightly bound
    • Slime layer: thin, loosely bound
    • Functions:
    • Protects pathogens from macrophage uptake
    • Aids adherence to surfaces
    • Provides environmental protection (drying, chemicals, etc.)
    • May provide nutrients
  • Flagella
    • Long, filamentous appendages used primarily for motility.
    • Structure: hook, filament, basal body; filament composed of flagellin; hook connects filament to basal body; basal body anchors to cell membrane.
    • Motility: rotation propels cell (like a ship propeller); can also aid in binding to cells/substrates and in secretion.
    • Arrangements (common types):
    • Atrichous: no flagella
    • Monotrichous: single flagellum at pole
    • Lophotrichous: two or more flagella at a pole
    • Amphitrichous: flagella at both ends
    • Peritrichous: flagella over the entire surface
  • Axial filaments
    • Found in spiral-shaped bacteria
    • Similar to an internal flagellum embedded in the membrane (outer sheath external to cell wall)
    • Contraction of opposing axial filaments causes rotation, producing locomotion (corkscrew-like motion)
  • Pili (fimbriae)
    • Short, thin fibers on many Gram-negative bacteria and some Gram-positives
    • Functions:
    • Adhesion to surfaces, other bacteria, and host cells
    • Some pili enable twitching motility
    • Sex pili
    • Used for conjugation (DNA transfer between bacteria)
    • DNA frequently carried on plasmids

4) The Cell Wall (2.2)

  • Location and general function
    • Exterior to the plasma membrane
    • Functions include:
    • Maintaining cellular shape
    • Protection from physical insults
    • Protection from osmotic lysis (prevents bursting when intracellular solute concentrations are high)
  • Composition: peptidoglycan (murein)
    • Backbone: alternating N-acetylmuramic acid (NAM) and N-acetylglucosamine (NAG)
    • NAM contains a 4-amino-acid peptide side chain
    • Backbone is cross-linked by peptide bridges between side chains
  • Variations in cell wall structure: Gram-positive vs Gram-negative
    • Gram-positive:
    • Thick, multi-layered peptidoglycan
    • Teichoic acids may regulate cation movement, inhibit excessive wall breakdown, and contribute antigenicity
    • Gram-negative:
    • Thin peptidoglycan layer (often 1 layer thick) with less cross-linking
    • Outer membrane external to the cell wall
    • Outer membrane functions: protection from immune defenses and damaging chemicals
    • Outer membrane components include lipopolysaccharide (LPS)
  • Lipopolysaccharide (LPS) in Gram-negative outer membrane:
    • O polysaccharide components function as antigens
    • Lipid A acts as an endotoxin that can cause endotoxic shock
    • Outer membrane also contains porins for small molecule transport
  • Gram staining (differential staining technique)
    • Developed by Christian Gram in 1884
    • Steps overview:
    • Heat-fix bacterial smear (small amounts; avoid roasting)
    • Primary stain: crystal violet (1 minute) → all cells purple
    • Mordant: Gram’s iodine (1 minute) → forms crystal violet-iodine complexes
    • Decolorization: acetone-alcohol → dehydrates Gram-positive thicker walls; Gram-negative lose stain
    • Counterstain: safranin (1 minute) → Gram-negative appear pink; Gram-positive remain purple
    • Result interpretation:
    • Gram-positive: purple after decolorization and counterstain
    • Gram-negative: pink after counterstain
  • Atypical cell walls (exceptions to the Gram rule)
    • Mycoplasma: lack cell walls; sterols in membranes provide osmotic protection
    • Mycobacterium: thick, waxy cell walls containing mycolic acids; resistant to many stains; acid-fast staining is used for detection
  • Additional functions of the cell wall and transport
    • Embedded membrane components aid in transport (cross-membrane movement of materials)
    • Transport can be:
    • Active transport: requires ATP; transport against a gradient
    • Passive transport: no ATP; moves down a gradient
  • Group translocation (a special active transport mechanism)
    • Substance is chemically modified during transport to prevent back flow
    • Example: glucose + phosphate (from phosphoenolpyruvate, PEP) → glucose-6-phosphate (G6P), which is impermeable to the membrane
    • Notation: ext{Glucose} + ext{PO}_4^{3-}
      ightarrow ext{Glucose-}6 ext{phosphate} (illustrative)

5) Internal Structures (2.3)

  • Plasma membrane (cell membrane)
    • Encloses cytoplasm; phospholipid bilayer with polar (hydrophilic) heads and nonpolar (hydrophobic) tails
    • Structure: lipid bilayer with embedded integral proteins and peripheral proteins
    • Function: selective permeability; regulates entry/exit of substances
    • Fragility: can be disrupted by alcohols and cell lysis
  • Osmotic considerations
    • Osmotic pressure: pressure needed to stop net water flow across the membrane
    • Water moves from areas of low solute concentration to high solute concentration
    • Bacteria may experience isotonic, hypotonic, or hypertonic solutions
    • Isotonic: solute concentration equal to the cell interior
    • Hypotonic: outside solute concentration is lower
    • Hypertonic: outside solute concentration is higher
  • Cytoplasm
    • Internal, fluid component rich in water
    • Contains inorganic/organic molecules, DNA, ribosomes, and inclusions
  • Cytoskeleton (prokaryotic equivalent)
    • Protein framework providing structural support and shape
    • Recent discoveries show prokaryotic cytoskeletal proteins participate in cell division, shape maintenance, and movement/diffusion of macromolecules
  • Bacterial DNA structure
    • Nucleoid: central region where DNA aggregates; not membrane-bound
    • Chromosome: circular; occupies ~20% of cell volume; attached to plasma membrane
    • Plasmids: small circular DNA molecules that replicate independently; can be gained/lost without losing essential functions; often carry advantageous genes
  • Plasmids (functional significance)
    • Carry genes for antibiotic resistance, metal tolerance, toxin production, and enzyme synthesis
    • Can be transferred between bacteria (horizontal gene transfer)
    • Highly useful in molecular biology and biotechnology (e.g., cloning vectors)
  • Ribosomes
    • Sites of protein synthesis; present in both prokaryotes and eukaryotes
    • Prokaryotic ribosomes are 70S (sedimentation coefficient)
    • Subunit composition:
    • 50S subunit: contains 23S rRNA, 5S rRNA, and ~34 proteins
    • 30S subunit: contains 16S rRNA and ~21 proteins
    • The 70S ribosome is composed of the two subunits: 70\text{S} = 50\text{S} + 30\text{S}
  • Inclusions
    • Reserve deposits of macromolecules for later use; help reduce osmotic pressure by storing excess solutes
    • Metachromatic granules (volutin): large inclusions that stain red with methylene blue; reserves of inorganic phosphate for ATP synthesis; example: Corynebacterium diphtheriae (diphtheria)
    • Polysaccharide granules: glycogen and starch; detected with iodine
    • Lipid inclusions: storage of fats; detectable with fat-soluble Sudan dyes
    • Sulfur granules: store sulfur; energy reserve for bacteria energy via oxidation of sulfur compounds
  • Other inclusions
    • Carboxysomes: store RuBisCO (ribulose-1,5-bisphosphate carboxylase) for CO₂-fixing bacteria
    • Gas vacuoles: hollow cavities to maintain buoyancy for access to oxygen, light, and nutrients
    • Magnetosomes: store iron oxide; act like magnets to pull bacteria to attachment sites and may protect against hydrogen peroxide (host immune mechanism)
  • Endospores (2.4)
    • Resting, highly durable structures formed by some bacteria under inhospitable conditions; non-reproductive but highly resistant
    • Spores form internally within the cell (sporulation or sporogenesis)
    • Common spore-formers: Bacillus and Clostridium
    • Structure: very thick wall with multiple protective layers
    • Germination (exsporulation) returns endospores to vegetative state
    • Sporulation process overview (sequence):
    • Spore septum begins to isolate DNA and a portion of cytoplasm
    • Plasma membrane engulfs the isolated material, forming a forespore
    • Peptidoglycan layer forms between membranes
    • Spore coat forms around the forespore
    • Endospore is released via lysis of the original cell
    • Notable historical note: prehistoric endospores detected in 2000 (250 million years old) demonstrated germination after extreme time spans, raising questions about longevity and resilience of spores
  • Practical examples and notes
    • E. coli sex pili illustrate conjugation and plasmid transfer
    • Mycobacterium staining requires acid-fast techniques due to waxy cell walls
    • The Gram stain remains a foundational lab technique for bacterial classification and antibiotic targeting considerations

6) Interconnections and Practical Implications

  • Motility and chemotaxis/phototaxis influence colonization, host tissue invasion, and survival in varied environments
  • Capsule presence (glycocalyx) often correlates with pathogenicity and immune evasion; also impacts biofilm formation and antibiotic resistance
  • Outer membrane in Gram-negative bacteria contributes to innate immune recognition (LPS) and can be a target for antibiotics and detergents; porins affect permeability
  • Differences in ribosome structure (70S vs eukaryotic 80S) make bacterial ribosomes a prime target for many antibiotics
  • Plasmids enable rapid genetic adaptation (antibiotic resistance genes, toxins, metabolic capabilities) and are essential tools in biotechnology
  • Endospores allow survival through extreme environmental stresses, contributing to persistence and public health concerns (e.g., Bacillus and Clostridium species)
  • Understanding cell wall composition informs staining strategies, antibiotic choices, and interpretation of lab results in clinical microbiology

7) Quick Reference Formulas and Key Facts

  • Size ranges: 0.2-2\,\mu\mathrm{m} (diameter), 2-8\,\mu\mathrm{m} (length)
  • 1 μm = 10^{-6} m
  • Ribosome composition: 70S = 50S + 30S
    • 50S subunit: 23S rRNA, 5S rRNA, 34 proteins
    • 30S subunit: 16S rRNA, 21 proteins
  • Peptidoglycan backbone: NAM-NAG with peptide cross-bridges
  • Group translocation example: glucose + phosphate (from PEP) → glucose-6-phosphate (G6P)
    • Represented as: \text{Glucose} + \text{PO}_4^{3-} \rightarrow \text{Glucose-6-phosphate}
  • Osmotic states definitions:
    • Isotonic: solute concentration equal to cell interior
    • Hypotonic: outside solute concentration lower than inside
    • Hypertonic: outside solute concentration higher than inside

Notes:

  • This set of notes is designed to mirror the structure and content of the provided transcript, including all major concepts, definitions, and laboratory considerations. It emphasizes the relationships between structure and function, as well as practical lab techniques and clinical relevance.