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Ch4 PPT Prokaryotic Cells - Comprehensive Study Notes

Prokaryotic Cells: Overview and Key Differences

  • Chapter focus: Prokaryotic Cells (Chapter 4)
  • Quick contrast with Eukaryotes:
    • Prokaryotes have no membrane-bound organelles; Eukaryotes have organelles.
    • Prokaryotic DNA is free, circular, and typically not associated with histones; Eukaryotic DNA is enclosed linear molecules packaged with histones.
    • Prokaryotes have complex cell walls with peptidoglycan; Eukaryotes have varied cell walls (if present) made of polysaccharides or different materials.
  • Core definitions:
    • Prokaryote: organism lacking a membrane-bound nucleus and organelles; typically small cells with simple structure.
    • Eukaryote: organism with a true nucleus and membrane-bound organelles; often larger and more complex.
  • Key takeaways for exam: structural differences drive differences in genetics, cell processes, and susceptibility to antibiotics.
  • Slide note: In-class reminder that slides may be updated shortly before class; reliance on latest material is important.

External and Internal Structures of Prokaryotes

  • External structures
    • Flagella (for motility)
    • Pili (fimbriae) – attachment; some specialized pili for DNA transfer
    • Glycocalyx – capsule or slime layer; exterior to cell wall; may be organized (capsule) or loose (slime layer)
    • Cell wall – structural support; peptidoglycan-containing in most bacteria
    • Plasma membrane (cell membrane)
  • Internal structures
    • Cytoplasm
    • Nucleoid (chromosome, single circular DNA, not enclosed by a membrane)
    • Ribosomes (protein synthesis; 70S in bacteria; target for many antibiotics)
    • Inclusions (storage bodies, granules)
    • Endospores (dormant, highly resistant structures formed under harsh conditions)
  • Note: Not every prokaryote has all of these structures; variability exists among species.

Structure of Flagella

  • Flagellum consists of three main parts:
    • Filament – made of flagellin
    • Hook – attaches filament to basal body and rotates
    • Basal body – anchors flagellum to cell wall and membrane
  • Function: propulsion via rotation; enables movement toward/away from stimuli (taxis)

Taxis and Motility

  • Taxis: movement toward or away from stimuli (e.g., phototaxis, chemotaxis)
  • Flagellar movement pattern: rotate to run or tumble; switching between runs and tumbles changes direction
  • Special case: Spirochetes use axial filaments (protein bundles wrapped around cell) to move; axial filaments cause corkscrew motion
  • Visual concept: chemotaxis example – bacteria are attracted to a sugar crystal

Flagellar Movements and Axial Filaments (Details)

  • Run-and-tumble dynamics
    • Run: smooth swimming
    • Tumble: reorientation
    • Alternation enables chemotaxis toward favorable environments
  • Axial filaments (periplasmic flagella)
    • Anchored at one end of the cell
    • Rotation causes cell to move in a screw-like fashion
    • Outer sheath and cell wall interactions support this motion
    • SEM representation shows axial filament between outer sheath and cell wall

Pili and Glycocalyx

  • Pili (pilus = pilus singular; pili = multiple)
    • Composed of pilin
    • Fimbriae – short, numerous; facilitate attachment to surfaces or other cells
    • Sex pili – long, typically one; used to transfer DNA between cells (conjugation)
  • Glycocalyx (sugar coat)
    • Outside cell wall; composed of polysaccharides and/or proteins
    • Capsule – neatly organized, firmly attached
    • Slime layer – unorganized, loose
    • Functions: attachment to surfaces, protection from harsh conditions, evasion of host defenses

Biofilms

  • Biofilm: complex communities of bacteria embedded in a matrix of slime layers and extracellular polymeric substances
  • Functions: surface attachment, protection, and enhanced infection potential
  • Biofilm life cycle (summary of cyclical process):
    1. Single free-floating bacteria land on a surface
    2. Bacterial cells aggregate and attach
    3. Growth and division leading to biofilm formation
    4. Mature biofilm develops
    5. Part of biofilm disperses to release free-floating bacteria for further colonization
    6. Cycle repeats
  • Note: Biofilms contribute to chronic infections and resistance to antimicrobial agents

Cell Wall: Protection, Shape, and Antibiotic Targeting

  • General roles: protection, maintenance of shape; site of many antibiotics
  • Primary constituent in eubacteria: peptidoglycan
  • Key components labeled in cell-wall diagrams:
    • Peptidoglycan layer
    • Capsule/slime layer outside the wall
    • Cell membrane under the wall
    • Cytoplasm and nucleoid inside
  • Peptidoglycan (PG) overview
    • Polymer of two carbohydrate constituents: N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM)
    • NAG-NAM repeating disaccharide backbone
    • Side chains consist of amino acids forming a peptide cross-bridge
    • Tetrapeptide side chain involved in cross-linking
    • Linkages create a strong matrix capable of withstanding turgor pressure
    • Cross-links give rigidity; cross-bridges differ between Gram-positive and Gram-negative organisms
  • Illustrative structure (conceptual):
    • Repeating unit: ext{NAG} - ext{NAM} with attached tetrapeptide cross-bridge; cross-links between tetrapeptides provide 3D rigidity
    • In Gram-positive bacteria, the PG layer is thick with teichoic acids embedded in the cell wall
    • In Gram-negative bacteria, the PG layer is thinner and located in the periplasm between the inner and outer membranes

Gram-Positive, Gram-Negative, and Acid-Fast Walls

  • Gram-positive cell walls
    • Thick peptidoglycan layer
    • Teichoic acids present
    • No outer membrane
    • Retains crystal violet dye in Gram stain
  • Gram-negative cell walls
    • Thin peptidoglycan layer
    • Outer membrane containing lipopolysaccharide (LPS)
    • Periplasmic space between membranes
    • Porin proteins form channels in outer membrane
    • Stain counterstained pink/red by safranin in Gram stain
  • Acid-fast cell walls (e.g., Mycobacteria)
    • Very thick mycolic acids and waxes embedded in the cell wall
    • Mycolic acids confer extreme resistance to desiccation and chemicals
    • Outer wall composition includes lipids and arabinogalactan–mycolic acid complex
  • LPS in Gram-negative outer membrane
    • Lipid A: endotoxin component
    • O polysaccharide: antigenic determinant
    • Contributes to immune recognition and pathogenicity
  • Teichoic Acids in Gram-Positive walls
    • Include wall teichoic acids and lipoteichoic acids
    • Involved in cation regulation and antigenic variation

Gram Stain Method and its Significance

  • Gram staining separates bacteria into two groups using two dyes: a violet stain (primary) and a red counterstain
  • Results:
    • Gram-positive bacteria retain violet dye due to thick peptidoglycan with teichoic acids
    • Gram-negative bacteria retain red dye due to thinner peptidoglycan and outer membrane that does not retain violet
  • Chemical basis: cell wall structure dictates dye retention and staining outcome
  • Practical memory aids (study tips):
    • Memory trick: P words go together → Positive = Purple = Peptidoglycan (thick)
    • Negative = Not thick, Needs outer membrane
  • Note: The Gram stain is a key diagnostic tool and relates directly to antibiotic susceptibility and cell-wall-targeting strategies

Plasma Membrane and Cytoplasm

  • Plasma membrane structure
    • Phospholipid bilayer
    • Proteins: peripheral (on the surface; signaling, support, enzymes) and integral (embedded; transport and signaling)
    • Fluid Mosaic Model: membrane components are dynamic and mobile within the lipid bilayer
  • Cytoplasm
    • The intracellular substance enclosed by the plasma membrane
  • Nucleoid
    • Location of the bacterial chromosome; DNA is not enclosed in a membrane
  • Ribosomes
    • Site of protein synthesis; composed of RNA and protein
    • Bacterial ribosomes are 70S (50S + 30S subunits)
    • Target of many antibiotics (e.g., tetracyclines, macrolides, aminoglycosides)

Inclusions, Magnetosomes, and Endospores

  • Inclusions
    • Storage deposits (granules)
    • Nomenclature often ends with -some (e.g., lipid granule, magnetosome)
    • Magnetosomes: magnetic iron (magnetite or greigite) crystals enabling orientation along Earth's magnetic field
    • Function: helps aquatic bacteria orient toward optimal oxygen concentrations
  • Endospores
    • Dormant, tough, and resistant structures formed under unfavorable conditions
    • Key terms:
    • Sporulation: endospore formation
    • Germination: return to vegetative state
    • Examples: Clostridium botulinum (botulism), Bacillus anthracis (anthrax)
    • Relevance: endospores aid survival during extreme heat, desiccation, chemicals, and radiation; important in healthcare due to persistence

Sporulation and Spore Architecture

  • Sporulation is a survival strategy, not reproduction: one vegetative cell becomes one endospore and later returns to a vegetative cell
  • Key vocabulary and structures:
    • Vegetative cell: actively growing cell
    • Sporangium: mother cell that produces the spore
    • Forespore: developing spore inside the sporangium
    • Exosporium: thin outermost protein layer of the spore
    • Spore coat:Multiple protective protein layers beneath the exosporium
    • Cortex: thick layer of specialized peptidoglycan under the spore coat
    • Core: innermost region containing DNA, ribosomes, and enzymes in a dehydrated state
  • Sporulation cycle (conceptual flow):
    • Chromosome duplication and segregation
    • Sporangium engulfs forespore, deposition of cortex and outer coat layers
    • Maturation of the spore and disintegration of the sporangium
    • Free spore released upon sporangium breakdown

Prokaryotic Shapes and Arrangements

  • Shapes (monomorphic vs pleomorphic)
    • Coccus: spheres
    • Bacillus (bacilli): rods
    • Spirals: twisted shapes
  • Arrangements (for cocci and bacilli)
    • Diplo-: pairs (2)
    • Tetra-: groups of four
    • Sarcina: cube-like clusters (8–64)
    • Strepto-: chains
    • Staphylo-: clustered grape-like groups
  • Spiral shapes
    • Vibrio: short curved rod
    • Spirillum: helical shape; uses flagella to move
    • Spirochete: flexible helical shape; moves via axial filaments
  • Visual cues: slide diagrams illustrate single bacilli, diplo-bacilli, strepto-bacilli, cocci arrangements, etc.

Problems in Bacterial Classification and Taxonomy

  • Challenges in classifying bacteria
    • Many unidentified species
    • Limited knowledge about identified species
    • Lateral (horizontal) gene transfer complicates phylogenetic history because genetic material can move between organisms not through descent
  • Important resources for taxonomy
    • American Type Culture Collection (ATCC): collects organisms, information, and distributes organisms; atcc.org
    • Bergey’s Manuals: internationally recognized for bacterial classification; undergo editions with changes; Bergeys.org

Universal Phylogenetic Tree and Major Groups

  • Concept: three-domain system includes Bacteria, Archaea, and Eukarya
  • The universal tree includes: Bacteria and Archaea (prokaryotes) and Eukarya (plants, animals, fungi, protists)
  • Positioning:
    • Bacteria: diverse groups including Proteobacteria, Cyanobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and others
    • Archaea: diverse groups including thermophiles, methanogens, halophiles
    • Eukarya: plants, animals, fungi, many protists
  • Practical takeaway: taxonomy reflects evolutionary relationships, ecological niches, and metabolic capabilities

Eubacteria (True Bacteria): Major Groups and Characteristics

  • Proteobacteria: largest grouping; examples include Escherichia coli (E. coli), Salmonella, Vibrio cholerae, Helicobacter pylori
  • Photosynthetic bacteria: Cyanobacteria (blue-green algae)
  • Firmicutes: mostly Gram-positive; typically low G+C content (example: Staphylococcus)
  • Actinobacteria: Gram-positive with high G+C content; many soil bacteria; notable pathogens include Mycobacterium tuberculosis and Mycobacterium leprae
  • Other: miscellaneous groups not easily categorized into the above

Archaea: Notable Groups and Roles

  • Thermophiles
    • Example: Pyrodictium
    • Habitat: deep-sea hydrothermal vents; temperatures > 100°C
    • Morphology: disc-shaped with tubules
    • Biotechnological relevance: Taq polymerase derived from thermophilic archaea used in PCR
  • Methanogens
    • Example: Methanobacterium
    • Metabolism: obligate anaerobes; produce methane; part of human flora; contribute to sewage treatment
  • Halophiles
    • Example: Halobacterium
    • Habitat: high-salt environments (e.g., Great Salt Lake)

Practical Implications and Key Concepts

  • Antibiotics targeting: many antibiotics target bacterial ribosomes (70S) or cell-wall synthesis involving peptidoglycan
  • Pathogenicity factors: LPS endotoxin (Gram-negative) and mycolic acids (acid-fast) influence virulence and immune response
  • Environmental and medical relevance:
    • Biofilms contribute to persistent infections and antibiotic resistance
    • Endospores enable survival in extreme conditions and complicate sterilization
    • Horizontal gene transfer drives rapid evolutionary change and can spread antibiotic resistance
  • Conceptual links: understanding cell-wall architecture informs understanding of staining, antibiotic selection, and disease processes

Quick Reference: Key Terms and Concepts

  • Nucleoid: region containing bacterial chromosome
  • Peptidoglycan: PG; backbone of NAG–NAM disaccharide with peptide cross-links
  • Teichoic acids: present in Gram-positive cell walls; contribute to permeability and antigenicity
  • Lipopolysaccharide (LPS): outer membrane component in Gram-negative bacteria; Lipid A, O polysaccharide
  • Porin: channel-forming proteins in Gram-negative outer membrane
  • Teichoic vs Lipoteichoic acids: types of teichoic acids related to wall and membrane interactions
  • Capsule vs slime layer: organized vs unorganized glycocalyx; roles in attachment and protection
  • Magnetosome: magnetite/greigite-containing inclusions aiding orientation in magnetic fields
  • Sporulation vs germination: survival cycle vs return to active growth
  • Sporangium, forespore, exosporium, cortex, core: structural components of endospores
  • Diplo-, Strepto-, Staphylo-, Sarcina: arrangement prefixes for cocci and bacilli
  • Vibrio, Spirillum, Spirochete: spiral morphologies with distinct motility mechanisms
  • ATCC and Bergey’s Manuals: taxonomy resources
  • Universal Phylogenetic Tree: conceptual map of Bacteria, Archaea, and Eukarya

Equations and Notation (LaTeX)

  • Peptidoglycan repeating unit (conceptual):
    • Repeating disaccharide backbone: ext{NAG-NAM}
    • Attached peptide cross-bridge forming cross-links (tetrapeptide): ext{Cross-bridge} = ext{tetrapeptide}
  • For readability, the cell-wall-related density and structural ideas are not expressed as a single numerical formula, but the following captures key components:
    • The thicker PG layer in Gram-positive bacteria leads to stronger retention of Gram stain due to the dense network of cross-links: ext{PG}_{ ext{thick}}
      ightarrow ext{violet retained}
    • The thinner PG layer with an outer membrane in Gram-negative bacteria allows dye leakage and red counterstain retention: ext{PG}_{ ext{thin}} + ext{outer membrane}
      ightarrow ext{red retained}

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