The Biology of Microorganisms - Prokaryotes and Microorganisms Review Flashcards

The Prokaryotes (Bacteria and Archaea)

  • Overview

    • Bacteria and Archaea are prokaryotes with diverse morphologies and metabolisms but share key cellular features.
    • Major topics covered: morphology, reproduction, metabolism, genetics (vertical and horizontal gene transfer), cell envelopes, transport, cell wall chemistry, outer structures, inclusions, and growth/reproduction mechanisms.

  • Review: Properties of all cells

    • Common cell components
    • Cytoplasmic membrane, cytoplasm, genome (DNA), and ribosomes.
    • Metabolism: use information in DNA to make RNA and proteins; take up nutrients, transform them, conserve energy, expel wastes.
    • Core processes
      • Catabolism: transforming molecules to produce energy and building blocks.
      • Anabolism: synthesizing macromolecules.
    • Growth: information from DNA is converted into proteins that perform work; proteins convert environmental nutrients into new cells.
    • Evolution: chance mutations in DNA yield new properties; phylogenetic trees based on DNA sequence reveal evolutionary relationships.
    • Differentiation: some cells form new structures (e.g., spores).
    • Communication: cells interact via chemical messengers.
    • Motility: some cells self-propel (e.g., via flagella).
    • Horizontal gene transfer: exchange genes by conjugation, transduction, transformation; contributes to genetic diversity.

  • The Prokaryotes (Bacteria and Archaea)

    • A. Morphology (Shape and Arrangement)
    • Cocci in clusters; Bacilli; Coccobacilli; Bacilli of varying sizes.
    • Arrangements: in chains, in pairs, in tetrads, diplococci, palisading, fusiform bacilli, spirochetes.
    • Example terms from the slides: Cocci, Bacilli, Coccobacilli, Bacilli in chains, In clusters, In tetrads, In pairs, Fusiform bacilli, Palisading, Spirochetes.
    • Note: not all bacteria have all shapes; morphology varies with species and conditions.
    • B. Morphology (Size)
    • Size measurements (examples given in the material; approximate values in micrometers):
      • Red blood cell: approx. 1.3 × 4.0 μm
      • Streptococcus: 0.8–1.0 μm
      • E. coli (example): 1.3 × 4.0 μm
      • Bacteriophage T2: 0.065 × 0.095 μm
      • Tobacco mosaic virus (TMV): 0.015 × 0.300 μm
      • Pollen: ~0.027 μm (example)
    • Rationale for small size: microbes are small to maximize surface area-to-volume ratio.
    • Surface area and volume relationships for spheres:
      • Surface area: SA=4πr2SA = 4\pi r^2
      • Volume: V=43πr3V = \frac{4}{3}\pi r^3
      • Surface area–to–volume ratio: SAV=3r\frac{SA}{V} = \frac{3}{r}
      • Implication: smaller cells have higher SA:V, facilitating nutrient uptake and waste removal.
    • C. Bacterial Cell Structures
    • Structures often present but not simultaneously universal:
      • Capsule, Ribosomes, Plasmid, Cytoplasmic membrane, Extracellular vesicle, Inclusion, Flagellum, (Archaea) archaellum (note spelling in slides varies).
    • Key point: no single bacterium possesses all structures at all times; presence depends on cell type, conditions, and life cycle stage.
    • D. The Cell Envelope
    • Layered structures surrounding the cytoplasm; govern interactions with the environment; regulate transport; site of energy conservation; determine cell shape; protect against stress.
    • Major components include:
      • Cytoplasmic membrane (plasma membrane)
      • Cell wall
      • Outer membrane (in Gram-negative bacteria)
      • Integral membrane proteins
      • Glycolipids, peripheral membrane proteins, oligosaccharides, and lipid–protein interactions
    • Functional themes:
      • Selective permeability barrier
      • Energy conservation and transduction
      • Anchorage and structural integrity
    • Notable adaptations:
      • Functional membrane microdomains organize protein complexes.
      • Hopanoids (bacterial lipids) act as stabilizers of membranes and influence fluidity; resemble eukaryotic sterols functionally but are distinct molecules (hopanoids are more hydrophobic and do not have the same amphipathic structure as cholesterol).
      • In some bacteria, hopanoids contribute to functional membrane microdomains, aiding organization of secretion systems and environmental signaling.
    • E. Transport mechanisms for nutrient uptake
    • Cells import nutrients via membrane-spanning proteins; transport can be active or passive.
    • Mechanisms described:
      • Simple transport: driven by the proton motive force (PMF), with a transporter protein spanning the membrane.
      • Group translocation: chemical modification of the transported substance driven by phosphoenolpyruvate (PEP) during transport.
      • ABC transporters: consist of a binding protein, transmembrane transporter, and ATP-hydrolyzing protein; energy from ATP; often high affinity and substrate specificity.
    • Example transporters shown in the material:
      • Lac permease (lactose transporter) and glucose transport, with binding proteins and ATP involvement in ABC systems.
      • Na+/H+ antiporters and other transmembrane transporters that couple solute uptake to ion gradients.
    • F. Cell Wall
    • Rigid layer containing peptidoglycan that surrounds the plasma membrane (except in mycoplasmas).
    • Functions:
      • Provides shape to the cell
      • Protects against osmotic lysis
      • Anchors the flagellum
      • Contributes to pathogenicity and protection against toxins
    • Peptidoglycan composition: a heteropolymer of glycan chains cross-linked by amino acids.
    • Classification: Gram-positive walls vs Gram-negative walls.
    • G. Chemical composition of peptidoglycan
    • Core components:
      • Glycan strands of alternating N-acetylmuramic acid (NAM) and N-acetylglucosamine (NAG)
      • Cross-links via peptide interbridges between stem peptides
    • Key residues in stem peptides (typical for many bacteria):
      • L-alanine (L-Ala)
      • D-glutamic acid (D-Glu)
      • L-lysine or meso-diaminopimelic acid (DAP)
      • D-alanine (D-Ala) x 2
    • Glycosidic bonds: covalent bonds joining sugars in glycan strands; provide rigidity in one direction.
    • Example interpeptide bridges (illustrative):
      • D-Ala at position 4 linked to L-Lys; several known bridges exist across species (e.g., Staphylococcus aureus, S. epidermidis, Micrococcus roseus, Streptococcus thermophilus, etc.).
      • In Corynebacterium, a bridge between D-ornithine (orn) and D-Ala may occur; L-homoserine can occupy position 3 in some species.
    • Cross-link variation largely determines peptidoglycan architecture among bacteria.
    • H. Teichoic and Lipoteichoic acids (Gram-positive)
    • Polymers of glycerol or ribitol linked by phosphate groups; embedded in the cell wall or membrane.
    • Lipoteichoic acids anchor the wall to the plasma membrane; teichoic acids contribute to wall structure and ion uptake.
    • Roles:
      • Important during cell division
      • Protect cells from harmful substances (antibiotics, host defenses)
      • Involved in binding pathogens to host tissues and may influence virulence
    • I. Gram-negative cell envelope (outer membrane and periplasm)
    • Outer membrane contains specific components such as porins and lipopolysaccharide (LPS).
    • Lipopolysaccharide (LPS) structure and functions
      • LPS is a large, complex molecule with three parts: lipid A, core polysaccharide, and O-side chain (O-antigen)
      • Roles:
      • Contributes to negative surface charge and outer membrane stability
      • Provides a permeability barrier and protection against host defenses
      • Lipid A can act as endotoxin (septic shock) when released
    • Outer membrane and periplasmic space lie outside the thin peptidoglycan layer and are covalently linked to the cell wall by Braun's lipoprotein.
    • J. Porins and periplasm
    • Porins are trimers spanning the outer membrane; allow passage of nutrients and hydrophilic molecules smaller than ~600 Da.
    • The periplasm contains hydrolytic enzymes, transport proteins, and components involved in peptidoglycan synthesis and compound modification that can harm the cell.
    • Example: E. coli has multiple porins (typical cell ~100,000 porin molecules).
    • K. Bacteria that lack cell walls
    • Some bacteria lack a rigid cell wall (e.g., Mycoplasma). Penicillin inhibition of wall synthesis can be ineffective in these organisms; they require isotonic conditions to prevent lysis in hypotonic environments.
    • L. Layers outside the cell wall
    • Capsule (glycocalyx): compact, well-organized; firmly attached; excludes India ink; can be antigenic and used in vaccines.
    • Slime layer: diffuse, unorganized; not tightly attached; does not exclude particles.
    • Capsule and slime layers contribute to:
      • Exclusion of viruses and hydrophobic toxins
      • Protection from physical injury
      • Attachment to surfaces
      • Resistance to phagocytosis
      • Reservoir of stored nutrients and prevention of desiccation
      • Contribution to pathogenicity
    • S-layers: regular two-dimensional crystalline protein arrays on the surface; roles include protection against environmental stress, promoting adhesion, and contributing to virulence in some pathogens.
    • M. Surface appendages: Pili and Fimbriae
    • Fimbriae: hundreds of short, bristle-like fibers used for attachment to surfaces; can act as receptors for certain viruses.
    • Sex pili: longer, fewer in number; mediate conjugation (gene transfer between bacteria).
    • N. Granules and Globules (Cell Inclusions)
    • Inclusions are distinct cytoplasmic bodies serving as energy reserves or carbon reservoirs; usually enclosed by a single-layer membrane.
    • Organic or inorganic inclusions: PHB, cyanophycin granules, carboxysomes, magnetosomes, sulfur globules, gas vesicles, wax esters, triglycerides, etc.
    • O. Specific Inclusions (examples mentioned in slides)
    • Poly-β-hydroxybutyric acid (PHB): common storage polymer; PHB is a type of polyhydroxyalkanoate (PHA) used for carbon and energy storage; accumulates under imbalanced growth conditions.
    • Cyanophycin granules: storage polymer of nitrogen, formed from arginine and aspartic acid; composition roughly repeating units of arginine and aspartic acid; enzyme cyanophycin synthetase (CphA) catalyzes synthesis.
      • Composition: Arg–Asp polymers with the approximate roles in nitrogen storage.
    • Carboxysomes: polyhedral bodies (~120 nm) that contain RuBisCO; may serve as sites for CO2 fixation.
    • Magnetosomes: intracellular chains of magnetic particles (e.g., magnetite Fe3O4, greigite Fe3S4, pyrite FeS2) that orient bacteria along the Earth's magnetic field.
    • Sulfur globules: intracellular chains of sulfur granules; can serve as electron acceptors under anoxic conditions, enabling anaerobic respiration in some bacteria.
    • Gas vesicles: gas-filled, protein-bound, rigid, buoyant structures; confer buoyancy and help position cells in water columns to optimize light/oxygen exposure.
    • Wax esters and triacylglycerols: insoluble cytoplasmic inclusions storing carbon and energy; less common than PHAs.
    • Other inclusions: rhapidosomes, R-bodies, calcite deposits, selenium spheres, insecticidal protein crystals, recombinant protein bodies, proteasomes, phycobilisomes, pirrellulosomes, anammoxosomes.

  • Growth and Reproduction in Prokaryotes

    • Growth defined as an increase in cell numbers via cell division.
    • The most common mode of reproduction is binary fission, producing two physiologically and genetically identical daughter cells.
    • Other modes of reproduction include:
    • Budding: a new daughter cell forms while the mother cell remains; observed in Planctomycetes, Cyanobacteria, Firmicutes, prosthecate Proteobacteria.
    • Intracellular offspring production (baeocytes): observed in some cyanobacteria like Stanieria; an intracellular process yields multiple small offspring.
    • Binary fission process (overview)
    • DNA replication occurs prior to division.
    • DNA segregation to opposite ends of the cell.
    • Division-site selection and invagination of the cell envelope.
    • Synthesis of new cell wall to form two daughter cells.
    • FtsZ ring formation at the center of the cell coordinates cytokinesis and cell wall synthesis.
    • Growth phases in batch culture
    • Lag phase: adaptation to new environment; low or no net growth.
    • Log (exponential) phase: rapid growth with constant rate; cells are physiologically active.
    • Stationary phase: growth rate slows as resources become limiting; death rate may balance growth.
    • Death phase: cells die at a higher rate than they are formed.
    • Terminology: growth involves both population increase and reproductive strategies (binary fission, budding, baeocyte production) depending on species.

  • Horizontal Gene Transfer (HGT) and Evolution (from the review material)

    • Horizontal gene transfer mechanisms enable exchange of genetic material between cells, contributing to genetic diversity and evolution.
    • Mechanisms include conjugation (via sex pili and mating bridges), transduction (phage-mediated transfer), and transformation (uptake of naked DNA).
    • HGT complements vertical gene transfer (from parent to offspring) and influences traits like antibiotic resistance and metabolic capabilities.

  • Key concepts and connections to broader biology

    • Cells are defined by a cytoplasmic membrane, cytoplasm, DNA, and ribosomes, but prokaryotes lack membrane-bound organelles.
    • The lipid bilayer is amphipathic: hydrophilic heads interact with water; hydrophobic tails form the interior of the membrane.
    • Membrane structure includes integral and peripheral proteins; membrane microdomains organize protein complexes involved in signaling, transport, and secretion.
    • Hopanoids in bacteria function similarly to sterols in eukaryotes, stabilizing membranes and contributing to microdomain organization.
    • The Gram stain-based distinction (Gram-positive vs Gram-negative) corresponds to differences in cell wall structure, peptidoglycan thickness, Teichoic acids, and outer membrane composition (LPS in Gram-negatives).
    • The periplasmic space in Gram-negatives houses enzymes and transport proteins; the outer membrane contains porins that regulate solute passage.
    • Capsule and glycocalyx provide protective and adhesive functions and can influence pathogenesis and vaccine design.
    • Inclusions serve as energy and nutrient reserves; storage compounds (PHAs, cyanophycin) enable survival during nutrient fluctuations.
    • Growth and reproduction strategies are adapted to environmental conditions; different modes affect population dynamics and ecological roles.

  • Formulas and numerical references (LaTeX)

    • Surface area of a sphere: SA=4πr2SA = 4\pi r^2
    • Volume of a sphere: V=43πr3V = \frac{4}{3}\pi r^3
    • Surface area–to–volume ratio: SAV=3r\frac{SA}{V} = \frac{3}{r}
    • Notes on dimensions and measurements in the slides provide example sizes in micrometers (μm) for various cells/viruses:
    • E.g., Streptococcus ~0.8–1.0 μm; E. coli ~1.3 × 4.0 μm; Tobacco mosaic virus ~0.015 × 0.300 μm; Bacteriophage ~0.065 × 0.095 μm; Pollovirus ~0.027 μm.

  • Summary of major terms to remember

    • Capsule, slime layer, glycocalyx; S-layers; porins; Braun’s lipoprotein; LPS; Lipid A; core polysaccharide; O-antigen; teichoic acids; lipoteichoic acids; peptidoglycan; NAM; NAG; D-alanine; DAP; interpeptide bridges; Gram-positive vs Gram-negative cell walls; FtsZ; binary fission; budding; baeocytes; PEP-PTS; ABC transporter; PMF; hopanoids; functional membrane microdomains; carboxysomes; RuBisCO; magnetosomes; gas vesicles; sphingolipids (in some archaea); archaellum.

  • References to foundational principles and real-world relevance

    • Prokaryotic cell structure underpins antibiotic targets (e.g., cell wall synthesis; beta-lactams inhibit cross-linking in peptidoglycan).
    • Horizontal gene transfer drives rapid dissemination of antibiotic resistance and new metabolic capabilities across taxa.
    • Understanding cell envelopes informs vaccine design (capsule antigens) and host–pathogen interactions.
    • Storage inclusions and organelles (carboxysomes, magnetosomes) illustrate metabolic specialization and ecological adaptation.

  • Ethical, philosophical, and practical implications

    • HGT challenges the notion of a single species boundary and has implications for antibiotic stewardship and public health.
    • The study of microbial structures informs bioengineering, biotechnology, and biosafety considerations when handling genetically diverse microbes.

  • Notable reminders and caveats

    • Not every bacterium has all structures; environment and life cycle stage strongly influence presence.
    • Some bacteria lack cell walls (e.g., Mycoplasma), affecting antibiotic susceptibility and cell stability in different environments.
    • The material emphasizes illustrative examples; actual sizes/structures can vary across species and conditions.