Chapter 4: Anatomy of Prokaryotes and Eukaryotes — Vocabulary

Prokaryotes: Overview

• Prokaryotes are organisms whose name means “pre-nucleus.”

• They are bacteria, unicellular, and reproduce asexually.

• Morphology refers to shape:

  • Cocci: round cells. Singular: coccus.

  • Bacilli (bacillus): rod-shaped cells.

  • Spirochetes: spiral-shaped cells.

  • Pleomorphic: no distinct shape.

• Two main classes of prokaryotes:

  • Eubacteria: the more “typical” bacteria (examples: Escherichia coli, Staphylococcus aureus, Salmonella).

  • Archaea: extremophiles; live in extreme environments (e.g., very low pH, very high temperature).

  • Note: Anatomical features discussed here are primarily described with respect to eubacteria; archaea are mentioned for context.

• Not every bacterium possesses every feature described below; these are potential features you may encounter.

• Organization: start from the outside of the cell and work inward.

Prokaryotic Morphology and Classification (Expanded)

• Shapes:

  • Cocci: spherical.

  • Bacilli/Bacillus: rod-shaped.

  • Spirochetes: spiral.

  • Pleomorphic: variable shape.

• Prokaryotes have two major groups by cell wall chemistry and outer layers:

  • Eubacteria: typical bacteria (some Gram-positive, some Gram-negative).

  • Archaea: may lack peptidoglycan in their cell walls; often contain other polymers and sterols in membranes.

• Important note on archaea:

  • They lack peptidoglycan because of harsh living conditions; cell walls may contain sterols.

Glycocalyx (Outer Surface)

• Composition: polysaccharides and/or polypeptides; synthesized inside the cell and secreted out.

• Two organizational forms:

  • Capsule: polysaccharides/polypeptides are highly organized and firmly attached to the cell wall. Associated with increased pathogenic potential and resistance to immune defenses.

  • Slime layer: polysaccharides/polypeptides loosely organized and not firmly attached. Benefits: attachment to surfaces/other cells, some protection, and communication.

Flagellum and Motility (Taxis)

• Flagellum: embedded in the cell wall and plasma membrane; enables motility (propulsion).

• Flagella organization can be at opposite poles or surrounding the cell.

• Motility terminology is described as taxis (directed movement):

  • Positive taxis: movement toward a stimulus (forward).

  • Negative taxis: movement away from a stimulus (backward).

  • Chemotaxis: movement toward/away from chemicals.

  • Phototaxis: movement toward/away from light.

Axial Filaments (Endoflagella)

• Found in spirochetes.

• 2–200 axial filaments (endoflagella) enclosed within the outer sheath.

• Each filament attaches at one end to the cytoplasmic membrane; they rotate the cell body like a corkscrew to move.

Pili and Fimbriae (Attachment Structures)

• Both made of the protein pilin.

• Primary roles: attachment to surfaces or host cells; not major drivers of movement.

• Types:

  • Conjugation pili (F pilus): long pili used for genetic exchange between bacteria.

  • Fimbriae: many short pili (up to hundreds) used for attachment to surfaces and host tissues; important for pathogenicity.

• Note: Fimbriae can facilitate attachment to host cells, aiding colonization and disease.

Bacterial Cell Wall

• Main constituent: peptidoglycan (also called murein).

• Peptidoglycan structure: polysaccharides cross-linked by peptides.

• The cell wall contains pores called porins that permit selective passage of molecules.

• Classification by peptidoglycan content:

  • Gram-positive: thick peptidoglycan layer.

  • Gram-negative: thin peptidoglycan layer; outer membrane present containing lipopolysaccharides (LPS), lipoproteins, and phospholipids.

• Archaea note: archaea generally do not have peptidoglycan and may have sterols in their cell walls to support structure.

Cytoplasmic (Plasma) Membrane

• Internal boundary: phospholipid bilayer (fluid mosaic model).

• Components: phospholipids, proteins (peripheral and integral), glycoproteins (proteins attached to carbohydrates), and glycolipids (proteins attached to lipids).

• Phospholipids have:

  • Hydrophilic (water-loving) phosphate head facing aqueous environments.

  • Hydrophobic (water-fearing) fatty acid tails inside the membrane.

• Function: selectively permeable barrier; controls entry/exit of substances.

• Transport across membrane: energy-independent (passive) and energy-requiring (active).

Passive vs Active Transport

• Passive transport: no energy expenditure; substances move down concentration gradient.

  • Diffusion: movement of molecules across the membrane; can be simple or facilitated.

  • Facilitated diffusion: uses integral membrane proteins as channels or carriers.

  • Osmosis: diffusion of water across a membrane.

• Active transport: requires cellular energy to move substances against the concentration gradient (uphill).

Cytoplasm and Cytoskeleton

• Cytoplasm: the watery internal milieu, about 80% water; provides reduced friction for macromolecule movement.

• Cytoskeleton (prokaryotes): protein-based framework supporting the cell.

• Nucleoid: region where the main circular, double-stranded DNA resides (not enclosed by a membrane).

• Plasmids: circular, double-stranded DNA outside the main chromosome; carry accessory genes; can be transferred via pili.

• Ribosomes: protein synthesis factories; composed of RNA and proteins.

  • Prokaryotic ribosome: 70S total; subunits are 50S and 30S.

  • The S (Svedberg) unit reflects size/shape, not a direct additive weight (i.e., 30S + 50S ≠ 70S due to interaction effects).

  • Formula: 70S = 50S + 30S (conceptual, for understanding subunit composition).

Inclusions (Storage Bodies) and Magnetosomes

• Inclusions: storage compartments within the cytoplasm.

  • Metachromatic inclusions: store inorganic phosphate.

  • Polysaccharide inclusions: store starch.

  • Lipid inclusions and sulfur inclusions: store lipids or sulfur, respectively.

• Magnetosomes: iron oxide-containing inclusions; aid in hydrogen peroxide detoxification and other metabolic processes (lab focus upcoming).

Endospores (Dormant Cells)

• Endospores are highly durable defense structures, primarily in Gram-positive bacilli.

• They enable survival under adverse conditions; provide long-term resistance.

• Structure: multi-layered protective coat around DNA, forming a hard shell.

• States:

  • Vegetative state: actively replicating and metabolizing.

  • Endospore: dormant, with no replication or metabolism.

• Sporulation (sporogenesis): process of endospore formation in response to stress.

• Germination: return from the endospore to the vegetative state when conditions become favorable.

• Location of endospore formation can be terminal or middle along the cell, varying by species.

• Importance: endospores can survive for years or even thousands of years and germinate when conditions improve.

Eukaryotes: Overview

• Eukaryotes can be unicellular or multicellular.

• Reproduction: asexual or sexual, depending on the organism.

• General characteristics: typically pleomorphic and larger than prokaryotic cells (roughly about 10x the volume on average).

• Note: Not all features described apply to every eukaryote.

Eukaryotic Motility: Flagella and Cilia

• Flagellum: moves in a back-and-forth (tail-wagging) manner; structurally different from prokaryotic flagella.

• Cilia: short, numerous projections that beat back and forth; provide motility or create currents; less motile than flagella.

• Some eukaryotes move using flagella; others may rely on cilia or other mechanisms.

Glycocalyx and Cell Wall in Eukaryotes

• Glycocalyx: present and composed of glycoproteins and glycolipids (like in prokaryotes).

• Cell wall: may be present or absent depending on the eukaryote; if present, it is not made of peptidoglycan.

  • If present, common components include chitin, cellulose, or silica, rather than peptidoglycan.

• Key note: Peptidoglycan is specific to prokaryotes.

Cytoplasmic Membrane in Eukaryotes

• Similar to prokaryotes: phospholipid bilayer with sterols (e.g., cholesterol) in many cells.

• Passive and active transport occur here as well (same concepts as in prokaryotes).

• Endocytosis: process by which a cell ingests material via engulfment.

  • Phagocytosis: ingestion of large particles (e.g., immune cells engulfing pathogens).

  • Pinocytosis: ingestion of fluids and small molecules.

  • Receptor-mediated endocytosis: targeted uptake after ligand binding to cell receptors.

Environmental Interactions and Tonicity (Eukaryotes)

• Environments types:

  • Isotonic: ideal environment; balanced water and solute concentrations between inside and outside the cell; constant water movement.

  • Hypotonic: outside environment has lower solute concentration; water tends to move into the cell; can cause lysis if excessive.

  • Hypertonic: outside environment has higher solute concentration; water moves out of the cell; can cause dehydration and plasmolysis.

• Outcome:

  • Hypotonic stress can lead to cell lysis.

  • Hypertonic stress can lead to cell dehydration and death.

  • Isotonic is the preferred balance for stable cell volume.

Cytoplasm, Cytoskeleton, and Cytoplasmic Streaming (Eukaryotes)

• Cytoplasm (cytosol): fluid portion of the cytoplasm; provides medium for biochemical reactions.

• Cytoskeleton: microfilaments (actin), microtubules (tubulin); provides structural support and transport pathways.

• Cytoplasmic streaming: directed flow of cytoplasm in some eukaryotic cells; helps distribute nutrients and organelles.

• Note: Cytoplasmic streaming is not observed in prokaryotes due to the lack of a complex cytoskeleton and endomembrane system.

Ribosomes in Eukaryotes

• Eukaryotic ribosome: 80S (60S + 40S subunits).

• Ribosome location: both free-standing ribosomes in the cytosol and attached ribosomes on the endoplasmic reticulum.

• Compare to prokaryotes: prokaryotic ribosome is 70S (50S + 30S).

Organelles and the Endomembrane System (Eukaryotes)

• Organelles: membrane-bound structures forming the endomembrane system; direct or indirect interactions between organelles (direct contact or through vesicle transport).

• Nucleus: site of DNA in eukaryotes.

  • DNA is associated with histones (and non-histones).

  • Nuclear envelope surrounds the DNA and contains pores for molecular traffic.

  • Nucleoli: regions within the nucleus where ribosomal RNA (rRNA) synthesis occurs.

• Golgi apparatus: site of protein modification and membrane formation; stacked flattened membranes called cisternae.

  • Cis face: receiving side; where transport vesicles enter.

  • Trans face: shipping side; where secretory vesicles leave.

  • Functions include adding cofactors or other modifications to proteins.

• Endoplasmic reticulum (ER): network of flattened membranes (cisternae) connected to the nuclear envelope; two regions:

  • Rough ER: studded with ribosomes; site of protein synthesis and initial processing.

  • Smooth ER: lacks ribosomes; site of lipid synthesis.

• Mitochondrion: site of cellular energy production (ATP).

  • Has outer and inner membranes; inner membrane folds into cristae; innermost region is the matrix.

  • Mitochondria can replicate independently; contain their own circular DNA and ribosomes resembling bacterial systems.

• Lysosomes: digestive enzyme-containing vesicles; part of endomembrane traffic.

• Peroxisomes: contain enzymes like catalase; help break down hydrogen peroxide (H₂O₂) as part of cellular defense/metabolism.

• Centrosomes: near the nucleus; composed of pericentriolar material and centrioles (microtubule organizing center); organize mitotic spindle during cell division.

• Other organelles (not exhaustively listed here): chloroplasts in plants/algae (also evidence for endosymbiosis, discussed later in the endosymbiotic theory).

Endomembrane System: Direct and Indirect Relationships

• Direct relationships: organelles physically connected or directly exchanging materials.

• Indirect relationships: materials transported via vesicles between organelles.

Endosymbiotic Theory (Origin of Eukaryotes)

• Hypothesis: eukaryotes originated when a larger prokaryotic cell engulfed a smaller prokaryotic cell; over time, the engulfed cell evolved into organelles (mitochondria and chloroplasts).

• Supporting evidence:

  • Mitochondria and chloroplasts resemble bacteria in size and shape.

  • They contain circular DNA and can replicate on their own.

  • They have protein synthesis machinery similar to bacteria.

• Implication: Eukaryotes arose through symbiotic partnerships rather than simple enlargement.

Quick comparative notes: Prokaryotes vs. Eukaryotes (in context of anatomy)

• Complexity: Eukaryotic cells generally contain many more organelles and a true nucleus; prokaryotes lack a nucleus and many organelles.

• Size: Eukaryotes are typically larger (about 10x the volume on average).

• Genetic organization: Prokaryotes have a nucleoid with circular DNA and often plasmids; eukaryotes have a membrane-bound nucleus with linear DNA and multiple chromosomes.

• Ribosomes: 70S in prokaryotes vs. 80S in eukaryotes (with 50S+30S vs. 60S+40S subunits, respectively).

• Cell wall: Prokaryotic walls commonly contain peptidoglycan; many eukaryotes lack a cell wall or have walls made of cellulose, chitin, or silica (not peptidoglycan).

• Endomembrane system: Present in eukaryotes; largely absent or reduced in prokaryotes.

Connections to Foundations and Real-World Relevance

• The glycocalyx and fimbriae/pili play critical roles in pathogenicity and host interactions; understanding these can elucidate mechanisms of infection and bacterial adhesion.

• The Gram stain classification (Gram-positive vs Gram-negative) hinges on peptidoglycan thickness and outer membrane composition; this informs antibiotic susceptibility and disease processes.

• Endospores represent a key survival strategy for certain bacteria (e.g., in food safety, clinical infections, and sterilization challenges).

• Endomembrane system and organelle functions underpin cellular metabolism, protein synthesis, and signaling—core to understanding cellular biology and disease mechanisms.

• Endosymbiotic theory links to broader evolutionary biology, highlighting how complex cells may have evolved through microbial partnerships; this has implications for understanding organelle origins and mitochondrial diseases.

Notation and Key Terms (for quick review)

• 70S, 50S, 30S: Prokaryotic ribosomes and subunits.

• 80S, 60S, 40S: Eukaryotic ribosomes and subunits.

• Peptidoglycan (murein): main cell wall component in most bacteria.

• Porins: channels in the cell wall that allow molecule passage.

• LPS: lipopolysaccharide component of the outer membrane in Gram-negative bacteria.

• Isotonic, Hypotonic, Hypertonic: tonicity states affecting water movement and cell volume.

• Endocytosis types: Phagocytosis, Pinocytosis, Receptor-mediated endocytosis.

• Endomembrane system: nucleus, ER, Golgi, lysosomes, endosomes, plasma membrane, and related vesicles.

• Endospore: dormant, highly resistant bacterial cell form.

• Sporulation/Sporogenesis: endospore formation.

• Germination: return to vegetative, metabolically active state.

• Endosymbiotic theory: origin of mitochondria and chloroplasts via symbiotic events.

Summary Takeaway

• Prokaryotes exhibit a set of potential outer-to-inner features (glycocalyx, flagella, pili, cell wall, membrane, cytoplasm, nucleoid, ribosomes, inclusions, endospores) with variation across species.

• Eukaryotes add a complex endomembrane system, true nucleus, mitochondria, and cytoskeleton, enabling greater cellular diversity and functionality; many features arose via endosymbiotic events and organelle specialization.

• Understanding these structures helps explain microbial physiology, disease mechanisms, antibiotic targets, and evolutionary biology.

1. Prokaryotes: Fundamental Characteristics

• Definition: Organisms whose name means “pre-nucleus.”

• Examples: Bacteria, Archaea.

• Cellularity: Unicellular.

• Reproduction: Asexual.

• Morphology (Shapes):

  • Cocci: Round cells (Singular: coccus).

  • Bacilli (bacillus): Rod-shaped cells.

  • Spirochetes: Spiral-shaped cells.

  • Pleomorphic: No distinct shape.

• Classes:

  • Eubacteria: “Typical” bacteria (e.g., Escherichia coli, Staphylococcus aureus, Salmonella).

  • Archaea: Extremophiles; live in extreme environments (e.g., very low pH, very high temperature).

2. Prokaryotic Cell Structures (Eubacteria Focus)

2.1. Glycocalyx (Outer Surface)

• Composition: Polysaccharides and/or polypeptides, synthesized inside and secreted out.

• Forms:

  • Capsule: Highly organized, firmly attached. Associated with increased pathogenic potential and resistance to immune defenses.

  • Slime layer: Loosely organized, not firmly attached. Benefits: attachment, some protection, communication.

2.2. Flagellum and Motility (Taxis)

• Function: Enables motility (propulsion), embedded in cell wall and plasma membrane.

• Organization: Can be at opposite poles or surrounding the cell.

• Taxis (Directed Movement):

  • Positive taxis: Movement toward a stimulus.

  • Negative taxis: Movement away from a stimulus.

  • Chemotaxis: Movement toward/away from chemicals.

  • Phototaxis: Movement toward/away from light.

2.3. Axial Filaments (Endoflagella)

• Found In: Spirochetes.

• Structure: 2–200 filaments enclosed within the outer sheath, attached to the cytoplasmic membrane.

• Mechanism: Rotate the cell body like a corkscrew for movement.

2.4. Pili and Fimbriae (Attachment Structures)

• Composition: Pilin protein.

• Primary Roles: Attachment to surfaces or host cells; not major drivers of movement.

• Types:

  • Conjugation pili (F pilus): Long pili for genetic exchange between bacteria.

  • Fimbriae: Many short pili (hundreds) for attachment to surfaces and host tissues; important for pathogenicity.

2.5. Bacterial Cell Wall

• Main Constituent: Peptidoglycan (murein) – polysaccharides cross-linked by peptides.

• Porins: Pores allowing selective passage of molecules.

• Classification by Peptidoglycan Content:

  • Gram-positive: Thick peptidoglycan layer.

  • Gram-negative: Thin peptidoglycan layer, outer membrane containing lipopolysaccharides (LPS), lipoproteins, and phospholipids.

• Archaea Note: Generally lack peptidoglycan; may have sterols in cell walls.

2.6. Cytoplasmic (Plasma) Membrane

• Structure: Phospholipid bilayer (fluid mosaic model).

• Components: Phospholipids, proteins (peripheral and integral), glycoproteins, glycolipids.

• Phospholipids: Hydrophilic phosphate head, hydrophobic fatty acid tails.

• Function: Selectively permeable barrier; controls substance entry/exit.

2.7. Transport Across Membrane

• Passive Transport (No Energy): Substances move down concentration gradient.

  • Diffusion: Simple or facilitated (using integral membrane proteins).

  • Osmosis: Diffusion of water.

• Active Transport (Requires Energy): Substances move against concentration gradient.

2.8. Cytoplasm and Cytoskeleton

• Cytoplasm: Watery internal milieu (approx. 80% water).

• Cytoskeleton (Prokaryotes): Protein-based framework.

2.9. Genetic Material and Ribosomes

• Nucleoid: Region with main circular, double-stranded DNA (not membrane-enclosed).

• Plasmids: Circular, double-stranded DNA outside main chromosome; carry accessory genes; transferable via pili.

• Ribosomes: Protein synthesis factories (RNA and proteins).

  • Prokaryotic Ribosome: 70S total; subunits are 50S and 30S (70S = 50S + 30S conceptual).

2.10. Inclusions (Storage Bodies) and Magnetosomes

• Inclusions: Cytoplasmic storage compartments.

  • Metachromatic: Inorganic phosphate.

  • Polysaccharide: Starch.

  • Lipid/Sulfur: Lipids or sulfur.

• Magnetosomes: Iron oxide-containing inclusions; aid in hydrogen peroxide detoxification.

2.11. Endospores (Dormant Cells)

• Function: Highly durable defense structures (primarily Gram-positive bacilli); enable survival under adverse conditions.

• Structure: Multi-layered protective coat around DNA.

• States:

  • Vegetative: Actively replicating and metabolizing.

  • Endospore: Dormant, no replication or metabolism.

• Processes:

  • Sporulation (sporogenesis): Endospore formation due to stress.

  • Germination: Return to vegetative state when conditions are favorable.

• Key Importance: Can survive for years, resisting harsh conditions.

3. Eukaryotes: Fundamental Characteristics

• Cellularity: Unicellular or multicellular.

• Reproduction: Asexual or sexual.

• General Characteristics: Typically pleomorphic; larger than prokaryotic cells (approx. 10x volume on average).

4. Eukaryotic Cell Structures

4.1. Motility: Flagella and Cilia

• Flagellum: Moves in a back-and-forth (tail-wagging) manner; structurally distinct from prokaryotic flagella.

• Cilia: Short, numerous projections; beat back and forth for motility or to create currents.

4.2. Glycocalyx and Cell Wall

• Glycocalyx: Present; composed of glycoproteins and glycolipids.

• Cell Wall: May be present or absent; if present, not made of peptidoglycan.

  • Components (if present): Chitin, cellulose, or silica.

  • Key Note: Peptidoglycan is specific to prokaryotes.

4.3. Cytoplasmic Membrane

• Structure: Phospholipid bilayer with sterols (e.g., cholesterol) in many cells.

• Transport: Passive and active transport (same concepts as prokaryotes).

• Endocytosis: Cell ingests material via engulfment.

  • Phagocytosis: Ingestion of large particles (e.g., pathogens).

  • Pinocytosis: Ingestion of fluids and small molecules.

  • Receptor-mediated endocytosis: Targeted uptake after ligand binding.

4.4. Environmental Interactions and Tonicity

• Isotonic: Ideal; balanced water/solute; constant water movement.

• Hypotonic: Lower solute outside; water moves into cell; can cause lysis.

• Hypertonic: Higher solute outside; water moves out; causes dehydration and plasmolysis.

• Outcome: Isotonic is preferred for stable cell volume.

4.5. Cytoplasm, Cytoskeleton, and Cytoplasmic Streaming

• Cytoplasm (cytosol): Fluid portion; medium for reactions.

• Cytoskeleton: Microfilaments (actin), microtubules (tubulin); structural support and transport.

• Cytoplasmic Streaming: Directed flow of cytoplasm; distributes nutrients/organelles (not in prokaryotes).

4.6. Ribosomes

• Eukaryotic Ribosome: 80S total (60S + 40S subunits).

• Location: Free-standing in cytosol and attached to endoplasmic reticulum.

4.7. Organelles and the Endomembrane System

• Organelles: Membrane-bound structures; interact directly or via vesicles.

  • Nucleus: Site of DNA (associated with histones); nuclear envelope with pores.

    • Nucleoli: rRNA synthesis.

  • Golgi apparatus: Stacked flattened membranes (cisternae); protein modification and membrane formation.

    • Cis face: Receiving side.

    • Trans face: Shipping side.

  • Endoplasmic Reticulum (ER): Network of cisternae connected to nuclear envelope.

    • Rough ER: Studded with ribosomes; protein synthesis and processing.

    • Smooth ER: Lacks ribosomes; lipid synthesis.

  • Mitochondrion: Site of ATP production; outer/inner membranes, cristae, matrix.

    • Key Point: Replicate independently, contain circular DNA and bacterial-like ribosomes (evidence for endosymbiosis).

  • Lysosomes: Contain digestive enzymes.

  • Peroxisomes: Contain enzymes like catalase; break down H2O2.

  • Centrosomes: Near nucleus; pericentriolar material and centrioles (microtubule organizing center); organize mitotic spindle.

5. Endosymbiotic Theory (Origin of Eukaryotes)

• Hypothesis: Larger prokaryote engulfed smaller prokaryote, which evolved into organelles (mitochondria, chloroplasts).

• Supporting Evidence:

  • Mitochondria/chloroplasts resemble bacteria in size/shape.

  • Contain circular DNA, replicate independently.

  • Protein synthesis machinery similar to bacteria.

• Implication: Eukaryotes arose through symbiotic partnerships.

6. Quick Comparative Notes: Prokaryotes vs. Eukaryotes

7. Real-World Relevance & Key Terms

• Pathogenicity: Glycocalyx, fimbriae/pili play critical roles in infection and adhesion.

• Gram Stain: Classification (Gram-positive/negative) based on peptidoglycan and outer membrane; informs antibiotic susceptibility.

• Endospores: Key survival strategy for certain bacteria (food safety, clinical infections, sterilization).

• Endomembrane System: Core to cellular metabolism, protein synthesis, and signaling; understanding disease mechanisms.

• Endosymbiotic Theory: Links to evolutionary biology; understanding organelle origins and mitochondrial diseases.

Key Terms for Review:

• 70S, 50S, 30S: Prokaryotic ribosomes and subunits.

• 80S, 60S, 40S: Eukaryotic ribosomes and subunits.

• Peptidoglycan (murein): Main bacterial cell wall component.

• Porins: Channels in cell wall.

• LPS: Lipopolysaccharide in Gram-negative outer membrane.

• Isotonic, Hypotonic, Hypertonic: Tonicity states.

• Endocytosis types: Phagocytosis, Pinocytosis, Receptor-mediated endocytosis.

• Endomembrane system: Nucleus, ER, Golgi, lysosomes, endosomes, plasma membrane, and vesicles.

• Endospore: Dormant, highly resistant bacterial cell form.

• Sporulation/Sporogenesis: Endospore formation.

• Germination: Return to vegetative state.

• Endosymbiotic theory: Origin of mitochondria and chloroplasts.