Prokaryotic Cell Structure and Function Notes

Cellular Level of Organization and Cell Theory

• Detailed study of the cell began in the 1830s.

• The foundational principles of Cell Theory originated from the pioneering work of German biologists Matthias Schleiden and Theodor Schwann between 1838 and 1839, with later contributions from German physician Rudolph Virchow in 1858.

• Tenets of the Cell Theory:

  • Composition: All organisms are composed of one or more cells. Formulated by German botanist Matthias Schleiden ($1804–1881$) and German zoologist Theodor Schwann ($1810–1882$).

  • Origin: Cells arise only from pre-existing cells because cells are self-reproducing structures. Formulated by German physician Rudolph Virchow ($1821–1902$).

  • Fundamental Unit: Cells are the basic structural and functional units of organization in all living organisms.

Cell Size, Surface-Area-to-Volume Ratio, and Microscopy

• Cell Size Ranges:

  • Cells typically range in size from $1\text{ millimeter (mm)}$ down to 1\text{ micrometer (̦m)} in diameter.

  • Maintenance of a small cell size is critical for maintaining an adequate exchange of materials across the plasma membrane.

• Surface-Area-to-Volume Relationships:

  • Cells require a large surface area relative to their volume to efficiently exchange nutrients, gases, and waste products with their environment.

  • As a cell grows larger, its internal volume increases much faster than its outer surface area. This decrease in the surface-area-to-volume ratio severely reduces the cell's transport efficiency.

  • Small cells possess a significantly larger surface-area-to-volume ratio, which provides a distinct physical advantage for molecular exchange.

• Mathematical Analysis of Surface-Area-to-Volume Ratio:

  • Single Large Cube ($4\text{ cm}$ cube):

  • Total Surface Area: $\text{height} \times \text{width} \times \text{number of sides} \times \text{number of cubes} = 4\text{ cm} \times 4\text{ cm} \times 6 \times 1 = 96\text{ cm}^2$

  • Total Volume: $\text{height} \times \text{width} \times \text{length} \times \text{number of cubes} = 4\text{ cm} \times 4\text{ cm} \times 4\text{ cm} \times 1 = 64\text{ cm}^3$

  • Surface Area to Volume Ratio: $96 : 64 = 1.5 : 1$

  • Eight Medium Cubes ($2\text{ cm}$ cubes):

  • Total Surface Area: $2\text{ cm} \times 2\text{ cm} \times 6 \times 8 = 192\text{ cm}^2$

  • Total Volume: $2\text{ cm} \times 2\text{ cm} \times 2\text{ cm} \times 8 = 64\text{ cm}^3$

  • Surface Area to Volume Ratio: $192 : 64 = 3 : 1$

  • Sixty-Four Small Cubes ($1\text{ cm}$ cubes):

  • Total Surface Area: $1\text{ cm} \times 1\text{ cm} \times 6 \times 64 = 384\text{ cm}^2$

  • Total Volume: $1\text{ cm} \times 1\text{ cm} \times 1\text{ cm} \times 64 = 64\text{ cm}^3$

  • Surface Area to Volume Ratio: $384 : 64 = 6 : 1$

• Principles of Microscopy:

  • Compound Light Microscope:

  • Light passes directly through a specimen and is focused through a series of glass lenses to form an image on the retina.

  • Maximum useful magnification is approximately $1,000\times$

  • Resolves objects separated by as little as 0.2\text{ ̦m}, which is $500\times$ better than the human eye (assuming the resolving power of the human eye is $1.0$).

  • Microscopy Metrics:

  • Magnification: The ratio between the size of an image and its actual physical size. Electron microscopes achieve magnifications hundreds of times greater than compound light microscopes.

  • Resolution: The minimum distance between two separate points that allows them to be distinguished as two distinct objects.

  • Contrast: The difference in shading/intensity between an object and its immediate background. Visualizing specific subcellular components (e.g., individual proteins) is frequently enhanced using fluorescently tagged antibodies.

• Microscopic Visualization Examples (Euglena gracilis):

  • Light Micrograph (LM): Shows live cell structures in color at $200\times$ magnification.

  • Transmission Electron Micrograph (TEM): Reveals internal ultrastructure cross-sections at $12,500\times$ magnification.

  • Scanning Electron Micrograph (SEM): Delivers three-dimensional surface topology at $1,520\times$ magnification.

Comparison of Prokaryotic and Eukaryotic Cells

• All living organisms belong to one of two structural categories:

  • Eukaryotic Cells:

  • Contain a membrane-enclosed nucleus housing genetic material.

  • Possess membrane-bound organelles that compartmentalize metabolic processes.

  • Considerably larger than prokaryotic cells.

  • Compartmentalization allows specific chemical reactions to be localized and isolated from conflicting metabolic processes.

  • Prokaryotic Cells:

  • Lack a membrane-bound nucleus; genomic DNA resides in a nucleoid region.

  • Structurally smaller and simpler than eukaryotic cells.

• Domains of Prokaryotic Life:

  • Domain Bacteria:

  • Ubiquitous ecological presence; act as key environmental decomposers.

  • Medically significant as disease-causing pathogens.

  • Economically important in manufacturing commercial products, biotechnology, and pharmaceuticals.

  • Domain Archaea:

  • Inhabit extreme, inhospitable environments (e.g., high temperature, extreme salinity, anaerobic conditions).

  • Biochemical Distinction: While Domain Bacteria and Domain Archaea share basic structural similarities, they exhibit profound differences in their biochemical composition, cell wall structure, and membrane lipids.

Prokaryotic Cell Morphology: Shapes and Structural Arrangements

• Dimensions: Typical prokaryotic cells measure 1.1\text{ to }1.5\text{ ̦m} in width and 2.0\text{ to }6.0\text{ ̦m} in length.

• Basic Cellular Shapes:

  • Coccus (plural: Cocci): Spherical or round cells.

  • Bacillus (plural: Bacilli): Rod-shaped cells; exhibit varying length-to-width ratios.

  • Spirillum (plural: Spirilla): Rigid, spiral-shaped cells.

  • Spirochete (plural: Spirochetes): Flexible, helical/spiral-shaped cells.

  • Vibrio (plural: Vibrios): Comma-shaped, curved rods.

  • Mycelium: A network of long, branching filamentous threads termed hyphae (resembling fungal growth forms).

  • Pleomorphic: Bacteria that display dynamic, variable, or irregular shapes depending on growth conditions.

• Cellular Arrangements:

  • Formed when prokaryotic cells divide during binary fission but remain attached to one another.

  • Cocci Arrangements:

  • Monococcus: Single, isolated spherical cell.

  • Diplococci: Cells divide in one plane and remain attached in pairs.

  • Streptococci: Cells divide continuously in a single plane to form long chains.

  • Staphylococci: Cells divide along random planes to form irregular, grape-like clusters.

  • Tetrads: Cells divide in two perpendicular planes to form a square packet of four cocci.

  • Sarcina: Cells divide systematically in three planes to produce a symmetrical cubic packet of eight cocci.

  • Bacilli Arrangements:

  • Monobacillus: Single rod-shaped cell.

  • Diplobacillus: Pairs of rod-shaped cells attached end-to-end.

  • Streptobacillus: Rods arranged end-to-end in chains.

  • Coccobacillus: Very short, oval rods that resemble cocci.

  • Palisades: Rods stacked side-by-side in a fence-like alignment.

  • Spore-former: Rods containing intracellular endospores.

  • Curved and Spiral Forms:

  • Vibrious: Comma-shaped cells.

  • Spirilla: Rigid helical filaments with tufts of flagella.

  • Spirochaetes: Highly flexible, thin spiral filaments.

The Bacterial Cell Envelope

• The cell envelope comprises the layered structures encasing the cytoplasm: the plasma membrane, cell wall, and outer layers (glycocalyx/capsules).

• Plasma Membrane:

  • A fluid phospholipid bilayer interspersed with integrated (transmembrane) proteins, peripheral proteins, carbohydrates, and specialized lipids like hopanoids (stiffening molecules analogous to eukaryotic cholesterol).

  • Functions in Bacteria:

  • Acts as a selectively permeable barrier regulating molecular transport.

  • Synthesizes cell wall precursors.

  • Participates directly in DNA replication.

  • Secretes extracellular proteins.

  • Drives cellular respiration and electron transport to generate energy ($\text{ATP}$).

  • Mesosomes: Internal invaginations or pouches formed by folded plasma membrane that expand the available surface area for enzymatic activities.

• Cell Wall Structure and Function:

  • Located external to the plasma membrane; provides structural integrity, maintains cell shape, and prevents lysis caused by internal osmotic pressure.

  • Composed of Peptidoglycan (Murein), a vast polymer consisting of alternating sugar chains:

  • $N\text{-acetylglucosamine (GlcNAc)}$

  • $N\text{-acetylmuramic acid (Mur2Ac)}$

  • Linked by $\beta(1 \rightarrow 4)$ glycosidic bonds (the specific site cleaved by the antimicrobial enzyme lysozyme).

  • Sugar chains are cross-linked by peptide chains attached to $N\text{-acetylmuramic acid}$, containing amino acids such as L-Alanine (L-Ala), D-Glutamic acid (D-Glu), L-Lysine (L-Lys), D-Alanine (D-Ala), and pentaglycine cross-bridges.

• Structural Variations in Bacterial Cell Walls:

  • Gram-Positive Cell Envelope:

  • Possesses a very thick, dense layer of peptidoglycan situated directly outside the plasma membrane.

  • Interwoven with acidic polysaccharides, including Teichoic acid and Lipoteichoic acid (which anchors the peptidoglycan layer to the underlying plasma membrane).

  • Gram-Negative Cell Envelope:

  • Contains a very thin layer of peptidoglycan residing within a gel-like periplasmic space between the inner plasma membrane and an outer membrane.

  • Outer Membrane Structure:

    • Asymmetric lipid bilayer containing phospholipids on the inner leaflet and Lipopolysaccharide (LPS) on the outer leaflet.

    • LPS Components: Lipid A (endotoxin), core polysaccharide, and O antigen (variable carbohydrate chain facing outward).

    • Porin Proteins: Transmembrane channels that span the outer membrane to allow passive transport of small molecules.

    • Murein Lipoproteins: Anchor the outer membrane to the underlying peptidoglycan meshwork.

  • Mycobacteria / Acid-Fast Cell Envelope:

  • Contains minimal peptidoglycan.

  • Dominated by a thick, waxy, highly protective outer lipid layer composed predominantly of Mycolic acids, linked via arabinogalactan polymers, glycolipids, and lipoarabinomannan.

• Extracellular Layers Outside the Cell Wall:

  • Capsule: Well-organized, firmly attached polysaccharide layer; resists removal; protects against desiccation, toxic chemicals, and host phagocytosis while aiding surface attachment.

  • Slime Layer: Unorganized, diffuse, loosely bound polysaccharide layer easily washed away.

  • Glycocalyx: General term for polysaccharide meshwork extending outward from the cell surface; aids attachment to solid bio-surfaces.

  • S-Layer: Rigid geometric array composed of protein or glycoprotein subunits; shields against osmotic and pH fluctuations, ion stress, and enzymatic attack.

Differential Staining: The Gram Stain Technique

• Staining Classification:

  • Simple Stain: Employs a single dye (e.g., iodine, methylene blue); does not differentiate specific organelles; used to evaluate overall cell size, shape, and arrangement.

  • Differential Stain: Utilizes multiple reagents/stains to categorize bacterial species based on underlying structural differences in their cell envelopes (e.g., Gram stain, Acid-Fast stain).

• The Gram Stain Protocol:

  • Formulated to distinguish Gram-positive from Gram-negative bacteria via a four-step chemical sequence:

1. Primary Stain (Crystal Violet):

   • Applied to a heat-fixed smear; stains all bacterial cells (both Gram-positive and Gram-negative) a deep purple color.

2. Mordant (Gram's Iodine):

   • Enters the cells and forms large, insoluble iodine-crystal violet complexes within the cytoplasm and cell wall.

3. Decolorizer (Acetone or Alcohol):

   • In Gram-Positive Bacteria: Dehydrates the thick peptidoglycan layer, causing its pores to shrink and trapping the large iodine-crystal violet complexes inside $\rightarrow$ cells remain purple.

   • In Gram-Negative Bacteria: Dissolves the outer membrane lipid bilayer and washes out through the thin, porous peptidoglycan layer $\rightarrow$ cells become colorless/clear.

4. Counterstain (Safranin):

   • Applied to stain all cleared cells.

   • Gram-positive cells retain the intense primary purple color, masking the lighter pink safranin $\rightarrow$ remain purple.

   • Decolorized Gram-negative cells absorb the safranin $\rightarrow$ appear pink or red.

Bacterial Cytoplasm, Internal Structures, and Extrachromosomal DNA

• Cytoplasm:

  • The internal semifluid matrix encased by the plasma membrane.

  • Composed of approximately $\frac{4}{5}$ ($80\text{ }$) water and $\frac{1}{5}$ ($20\text{ }$) dissolved organic and inorganic solutes, including metabolic enzymes, proteins, carbohydrates, lipids, and inorganic ions.

  • Serves as the primary site for metabolic reactions and enzymatic pathways.

• Intracytoplasmic Membranes:

  • Specialized plasma membrane infoldings/invaginations found in high-metabolic-rate bacteria, such as photosynthetic prokaryotes or obligate aerobes with elevated respiratory chains.

  • Can form aggregates of spherical vesicles or stacked internal lamellae.

• Bacterial Ribosomes:

  • Non-membrane-bound ribonucleoprotein complexes distributed throughout the cytoplasm.

  • Function as the sites of protein synthesis (translation).

  • Smaller and structurally distinct from eukaryotic ($80\text{S}$) ribosomes.

  • Designated as $70\text{S}$ Ribosomes, composed of two functional subunits:

  • $50\text{S}$ Large Subunit: Contains the peptidyl transferase center and three tRNA binding sites (A site, P site, E site).

  • $30\text{S}$ Small Subunit: Contains the mRNA-binding site.

• Nucleoid:

  • Irregularly shaped, non-membrane-bound cytoplasmic region housing the bacterial chromosome.

  • Contains a single, circular double-stranded DNA molecule associated with small amounts of RNA and specialized architectural proteins.

• Plasmids:

  • Small, circular, extrachromosomal DNA molecules that replicate independently of the bacterial chromosome.

  • Carry non-essential genes that provide strong selective advantages under specific environmental stresses (e.g., antibiotic resistance factors, heavy-metal tolerance, or virulence determinants).

  • Transferred horizontally between bacterial cells during conjugation.

• Bacterial Conjugation:

  • Direct physical transfer of genetic material (typically plasmids) from a donor bacterium to a recipient bacterium.

  • Mediated by a specialized, rigid extracellular tube called a conjugation pilus (sex pilus).

  • Process steps:

  1. Donor cell projects a sex pilus that attaches to the recipient cell.

  2. Pilus retracts, bringing the donor and recipient into direct cell-to-cell contact.

  3. A specialized protein complex (relaxosome/transferosome) cuts one strand of plasmid DNA and transfers it into the recipient.

  4. Both cells synthesize the complementary strand, transforming the recipient into a new plasmid donor.

Bacterial Appendages and Mechanisms of Locomotion

• Approximately half of all known bacterial species are motile and adjust their movements in response to chemical and environmental stimuli.

• Flagella Structure and Ultrastructure:

  • Long, thin, helical appendages that function like motorized propellers for cell movement.

  • Structurally distinct from and significantly simpler than eukaryotic flagella.

  • Composed of three functional parts:

  • Filament: Long, hollow helical cylinder extending from the cell surface to the tip, composed of flagellin proteins.

  • Hook: Short, curved flexible coupling segment connecting the filament to the basal motor.

  • Basal Body: The rotary motor embedded within the cell envelope.

    • Gram-negative flagella possess four anchor rings spanning the outer membrane, peptidoglycan layer, periplasmic space, and inner plasma membrane.

    • Gram-positive flagella possess two anchor rings attached directly to the inner plasma membrane and thick peptidoglycan wall.

• Flagellar Arrangements (Trichous = hair-like):

  • Atrichous: Lacking flagella entirely.

  • Monotrichous: Single polar flagellum attached at one end.

  • Amphitrichous: Single flagellum located at both opposing poles of the cell.

  • Cephalotrichous: Clusters/tufts of flagella emerging at one or both ends.

  • Lophotrichous: A distinct bundle or tuft of flagella originating from a single point.

  • Peritrichous: Flagella distributed randomly across the entire cell surface.

• Types of Bacterial Movement:

  • 1. Flagellar Motility:

  • Swimming: Individual cell movement driven by rapid flagellar rotation (up to $1100\text{ revolutions/sec}$). Counterclockwise rotation results in a smooth forward run, while clockwise rotation causes flagellar bundle dispersal, resulting in a random tumble to reorient the cell.

  • Swarming: Rapid, coordinated group movement across moist solid/semi-solid agar surfaces; executed in unison by cells typically possessing peritrichous flagella.

  • Spirochete Motility: Internal flagella termed periplasmic flagella or axial fibrils reside within the periplasmic space between the protoplasmic cylinder and flexible outer membrane. Rotation creates a corkscrew-like flexing and spinning motion allowing movement through viscous fluids.

• 2. Twitching and Gliding Motility:

  • Flagella-independent movement occurring on solid surfaces.

  • Twitching Motility: Mediated by the rapid extension, attachment, and retraction of Type IV pili ("grappling hook" motion).

  • Gliding Motility: Smooth, continuous movement along surfaces without visible external appendages.

• 3. Chemotaxis:

  • Directed movement toward chemical attractants (e.g., nutrients like sugars/amino acids) or away from chemical repellents (e.g., toxins, waste products).

  • Surface chemoreceptors detect concentration gradients and transmit signals to the flagellar rotary motor.

  • In an attractant gradient, forward runs become longer and tumbles occur less frequently, resulting in net migration toward the favorable stimulus.

  • Non-Motile Surface Appendages (Pili and Fimbriae):

• Pili (singular: Pilus): Tiny, hollow protein cylinders protruding from the cell surface; primarily found in Gram-negative bacteria.

  • Conjugation Pili (Sex Pili): Long, specialized pili that attach donor and recipient cells to mediate genetic transfer.

  • Type IV Pili: Facilitate twitching motility and surface adherence.

• Fimbriae (singular: Fimbria): Short, thin, hair-like bristle projections sprouting across the cell surface; present in both Gram-positive and Gram-negative bacteria; critical for host cell adherence, tissue colonization, and pathogenicity.

Endospores and the Process of Sporulation

• Definition and Function:

  • A dormant, highly resistant non-reproductive structure produced inside certain bacterial cells (predominantly Gram-positive rods like Bacillus and Clostridium).

  • Serves strictly as a survival mechanism in response to harsh, adverse environmental conditions (e.g., nutrient starvation, extreme temperatures, high ultraviolet or ionizing radiation, desiccation, and chemical disinfectants).

  • Endospores are exceptionally difficult to destroy and can remain viable in a cryptobiotic state for thousands of years.

• Endospore Layers (from inside to outside):

  • Core (Spore Core): Contains dehydration-stabilized DNA, ribosomes, glycolytic enzymes, and high concentration of calcium dipicolinate.

  • Core Wall: Inner peptidoglycan layer surrounding the core.

  • Cortex: Thick, loosely cross-linked peptidoglycan layer.

  • Spore Coat: Dense, multi-layered protein shell providing chemical resistance.

  • Exosporium: Thin, delicate lipid-protein outer layer.

• The Sporulation Process Cycle:

  • An organized multi-step developmental program taking several hours, initiated when vegetative cell growth halts due to nutrient deprivation:

• Stage I: Axial Filament Formation: The bacterial chromosome replicates and stretches into an axial filament along the longitudinal cell axis.

• Stage II: Septum Formation: The plasma membrane invaginates near one pole to form an asymmetric spore septum, isolating a portion of DNA.

• Stage III: Forespore Engulfment: The mother cell membrane grows around the isolated forespore, engulfing it within a double membrane envelope.

• Stage IV: Cortex Formation: A thick peptidoglycan cortex is synthesized between the two internal membranes, accompanied by accumulation of calcium and dipicolinic acid.

• Stage V: Coat Synthesis: Highly resistant protein coat layers are deposited around the cortex.

• Stage VI: Endospore Maturation: Spore dehydration is finalized, conferring thermal stability and enzymatic dormancy.

• Stage VII: Sporangium Lysis: The surrounding mother cell (sporangium) lyses and releases the fully mature free endospore into the environment.

• Germination: When environmental conditions become favorable (nutrients, moisture), the endospore breaks dormancy and germinates back into an active, dividing vegetative cell.