Prokaryotic Microorganisms - BIOL3420 Study Notes

Goals and Objectives

• Understand main characteristics of prokaryotes.
• After this lecture students should be able to:
  • List components of a prokaryotic cell.
  • Explain structure and function of external appendages present in prokaryotes.
  • Classify bacteria according to the number and position of flagella.
  • Explain chemotaxis and phototaxis in bacteria.
  • Describe structure and function of external surface layers present in bacteria.
  • Describe differences in the structure of the cell envelope between gram-positive and gram-negative bacteria and explain why they stain differently in Gram staining.
  • Describe organization of genetic material in bacteria.
  • Describe structure and function of bacterial ribosomes.
  • Name types of bacteria according to their cell shape and aggregation of cells they form.
  • Explain pleomorphism in bacteria.
  • Describe germination and sporulation in bacteria.
  • Explain the importance of bacterial endospores and their medical implications.

Tree of Life

• Three domains: Bacteria, Archaea, Eukarya.
• Four eukaryotic kingdoms: Animalia, Plantae, Fungi, Protista.
  • Protista has two subkingdoms: Algae and Protozoa.
• Viruses are not living organisms.

Bacterial Cell

External Elements

• Appendages: Flagella, Pili, Fimbriae.
• Surface layers: S layers, Glycocalyx (Capsulae and Slim Layer).
• Cell envelope components: Outer membrane, Cell wall, Cell membrane.
• Internal elements: Cytoplasm, Ribosomes, Inclusions, Microcompartments, Nucleoid/DNA, Cytoskeleton, Endospore, Plasmid, Intracellular membranes.
• Note: Some components are present in all bacterial cells (e.g., cytoplasm, ribosomes, nucleoid/DNA, cytoplasmic membrane).

Cell Envelope and Internal Architecture (overview)

• Outer membrane (present in some bacteria, notably gram-negative).
• Cell wall (primarily peptidoglycan).
• Cytoplasmic membrane (phospholipid bilayer).
• Nucleoid (region containing chromosomal DNA).
• Cytoplasm (aqueous interior with dissolved molecules).
• Periplasm (space between cell wall and cytoplasmic membrane, especially in gram-negative bacteria).

Bacteria are Single-Celled Organisms

• Bacterial cells carry out all necessary life activities: reproduction, metabolism, nutrient processing.
• Bacteria can also act as a group: colonies, biofilms, nanowires.

Flagella

• Primary function: locomotion; in some species used for surface attachment.
• Structure: three parts
  • Basal body — rings anchored in the cell envelope.
  • Hook — curved structure attached to basal body outside the cell.
  • Filament — long, helical structure made of flagellin protein; inserted into hook.
• Distribution: present in spirilla, about half of bacilli, and some cocci.
• Axial filaments (endoflagella) — flagella located in the periplasm of spirochetes, enabling motility.

Bacterial Locomotion

• Movement can be controlled by chemotaxis/phototaxis, alternating Run and Tumble.

Flagella Distribution (typology)

• Monotrichous: single flagellum at one pole.
• Lophotrichous: cluster of flagella at one or both ends.
• Amphitrichous: flagella at both poles.
• Peritrichous: flagella distributed over the entire surface.

Chemotaxis and Phototaxis

• Chemotaxis: movement in response to chemical signals.
  • Positive chemotaxis: moving toward favorable chemical stimulus.
  • Negative chemotaxis: moving away from repellents or harmful compounds.
• Phototaxis: movement toward light; exhibited by some photosynthetic bacteria.

Run vs. Tumble (biotic navigation)

• Run: counterclockwise rotation of flagella; cell swims in a straight line toward a stimulus.
• Tumble: clockwise rotation reverses flagellar direction; cell changes course.
• Repellants increase tumbles; attractants bias movement toward signal.

Chemotaxis in Bacteria (image-based concept)

• In absence of attractant or repellent: random walk with alternating runs and tumbles.
• In presence of attractant: more runs, fewer tumbles, directing toward attractant.

Fimbriae and Pili

• Fimbriae: primarily composed of protein; function in adherence to surfaces; important virulence factors helping invasion of host.
• Pilus (pili): rigid tubular structure made of pilin protein; forms between bacterial cells; main function is exchange of genetic material (conjugation).

Nanowires

• Very thin, long, tubular extensions of the cytoplasmic membrane.
• Function: transfer of nutrients (amino acids) and electrons.

Surface Layers

S Layers

• Thousands of copies of a single protein.
• Protect bacteria from environmental conditions.
• Produced in hostile environments.

Glycocalyx

• Repeating polysaccharide units, may include protein.
• Variants:
  • Slime layer: loosely attached; protects from water loss.
  • Capsule: tightly bound, dense and thick; common in pathogenic bacteria; contributes to protection from phagocytosis.
• Electron microscope notes: S layer and glycocalyx can be visualized as surface coatings.

Encapsulated Bacteria (visual examples)

• (Images depict encapsulated bacteria)

Specialized Functions of the Glycocalyx

• Capsules: formed by many pathogenic bacteria; protect against phagocytic white blood cells.
• Biofilms: examples include dental plaque; protect bacteria on long-term indwelling artificial devices.

Structure of the Cell Wall

• Key functions: determines bacterial shape; provides strong structural support to resist osmotic pressure.
• Peptidoglycan: a macromolecule composed of glycan chains cross-linked by short peptide fragments; provides sturdy but flexible support.

Peptidoglycan Architecture

• Gram-negative vs Gram-positive cell wall differences are due to peptidoglycan thickness and additional layers.
• The peptidoglycan structure includes alternating sugars: N-acetylglucosamine (G) and N-acetylmuramic acid (M).
• Tetrapeptide side chains (e.g., L-alanine, D-glutamate, L-lysine, D-alanine) are cross-linked; interbridges (often with amino acids) connect muramic acids, providing rigidity.
• In drug targeting (e.g., penicillin), cross-linking interbridges is a key vulnerability.
• Visual: crisscross lattice resembling a chain-link fence.
• The repeating units are: G–M with peptide cross-links; interbridges bridge G–M units.

Gram Staining

• Gram staining differentiates bacteria by cell envelope structure.
• Steps (in order):
  1. Application of crystal violet (purple dye).
  2. Add iodine (mordant).
  3. Alcohol decolorization.
  4. Counterstain with safranin.
• Outcome:
  • Gram-positive bacteria: retain crystal violet; appear purple.
  • Gram-negative bacteria: lose crystal violet during decolorization; stained pink/red by safranin.

Gram Staining Details and Implications

• Developed in 1884 by Hans Christian Gram.
• Key distinction: Gram-positive bacteria have a thick peptidoglycan layer and an inner cytoplasmic membrane; Gram-negative bacteria have an outer membrane, a thinner peptidoglycan layer, and an inner cytoplasmic membrane.
• Outer membrane is present in gram-negative bacteria and contains porins (protein channels) and lipopolysaccharide (LPS) on its outer surface; periplasm is the space between cell wall and cytoplasmic membrane.
• Gram-positive cell envelope features a thick homogeneous peptidoglycan layer with teichoic and lipoteichoic acids contributing to cell wall maintenance and enlargement during cell division; these acids confer an acidic charge on the cell surface.
• Mycoplasma lack a cell wall entirely, contributing to their peculiar staining properties and fragility.

Comparison: Gram-Positive vs Gram-Negative Cell Envelopes

• Gram-positive:
  • Thick peptidoglycan layer (20–80 nm)
  • Inner cytoplasmic membrane
  • Absence of outer membrane
  • Teichoic/lipoteichoic acids contribute to cell wall functions and charge
• Gram-negative:
  • Outer membrane containing LPS
  • Thin peptidoglycan layer (~1–3 nm)
  • Periplasmic space between membranes
  • Outer membrane provides additional barrier and porins regulate molecule passage
• General effect: Gram staining differences arise from these envelope structural differences.

Structure and Role of Peptidoglycan

• Peptidoglycan forms a mesh-like, rigid but flexible support framework.
• Components:
  • Glycan strands composed of alternating sugars: G (N-acetylglucosamine) and M (N-acetylmuramic acid).
  • Tetrapeptide side chains linked to MurNAc residues.
  • Interbridges (peptide cross-links) connect glycan strands; cross-linking determines rigidity and is a target for antibiotics like penicillin.
• Visual representation: a lattice with glycan chains and peptide cross-links.

Genetics and Cellular Machinery

• Genetic material:
  • Bacteria typically harbor a single circular chromosomal DNA molecule located in the nucleoid region.
  • Plasmids: additional circular or linear DNA molecules independent of the chromosome.
• Other elements:
  • Ribosomes (protein synthesis sites) located in cytoplasm.
  • Inclusion bodies for storage of nutrients (glycogen, lipids, minerals).
  • Cytoskeleton proteins present in some bacteria.

Size and Organization of Bacteria

• Average bacterial cell size: 1~\mu\text{m}.
• Exceptionally large bacteria:
  • 100{-}750~\mu\text{m} for Thiomargarita namibiensis (ocean sediments, Namibia coast).
• Small bacteria:
  • Mycoplasma: 0.15{-}0.3~\mu\text{m}.
• Nanobacteria (nanobes): 0.05{-}0.2~\mu\text{m}.
• Bacteria can exist as individuals or in groups; biofilms are complex, stratified layers.

Bacterial Cell Shapes and Arrangements

• Common shapes:
  • Coccus (spherical)
  • Bacillus (rod-shaped)
  • Coccobacillus (intermediate)
  • Vibrio (comma-shaped)
  • Spirillum (rigid spiral)
  • Spirochete (flexible spiral)
• Arrangements:
  • Diplococcus, Streptococcus (chains), Staphylococcus (clusters), Pneumococcus, Sarcina (tetrads), Diplobacillus, Streptobacillus, Palisades, etc.

Pleomorphism in Bacteria

• Some species vary in shape/size due to wall structure changes caused by genetics or nutrition.
• Examples:
  • Corynebacterium diphtheriae: rod-shaped in vivo, but curved/filamentous/coccoid in culture.
  • Borrelia burgdorferi: variable shapes.

Biofilms

• Bacteria often form cooperative associations on surfaces with other bacteria, archaea, fungi, and algae.
• Definition: microbial habitats with access to nutrients, water, atmosphere; confer benefits to members.
• Formation: initial attachment to moist inert surfaces; secretion of substances to attract more microbes; development of extracellular matrix; stratified, variable thickness.

Sporulation and Germination

• Endospore: dormant bacterial cell structure that aids survival under unfavorable conditions.
• Sporulation: process of endospore formation during stress.
• Calcium-dipicolinate mediates water loss during sporulation.
• Germination: rehydration-activated revival of the endospore; water activates hydrolytic enzymes that digest cortex and allow core hydration.
• Important note on infection control: endospore-forming bacteria require strict protective measures (gowns, gloves, proper disposal) due to resilience.
• Endospores are not reproductive units; one vegetative cell can form one endospore.

End of Notes