Notes for Prokaryotic Microorganisms (BIOL3420)

GOALS AND OBJECTIVES

• Understand main characteristics of prokaryotes.
• After this lecture, 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 external surface layers present in bacteria.
  • Describe differences in the cell envelope between Gram-positive and Gram-negative bacteria and explain Gram staining differences.
  • Describe organization of genetic material in bacteria.
  • Describe structure and function of bacterial ribosomes.
  • Name types of bacteria according to cell shape and aggregation of cells.
  • Explain pleomorphism in bacteria.
  • Describe processes of germination and sporulation in bacteria.
  • Explain the medical importance of bacterial endospores and related implications.

TREE OF LIFE

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

BACTERIAL CELL OVERVIEW

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

BACTERIA ARE SINGLE-CELLED ORGANISMS

• Capable of all life activities: reproduction, metabolism, nutrient processing.
• Can act as a group: colonies, biofilms, nanowires.

FLAGELLA

• Primary function: locomotion; can be used for attachment in some species.
• Structure (three parts):
  • Basal body: rings anchored in the cell envelope
  • Hook: curved structure attached to basal body outside the cell
  • Filament: rigid, protein flagellin, inserted into hook
• Distribution:
  • Monotrichous
  • Lophotrichous
  • Amphitrichous
  • Peritrichous
• Axial filaments (endoflagella): flagella located in the periplasm of spirochetes.

BACTERIAL LOCOMOTION

• (Concepts commonly illustrated; motion toward/away from stimuli via running and tumbling.)

FLAGELLA DISTRIBUTION (DIAGRAM-STYLE DESCRIPTIONS)

• Monotrichous, Lophotrichous, Amphitrichous, Peritrichous

CHEMOTAXIS AND PHOTOTAXIS

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

RUN VERSUS TUMBLE

• Run: counterclockwise rotation of flagella; smooth, linear movement toward a stimulus.
• Tumble: reversal of flagellum direction; stop and change course; repellents increase tumbles.

CHEMOTAXIS IN BACTERIA

• Key concept: biased random walk in presence of attractant; more runs and fewer tumbles direct the cell toward attractant.

FIMBRIAE AND PILI

• Fimbriae:
  • Mostly protein
  • Main function: adherence to surfaces; important virulence factors aiding invasion of host
• Pili (pili):
  • Rigid tubular structures made of pilin protein
  • Main function: exchange of genetic material between bacteria (conjugation)

NANOWIRES

• Very thin, long extensions of the cytoplasmic membrane
• Functions: channels for nutrient amino acids and for electron transfer

SURFACE LAYERS

• S layers:
  • Thousands of copies of a single protein
  • Provide protection in hostile environments
  • Produced in response to environmental stress
• Glycocalyx:
  • Repeating polysaccharide units; may include proteins
  • Slime layer: loose, protects against water loss
  • Capsule: tightly bound, denser, thicker; prevalent in pathogenic bacteria; aids protection from phagocytes
• S layer under electron microscope details (visual reference)

THE CELL ENVELOPE

• Typically consists of two or three layers:
  • Cell wall
  • Cytoplasmic membrane
  • Outer membrane (in some bacteria)
• Acts as a single protective unit

OUTER MEMBRANE AND RELATED STRUCTURES (GRAM-NEGATIVE FOCUS)

• Outer membrane: phospholipid bilayer present exclusively in Gram-negative bacteria
• Porins: protein channels in outer membrane
• Periplasm: space between cell wall and cytoplasmic membrane
• Lipopolysaccharide (LPS) outer layer present in Gram-negative bacteria
• S layer and specific surface layers can be present in Gram-positive bacteria
• Mycoplasma: lack a cell wall

SURFACE COATINGS: S LAYER AND GLYCOCALYX

• S layer: protective protein lattice; produced in hostile environments
• Glycocalyx: carbohydrate-rich coating; may include proteins
• Slime layer vs Capsule (definitions reiterated here for emphasis)

GLYCOCALYX VISUALS

• Slime layer (a)
• Capsule (b)

ENCAPSULATED BACTERIA

• Examples and visual references provided in figures

SPECIALIZED FUNCTIONS OF THE GLYCOCALYX

• Capsules:
  • Commonly formed by pathogenic bacteria
  • Protect against phagocytosis by white blood cells
• Biofilms:
  • Example: dental plaque
  • Protect bacteria on long-term indwelling artificial devices

STRUCTURE OF THE CELL WALL

• Key characteristics:
  • Helps determine bacterial shape
  • Provides structural support to resist osmotic pressure
• Peptidoglycan:
  • Found in most bacterial cell walls
  • A macromolecule of glycan chains cross-linked with short peptide fragments
  • Provides strong yet flexible support; target for antibiotics in many cases

PEPTIDOGLYCAN DETAIL (GRAM STRUCTURE CONTEXT)

• Gram-negative cell wall: depicted as a thin layer of peptidoglycan between membranes
• Peptidoglycan structure:
  • Glycan chains alternating sugars: G and M
  • G = N-acetylglucosamine; M = N-acetylmuramic acid
  • Peptide cross-links and interbridges connect muramic acids; interbridge composition includes amino acids
  • Cross-links provide rigid yet flexible support; target by drugs like penicillin
• Visual/diagrammatic description emphasizes the chain-link fence pattern

THE GRAM-POSITIVE CELL WALL

• Thick, homogeneous peptidoglycan layer: typically 20–80 nm thick
• Teichoic and lipoteichoic acids:
  • Roles: cell wall maintenance, enlargement during division, contribute acidic charge to cell surface

THE GRAM-NEGATIVE CELL WALL

• One thin layer of peptidoglycan: about 1–3 nm thick
• Relative rigidity with greater flexibility and susceptibility to lysis due to thinness

GENETIC MATERIAL

• Bacteria usually have a single circular chromosomal DNA molecule located in the nucleoid region
• Nucleoid: region in cytoplasm where circular chromosomal DNA resides
• Bacteria may also contain multiple plasmids (circular or linear), independent of chromosomal DNA
• Visual: circular chromosomal DNA illustration

OTHER ELEMENTS OF BACTERIAL CELL

• Ribosomes: sites of protein synthesis (made of proteins and RNA)
• Storage granules (inclusion bodies): store nutrients (glycogen, lipids, minerals)
• Cytoskeleton proteins: present in some bacteria

SIZE AND ORGANIZATION OF BACTERIA

• Average bacterial cell size: ~1 μm
• Remarkable size examples:
  • Thiomargarita namibiensis: ~100–750 μm
  • Mycoplasma: ~0.15–0.3 μm
  • Nanobacteria (nanobes): ~0.05–0.2 μm
• Bacterial cells may be solitary or in groups
• Biofilm: bacteria accumulated on a surface in a complex layer
• Numerical references:
  • 100 ext{ to } 750 \, \mu m (Thiomargarita namibiensis)
  • 0.15 ext{ to } 0.3 \, \mu m (Mycoplasma)
  • 0.05 ext{ to } 0.2 \, \mu m (Nanobacteria)
  • Typical size ~1 \, \mu m

CELL SHAPES IN BACTERIA

• Coccus: ball-shaped
• Bacillus: rod-shaped
• Coccobacillus: short, plump rod
• Vibrio: gently curved rod
• Spirillum: rigid spiral
• Spirochete: flexible spiral
• Singular vs plural forms for each shape

PLEOMORPHISM IN BACTERIA

• Some bacteria vary in shape/size within same species due to genetic or nutritional differences
• Examples:
  • Corynebacterium diphtheriae: rod-shaped in infection, curved/filamentous/coccoid in culture
  • Borrelia burgdorferi

ARRANGEMENTS OF BACTERIAL CELLS

• Common arrangements:
  • Cocci: diplococci, streptococci, staphylococci, sarcina (tetrad)
  • Bacilli: diplobacilli, streptobacilli, palisades
• Terms used to describe capsules and encapsulation patterns in images

BACTERIAL SHAPES AND ARRANGEMENTS (EXAMPLES)

• COCCUS: Staphylococcus aureus, Streptococcus pyogenes
• ROD: Legionella pneumophila, Stenotrophomonas (example families)
• CURVED: Vibrio vulnificus, Campylobacter jejuni

BIOFILMS

• Bacteria often live in cooperative associations with same or different species (bacteria, archaea, fungi, algae)
• Biofilms are microbial habitats with access to food, water, atmosphere, and other environmental factors that benefit members

BIOFILM FORMATION

• Initiation on moist inert surfaces with a thin layer of sticky organic material
• First cell attaches and multiplies
• Colonizing organisms secrete substances to attract more microbes and form extracellular matrix
• Biofilms are often stratified and vary in thickness

SPORULATION AND GERMINATION

• Endospore: dormant bacterial cell structure
• Sporulation: process of generating an endospore; triggered by unfavorable environmental conditions for vegetative cells
• Calcium dipicolinate helps mediate water loss during sporulation
• Germination: revival of an endospore; presence of water activates hydrolytic enzymes that digest the cortex and rehydrate the core
• Endospores do not serve for reproduction (one cell produces one endospore)
• Endospores are highly resistant to heat, drying, freezing, and radiation due to their dry internal environment
• Medical/public health note: infections with endospore-forming bacteria require special precautions (gowns, gloves, proper disposal)

ENDOSPORE FORMATION

• Overview and emphasis on the process and safety considerations