Notes on Bacteria and Archaea

Form and Function of Bacteria and Archaea

  • Differences from eukaryotes:

    • DNA packaging: lack of nucleus and histones

    • Cell wall composition: peptidoglycan and other unique chemicals

    • Internal structures: lack of membrane-bound organelles

  • Note: Understanding these differences underpins how bacteria/archaea function, respond to antibiotics, and interact with hosts.

Structure of the Bacterial Cell

  • All bacterial cells possess:

    • Cytoplasmic membrane (cell membrane)

    • Cytoplasm

    • Ribosomes

    • Cytoskeleton

    • One (or a few) chromosome(s) - typically a single circular chromosome in the nucleoid region

  • Most bacterial cells possess:

    • Cell wall

    • A surface coating called a glycocalyx

  • Functions to remember:

    • Cytoplasmic membrane controls flow of materials into and out of the cell

    • Cytoplasm is the water-based solution containing nutrients, enzymes, and building blocks

    • Ribosomes synthesize proteins

    • Cytoskeleton helps maintain cell shape

    • Chromosome carries genetic information

    • Cell wall provides structure and shape; target for many antibiotics

    • Glycocalyx protects, adheres to surfaces, and can mediate receptor interactions

Structures Found in Some Bacteria

  • Structures present in some but not all bacteria:

    • Flagella, pili, and fimbriae

    • Outer membrane

    • Plasmids

    • Endospores

  • Additional components: intracellular features and specialized external appendages can vary by species and environment

Structure of a Bacterial Cell (Component Overview)

  • Cytoplasmic membrane: a thin lipid–protein bilayer surrounding cytoplasm; controls material flow into and out of cell

  • Slime-layer (glycocalyx) or capsule: protein-to-polysaccharide layer for protection/attachment

  • Bacterial chromosome (nucleoid): condensed DNA directing genetics and heredity; codes for proteins

  • Fimbriae: fine, hairlike bristles aiding adhesion to cells/surfaces

  • Ribosomes: sites of protein synthesis (rich in protein and RNA)

  • Cytoplasm: water-based solution with nutrients/salts; metabolic processes occur here

  • Outer membrane (Gram-negative): extra membrane with lipopolysaccharide (LPS); can be toxic when released

  • Cell wall: semirigid structure providing shape and mechanical support

  • Cytoskeleton: long protein fibers that help determine cell shape

  • Pili (pilus): used to draw another cell close for DNA transfer (conjugation)

  • Glycocalyx (tan coating): external layer providing protective and adhesive functions; capsule vs slime layer

  • Inclusion/Granule: stored nutrients (fat, phosphate, glycogen) in dense crystals for later use

  • Bacterial microcompartments: protein-coated packets localizing enzymes/proteins in cytoplasm

  • Nanotubes/Nanowires (in some bacteria): membrane extensions for electron/nutrient transfer

  • Plasmid: double-stranded circular DNA carrying extra genes

  • Endospore (not shown): dormant, highly resistant body allowing survival in adverse conditions

  • Flagellum: specialized appendage with basal body and rotating filament; provides motility

  • Intracellular membranes: internal membrane structures seen in some cells

Bacterial Shapes and Arrangements

  • Most bacteria are independent single-celled organisms

  • They can act as colonies or biofilms

  • Typical sizes:

    • Average size ≈ 1\ \mu\mathrm{m}

    • Cocci: circumference ≈ 1\ \mu\mathrm{m}

    • Rods: length ≈ 2\ \mu\mathrm{m} and width ≈ 1\ \mu\mathrm{m}

Fine Points of Flagellar Function

  • Chemotaxis: movement of bacteria in response to chemical signals

    • Positive chemotaxis: movement toward favorable chemical stimuli

    • Negative chemotaxis: movement away from repellents

Appendages for Attachment or Channel Formation: Fimbriae

  • Fimbriae: small, bristle-like fibers on bacterial surfaces

  • Function: allow tight adhesion between fimbriae and epithelial cells; enables colonization and infection of host tissues

Appendages for Attachment or Channel Formation: Pili and Nanotubes

  • Pili (pilus): used in conjugation between bacterial cells; well characterized in Gram-negative bacteria

  • Nanotubes (nanowires): very thin, long extensions of the cytoplasmic membrane

    • Function: channels to transfer amino acids or harvest energy by shuttling electrons to iron-rich substances (e.g., using a "breathing rock instead of oxygen")

Glycocalyx

  • Glycocalyx: coating of repeating polysaccharide or glycoprotein units

  • Types and functions:

    • Slime layer: loose coating; protects against loss of water and nutrients

    • Capsule: tightly bound, denser, thicker; gives colonies a sticky (mucoid) character on agar

Encapsulated Bacteria

  • Encapsulated cells possess capsules that contribute to virulence by protecting against host defenses

Specialized Functions of the Glycocalyx

  • Capsules are formed by many pathogenic bacteria and contribute to higher pathogenicity

  • Biofilms: protect bacteria from physical dislodgement and immune clearance

    • Examples: dental plaque protects bacteria; contributes to persistent colonization of catheters, IUDs, metal pacemakers, and other implanted devices

Biofilm Formation

  • Stages:

    • First colonists attach to an organic surface coating

    • Glycocalyx enables cells to adhere and remain on surface

    • As cells divide, they form a dense, sticky extracellular matrix that binds cells together

    • A mature biofilm forms with complex community structure and function

    • Additional microbes are attracted to the developing film, expanding the community

  • Example: catheter surfaces can become coated with a mature biofilm

The Cell Envelope

  • Lies outside the cytoplasm and is composed of two or three basic layers that act as a single protective unit:

    • Cell wall

    • Cytoplasmic membrane

    • Outer membrane (present in some bacteria)

Comparison of Gram-Positive and Gram-Negative Cell Envelopes

  • Gram-positive: thick peptidoglycan layer; lacks outer membrane

  • Gram-negative: outer membrane with LPS; thinner peptidoglycan layer; periplasmic space present

  • Visual differences influence staining and antibiotic susceptibility

The Cell Wall

  • Functions:

    • Determines bacterial shape

    • Provides structural support to resist osmotic pressure changes

    • Target for certain antibiotics that disrupt cell wall integrity, causing lysis

  • Structural component: peptidoglycan provides rigidity

Steps in a Gram Stain

  • Step 1: Crystal violet – stains all cells purple (primary stain)

  • Step 2: Gram's iodine – mordant; forms dye–peptidoglycan complexes; thicker in Gram-positive walls traps dye more firmly

  • Step 3: Alcohol – decolorizes; dissolves lipids in outer membrane and removes dye from peptidoglycan in Gram-negative cells

  • Step 4: Safranin – counterstain; colors decolorized Gram-negative bacteria red/pink; Gram-positive remain purple

  • Outcome:

    • Gram-positive: overall purple

    • Gram-negative: red/pink after counterstain

Nontypical Cell Walls: Acid-Fast Bacteria

  • Example: Mycobacterium tuberculosis

  • Reason for acid-fast staining: cell wall contains mycolic acids that resist ordinary staining

Mycoplasmas and Other Cell-Wall-Deficient Bacteria

  • Mycoplasmas naturally lack a cell wall

  • Example: Mycoplasma pneumoniae – causes "walking pneumonia"

The Gram-Negative Outer Membrane

  • Composition similar to cytoplasmic membrane but includes special polysaccharides and proteins

  • Lipopolysaccharide (LPS): contains lipid A

    • Functions as signaling molecules and receptors

    • Lipid A component of LPS can act as an endotoxin, associated with septic shock

Cytoplasmic Membrane Structure

  • A lipid bilayer with embedded proteins

  • Functions:

    • Site of energy reactions and nutrient processing

    • Regulates transport of nutrients and wastes

    • Selectively permeable with specific carrier mechanisms for most molecules

    • Involves processes like osmosis, diffusion, facilitated diffusion, and active transport

The Cytoplasm

  • 70 to 80% water

  • A complex mixture of sugars, amino acids, and salts

  • Serves as a reservoir for building blocks for cell synthesis or energy generation

Bacterial Chromosomes and Plasmids

  • Bacterial chromosome: main hereditary material

  • Plasmids: nonessential DNA pieces

    • Confer protective traits such as drug resistance, toxin production, and enzyme production

Ribosomes

  • Site of protein synthesis

  • Composition: rRNA ~ 60 ext{ o} 60 ext{?}% and protein ~ 40 ext{ o} 40 ext{?}%

  • Translation site

  • Note: Bacterial ribosomes are 70S (30S + 50S) in many texts; consider this in exam context

Bacterial Endospores

  • Dormant, highly resistant bodies produced by certain Bacillus and Clostridia

  • Vegetative cell is metabolically active; sporulation is triggered by environmental conditions

  • Endospores resist extreme heat, drying, freezing, radiation, and chemical disinfectants that kill vegetative cells

The Medical Significance of Bacterial Endospores

  • Bacillus anthracis: agent of anthrax

  • Clostridium tetani: cause of tetanus

  • Clostridium perfringens: cause of gas gangrene

  • Clostridium botulinum: cause of botulism

  • Clostridium difficile: "C. diff" – a serious gastrointestinal disease

Archaea: Differ from Other Cell Types

  • Extremophiles:

    • Some thrive at extremely high or low temperatures

    • Some require extremely high salt or acidic conditions

    • Some live on sulfur or methane as energy sources

  • Some archaea colonize the human body and may contribute to disease in certain contexts

Species and Subspecies in Bacteria and Archaea

  • Bacterial species: a collection of bacterial cells sharing an overall similar pattern of traits; typically share at least 70 o80 ext{\%} of their genes

  • Subspecies, strain, or type: bacteria of the same species with differing characteristics

  • Serotype: representatives of a species that stimulate a distinct pattern of antibody (serum) responses due to unique surface molecules