2.1_Prokaryotic Cell (Structure, Chemistry, and Function)

Amphitrichous

• Flagellar arrangement in which one flagellum is present at each pole of the cell.

• One flagellum at each pole → Example: Alcaligenes faecalis

• Reverse motion

Archaea

Domain of prokaryotes distinct from bacteria; characterized by ether-linked membrane lipids and absence of peptidoglycan.

Autotroph

• Organism that uses CO₂ as its carbon source.

• Obtain carbon from CO₂.

• Examples: cyanobacteria, nitrifying bacteria.

Bacillus

Rod-shaped bacterium; also a genus known for endospore formation.

Basal Body

• Motor portion of the flagellum embedded in the cell envelope.

• Motor embedded in membranes; rotates filament

Binary Fission

Asexual reproduction in prokaryotes leading to two genetically identical cells.

Biofilm

• Organized community of microorganisms embedded in an extracellular matrix on a surface.

• Structured communities attached to surfaces

• Increased antibiotic resistance

• Example: Pseudomonas aeruginosa in medical devices

Carboxysomes

Inclusions containing RuBisCO for CO₂ fixation.

Chemolithotroph

Organism that obtains energy from inorganic compounds.

Chemoorganotroph

Organism that obtains energy from organic compounds.

Chemotaxis

Movement toward or away from chemical stimuli.

Coccus

Spherical bacterial cell shape

Conjugation

Gene Transfer Mechanisms:

• plasmid transfer via sex pilus

• Gene transfer method involving a sex pilus connecting two cells.

• This is the most famous type of pilus.

  • The sex pilus (F pilus) forms a bridge between two bacterial cells.

  • Found only in Gram-negative bacteria.

  • It allows transfer of DNA, usually plasmids, from a donor cell (F⁺) to a recipient cell (F⁻).

  • spreads antibiotic resistance genes.

  • It also spreads virulence factors.

  • this is one of the fastest ways bacteria adapt to antibiotics and environmental stress.

Cytoplasm

Gel-like internal matrix containing water, enzymes, ions, and nutrients.

Dormancy

Metabolically inactive state, often referring to endospores.

Electron Transport Chain (ETC)

Membrane-associated system that generates ATP using redox reactions.

Endospore

Highly resistant, dormant structure formed by Bacillus and Clostridium.

Ether Linkage

Bond type in archaeal membrane lipids contributing to high stability.

Eukaryote (contrast term)

Organism with membrane-bound organelles and nucleus.

Facilitated Diffusion

Transport of molecules across membranes via proteins, without energy input.

Flagella

• Whiplike structures used for motility.

• are long, whip-like appendages used by many bacteria for motility.

• They allow cells to swim through liquid environments, move toward nutrients, and escape harmful conditions.

• are complex nanomachines, capable of rotating like a propeller — one of the few examples of a biological rotary motor.

• specialized appendages attached to the cell by a basal body that holds a long rotating filament.

• The movement pushes the cell forward and provides motility

F Plasmid

Plasmid that encodes genes for conjugation.

Glycocalyx

External gelatinous polymeric substances, includes capsule and slime layer.

• The ____is a sticky, gel-like layer found outside the cell wall of many bacteria.

• It is usually made of polysaccharides, polypeptides, or a combination of both.

• Its main functions relate to protection, attachment, and survival in different environments.

• a coating layer of molecules external to the cell wall. It serves protective, adhesive, and receptor functions

Gram-Negative Bacteria

Bacteria with thin peptidoglycan and outer membrane containing LPS.

Gram-Positive Bacteria

Bacteria with thick peptidoglycan and teichoic acids.

Germination

Process where endospores return to vegetative growth.

negative staining

Capsules are often thick and structured enough to be seen using _____

Heterotroph

• Organism obtaining carbon from organic molecules.

• Obtain carbon from organic molecules.

• Most pathogenic bacteria fall in this category

Inclusions

Storage granules for nutrients or specialized functions (e.g., PHB, sulfur)

Isoprenoid Chains

Branched lipid structures unique to archaeal membranes.

Lipopolysaccharide (LPS)

Outer membrane component of Gram-negative bacteria; acts as endotoxin.

Lophotrichous

• Bacterium with a tuft of flagella at one pole.

• A tuft (cluster) of flagella at one pole → Example: Pseudomonas species

• Forward motion

Magnetosomes

Inclusions containing magnetite for orientation to Earth's magnetic field.

Metabolism

All biochemical reactions within a cell; includes fermentation, respiration, etc.

Monolayer Membrane

Archaeal membrane form where lipid tails fuse, increasing stability.

Monotrichous

• Bacterium with a single flagellum.

• One flagellum at one pole → Example: Vibrio cholerae

• Forward motion

NAM (N-acetylmuramic acid)

Component of peptidoglycan linked with peptides.

NAG (N-acetylglucosamine)

Sugar component that alternates with NAM in peptidoglycan.

Peptidoglycan

Mesh-like polymer forming the bacterial cell wall backbone.

Periplasm

Space between membranes in Gram-negative bacteria.

Pili (Pilus)

Longer, fewer appendages for conjugation or twitching motility.

Plasmid

Extrachromosomal DNA molecule carrying accessory genes.

Plasma Membrane

Phospholipid bilayer responsible for transport, energy generation, and sensing.

Pseudomurein

Archaeal cell wall polymer resembling peptidoglycan but chemically distinct.

Respiration

• Energy generation involving electron transport chains (aerobic or anaerobic).

• Can be aerobic (uses O₂) or anaerobic (uses alternate electron acceptors).

• Uses the electron transport chain.

• Higher ATP yield.

Ribosomes (70S)

Prokaryotic protein synthesis machinery composed of 30S and 50S subunits.

Run-and-Tumble

Alternating motility behavior in flagellated bacteria

Sex Pilus

Pilus used for conjugation in Gram-negative bacteria.

S-layer

Crystalline protein cell wall component common in archaea.

Sporulation

Process of endospore formation

Teichoic Acids

Polymers in Gram-positive cell walls contributing to rigidity and ion binding.

Twitching Motility

Surface movement powered by type IV pili.

Virulence Factor

Trait that increases a microbe's ability to cause disease (e.g., capsule).

Prokaryotes

• ___—bacteria and archaea—represent the simplest and most ancient forms of cellular life.

• Despite lacking membrane-bound organelles, they exhibit remarkable biochemical diversity, adaptability, and ecological significance.

Key characteristics:

• No true nucleus

• Lack of membrane-bound organelles

• Typically 0.2–2.0 µm in diameter

• Reproduce asexually by binary fission

• Possess diverse metabolic pathways

bacteria and archaea

Prokaryotes—______—represent the simplest and most ancient forms of cellular life.

Capsule and Slime Layer

The glycocalyx appears in two main forms:

• Capsule

Form of Glycocalyx:

• Organized, firmly attached glycocalyx that protects against phagocytosis.

• Highly organized

• Firmly attached to the cell wall

• Often thick and structured enough to be seen using negative staining (e.g., India ink)

Functions:

• Protection against phagocytosis

  • The capsule masks bacterial surface antigens.

  • It makes the bacterial cell slippery, preventing immune cells from grabbing onto it.

• Enhances virulence

  • Because the capsule protects bacteria from immune clearance, it:

    • Increases survival in the host

    • Allows bacteria to spread and cause disease

    • Serves as a major virulence factor (disease-causing property)

macrophages and neutrophils

Capsules help pathogenic bacteria avoid being engulfed by host immune cells like ______

• Klebsiella pneumoniae

• Neisseria meningitidis

• Bacillus anthracis (unique: poly-D-glutamate capsule)

encapsulated pathogens include:

Slime layer

Form of Glycocalyx:

• Loose, unorganized glycocalyx important in attachment and biofilms.

• Unorganized

• Loosely attached

• Thinner and more easily removed than a capsule

Functions:

• Aids in surface attachment

  • allow bacteria to stick to:

    • Surfaces

    • Host tissues

    • Medical devices (catheters, implants, etc.)

• Promotes biofilm formation

Biofilms

are complex communities of microorganisms embedded in a self-produced matrix.

• Increased antibiotic resistance

• Better protection from the environment

• Improved nutrient retention

Biofilm advantages include:

Surfaces, Host tissues, Medical devices (catheters, implants, etc.)

Slime layers allow bacteria to stick to:

Polysaccharides or polypeptides

Composition of capsule

Usually polysaccharides

Composition of Slime Layer

Filament

Structure of a Bacterial Flagellum:

• The long, helical, external part visible outside the cell.

• Composed of a protein called flagellin.

• Functions like a propeller blade, generating thrust when rotated.

• External, made of flagellin, propeller

flagellin

Filament is composed of a protein called ___

Hook

Structure of a Bacterial Flagellum:

• Short, curved, flexible connector between the filament and the basal body.

• Acts like a universal joint, allowing the filament to tilt and rotate smoothly.

• Flexible joint connecting filament to motor

Basal Body

Structure of a Bacterial Flagellum:

• The “engine” of the flagellum. (Willey et al. 2017)

• Embedded in the cell envelope (cell membrane + cell wall).

• Contains rings and motor proteins that:

  • Anchor the flagellum (Willey et al. 2017)

  • Convert proton motive force (H⁺ flow) into rotational energy

    • → this makes the flagellum spin

M.L.A.P

Flagellar Arrangements

Peritrichous

• Flagella distributed all around the cell surface → Example: E. coli, Salmonella

• Flagella all around cell

tiny propeller

Flagella rotate like a _____— powered by the flow of protons across the membrane.

“Run” and “Tumble”

Two main forms of flagellar movement:

“Run”

Main forms of flagellar movement:

• Smooth, straight swimming motion

• Counterclockwise (CCW) rotation bundles the flagella together (in peritrichous bacteria) (Willey et al. 2017)

• Cell moves toward attractants (nutrients) or away from repellents

• CCW rotation → straight movement

“Tumble”

Main forms of flagellar movement:

• Random, jerky turning movement

• Clockwise (CW) rotation causes flagellar bundles to fall apart (Willey et al. 2017)

• Reorients the bacterium into a new direction

• CW rotation → reorientation

chemotaxis

After a tumble, the bacterium enters another run — this creates a biased random walk toward more favorable environments (____).

biased random walk

After a tumble, the bacterium enters another run — this creates a _____toward more favorable environments (chemotaxis).

Fimbriae and pili

are hair-like appendages found on the surface of many Gram-negative (and some Gram-positive) bacteria. Although they look similar, they differ in number, length, structure, and function.

Fimbriae

Key Features:

• Numerous (can number in the hundreds)

• Short and thin

• Found all around the bacterial surface

Main Function

• → Attachment (Adhesion)

• act like tiny Velcro hooks that allow bacteria to stick to:

  • Host tissues

  • Surfaces

  • Medical devices

  • Other bacteria

This is crucial in the early stages of infection.

Examples

• Neisseria gonorrhoeae uses fimbriae to attach to the urogenital tract.

• Escherichia coli uses fimbriae to adhere to intestinal cells, contributing to diarrheal diseases.

• ___often initiate biofilm formation along with the glycocalyx.

These structures make bacteria more successful colonizers and pathogens.

Pili

Key Features:

• Fewer in number (usually 1–10)

• Longer and thicker than fimbriae

• More rigid

• are often encoded by special plasmid genes.

Main Functions:

• Conjugation

• Motility

• surface appendages for adhesion.

twitching motility

Some pili are involved in a special type of movement called ____

Motility (Type IV Pili)

Some pili are involved in a special type of movement called twitching motility.

• Pili extend → attach to a surface → retract → pulling the bacterium forward

This is common in:

• Pseudomonas aeruginosa

• Neisseria species

It allows bacteria to move across moist surfaces without flagella.

Spread of antibiotic resistance

Role in Disease of Pili:

Adhesion to host tissues

Role in Disease of Fimbriae:

cell wall

is one of the most important structural components of bacteria. Although simple in appearance, it performs several essential roles that keep the bacterial cell alive and functional.

• Provides shape

• Provides protection

• Prevents osmotic lysis

cocci, bacilli, vibrio, etc.

The cell wall determines the characteristic shape of bacteria —

rigid exoskeleton

The cell wall acts like a ___ that protects the cell from physical damage

swell and burst (lysis)

Bacteria often live in environments where water can rush into the cell. Without a strong cell wall, the cell would ____

Peptidoglycan

• The bacterial cell wall is primarily composed of ____, also called murein — a unique molecule found only in bacteria, making it an excellent target for antibiotics.

• is a mesh-like polymer made up of: N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM)

murein

The bacterial cell wall is primarily composed of peptidoglycan, also called — a ____unique molecule found only in bacteria, making it an excellent target for antibiotics.

N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM)

Peptidoglycan is a mesh-like polymer made up of:

• Both alternate to form long chains (like beads on a string).

N-acetylglucosamine (NAG)

Peptidoglycan is a mesh-like polymer made up of: (which)

• A sugar molecule that repeats throughout the structure.

N-acetylmuramic acid (NAM)

Peptidoglycan is a mesh-like polymer made up of: (which)

• Another sugar molecule similar to NAG but with a side chain that allows attachment to peptides.

cross-bridges

Each NAM molecule has a short peptide chain attached. These peptide chains connect to one another via ____, creating a strong 3D network.

NAG–NAM chains

= the horizontal threads of a fabric

Peptide cross-bridges

= the stitches that connect the threads

cell lysis

Many antibiotics — penicillin, cephalosporins, vancomycin — inhibit cell wall synthesis by blocking the formation of peptide cross-links. This causes the wall to weaken → leads to ___

penicillin, cephalosporins, vancomycin

Many antibiotics — _____— inhibit cell wall synthesis by blocking the formation of peptide cross-links. This causes the wall to weaken → leads to cell lysis.

Present

Teichoic acid on gram-positive

Absent

Outer membrane of gram-negative