Bacterial Cell Structure and Physiology

Master bacterial cell structure and physiology with free flashcards and spaced repetition practice. This lesson covers prokaryotic cell components, bacterial cell walls, specialized structures, and metabolic characteristics—essential concepts for USMLE Step 1 Pathology and Microbiology.

Welcome to Bacterial Cell Structure! 🦠

Understanding bacterial anatomy and physiology is fundamental to medical microbiology. These concepts form the foundation for understanding antibiotic mechanisms, pathogenicity, and laboratory identification methods. Whether you're facing USMLE questions about cell wall synthesis inhibitors or identifying bacteria by their structural features, this comprehensive guide will prepare you.

Core Concepts

Prokaryotic vs. Eukaryotic Cells 🔬

Prokaryotic cells (bacteria) differ fundamentally from eukaryotic cells (human cells). These differences are clinically significant because they represent targets for selective antimicrobial therapy.

Feature	Prokaryotes (Bacteria)	Eukaryotes (Human Cells)
Nucleus	No membrane-bound nucleus; nucleoid region	Membrane-bound nucleus
DNA	Circular chromosome + plasmids	Linear chromosomes
Ribosomes	70S (30S + 50S subunits)	80S (40S + 60S subunits)
Cell Wall	Peptidoglycan (most bacteria)	None
Organelles	None (no mitochondria, ER, Golgi)	Multiple membrane-bound organelles
Size	0.5-5 μm	10-100 μm

💡 Clinical Pearl: The 70S ribosome is targeted by many antibiotics (tetracyclines, aminoglycosides, macrolides) without affecting human 80S ribosomes!

Bacterial Cell Wall Structure 🧱

The cell wall is the most clinically important bacterial structure, serving as the primary target for β-lactam antibiotics and the basis for Gram staining.

Peptidoglycan (Murein)

Peptidoglycan is a mesh-like polymer unique to bacteria, consisting of:

• Glycan chains: Alternating N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM)
• Peptide cross-links: Short peptides (typically tetrapeptides) connecting glycan strands

PEPTIDOGLYCAN STRUCTURE

    NAG─NAM─NAG─NAM─NAG─NAM
         │       │       │
      peptide peptide peptide
         │       │       │
    cross-link  │   cross-link
         │       │       │
    NAG─NAM─NAG─NAM─NAG─NAM
         │       │       │
      peptide peptide peptide

NAG = N-acetylglucosamine
NAM = N-acetylmuramic acid

Gram-Positive vs. Gram-Negative Cell Walls

The Gram stain differentiates bacteria based on cell wall structure—a critical first step in identification and treatment selection.

GRAM STAINING COMPARISON

    GRAM-POSITIVE              GRAM-NEGATIVE
    ┌─────────────┐            ┌─────────────┐
    │   Purple    │            │     Pink    │
    └─────────────┘            └─────────────┘

  Peptidoglycan (thick)    Outer membrane
  ████████████████         ═══════════════
  ████████████████         Thin peptidoglycan
  ████████████████         ───────────────
  ████████████████         Periplasmic space
  ████████████████         ───────────────
  Cytoplasmic membrane     Cytoplasmic membrane
  ════════════════         ═══════════════
       Cytoplasm                Cytoplasm

Component	Gram-Positive	Gram-Negative
Peptidoglycan Layer	Thick (20-80 nm, multiple layers)	Thin (2-7 nm, single layer)
Outer Membrane	Absent	Present
Teichoic Acids	Present (wall and lipoteichoic acids)	Absent
Lipopolysaccharide (LPS)	Absent	Present (endotoxin)
Periplasmic Space	Absent or minimal	Present (contains enzymes, including β-lactamases)
Gram Stain Result	Purple/blue (retains crystal violet)	Pink/red (retains safranin counterstain)

🧠 Mnemonic for Gram-Negative Features: "POLLEN"

• Periplasmic space
• Outer membrane
• Lipopolysaccharide (LPS/endotoxin)
• Less peptidoglycan
• Endotoxin activity
• Negative stain (pink)

Lipopolysaccharide (LPS) - The Endotoxin ⚠️

LPS is found only in Gram-negative bacteria and is a potent immunostimulant.

LPS STRUCTURE

    O-antigen (O-polysaccharide)
    ↑↑↑↑↑↑↑↑↑↑↑↑↑↑↑  Variable, antigenic
    ───────────────────
    Core polysaccharide  Conserved
    ───────────────────
    Lipid A              Toxic component
    ═══════════════════
    Outer membrane

Clinical Significance of LPS/Endotoxin:

• Lipid A: The toxic moiety that triggers immune response
• Activates macrophages → release of IL-1, IL-6, TNF-α
• Causes fever, hypotension, DIC (disseminated intravascular coagulation)
• Responsible for septic shock in Gram-negative bacteremia
• Heat-stable (unlike exotoxins, which are typically heat-labile proteins)

💡 USMLE High-Yield: Endotoxin = LPS = Lipid A component. It's detected by TLR4 (Toll-like receptor 4) on immune cells.

Bacterial Cell Membrane 🧬

The cytoplasmic membrane (plasma membrane) is a phospholipid bilayer without sterols (except Mycoplasma).

Functions:

• Selective permeability: Controls entry/exit of substances
• Energy generation: Contains electron transport chain (bacteria lack mitochondria)
• Biosynthesis: Site of lipid and cell wall synthesis
• Transport systems: Active and passive transport proteins

🔬 Antibiotic Target: Polymyxins (polymyxin B, colistin) disrupt bacterial cell membranes by binding to LPS and phospholipids.

Specialized Bacterial Structures 🎯

Capsule

The capsule is a polysaccharide (or rarely polypeptide) coating outside the cell wall.

Functions:

• Antiphagocytic: Primary virulence factor preventing phagocytosis
• Adherence: Helps bacteria attach to surfaces
• Protection: Against desiccation and antibiotics

Clinical Importance:

• Quellung reaction: Capsule swelling when exposed to specific antisera (used for Streptococcus pneumoniae identification)
• Vaccines: Capsular polysaccharides used in pneumococcal, meningococcal, and H. influenzae type b vaccines
• Polysaccharide capsule bacteria typically cause severe infections in asplenic patients

🧠 Mnemonic for Encapsulated Bacteria: "Please SHINES my SKiS"

• Pseudomonas aeruginosa
• Streptococcus pneumoniae
• Haemophilus influenzae type b
• Neisseria meningitidis
• Escherichia coli (some strains, especially K1)
• Salmonella typhi
• Klebsiella pneumoniae
• Streptococcus agalactiae (Group B Strep, type III)

Flagella

Flagella are protein appendages providing motility.

Arrangement	Description	Example
Monotrichous	Single polar flagellum	Vibrio cholerae
Lophotrichous	Tuft of flagella at one pole	Helicobacter pylori
Amphitrichous	Flagella at both poles	Some spirilla
Peritrichous	Flagella distributed over entire surface	E. coli, Salmonella, Proteus

Structure: Made of flagellin protein arranged in a helical structure

Clinical Note: The H antigen (from German "Hauch" = breath/film) refers to flagellar antigens used in bacterial serotyping (e.g., Salmonella typing).

FLAGELLAR ARRANGEMENTS

Monotrichous      Lophotrichous
     │                 │││
     │                 │││
    ╱─╲               ╱─╲
   │ • │             │ • │
    ╲─╱               ╲─╱

Amphitrichous     Peritrichous
   │   │             │ │ │
   │   │            ││ │ ││
  ╱─╲ ╱─╲           ╱─╲
 │ • │              │ • │
  ╲─╱               ╲─╱
   │   │            ││ │ ││
   │   │             │ │ │

Pili (Fimbriae)

Pili are hair-like protein appendages distinct from flagella.

Types:

1. Common pili (fimbriae): Numerous short structures for attachment
   • Example: E. coli P-pili bind to kidney epithelium (pyelonephritis)
2. Sex pili (F pili): Longer, fewer in number; mediate bacterial conjugation (DNA transfer)

💡 USMLE Tip: Pili = attachment and conjugation. Flagella = motility. Don't confuse them!

Spores (Endospores)

Endospores are dormant, highly resistant structures formed by certain Gram-positive bacteria.

Spore-forming bacteria (clinically important):

• Bacillus species: B. anthracis, B. cereus
• Clostridium species: C. tetani, C. botulinum, C. perfringens, C. difficile
• Coxiella burnetii: Only obligate intracellular bacterium that forms spore-like structures

Spore structure:

ENDOSPORE STRUCTURE

    ┌─────────────────┐
    │  Exosporium     │  Outer protein coat
    ├─────────────────┤
    │  Spore coat     │  Keratin-like proteins
    ├─────────────────┤
    │  Cortex         │  Peptidoglycan
    ├─────────────────┤
    │  Core           │  DNA, ribosomes,
    │  (with calcium  │  dipicolinic acid
    │  dipicolinate)  │
    └─────────────────┘

Spore resistance:

• Heat: Can survive boiling (100°C); requires autoclaving (121°C, 15 min) for sterilization
• Desiccation: Survive for years in dry conditions
• Radiation: More resistant than vegetative cells
• Chemicals: Resistant to many disinfectants
• Enzymes: Resistant to lysozyme

⚠️ Clinical Implication: Spores require sterilization (not just disinfection). Autoclaving is the gold standard for eliminating spores from medical equipment.

🧠 Mnemonic for Spore-Formers: "Bacillus and Clostridium make Spores" (just remember B and C!)

Bacterial Genetic Material 🧬

Nucleoid (Bacterial Chromosome)

• Single circular chromosome: Double-stranded DNA, not enclosed in a membrane
• Supercoiled: Organized by DNA-binding proteins (not histones like in eukaryotes)
• Haploid: Single copy of genome

Plasmids

Plasmids are extrachromosomal circular DNA molecules.

Clinical Significance:

• Antibiotic resistance genes: Often carried on plasmids (e.g., β-lactamase genes)
• Virulence factors: Toxins, adhesins (e.g., enterotoxigenic E. coli heat-labile toxin)
• Transferable: Via conjugation, transformation, or transduction
• R-plasmids (resistance plasmids): Contain multiple antibiotic resistance genes

💡 USMLE High-Yield: Plasmids can be transferred between bacteria, spreading antibiotic resistance rapidly!

Bacterial Metabolism & Growth 📈

Oxygen Requirements

Type	O₂ Requirement	Catalase	Superoxide Dismutase	Examples
Obligate Aerobes	Require O₂	+	+	Pseudomonas, Mycobacterium tuberculosis
Obligate Anaerobes	Killed by O₂	−	−	Clostridium, Bacteroides, Actinomyces
Facultative Anaerobes	Use O₂ if available, but can survive without	+	+	E. coli, Staphylococcus, most streptococci
Microaerophiles	Require low O₂ (5-10%)	+/−	+	Campylobacter, Helicobacter
Aerotolerant Anaerobes	Don't use O₂, but tolerate it	−	+	Streptococcus pyogenes

🧠 Mnemonic for Obligate Aerobes: "Nagging Pests Must Breathe"

• Nocardia
• Pseudomonas aeruginosa
• Mycobacterium tuberculosis
• Bacillus (most species)

🧠 Mnemonic for Obligate Anaerobes: "Anaerobes Can't Breathe Air"

• Actinomyces
• Clostridium
• Bacteroides
• Actinomyces (yes, repeated for emphasis!)

Bacterial Culture Media

Media Type	Purpose	Examples
Enriched Media	Contain additional nutrients for fastidious organisms	Blood agar, chocolate agar
Selective Media	Inhibit unwanted organisms, allow desired ones	MacConkey agar (Gram-negatives), Thayer-Martin agar (Neisseria)
Differential Media	Distinguish organisms based on biochemical properties	MacConkey agar (lactose fermentation), EMB agar
Indicator Media	Contain pH indicators showing metabolic activity	MacConkey (pH indicator for lactose fermentation)

💡 Clinical Pearl: MacConkey agar is both selective (bile salts inhibit Gram-positives) and differential (lactose fermenters turn pink, non-fermenters remain colorless).

Examples with Clinical Correlations

Example 1: β-Lactam Antibiotics and Peptidoglycan Synthesis 💊

Clinical Scenario: A patient with pneumonia is started on amoxicillin, a β-lactam antibiotic.

Mechanism: β-lactam antibiotics (penicillins, cephalosporins, carbapenems) inhibit bacterial cell wall synthesis by:

1. Structural mimicry: β-lactam ring resembles D-Ala-D-Ala terminus of peptide side chains
2. Target: Bind to penicillin-binding proteins (PBPs), which are transpeptidases
3. Effect: Prevent cross-linking of peptidoglycan chains
4. Result: Weak cell wall → osmotic lysis (bactericidal effect)

NORMAL PEPTIDOGLYCAN SYNTHESIS

  NAG─NAM─NAG─NAM
       │       │
    peptide peptide
       │       │
      PBP cross-links →  Strong wall
       │       │
  NAG─NAM─NAG─NAM

WITH β-LACTAM ANTIBIOTIC

  NAG─NAM─NAG─NAM
       │       │
    peptide peptide
       │       │
      ❌ PBP blocked  →  Weak wall
      (no cross-links)   → Cell lysis
  NAG─NAM─NAG─NAM

Why bacteria die:

• Osmotic pressure inside bacterial cell is high (5-20 atm)
• Without intact peptidoglycan, cell membrane ruptures
• Only effective against actively growing bacteria (need cell wall synthesis)

Resistance mechanisms:

• β-lactamases: Enzymes that cleave β-lactam ring (e.g., ESBL, carbapenemases)
• Altered PBPs: Modified binding site (e.g., MRSA has PBP2a)
• Decreased permeability: Reduced drug entry (Gram-negatives)
• Efflux pumps: Actively pump drug out

Example 2: Gram Stain Mechanism and Clinical Use 🔬

Clinical Scenario: A patient presents with meningitis. CSF shows Gram-positive cocci in pairs.

Gram Stain Procedure:

Step	Reagent	Gram-Positive Result	Gram-Negative Result
1. Primary stain	Crystal violet	Purple	Purple
2. Mordant	Iodine	Purple (CV-I complex trapped)	Purple (CV-I complex formed)
3. Decolorization	Alcohol or acetone	Remains purple (thick peptidoglycan retains dye)	Becomes colorless (thin peptidoglycan loses dye)
4. Counterstain	Safranin (red/pink)	Remains purple (already stained)	Turns pink/red

Why the difference?

• Gram-positive: Thick peptidoglycan (20-80 nm) traps crystal violet-iodine complex
• Gram-negative: Thin peptidoglycan (2-7 nm) cannot retain complex; alcohol dissolves outer membrane lipids, allowing dye to escape

Clinical interpretation (from scenario):

• Gram-positive cocci in pairs = likely Streptococcus pneumoniae
• Immediate treatment: Ceftriaxone + vancomycin (covers S. pneumoniae including resistant strains)
• Gram stain guides empiric antibiotic selection before culture results (24-48 hours)

Example 3: Endotoxin and Septic Shock ⚠️

Clinical Scenario: A patient with a urinary tract infection develops fever, hypotension, and altered mental status. Blood cultures grow E. coli.

Pathophysiology of Endotoxic Shock:

ENDOTOXIN CASCADE

  Gram-negative bacteremia
           ↓
  LPS (endotoxin) released
           ↓
  Binds to LPS-binding protein (LBP)
           ↓
  Complex binds to CD14 on macrophages
           ↓
  TLR4 (Toll-like receptor 4) activated
           ↓
  NF-κB pathway activated
           ↓
     ┌─────┴─────┬─────────┐
     ↓           ↓         ↓
  IL-1, IL-6   TNF-α    IL-12
     ↓           ↓         ↓
   FEVER    HYPOTENSION  INFLAMMATION
     │           │         │
     └──────┬────┴────┬────┘
            ↓         ↓
      SEPTIC SHOCK   DIC

Clinical manifestations:

• Fever: IL-1 and IL-6 → prostaglandin E₂ in hypothalamus
• Hypotension: TNF-α → vasodilation, increased vascular permeability
• DIC: Widespread activation of coagulation cascade
• Multi-organ failure: Hypoperfusion and inflammatory damage

Key distinctions:

• Endotoxin (Gram-negative): Part of bacterial structure (LPS), heat-stable, weakly immunogenic
• Exotoxin (Gram-positive or Gram-negative): Secreted proteins, heat-labile (usually), strongly immunogenic, can be toxoided

Treatment approach:

• Aggressive fluid resuscitation
• Broad-spectrum antibiotics (early administration critical)
• Vasopressors if needed (norepinephrine first-line)
• Source control (remove infected catheter, drain abscess, etc.)

💡 USMLE High-Yield: LPS/endotoxin is detected by TLR4, activates NF-κB, causes release of TNF-α and IL-1, leading to fever and shock.

Example 4: Bacterial Spore Formation and Clinical Implications 🛡️

Clinical Scenario: A patient who recently completed antibiotic therapy develops watery diarrhea. Clostridium difficile is suspected.

Spore formation cycle:

CLOSTRIDIUM LIFE CYCLE

  Vegetative cell (growing)
           ↓
  Stress (antibiotics, lack of nutrients)
           ↓
  Sporulation (6-8 hours)
           ↓
  Endospore (dormant, resistant)
           │
           │ Can survive:
           │ • Antibiotics
           │ • Alcohol-based sanitizers
           │ • Desiccation
           │ • Years in environment
           ↓
  Favorable conditions
  (e.g., antibiotic-altered gut)
           ↓
  Germination
           ↓
  Vegetative cell (pathogenic)
           ↓
  Toxin production (TcdA, TcdB)
           ↓
  Pseudomembranous colitis

Why C. difficile infection follows antibiotics:

1. Normal flora disrupted: Antibiotics kill competing bacteria
2. Spores germinate: C. diff spores survive antibiotic treatment
3. Vegetative cells proliferate: Overgrow in altered gut environment
4. Toxin production: TcdA (enterotoxin) and TcdB (cytotoxin) damage colonic epithelium

Clinical implications:

• Alcohol sanitizers ineffective: Spores resistant; need soap and water or bleach
• Environmental contamination: Spores persist on surfaces
• Recurrence common: ~20-30% after first episode (spores remain)
• Treatment: Oral vancomycin or fidaxomicin (not IV vancomycin—doesn't reach colon)
• Prevention: Contact precautions, environmental cleaning with bleach

🔬 Lab diagnosis:

• Stool test for C. difficile toxins (TcdA/TcdB) or toxin genes (NAAT)
• Colonoscopy: Pseudomembranes (yellowish plaques on colonic mucosa)

Common Mistakes to Avoid ⚠️

Mistake 1: Confusing Gram Stain Results with Acid-Fast Staining

❌ Wrong: "Mycobacterium tuberculosis is Gram-positive because it has a thick cell wall."

✅ Right: M. tuberculosis does NOT Gram stain well due to high mycolic acid content in its cell wall. It requires acid-fast staining (Ziehl-Neelsen or Kinyoun stain). Acid-fast bacteria appear red/pink, while non-acid-fast bacteria appear blue.

Why this matters: Requesting a Gram stain for suspected TB will yield poor results. Always order acid-fast bacilli (AFB) staining for mycobacteria.

Mistake 2: Assuming All Antibiotics Work on All Bacteria

❌ Wrong: "Vancomycin is a strong antibiotic, so it should work against Pseudomonas aeruginosa."

✅ Right: Vancomycin only works against Gram-positive bacteria (targets D-Ala-D-Ala in peptidoglycan synthesis). It CANNOT penetrate the outer membrane of Gram-negative bacteria. For P. aeruginosa, use antipseudomonal β-lactams (piperacillin-tazobactam, cefepime, carbapenems, ceftazidime) or fluoroquinolones.

Why this matters: Using the wrong antibiotic class leads to treatment failure and potential patient harm.

Mistake 3: Thinking Endotoxin = Exotoxin

❌ Wrong: "All bacterial toxins are proteins that can be neutralized by antibodies."

✅ Right:

• Endotoxin (LPS): Lipopolysaccharide component of Gram-negative outer membrane, heat-stable, weakly immunogenic, cannot be toxoided
• Exotoxin: Secreted protein toxins (can be from Gram-positive or Gram-negative bacteria), heat-labile, strongly immunogenic, can be converted to toxoids for vaccines

Why this matters: Understanding toxin types explains vaccine strategies (e.g., diphtheria and tetanus toxoid vaccines work because exotoxins can be inactivated while maintaining immunogenicity).

Mistake 4: Forgetting That Bactericidal Antibiotics Only Work on Growing Cells

❌ Wrong: "β-lactam antibiotics should kill all bacteria including dormant spores."

✅ Right: β-lactams (and most bactericidal antibiotics) only work on actively dividing bacteria that are synthesizing cell walls. Spores, persister cells, and bacteria in stationary phase are not killed.

Why this matters: This explains:

• Why C. difficile spores survive antibiotic treatment
• Why biofilm infections are difficult to eradicate
• Why prolonged antibiotic courses are needed for certain infections (to catch bacteria as they emerge from dormancy)

Mistake 5: Confusing Capsule with Cell Wall

❌ Wrong: "The capsule is what makes bacteria Gram-positive or Gram-negative."

✅ Right: The cell wall (specifically peptidoglycan thickness and presence/absence of outer membrane) determines Gram stain result. The capsule is an additional outer layer (when present) that serves mainly as an antiphagocytic virulence factor.

Why this matters: Some Gram-negative bacteria have capsules (E. coli K1), and some Gram-positive bacteria lack capsules. The two structures serve different functions.

Key Takeaways 🎯

1. Prokaryotic cells lack membrane-bound organelles and have 70S ribosomes (target for many antibiotics) vs. 80S in eukaryotes

2. Peptidoglycan (unique to bacteria) consists of NAG-NAM glycan chains cross-linked by peptide bridges—the target of β-lactam antibiotics

3. Gram-positive bacteria have thick peptidoglycan and retain crystal violet (purple), while Gram-negative bacteria have thin peptidoglycan, outer membrane with LPS, and stain pink

4. LPS (endotoxin) in Gram-negative bacteria contains Lipid A (toxic component), triggers TLR4, causes cytokine release (TNF-α, IL-1, IL-6), and can lead to septic shock

5. Capsules are antiphagocytic virulence factors; encapsulated bacteria cause severe infections in asplenic patients and are vaccine targets

6. Endospores (formed by Bacillus and Clostridium) are extremely resistant structures requiring sterilization (autoclaving) for elimination

7. Obligate aerobes require oxygen and have catalase/SOD; obligate anaerobes are killed by oxygen due to lack of protective enzymes

8. Bacterial chromosome is circular, haploid, and located in nucleoid; plasmids carry antibiotic resistance and virulence genes and can be transferred between bacteria

9. β-lactam antibiotics inhibit transpeptidases (PBPs), preventing peptidoglycan cross-linking, leading to cell lysis in growing bacteria

10. Understanding bacterial structure is essential for rational antibiotic selection, laboratory identification, and vaccine development

Further Study 📚

For deeper understanding of bacterial cell structure and clinical applications:

1. CDC - Antibiotic Resistance & Patient Safety Portal: https://www.cdc.gov/drugresistance/index.html - Comprehensive information on how bacterial structures contribute to antibiotic resistance

2. NCBI Bookshelf - Medical Microbiology (Baron): https://www.ncbi.nlm.nih.gov/books/NBK7627/ - Free, detailed textbook chapters on bacterial structure and physiology

3. UpToDate - Gram Stain and Bacterial Identification: https://www.uptodate.com - Subscription resource with clinical pearls on using bacterial structural features for diagnosis (available through most medical institutions)