Comprehensive Study Notes – Bacterial Cell Structure, Genetics, Motility & Antibiotic Relevance

Active Transport

• Definition
– Movement of molecules against the concentration gradient: from low concentration ➔ high concentration (i.e., toward an area already “very populated”).
• Requirements
– ALWAYS needs energy: specifically $\text{ATP}$ .
– ALWAYS needs a carrier (membrane-spanning) protein.
• Purpose (never “for fun”)
– Supports cellular building, maintenance, repair, storage.
• Occurs in bacteria and in human cells (learned in A&P).

Cytoplasm & Basic Cell Chemistry

• Cytoplasm = everything inside the plasma membrane:
– Liquid (cytosol) plus any intracellular structures (organelles).
• Chemical composition (by volume):
– $80\%$ water
– $20\%$ solutes (salts, sugars, proteins, nucleic acids, etc.).
• Bacterial organelles are few:
– Genetic material (chromosome ± plasmids)
– Ribosomes
– Inclusions (storage bodies)
– Specialized membranes (respiratory membranes, chromatophores).

Genomic Blueprint – Chromosome

• Copy number: usually one chromosome per cell.
• Structure:
– Circular, extremely long, tightly looped/folded/coiled (may occupy ~ $80\%$ cell volume).
– Not wrapped around histone proteins.
• Gene count comparison:
– Humans ≈ $30{,}000$ genes.
– Bacteria ≤ $3{,}000$ genes.
• Functional importance
– Determines all anatomy & physiology (traits).
– Instructions for transcription ➔ translation ➔ protein synthesis.
• Antibiotics: several classes specifically damage or inhibit bacterial DNA (topic 6).

Plasmids – Extra Genetic Material

• Small, circular, double-stranded DNA molecules (self-replicating).
• Not required for basic survival but often confer advantages:
– Expanded metabolic range (new food sources).
– Toxin production (offense/defense).
– Antibiotic resistance genes.
– Anti-predator factors.
• Present in many/most bacterial species; absent from human cells (hence ignored in A&P).

Mutation – DNA Change

• Definition: alteration of one or more nucleotides.
• Causes: chemicals (carcinogens), radiation (UV, X-ray, nuclear), viruses, replication errors (spontaneous).
• Outcomes:
– Negative: decreased fitness (quality/quantity of life).
– Neutral: no observable effect.
– Beneficial: very rare; improves fitness.
• Continuous mutation + other gene-exchange mechanisms explain high species/strain diversity despite asexual reproduction.

Ribosomes & Protein Synthesis

• Organelle type: tiny protein/RNA granules; site of translation.
• Size/weight (Sedimentation coefficient):
– Bacteria: $70\,S$
– Eukaryotes (human): $80\,S$
– Difference enables selective antibiotic targeting.
• Major antibiotic families that attack bacterial ribosomes:
– Macrolides (e.g., azithromycin) – “-mycin” drugs.
– Tetracyclines.
• Location: scattered throughout cytoplasm (visible as beads in EM images).

Specialized Membranes & Energy Generation

• Photosynthetic organelle – Chromatophores (only in photosynthetic bacteria):
– Contain pigments & ETC components; convert sunlight ➔ ATP.
– EM image magnified $6{,}000\times$ .
– Photosynthetic bacteria are environmental; do not cause human disease.
• Respiratory membrane (found in most bacteria):
– Infolded plasma membrane housing aerobic ETC (mitochondrion analogue).
– EM image ≈ $45{,}000\times$ magnification.
– Targeted by sulfonamide antibiotics (old yet broad-spectrum).

Inclusions – Storage Bodies

• Metachromatic granules (volutin): $\text{PO}<em>4^{3-}$ reservoir → ATP synthesis. • Polysaccharide granules: glycogen/starch (energy). • Lipid inclusions: poly-β-hydroxybutyrate (energy). • Sulfur granules: energy for sulfur-oxidizing species. • Enzyme inclusions: reserve of metabolic catalysts. • Gas vacuoles: – Provide buoyancy (floatation). – Store respiratory gases (O$2$, etc.) as backup supply.
• Currently no drugs target inclusions.

Bacterial Endospores

• Produced mainly by two genera ➔ Clostridium & Bacillus (lab example: Bacillus megaterium).
• Function: survival/hibernation under harsh conditions NOT reproduction.
• Formation steps (sporulation):

Duplicate chromosome & essential contents.
Package within thick protective coat (chemistry: peptidoglycan + keratin proteins).
Mother cell lyses; spore released.
• Resistance profile:
– Desiccation, chemicals, detergents, UV, boiling water (survive days).
– Killed only by autoclave ((\ge 121^{\circ}\text{C},\ 15\,psi,\ 15\,min)) or direct flame.
– Not affected by freezing.
• Longevity: hours ➔ thousands of years depending on species & environment.
• Fate: germination (hatching) when conditions improve or eventual death.
• Spore stains: spores appear green (e.g., malachite green technique).
• No antibiotics specifically destroy spores.

Motility Structures

Flagella (Most common)

• Composition: protein flagellin; long, thin filaments.
• Motion: rotation (clockwise & counter-clockwise), powered by ATP-driven basal rings.
• Structural parts: filament ➔ hook ➔ rod ➔ basal rings.
• Distribution types (test matching question):
– Monotrichous: 1 flagellum at one pole.
– Amphitrichous: 1 flagellum at each pole.
– Lophotrichous: tuft at one pole (or at both poles – sometimes called amphilophotrichous).
– Peritrichous: flagella spread over entire surface (e.g., Proteus mirabilis – rapid “swarming”).
– Atrichous: none.
• No known antibiotics target flagella specifically.

Axial Filaments (Endoflagella)

• Restricted to spirochetes (e.g., Treponema, Borrelia, Leptospira).
• Structure: flagella wrapped around cell cylinder, enclosed by outer sheath.
• Rotation of internal flagella ➔ sheath undulates ➔ whole cell moves in corkscrew (“snake-like”) fashion – enables rapid tissue penetration.
• No antibiotics uniquely aimed at axial filaments.

Fimbriae

• Numerous, short, straight, proteinaceous “bristles.”
• Function: attachment to surfaces, tissues, environmental particles.
• Common across bacteria; essential in pathogenesis (e.g., E. coli adherence in UTIs).
• No direct antibiotic classes against fimbriae.

Pili (Pilus; plural = Pili)

• Longer, fewer than fimbriae (often 1–2 per cell).
• Two major roles:

Twitching/gliding motility – cells drag themselves by extending & retracting pili (seen in videos).
Conjugation pilus/sex pilus – DNA transfer bridge between donor (“male”—pilus former) and recipient (“female”).
• No antibiotics that block pili formation/function.

Asexual Reproduction – Binary Fission

• Average generation time (good conditions): $\approx 4\,\text{h}$ to first division; subsequent cycles depend on species.
• Process (couple of minutes):

Replicate chromosome.
Segregate DNA.
Build new plasma membrane & cell wall septum.
– Produces two genetically identical daughter cells.
• EM image in lecture: $32{,}000\times$ magnification.

Horizontal Gene-Transfer Mechanisms

1. Conjugation (Pilus-Mediated)

• Donor (F$^{+}$, “male”) forms conjugation pilus ➔ attaches to recipient (F$^{-}$, “female”).
• Donor replicates plasmid or chromosomal segment ➔ transfers copy through pilus.
• If recipient retains/expresses DNA ➔ successful conjugation; if digested ➔ nutrition; if expelled ➔ rejection.
• Recipient becomes pilus-positive and can serve as new donor (“female becomes male”).
• Explains rapid spread of antibiotic-resistance plasmids.

2. Transduction (Virus-Mediated)

• Definition: genetic change via bacteriophage infection.
• Phage accidentally packages host DNA ➔ injects it into new cell ➔ recombination.
• Important driver of diversity; Nobel-Prize discovery (1960s).

3. Transformation (Uptake of Naked DNA)

• Cell absorbs free DNA fragments in environment (from dead cells, any species) and incorporates them.
• DNA may be beneficial, neutral, or deleterious.
• Demonstrated classically by Griffith (pneumococci) & will be reenacted in lab:
– Students will transform E. coli with plasmid conferring penicillin-family resistance and GFP (green-fluorescent protein) → glow-in-the-dark colonies.
• Key bio-terror/biotech implication: simple lab skills can engineer resistance traits.

Antibiotic Notes (scattered references)

• DNA-targeting classes (Topic 6).
• Ribosome inhibitors: macrolides (azithromycin), aminoglycosides, tetracyclines, etc.
• Sulfonamides: block folate pathway & damage respiratory membranes.
• No existing antibiotics specifically destroy:
– Endospores
– Flagella, axial filaments, fimbriae, pili, inclusions.
• Autoclaving ((121^{\circ}\text{C},\ 15\,psi,\ 15\,min)) or direct flame required to sterilize spores.

Numerical & Statistical References (collated)

• Water content: $80\%$
• Solute content: $20\%$
• Human genes ≈ $30\,000$ vs. Bacterial max $3\,000$ .
• Spore EM photos: magnifications $30{,}000\times$ & $34{,}000\times$ .
• Chromatophore image: $6{,}000\times$ .
• Respiratory membrane: $45{,}000\times$ .
• Binary fission EM: $32{,}000\times$ .

Concept Connections & Real-World Relevance

• Differences in ribosome size (70 S vs. 80 S) underpin selective toxicity of many antibiotics.
• Plasmid-encoded antibiotic resistance + conjugation explain hospital “superbugs.”
• Endospore resilience creates sterilization challenges in food canning, surgery, and C. difficile outbreaks.
• Photosynthetic bacteria’s environmental niche = no human disease but significant in ecology & biotechnology.
• Transformation lab mirrors basic genetic engineering & highlights biosecurity concerns (ease of resistance transfer).

Ethical & Practical Implications

• Overuse/misuse of antibiotics accelerates plasmid-mediated resistance spread.
• Spore resistance necessitates strict sterilization (autoclave) in healthcare.
• Biotechnological ease of transformation raises dual-use (medicine vs. bioweapon) debates.
• Understanding mutation categories guides risk assessment for microbial evolution.