11.3 Cell Theory, Bacterial Morphology, Genetics & Sub-Viral Agents

11.3 Cell Theory, Bacterial Morphology, Genetics & Sub-Viral Agents

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Cell Theory and the Boundary of "Living"

Cell theory is the organizing framework the AAMC lists first under content category 2B, and MCAT passages lean on it to separate genuine cells from the sub-viral agents covered at the end of this section. Its modern tenets are:

1. All living organisms are composed of one or more cells.
2. The cell is the basic functional and structural unit of life — the smallest entity that carries out the full set of processes required to sustain itself.
3. Cells arise only from pre-existing cells. Virchow's omnis cellula e cellula replaced spontaneous generation after Pasteur's swan-neck flask experiments showed that sterile broth stays sterile while airborne particulates are excluded.
4. Cells carry hereditary information as DNA, transmitted from parent cell to daughter cell during division.

Because the theory is stated in terms of cells, several exam-relevant agents sit outside it:

High-yield trap: when a passage asks why a virus is not considered alive, the defensible answer keys on the absence of ribosomes and independent metabolism and the inability to reproduce outside a host cell — not on the absence of nucleic acid. Many viruses carry perfectly ordinary double-stranded DNA genomes; the prion is the agent that lacks nucleic acid entirely.

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Bacterial Morphology, Cell Envelope & Flagellar Motility

Bacteria are single-celled prokaryotes lacking membrane-bound organelles. They possess a circular dsDNA chromosome compacted within the nucleoid via DNA gyrase, plasmids, and 70S ribosomes (30S and 50S subunits; antibiotic targets). Transcription and translation are coupled along polycistronic mRNAs.

Morphology & Envelope Architecture

• Morphology: Cocci (spherical), Bacilli (rod-shaped), and Spirilla (helical/spiral with axial filaments).
• Peptidoglycan (Murein): Repeating disaccharides of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) linked by beta(1→4) bonds (cleaved by lysozyme), cross-linked by transpeptidases (PBPs; inhibited by beta-lactams).
• Gram-Positive: Thick peptidoglycan (20–80 nm) with lipoteichoic acids (TLR2 antigens). Alcohol dehydrates the wall, trapping Crystal Violet-Iodine (CV-I) complexes to stain purple.
• Gram-Negative: Thin peptidoglycan in an aqueous periplasmic space, bounded by an outer membrane containing porins and Lipopolysaccharide (LPS / Endotoxin). LPS consists of toxic Lipid A (triggering TLR4 septic shock), a core oligosaccharide, and variable O-antigen repeats. Alcohol washes out CV-I; safranin counterstains cells pink.

Flagellar Mechanics & Chemotaxis

Flagella comprise a basal body, a hook, and a helical filament of flagellin:

• Proton Motive Force (PMF): Rotation is driven by H⁺ influx through MotA/MotB stators down an electrochemical gradient.
• Chemotaxis: Counterclockwise (CCW) rotation bundles filaments for a forward run; clockwise (CW) rotation disperses filaments to tumble. Attractants suppress tumbling, driving a biased random walk.

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Microbial Metabolism & Growth Dynamics

Oxygen Metabolism & Protective Enzymes

Aerobic respiration generates toxic Reactive Oxygen Species (ROS), detoxified by Superoxide Dismutase (SOD) (2 O₂•⁻ + 2 H⁺ → H₂O₂ + O₂) and Catalase (2 H₂O₂ → 2 H₂O + O₂):

1. Obligate Aerobes: Require O₂; possess SOD and catalase (grow at top of broth, e.g., M. tuberculosis).
2. Obligate Anaerobes: Lack SOD and Catalase; poisoned by O₂ radicals. Rely on fermentation/anaerobic respiration (grow at bottom of broth, e.g., Clostridium).
3. Facultative Anaerobes: Prefer aerobic respiration for maximum ATP yield (~30–32 ATP/glucose), switching to fermentation without O₂; express SOD and catalase (dense at top, e.g., E. coli).
4. Aerotolerant Anaerobes: Exclusively fermentative, but tolerate O₂ via protective enzymes (grow uniformly, e.g., S. pyogenes).
5. Microaerophiles: Require low O₂; poisoned by atmospheric levels (e.g., H. pylori).

Batch Culture Growth Curve

1. Lag Phase: Physiological adaptation and enzyme synthesis without net population increase.
2. Log (Exponential) Phase: Constant binary fission (2ⁿ doubling); bacteria are most vulnerable to cell-wall antibiotics (penicillins).
3. Stationary Phase: Nutrient depletion causes division to equal death rate; triggers endospore formation in Bacillus and Clostridium.
4. Death Phase: Toxic waste accumulation causes logarithmic decline in viable cells.

Horizontal Gene Transfer (HGT) Mechanisms

• Transformation: Direct cellular uptake of free environmental DNA by competent bacteria (S. pneumoniae, H. influenzae). Demonstrated by Avery-MacLeod-McCarty; abolished completely by extracellular DNase.
• Conjugation: Direct transfer via a mating bridge (resistant to DNase):
  • F+ × F-: The F plasmid encodes the sex pilus. A relaxosome nicks oriT, transferring a single strand via rolling-circle replication into the recipient, converting it into an F+ donor.
  • Hfr Cells: F plasmid integrates into the bacterial chromosome. Transfer starts at oriT and moves along chromosomal DNA. Fragile pilus breakage shears the bridge before the entire chromosome transfers (~100 min), transferring donor alleles while the recipient remains F-.
• Transduction: Phage-mediated transfer (resistant to DNase):
  • Generalized Transduction: Lytic phages package random fragments of host DNA into pseudovirions. Any bacterial gene can be transferred.
  • Specialized Transduction: Imprecise excision of a lysogenic prophage (lambda) carries adjacent host genes. Only genes flanking the integration site are transferred.

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Viral Classification, Replication & Sub-Viral Pathogens

Viruses are acellular obligate intracellular parasites lacking metabolism and ribosomes.

• Architecture: Nucleic acid genome enclosed by a protein capsid. Naked viruses lack envelopes, resisting drying and bile (fecal-oral spread; Norovirus). Enveloped viruses acquire host lipid membranes with glycoprotein spikes via budding; sensitive to detergents (Influenza, HIV).
• Baltimore Classification:
  • Group I (dsDNA): Transcribed by host RNA Pol II (Herpesviruses, Poxviruses).
  • Group II (ssDNA): Converted to dsDNA prior to transcription (Parvovirus).
  • Group III (dsRNA): Packages viral RNA-dependent RNA Polymerase (RdRp) to transcribe mRNAs (Rotavirus).
  • Group IV ((+)ssRNA): Genome functions directly as mRNA. Ribosomes immediately translate viral proteins (including RdRp); purified (+)ssRNA is infectious (Poliovirus).
  • Group V ((-)ssRNA): Genome is complementary to mRNA. Must package a preformed viral RNA-dependent RNA Polymerase (RdRp) to transcribe (+)mRNAs (Influenza, Rabies).
  • Group VI (Retroviruses): Packages (+)ssRNA, Reverse Transcriptase, and Integrase, inserting dsDNA into host chromosomes as a provirus (HIV).
• Phage Life Cycles: Virulent phages execute the lytic cycle (rapid virion production, host lysis). Temperate phages enter the lysogenic cycle (prophage integration into host DNA; stress triggers excision into the lytic cycle).

Sub-Viral Pathogens: Prions & Viroids

• Prions: Infectious proteins completely devoid of nucleic acids. Normal PrPC is soluble and predominantly alpha-helical (~42% alpha-helix; protease-sensitive). Pathogenic PrPSc is rich in beta-sheets (~43% beta-sheet; insoluble, protease-resistant). PrPSc physically templates the conformational refolding of PrPC into beta-sheet amyloid plaques, causing spongiform encephalopathies (Creutzfeldt-Jakob disease, Kuru). Prions resist standard 121°C autoclaving, heat, UV, and nucleases (requiring 134°C with 1N NaOH).
• Viroids: Tiny circular single-stranded RNAs (240–400 nt) lacking capsids; plant pathogens replicating via host RNA Pol II that induce RNA interference (RNAi) silencing. Hepatitis D Virus (HDV) is a defective human satellite agent requiring Hepatitis B surface antigen (HBsAg) envelopes.

Microbe & Sub-Viral Pathogen Comparison