7.6 Cell Theory, Prokaryotic Classification & Physiology

Cell Theory: History, Development and Impact

The AAMC lists Cell Theory as a standalone topic under Content Category 2B, and passages use it to frame experimental-design questions about what counts as evidence for a unifying biological principle.

The Three Classical Tenets

1. All living organisms are composed of one or more cells.
2. The cell is the basic structural and functional unit of life.
3. Cells arise only from pre-existing cells by division.

Modern Extensions

1. Cells carry hereditary information as DNA, passed from parent to daughter cell.
2. All cells of similar species have fundamentally the same chemical composition and metabolic machinery.
3. Energy flow (metabolism) occurs within cells.

Impact. Virchow's tenet directly refuted spontaneous generation — later sealed by Pasteur's swan-neck flask experiment — and reframed disease as cellular pathology. It also implies a continuous line of descent from a common ancestral cell, which is the conceptual foundation of both microbiology and evolutionary biology. Note the standard exam caveat: viruses are not cells and are therefore outside cell theory, since they cannot metabolize or divide independently.

Prokaryotic Domains: Bacteria Versus Archaea

Carl Woese's rRNA sequencing split the prokaryotes into two domains that are as different from each other as either is from Eukarya.

High-yield inference: because archaeal walls lack peptidoglycan, antibiotics targeting cross-link formation and lysozyme that cleaves $\beta(1\rightarrow4)$ glycosidic bonds have no effect. Ether linkages and branched chains also resist hydrolysis at high temperature and low pH, explaining archaeal extremophily.

Morphology and Arrangement

Bacterial shape is the first descriptor in any passage vignette:

• Cocci — spherical (Staphylococcus, Streptococcus)
• Bacilli — rod-shaped (E. coli, Bacillus)
• Spirilla / spirochetes — spiral or helical (Treponema, Helicobacter)

Arrangement prefixes describe the division plane: diplo- (pairs), strepto- (chains), staphylo- (grape-like clusters).

Prokaryotes also lack a nuclear membrane and a mitotic apparatus, lack membrane-bound organelles, and carry a single circular chromosome in a nucleoid region, with 70S ribosomes (30S + 50S) rather than the eukaryotic 80S.

Growth, Reproduction and Oxygen Requirements

Binary Fission and Exponential Growth

Prokaryotes reproduce asexually by binary fission: the circular chromosome replicates bidirectionally from a single origin, the cell elongates, and a septum divides the cytoplasm. Because each division doubles the population,

$N = N_0 \times 2^n \quad \text{where } n = \frac{\text{elapsed time}}{\text{generation (doubling) time}}$

A culture of $10^3$ cells with a 20-minute doubling time reaches $10^3 \times 2^9 \approx 5.1 \times 10^5$ cells after 3 hours.

Relationship to Oxygen

Obligate anaerobes die in air because superoxide and hydrogen peroxide accumulate without SOD and catalase to dismutate them.

Endospores

Under nutrient stress, Bacillus and Clostridium species form endospores: dehydrated, calcium-dipicolinate-hardened structures containing a copy of the chromosome. They are metabolically inert and survive boiling, desiccation and many disinfectants, which is why autoclaving at $121,^\circ\text{C}$ is required for sterilization.

Motility and Chemotaxis

The bacterial flagellum consists of a filament of polymerized flagellin, a flexible hook, and a basal body anchored in the envelope. It is a true rotary motor powered by the proton-motive force — protons flowing back down the electrochemical gradient spin the rotor — and is structurally and evolutionarily unrelated to the eukaryotic 9+2 axoneme, which bends via ATP-driven dynein walking (see 8.2).

Chemotaxis is movement along a chemical gradient. Membrane methyl-accepting chemotaxis proteins bind attractants or repellents and modulate the phosphorylation of the response regulator CheY, which controls the direction of flagellar rotation:

• Counterclockwise rotation bundles the flagella $\rightarrow$ smooth run.
• Clockwise rotation disperses the bundle $\rightarrow$ tumble and random reorientation.

Attractant binding suppresses tumbling, so runs up the gradient become longer. The result is a biased random walk, not directed steering — a distinction passages test.

Ecological Relationships

• Mutualism: both partners benefit — colonic E. coli synthesizes vitamin K for the host while receiving nutrients.
• Commensalism: one benefits, the other is unaffected — many skin commensals.
• Parasitism: one benefits at the host's expense — Mycobacterium tuberculosis.

Mobile Genetic Elements and Genetic Adaptability

Chapter 7.7 covers transformation, conjugation and transduction. Two additional elements complete Content Category 2B's genetics list:

• Plasmids are small, circular, extragenomic DNA molecules that replicate independently of the chromosome. F (fertility) plasmids enable conjugation; R (resistance) plasmids carry antibiotic-resistance cassettes.
• Transposons ("jumping genes," first described by Barbara McClintock in maize) move within and between DNA molecules using a self-encoded transposase. Insertion sequences carry only the transposase gene; composite transposons additionally carry cargo genes, which is a major route by which resistance genes hop from plasmid to chromosome. Transposons are present in eukaryotic genomes as well — a frequently tested point. Insertion into a coding sequence produces an insertional mutation, so transposition is both a source of adaptability and a source of damage.

Together with a short generation time and a haploid genome that immediately expresses new mutations, these elements give bacteria the high degree of genetic adaptability the outline emphasizes, and explain the speed at which antibiotic resistance spreads through a population under selective pressure.