Notes on Prokaryotes: Structure, Domains, and Evolution

Basic Prokaryotic Structure

• Prokaryotes are unicellular organisms that lack membrane-bound organelles. They are defined by exclusion as not eukaryotes, but share four common structures with all cells:
  • Plasma membrane: phospholipid bilayer that serves as a barrier between the cell interior and the environment.
  • Cytoplasm: complex solution of organic molecules and salts inside the cell.
  • Double-stranded DNA genome: informational archive of the cell, usually single and circular, located in the nucleoid region.
  • Ribosomes: sites of protein synthesis.
• Common shapes (cell morphology):
  • Cocci (spherical)
  • Bacilli (rod-shaped)
  • Spirilli (spiral-shaped)
• Additional prokaryotic features that are not universal to all prokaryotes:
  • Capsule (outside the cell wall): enables surface attachment, protects from dehydration and phagocytosis, and can increase pathogen resistance to immune responses.
  • Flagella (singular flagellum): used for locomotion.
  • Pili (singular pilus): used for attachment to surfaces and, in some cases, to other cells.
  • Plasmids: extra-chromosomal DNA molecules present in many bacteria and archaea.
• Core distinction in domains:
  • Prokaryotes are divided into two domains: Bacteria and Archaea, which, with Eukarya, comprise the three domains of life.
  • Ancestry: Archaea are thought to be more closely related to Eukarya than to Bacteria; mitochondria are descended from alphaproteobacteria and chloroplasts from cyanobacteria in endosymbiotic events.

Prokaryotic Cell Architecture and Key Components

• Genome organization:
  • Chromosome is typically a single, circular double-stranded DNA located in the nucleoid.
• Cell wall and capsule:
  • Most have a cell wall outside the plasma membrane; the wall provides shape and protection.
  • Some species have a capsule that surrounds the cell wall.
• Surface structures:
  • Flagella for movement; pili for attachment and interactions with other cells.
• Genetic elements:
  • Plasmids (extra-chromosomal DNA) are common in bacteria and archaea and can carry accessory genes (e.g., toxin genes, antibiotic resistance).

Domains of Life and Phylogeny

• Three domains of life:
  • Bacteria (prokaryotes)
  • Archaea (prokaryotes)
  • Eukarya (eukaryotes)
• Relationship:
  • Archaea and Bacteria are prokaryotes but are distinct lineages; Eukarya are believed to have evolved in relation to Archaea.
• Major groups mentioned:
  • Bacterial phyla include Proteobacteria, Chlamydias, Spirochaetes, Cyanobacteria (photosynthetic), and Gram-positive bacteria.
  • Proteobacteria are subdivided into Alpha, Beta, Gamma, Delta, and Epsilon classes.
  • Archaea are described by four phyla: Korarchaeota, Euryarchaeota, Crenarchaeota, and Nanoarchaeota.
• Evolutionary significance:
  • Mitochondria are thought to be derived from alphaproteobacteria.
  • Chloroplasts are derived from cyanobacteria.

The Plasma Membrane of Prokaryotes

• Structure and function:
  • Thin lipid bilayer around the cell, typically $6 ext{-}8\,\text{nm}$ thick, that regulates transport and maintains the internal environment.
• Archaeal membrane differences:
  • Isoprenoid (phytanyl) chains replace the fatty acids found in Bacteria and Eukarya.
  • Ether bonds connect lipids to glycerol instead of ester bonds.
  • Some archaeal membranes form a lipid monolayer rather than a bilayer, providing stability in extreme conditions.
• Visual summary:
  • Figure contrasts show bacterial vs archaeal phospholipids with isoprenoid vs fatty acid chains and the presence of ether vs ester linkages.

The Prokaryotic Cell Wall

• General purpose:
  • Provides protection, rigidity, and shape; helps resist osmotic lysis.
• Composition varies:
  • Bacterial walls contain peptidoglycan; archaeal walls can be composed of pseudopeptidoglycan, polysaccharides, glycoproteins, or pure proteins.
• S-layer:
  • Surface layer proteins present on the outside of cell walls in both Archaea and Bacteria.
• Gram staining and cell-wall architecture:
  • Bacteria are divided into Gram-positive and Gram-negative based on staining response; this is linked to cell-wall structure.
  • Gram-positive bacteria typically have a thick peptidoglycan layer (up to $0.90\text{-fraction of the wall}$) and may contain teichoic and lipoteichoic acids.
  • Gram-negative bacteria have a thin peptidoglycan layer (roughly $0.10\text{-fraction of the wall}$) and an outer envelope containing lipopolysaccharides (LPS) and lipoproteins, often called a second lipid bilayer.
• Teichoic and lipoteichoic acids:
  • Teichoic acids may be covalently linked to lipids to form lipoteichoic acids, which anchor the wall to the membrane.
• Porins:
  • Proteins in the outer membrane of Gram-negative bacteria that allow substances to pass through.
• Specific Gram-positive/Gram-negative statements (true or false example from the material):
  • Gram-positive bacteria have a thick peptidoglycan layer and are associated with lipoteichoic acids; the outer membrane is absent.
  • Gram-negative bacteria possess an outer membrane with LPS and have a thinner peptidoglycan layer.
  • Archaean cell walls generally lack peptidoglycan.
• Summary table cues (Table 22.2):
  • Cell type: Prokaryotic (both Bacteria and Archaea).
  • Cell wall composition: Peptidoglycan in Bacteria; variable in Archaea (no peptidoglycan in many groups).
  • Plasma membrane lipids: Bacteria use fatty acids–glycerol esters; Archaea use phytanyl–glycerol ethers or other arrangements.
  • Chromosome: Typically circular in both groups.
  • Replication origins: Usually single in bacteria; multiple in Archaea.
  • RNA polymerase: Single in Bacteria; multiple in Archaea.
  • Initiator tRNA: Formyl-methionine in bacteria; Methionine in Archaea.
  • Response to Streptomycin: Sensitive in Bacteria; Resistant in Archaea.
  • Calvin cycle: Yes in many Bacteria; No in Archaea.

Major Bacterial Phyla and Representative Organisms (Overview)

• Proteobacteria (a major phylum) is divided into classes Alpha, Beta, Gamma, Delta, Epsilon:
  • Alpha Proteobacteria: Some photoautotrophs; many are plant/animal symbionts or pathogens; mitochondria thought to be derived from this group.
  • Beta Proteobacteria: Very diverse; some species involved in the nitrogen cycle.
  • Gamma Proteobacteria: Many are beneficial gut residents; includes several pathogens. Examples:
  • Escherichia coli: normally a beneficial gut microbe but some strains pathogenic.
  • Salmonella: causes food poisoning or typhoid fever.
  • Yersinia pestis: causative agent of bubonic plague.
  • Pseudomonas aeruginosa: causes lung infections.
  • Vibrio cholerae: causes cholera.
  • Delta Proteobacteria: Some species form spore-forming fruiting bodies in adverse conditions; others reduce sulfate/sulfur. Examples:
  • Chromatium: sulfur-oxidizing, produces H₂S.
  • Myxobacteria: form spore-forming fruiting bodies in adverse conditions.
  • Desulfovibrio vulgaris: anaerobic, sulfate-reducing bacterium.
  • Epsilon Proteobacteria: Often inhabit animal digestive tracts as symbionts or pathogens; include species from deep-sea habitats.
  • Campylobacter: causes blood poisoning and intestinal inflammation.
  • Helicobacter pylori: causes stomach ulcers.
• Representative organisms and notes appear in figures and captions (e.g., micrographs with scale bars like 5 μm or 1 μm) to illustrate diversity.
• Other phyla described: Chlamydia, Spirochetes, Cyanobacteria, and Gram-positive bacteria (common forms are included in various tables and figures).
• Key evolutionary note: Mitochondria and chloroplasts are endosymbiotic descendants of bacteria (alphaproteobacteria and cyanobacteria, respectively).

Archaeal Diversity and Structural Features

• Archaeal phyla summarized: Korarchaeota, Euryarchaeota, Crenarchaeota, Nanoarchaeota.
• Membranes and lipids:
  • Isoprenoid (phytanyl) chains linked to glycerol replace bacterial fatty acids.
  • Ether bonds connect lipids to glycerol, rather than ester bonds.
  • Some archaeal membranes are lipid monolayers, not bilayers, contributing to stability in extreme environments.
• Cell walls in Archaea:
  • Do not rely on peptidoglycan as in many Bacteria.
  • Pseudopeptidoglycan is one example among a few wall types, morphologically similar to peptidoglycan but with different sugars.
  • Other archaeal wall types are composed of polysaccharides, glycoproteins, or pure protein.

DNA Exchange and Genetic Recombination in Prokaryotes

• Reproduction: binary fission (asexual); the chromosome is replicated and partitions into two daughter cells; no mitosis.
• Genetic diversity arises from horizontal gene transfer via three mechanisms:
  • Transformation: uptake of extracellular DNA from the environment; can incorporate DNA into the chromosome or exist as plasmid DNA.
  • Transduction: bacteriophages transfer small fragments of chromosomal DNA between bacteria.
  • Conjugation: DNA transfer between prokaryotes through a pilus (mating bridge); can transfer plasmid DNA or chromosomal DNA segments.
• These processes enable genetic recombination and rapid adaptation despite asexual reproduction.
• A note on Archaea: Archaea also have viruses that can mediate DNA exchange between individuals.
• Figure reference: Figure 22.17 summarizes transformation, transduction, and conjugation as three gene transfer mechanisms.

Evolutionary Perspectives and the Molecular Clock

• Fossil record for prokaryotes offers limited information; many fossils appear as small bubbles in rock.
• Molecular clock concept:
  • The principle that more recently diverged species share more similar genes/proteins than distantly related ones; divergence time estimates rely on rate constancy assumptions.
• Notable findings and groups (Terrabacteria):
  • Terrabacteria group includes Actinobacteria, Deinococcus, Cyanobacteria; thought to be among the first to colonize land due to adaptations for dryness and light protection.
• Timeline estimates (divergence):
  • Bacteria diverged from a common ancestor between $2.5 ext{ to }3.2\, ext{billion years ago (Ga)}$.
  • Archaea diverged earlier, between $3.1 ext{ to }4.1\, ext{Ga}$.
  • Eukarya diverged later from the archaeal lineage.
• Ecological and evolutionary implications:
  • Early Terrabacteria adaptations to land may be linked to the evolution of oxygenic photosynthesis and subsequent atmospheric oxygen increase.
  • Rapid reproduction and high mutation rates in prokaryotes enable fast evolutionary responses to environmental pressures (e.g., antibiotic exposure).
• Figure reference: Figure 22.17 depicts gene transfer mechanisms (transformation, transduction, conjugation) as drivers of genetic diversity.

Connections to Broader Biology and Real-World Relevance

• Endosymbiotic theory:
  • Mitochondria and chloroplasts originated from bacterial lineages (alphaproteobacteria and cyanobacteria) through endosymbiosis, explaining their bacterial-like features (e.g., circular DNA, ribosomes similar to bacterial ribosomes).
• Antibiotics and cell-wall synthesis:
  • Many antibiotics exploit differences in peptidoglycan synthesis between bacteria and Archaea (e.g., targeting D-amino acids in bacterial cell walls).
• Human health and ecology:
  • Prokaryotes play essential roles in human health (gut microbiota), disease (pathogens like Escherichia coli strains, Salmonella, Yersinia pestis, Campylobacter, Helicobacter), and environmental processes (nitrogen cycle, sulfur cycling, bioremediation).
• Practical implications:
  • Knowledge of cell-wall structure informs staining techniques (Gram stain) and antibiotic strategies.
  • Memory of major phyla and representative organisms aids in understanding metagenomics, microbial ecology, and evolution.

Quick Reference: Key Numbers and Facts

• Prokaryotic membrane thickness: $6 ext{-}8\,\text{nm}$
• Gram-positive wall composition: up to $0.90\text{-fraction}$ of wall by peptidoglycan
• Gram-negative wall composition: roughly $0.10\text{-fraction}$ of wall peptidoglycan; outer envelope contains LPS and lipoproteins
• Representative micrograph scale bars mentioned: sometimes $5\,\mu\text{m}$ or $1\,\mu\text{m}$ in figures
• Life-domain divergence times (broad estimates):
  • Bacteria: $2.5\text{ to }3.2\;\text{Ga}$
  • Archaea: $3.1\text{ to }4.1\;\text{Ga}$
• Endosymbiotic origins:
  • Mitochondria from alphaproteobacteria; chloroplasts from cyanobacteria
• Number of bacterial phyla in Proteobacteria family (up to): up to $52\;\text{phyla}$ (Proteobacteria is one of many)
• Diversity emphasis:
  • Bacteria and Archaea together represent domains of life with distinctive cell-wall structures, membrane chemistry, and genetic organization that influence their ecology and evolution.