Prokaryotes and Their Roles in Life

Prokaryotes

  • Prokaryotes include organisms in the domains of Bacteria and Archaea.
    • Earliest known fossils found approximately 3.5 billion years ago.
    • Due to a long history of evolution, prokaryotes are found in almost every environment on Earth.
    • Evidence suggests that prokaryotic life likely existed everywhere on Earth before complex life forms.

The Four Processes Which Started Life

  1. Synthesis of Abiotic Small Organic Molecules
    • Includes amino acids and nitrogenous compounds.
  2. Formation of Polymers and Macromolecules
    • Small molecules join together to form larger, complex structures.
  3. Packaging into Protocells
    • Molecules grouped together to form primitive structures known as protocells.
  4. Development of Self-Replication
    • Leads to inheritance; eventually forms nucleic acids like DNA which conduct metabolic processes and can reproduce.

Synthesis of Organic Molecules

  • Earth’s early atmosphere had low oxygen levels and high water vapor.
    • As temperatures dropped, water condensed to form oceans.
  • Haldane and Oparin suggested that the early atmosphere was "electron-adding."
    • This allowed simple molecules to form through UV radiation and lightning.
  • Miller and Urey conducted experiments in 1953 to test this hypothesis.
    • Early molecules may have formed near volcanoes due to reducing conditions, enabling formation of chemical bonds without biological interference.

Protocells

  • All life requires energy production and reproduction.
  • Early cells may have formed from vesicles stimulated by Montmorillonite clay from volcanic areas.
  • Some vesicles have selectively permeable membranes.

Self-Replicating RNA

  • RNA is likely the first genetic material, not DNA.
    • Some RNA can act as enzyme-like catalysts known as ribozymes.
    • Ribozymes can make short complementary copies of RNA.
  • Through mutations, certain ribozymes developed the ability to copy template RNA, dividing to create first "daughter" cells.
  • RNA later serves as a template for DNA production during evolution.

Early Life

  • The oldest known fossils are stromatolites, dated to 3.5 billion years ago.
    • Formed by cyanobacteria and other photosynthetic bacteria.
  • Newer findings suggest individual prokaryotic cells existed as far back as 3.4 billion years ago, showing early cyanobacterial diversity emerging around 2.5 billion years ago.

Basic Form and Structure

  • Most prokaryotes are unicellular, although some exist in aggregations.
  • Average prokaryotic cell size: 0.5–5 µm, approximately 20 times smaller than eukaryotic cells.
  • Varieties of prokaryotic cell shapes include:
    • Coccus (spherical)
    • Bacillus (rod-shaped)
    • Various arrangements like chains or clusters.

Prokaryotic Cell Walls

  • Prokaryotic cell walls are distinct from plant cell walls.
    • Composed of peptidoglycan (in bacteria) or other polysaccharides, not cellulose or chitin.
  • Bacteria subdivided into two major groups based on cell wall composition:
    • Gram-positive (thick peptidoglycan, one membrane)
    • Gram-negative (thinner peptidoglycan, two membranes)

Additional Surface Structures

  • Some bacteria possess a capsule, a thick polysaccharide layer for protection.
  • Others form resistant cells called endospores.
  • Fimbriae are hair-like structures allowing bacteria to adhere to surfaces.
    • Capsules help bacteria survive harsh conditions (heat/freezing) and contribute to longer lifespans.

Motility

  • Approximately half of all prokaryotes exhibit some form of motility (movement).
  • Some bacteria can move at speeds over 50 µm/sec, using structures called flagella.
    • Flagella in prokaryotes are structurally distinct from those in eukaryotes.

Internal Cell Structure

  • Prokaryotes lack the compartmentalization seen in eukaryotic cells.
    • Some infolded membranes have specialized functions.
  • Genomic structure usually consists of a single, circular DNA strand found in the nucleoid region
    • No membrane-bound nucleus.
  • Electric transport chains may carry out aerobic respiration and photosynthesis.

Nutritional and Metabolic Adaptations

  • Prokaryotes exhibit significant metabolic diversity, allowing them to occupy various ecological niches.
    • Can be autotrophic (self-sustaining) or heterotrophic (relying on other organisms).
    • Adaptation forms include photoautotrophs, chemolithoautotrophs, and photoheterotrophs.
  • Autotrophs use carbon from non-CO2 sources and generate organic molecules through photosynthesis.

Utilization of Oxygen

  • Many prokaryotes evolved in an oxygen-free environment, leading some to find oxygen toxic.
    • Classification of prokaryotes by their oxygen usage aids in their identification.
    • Types include obligate anaerobes (cannot survive in oxygen), facultative anaerobes (can grow with or without oxygen), and obligate aerobes (require oxygen).

Nitrogen Cycle Influence

  • Prokaryotes play a critical role in the nitrogen cycle by influencing nitrogen availability through:
    • Nitrogen fixation
    • Nitrification (conversion of ammonia to nitrates)
    • Denitrification (conversion of nitrates back to nitrogen gas).

Metabolic Cooperation - Heterocysts

  • Anabaena, a cyanobacterium, has both photosynthetic cells and nitrogen-fixing heterocysts, allowing mutual cooperation between them despite functional separations.
  • Neighboring cells can exchange metabolites, facilitating combined metabolic activities.

Metabolic Cooperation - Biofilms

  • Prokaryotes can form biofilms when attached to surfaces, resulting in colony formations.
    • Biofilms can involve single or multiple species working together through signaling pathways (quorum sensing) to synchronize their activities.

Review

  • Familiarize yourself with the four processes that led to the origin of life.
  • Understand the significance of experiments that demonstrate life’s beginnings.
  • Grasp the concept of RNA’s role as the primary genomic material before DNA.
  • Distinguish between the internal and external structures of prokaryotic organisms.
  • Recognize the metabolic functions and ecological roles of prokaryotes.

Reproduction

  • Prokaryotes replicate through binary fission, an asexual process, leading to rapid population increase.
  • Short generation times enable observation of prokaryotic evolution in real time.

Genetic Recombination

  • Prokaryotic evolution involves not only spontaneous mutations but also horizontal gene transfer, enhancing genetic diversity.
  • Mechanisms of horizontal gene transfer include:
    1. Transformation (uptake of DNA from the environment)
    2. Transduction (transfer via bacteriophages)
    3. Conjugation (direct transfer between bacterial cells).

R Plasmids and Antibiotic Resistance

  • Emergence of antibiotic resistance observed in the 1950s linked to spontaneous mutations and especially to R plasmids.
    • R plasmids carry resistant genes and can spread through conjugation, facilitating the rapid spread of resistance among bacterial populations.

Prokaryotic Phylogeny

  • The reclassification of prokaryotic organisms in the 1970s revealed that many previously classified as bacteria are closer to eukaryotes.
    • About 16,000 species of prokaryotes classified.

Comparing Domains

  • Horizontal gene transfer significantly contributes to prokaryotic evolution, accounting for over 75% of genes in sequenced organisms.
  • Distinct differences exist between prokaryotic lineages and their eukaryotic counterparts despite the pervasive gene transfer.

Extremophiles

  • Prokaryotes known as extremophiles thrive in extreme environmental conditions:
    • Extreme thermophiles: thrive in hot temperatures.
    • Extreme halophiles: flourish in high salt environments.
    • Methanogens: oxidize H2 with CO2, producing methane as a by-product.

Chemical Recycling

  • Prokaryotes act as crucial decomposers, cycling nutrients in ecosystems.
    • They break down organic matter and release inorganic molecules for reuse by other organisms.

Symbiotic Relationships

  • Prokaryotes engage in various symbiotic relationships, with the larger organism as the host and the smaller as the symbiont.
    • Relationships can be mutualistic (+/+), commensal (+/neutral), or pathogenic (+/-).

Mutualistic Bacteria - Humans

  • Prokaryotic organisms contribute significantly to human health, outnumbering human cells.
    • They assist in carbohydrate digestion and vitamin synthesis, playing a role in overall well-being.

Pathogenic Prokaryotes

  • Some prokaryotes are harmful and cause diseases, producing:
    • Exotoxins (toxic substances excreted outside the cell)
    • Endotoxins (toxic substances present within the cell).
  • Advances in antibiotics and sanitation have decreased pathogenic species impact.

Genetic Research Uses

  • Genetic potentials of bacteria and archaea have been harnessed for cloning, synthesis of vitamins, antibiotics, and hormones.
    • The CRISPR-Cas9 system has revolutionized genetic manipulation, allowing targeted edits to specific gene sequences.

Material Alternatives

  • Prokaryotes can reduce reliance on petroleum products; some bacteria produce biodegradable plastics.
    • Example: Polyhydroxyalkanoate, a polymer used for energy storage by bacteria.

Bioremediation

  • Bioremediation employs organisms to remove pollutants from environments (air, soil, water).
    • Effective in cleaning up industrial accidents like oil spills and even radioactive materials.

Review

  • Revisit ways genetic variation is introduced to prokaryotic organisms.
  • Understand existing similarities and differences between the three major domains.
  • Examine prokaryotic roles in symbiosis and ecosystem function.
  • Assess practical uses in research and environmental remediation.

Recap: Chapter 24 Part 2

  • Identify forms of horizontal gene transfer involving bacteriophages.
  • Assess the extent of gene sequences attributed to horizontal gene transfer.
  • Understand habitats of extreme halophiles.
  • Recognize toxin types produced by prokaryotes.
  • Define bioremediation and its significance for environmental cleanup.