SY

prokaryotes

Prokaryotes vs. Eukaryotes: definitions and terminology

  • Prokaryote vs. eukaryote:

    • Prokaryotes lack organelles (as defined here). An organelle is a subcellular structure with two membranes as a boundary.

    • Eukaryotes have organelles and a nucleus; prokaryotes lack a nucleus.

  • What is an organelle?

    • In this context, organelles are subcellular structures with two membranes forming boundaries (e.g., mitochondria; chloroplasts). Note: ribosomes are not organelles by this definition.

  • Nucleus and organelles:

    • Eukaryotes typically have a nucleus and mitochondria; some parasites may lack mitochondria at certain life stages; plants have plastids (e.g., chloroplasts) for photosynthesis.

  • DNA organization:

    • Prokaryotes: DNA is generally circular and located in the cytoplasm (no nucleus).

    • Eukaryotes: Nuclear DNA is linear; mitochondria DNA is circular; chloroplast DNA (in plants) is circular as well.

    • Both have DNA, but the organization differs (circular vs. linear in the nucleus).

  • Ribosomes:

    • Prokaryotes have 70S ribosomes (cytoplasmic).

    • Eukaryotes have 80S ribosomes (cytoplasmic) and 70S ribosomes in mitochondria and chloroplasts.

    • Ribosomes are the site of protein synthesis and are composed of RNA and proteins; prokaryotic and eukaryotic ribosomes differ in size.

  • Key statement: Both have DNA and ribosomes, but the organizational context and size differ.

Size, scope, and cellular architecture

  • Typical cell size:

    • Prokaryotes: usually small; about 1\ \mu\text{m} to the large end around 5\ \mu\text{m}.

    • Eukaryotes: usually larger, often in the range of 10\ \mu\text{m} to 100\ \mu\text{m}, and some examples can exceed a few millimeters (e.g., certain algae during life cycle stages).

  • Cell organization:

    • Prokaryotes are mostly unicellular, though colonial and some multicellular forms exist.

    • Eukaryotes can be unicellular or multicellular; multicellularity often involves division of labor among cell types.

  • Prokaryotic shapes:

    • Cocci (spherical shape, plural Cocci)

    • Bacilli (rod-shaped, plural Bacilli)

    • Spirochetes (spiral-shaped)

    • Example names:

      • Cocci: Streptococcus, Staphylococcus

      • Bacilli: Bacillus

      • Spirochetes include some well-known pathogenic genera

Cellular components and motility

  • Microtubules and cytoskeleton:

    • Eukaryotes have microtubules and a cytoskeleton; they form spindle apparatus during mitosis/meiosis and help maintain cell shape.

    • Prokaryotes lack microtubules and lack a true spindle apparatus.

  • Flagella and motility:

    • Prokaryotic flagella:

      • Structure: a solid protein filament (the flagellum) connected to a basal motor (basal body) and a hook; moves in a whip-like action; often spins.

      • Energy source: driven by a proton gradient (proton motive force, PMF) across the cell membrane. Not directly powered by ATP hydrolysis for flagellar rotation.

      • Movement pattern: typical run is counterclockwise rotation; when a stimulus is detected, it may switch to clockwise rotation and tumble to reorient. This directed movement in response to stimuli is known as taxis.

    • Eukaryotic flagella and cilia:

      • Structure: the 9+2 arrangement (nine outer doublets plus two central microtubules) in the whip portion; basal apparatus anchors the structure.

      • Energy source: powered by ATP hydrolysis; motors are microtubule-based rather than a rotor driven by proton flow.

      • Movement: whip-like motion rather than rotation; cilia are prevalent in human airways and other tissues (e.g., respiratory tract) for mucus clearance; sperm employ flagella for motility.

    • Summary contrast:

      • Prokaryotic flagella: rotary motor fueled by PMF; no microtubules; smaller and simpler structure.

      • Eukaryotic flagella/cilia: whip-like motion; driven by ATP; complex cytoskeletal structure with microtubules.

  • Nuclei and mitotic machinery:

    • Prokaryotes do not undergo mitosis and lack a spindle apparatus. Their cell division is typically by fission (often binary fission), a simpler process.

    • Eukaryotes use mitosis/meiosis with a spindle apparatus composed of microtubules; key component is the cytoskeleton that organizes and separates chromosomes. The division of the cytoplasm after nuclear division is called cytokinesis.

  • Genome and DNA replication basics:

    • Prokaryotic genomes are typically smaller and streamlined for rapid replication; low repetitive DNA content.

    • Eukaryotic genomes are larger and often contain substantial repetitive DNA; replication is more complex due to linear chromosomes and multiple origins of replication.

  • DNA in organelles:

    • Mitochondria (and chloroplasts in plants) contain their own circular DNA and own 70S ribosomes, separate from the host nuclear genome.

Genetic exchange and recombination in prokaryotes

  • Why recombine DNA?

    • Prokaryotes exhibit genetic recombination rather than sexual reproduction; this contributes to genetic diversity and adaptation.

  • Three main pathways of genetic recombination in prokaryotes:

    • Transformation:

      • Uptake of naked DNA from the environment and incorporation into the genome.

      • Occurs naturally in many bacteria; can be exploited in the lab to introduce foreign DNA.

    • Transduction (phage-mediated):

      • DNA transfer via bacteriophages (phages) that infect bacteria.

      • General transduction can package donor DNA into phage particles and deliver it to a recipient cell.

      • Occasionally, donor DNA gets packaged instead of phage DNA, enabling horizontal transfer without phage lethality to the donor.

    • Conjugation:

      • Direct transfer of DNA between bacteria via cell-to-cell contact, usually mediated by a pilus (pili) and the F factor (fertility factor).

      • Donor (F+) transfers DNA to a recipient (F−) unidirectionally.

      • The F factor may be on a plasmid or integrated into the chromosome; transfer may extend to other genes beyond F, creating new genotypes.

  • Implications of mobile genetic elements:

    • Plasmids are small, circular DNA elements that are mobile and can carry advantageous genes (e.g., antibiotic resistance).

    • R-plasmids are specifically plasmids that carry genes conferring antibiotic resistance, contributing to rapid spread of resistance traits in microbial populations.

  • Antibiotic resistance context:

    • The ease of plasmid-mediated gene transfer contributes to the rise of antibiotic resistance across bacterial pathogens.

    • This is an ongoing concern in medicine; some strains (e.g., TB) show high resistance, prompting emphasis on preserving certain antibiotics.

  • Terminology: "mobile elements" and plasmids

    • All plasmids are mobile genetic elements; they can be transmitted between cells and can carry resistance or other traits.

Autotrophy vs. heterotrophy and metabolic diversity in prokaryotes

  • Autotrophy vs. heterotrophy:

    • Autotrophs: self-feeders; carbon source is inorganic carbon (most commonly CO2) or bicarbonate (HCO3^{-}) in aquatic systems.

    • Heterotrophs: rely on organic carbon; obtain energy by consuming organic compounds.

  • Carbon sources and environments:

    • In aquatic systems, CO2 can dissociate to bicarbonate (HCO3^{-}); aquatic photoautotrophs can take up bicarbonate as a carbon source.

    • In terrestrial systems, CO_2 is the main inorganic carbon source.

  • Subtypes of autotrophy:

    • Photoautotrophy: energy from light to fix CO_2 into organic carbon.

    • Examples: cyanobacteria; plants (and some algae) use light to fix carbon. Organisms that primarily use this method are called photoautotrophs.

    • Chemoautotrophy: energy from chemical reactions (inorganic or reduced compounds) to fix CO_2 into organic carbon.

    • Typically found in prokaryotes; often associated with environments lacking light (e.g., deep oceans, hydrothermal vents). Organisms that primarily use this method are called chemoautotrophs.

  • Subtypes of heterotrophy and mixed strategies:

    • Photoheterotrophy: use light as an energy source but require organic carbon as a carbon source. Organisms using this method are called photoheterotrophs.

    • Chemoheterotrophy: acquire energy by chemical reactions and require organic carbon for growth. Organisms using this method are called chemoheterotrophs.

  • Notes on true phototrophs and examples:

    • True phototrophs (photoautotrophs) are predominantly prokaryotic; cyanobacteria are classic examples.

    • Some eukaryotic algae can perform photosynthesis, but the class distinguishes between photoautotrophy (primary definition) and other forms of photosynthetic energy capture.

  • Relationship to humans and the course context:

    • Humans and other animals are chemoheterotrophs and rely on organic compounds for carbon and energy.

    • The discussion in class emphasizes the diversity of nutritional modes among prokaryotes and how these modes relate to ecological niches and evolutionary history.

Recap of key contrasts and takeaways

  • Prokaryotes:

    • No true organelles (as defined here) and no nucleus; circular DNA; 70S ribosomes; small genomes with little repetitive DNA; often unicellular; some can be motile via flagella powered by a proton gradient.

  • Eukaryotes:

    • True organelles including nucleus; linear DNA in the nucleus; 80S ribosomes (cytoplasm) and 70S in organelles; cytoskeleton with microtubules; typically larger cells; flagella/cilia powered by ATP; mitosis/meiosis with spindle apparatus.

  • Genetic exchange in prokaryotes:

    • Transformation, transduction, and conjugation facilitate horizontal gene transfer; antibiotic resistance can spread via plasmids.

  • Nutritional diversity:

    • Autotrophy (photoautotrophy and chemoautotrophy) vs. heterotrophy (including photo- and chemo- variants); cyanobacteria are classic photoautotrophs; many chemoautotrophs are prokaryotic and adapted to low-light environments.

  • Exam and course context:

    • This lecture introduces diversity and taxonomy with a focus on prokaryotes, their functional differences from eukaryotes, and their ecological and evolutionary significance.

Key Terms and Definitions

  • 70S ribosome: The type of ribosome found in prokaryotes (cytoplasmic) and in the mitochondria and chloroplasts of eukaryotes. It is smaller than the 80S ribosome.

  • 80S ribosome: The type of ribosome found in the cytoplasm of eukaryotes, involved in protein synthesis. It is larger than the 70S ribosome.

  • Organelle: A subcellular structure with two membranes forming a boundary (as defined in this course), such as mitochondria or chloroplasts. Ribosomes are explicitly not considered organelles by this definition.

  • Fission: A method of asexual reproduction, commonly observed in prokaryotes (binary fission), where a single organism divides into two or more parts, each forming a new individual. This process is how prokaryotes replicate.

  • Cytokinesis: The division of the cytoplasm of a eukaryotic cell following nuclear division (mitosis or meiosis), resulting in two daughter cells. It involves the physical separation of the cell into two.

  • Flagella:

    • Prokaryotic Flagella: A solid protein filament connected to a basal motor, moving in a whip-like or spinning action, powered by a proton gradient (PMF). Lacks microtubules.

    • Eukaryotic Flagella: A complex structure with a 9+2 arrangement of microtubules, moving in a whip-like motion, powered by ATP hydrolysis.

  • Microtubules: Components of the cytoskeleton in eukaryotes, forming structures like the spindle apparatus during cell division and aiding in maintaining cell shape and intracellular transport.

  • Coccus/Cocci: Spherical-shaped bacteria (e.g., Streptococcus, Staphylococcus).

  • Bacillus/Bacilli: Rod-shaped bacteria (e.g., Bacillus).

  • Spirochete: Spiral-shaped bacteria.

  • Taxis: Directed movement of an organism in response to an environmental stimulus (e.g., phototaxis to light, chemotaxis to chemicals).

  • Plasmid: Small, circular DNA elements in prokaryotes (and some eukaryotes) that are mobile and can carry advantageous genes, separate from the main chromosomal DNA.

  • R-plasmids: Plasmids that specifically carry genes providing resistance to antibiotics, contributing significantly to the spread of antibiotic resistance in bacterial populations.

  • Transformation: A pathway of genetic recombination in prokaryotes involving the uptake of naked DNA from the environment by a recipient cell and its subsequent incorporation into the recipient's genome.

  • Transduction: DNA transfer between bacteria mediated by bacteriophages (viruses that infect bacteria), where bacterial donor DNA is packaged into phage particles and delivered to a recipient cell.

  • Conjugation: Direct transfer of DNA between bacteria through cell-to-cell contact, typically facilitated by a pilus and often involving the transfer of an F factor (fertility factor) or other plasmid DNA.

  • Photoautotroph: An organism that uses light as an energy source and fixes inorganic carbon (e.g., CO_2 or bicarbonate) into organic compounds for growth (e.g., cyanobacteria, plants).

  • Chemoautotroph: An organism that obtains energy from chemical reactions involving inorganic or reduced compounds and fixes inorganic carbon (e.g., CO_2) into organic compounds (typically prokaryotic, found in environments lacking light).

  • Photoheterotroph: An organism that uses light as an energy source but requires organic carbon as a carbon source.

  • Chemoheterotroph: An organism that obtains both its energy and carbon from organic compounds through chemical reactions (e.g., humans, most animals).