BIO201 Prokaryotes, Eukaryotes, and Endosymbiosis Flashcards
Prokaryotes and Eukaryotes: Comprehensive Study Notes
Key opening ideas of the chapter:
- Bacteria and archaea are the most abundant and diverse life-forms on Earth, contrasted with eukaryotes.
- Core questions: Why and how do biologists study prokaryotes? What can be learned by asking questions and surveying lineages?
- Four overarching themes in their diversification: Gene transfer, Metabolism, Morphology, Ecological diversity.
- We will discuss a few representative examples and emphasize major concepts from microbiology.
Major groups and their broad distinctions:
- Prokaryotes include Bacteria and Archaea; Eukaryotes include all organisms with membrane-bound organelles and a nucleus.
- Prokaryotes are extremely diverse and ubiquitous; Eukaryotes represent a separate branch with distinctive cellular features.
Key differences among Bacteria, Archaea, and Eukarya (summarized from the cell-structure table):
- DNA arrangement:
- Bacteria: single, circular chromosome
- Archaea: single, circular chromosome
- Eukarya: multiple linear chromosomes
- Chromosomal proteins:
- Bacteria: histone-like proteins
- Archaea: histone-like proteins (more reminiscent of eukaryotic histones in some respects)
- Eukarya: histones (five major types)
- Genes organized in operons:
- Bacteria: yes
- Archaea: yes
- Eukarya: no
- Nuclear envelope:
- Bacteria: no
- Archaea: no
- Eukarya: yes
- Mitochondria:
- Bacteria: no
- Archaea: no
- Eukarya: yes
- Chloroplasts:
- Bacteria: no
- Archaea: no
- Eukarya: yes (in plants and algae)
- Peptidoglycan in cell wall:
- Bacteria: present
- Archaea: absent or greatly reduced
- Eukarya: absent
- Membrane lipids:
- Bacteria: unbranched; ester linkages
- Archaea: branched; ether linkages
- Eukarya: unbranched; ester linkages
- RNA polymerase:
- Bacteria: one type
- Archaea: multiple types
- Eukarya: multiple types
- Ribosomal proteins / translation start:
- First amino acid in bacterial proteins: Formylmethionine (fMet)
- In Archaea and Eukarya: Methionine (Met)
- Cell division and energy metabolism proteins: different in prokaryotes vs eukaryotes; details reflect distinct machinery.
- Sensitivity to antibiotics (e.g., chloramphenicol and streptomycin): mainly affect bacteria; archaea and eukaryotes have different sensitivities.
Cell size, shape, and motility (typical ranges and examples):
- Size: Most bacteria are about 1.0\,\mu\text{m} in diameter; some are much larger. Largest known: \approx 100\,\mu\text{m} (e.g., Thiomargarita namibiensis).
- Shapes: Rods, spheres, spirals; cells may adhere to form chains.
- Motility: Varies among species; some nonmotile; swimming and gliding are common.
- Examples:
- Swimming: \text{Pseudomonas aeruginosa}
- Spirals: \text{Campylobacter jejuni}
- Gliding: \text{Oscillatoria limosa}
- Visual summary: size range from sub-micron to tens of micrometers; diverse morphologies enable adaptation to environments.
Prokaryotic motility and surface structures:
- Most common motility is via flagella, which are structurally unlike eukaryotic flagella and are much smaller.
- Some prokaryotes glide; others move using gas bubbles or other mechanisms.
- Surface structures: Capsule and fimbriae; many prokaryotes live as unicells but can form colonies and biofilms in various environments.
Prokaryotic cell walls and staining (Gram categories):
- Gram-positive cell wall:
- Thick layer of polysaccharides (peptidoglycan-rich)
- Gram-negative cell wall:
- Outer membrane plus a thin peptidoglycan layer; additional features can affect permeability and antibiotic susceptibility
- The outer membrane in Gram-negative bacteria contributes to reduced antibiotic passage in many cases.
Gram-positive bacteria, notable members, and life strategies:
- Streptomyces: notable antibiotic producers
- Mycoplasmas: among the smallest cells (lacking cell walls)
- Endospores: many Gram-positive bacteria form endospores that can survive extremely long periods (up to ~1000 years or more) under harsh conditions; examples include agents of botulism and anthrax.
- Practical implication: Endospores contribute to persistence and transmission of certain pathogens; antibiotic production by Streptomyces underpins many medicines.
Reproduction and genetic transfer in prokaryotes:
- Asexual reproduction: binary fission (fission)
- Genetic transfer mechanisms (horizontal gene transfer):
- Conjugation: DNA transferred cell-to-cell via direct contact (often F-plasmid–mediated)
- Transformation: uptake of free DNA from the environment by cells
- Transduction: viral (bacteriophage) transfer of DNA
- Important note: In prokaryotes, reproduction and genetic transfer do not necessarily happen together in a single event.
Taxonomic placement and domain groups (overview):
- Domain Bacteria: includes diverse phyla such as Mycoplasma, Firmicutes, Cyanobacteria, Actinobacteria, Spirochaetes, Chlamydiae, Bacteroidetes, ε-Proteobacteria, δ-Proteobacteria, α-Proteobacteria, β-Proteobacteria, γ-Proteobacteria
- Domain Archaea: includes major groups such as Thaumarchaeota, Crenarchaeota, Korarchaeota, Euryarchaeota
- Domain Eukarya: includes all eukaryotic life
- Conceptual notes:
- The prokaryote/eukaryote dichotomy is a basis for comparing cell organization, not merely a superficial label; some features blur lines (e.g., Archaea share some traits with Eukarya in replication and transcription/translation processes).
- Several chapters discuss phylogeny and whether prokaryotes form a monophyletic group; emphasis is placed on a few key lineages for practical study.
Archaea: extremophiles and membrane biology
- Many Archaea are extremophiles, thriving in hot springs, hypersaline environments, and highly acidic conditions.
- Membrane structure in Archaea is distinctive (weird lipids) and markedly different from bacteria and eukaryotes; peptidoglycan is absent in most Archaea.
- Although prokaryotes overall, Archaea have unique features that set them apart from bacteria and eukaryotes.
Proteobacteria and their significance
- Proteobacteria (often colored as purple bacteria) constitute a large, diverse group.
- Includes photosynthetic members (many do not generate oxygen directly) and has numerous human pathogens (e.g., some strains of E. coli, Salmonella).
- They are important for understanding the probable origin of mitochondria (endosymbiotic theory).
- Nitrogen-fixing members are ecologically important for legumes and other plants.
- Notable pathogens include Yersinia pestis (Bubonic plague), Salmonella enterica serotypes (e.g., typhi).
The nitrogen cycle (conceptual overview with key steps):
- Atmospheric nitrogen: ext{N}_2 is fixed by bacteria to forms usable by organisms.
- Nitrogen fixation: \mathrm{N2 + 8 H^+ + 8 e^- + 16 ATP \rightarrow 2 NH3 + H2 + 16 ADP + 16 Pi}
- Ammonification (decomposition) converts organic nitrogen into ammonium: \mathrm{|\rightarrow NH_4^+}
- Nitrification: conversion of ammonium to nitrites and then to nitrates: \mathrm{NH4^+ \rightarrow NO2^- \rightarrow NO_3^-}
- Denitrification and assimilation processes close the cycle; denitrifying bacteria reduce nitrates back to nitrogen gas under anaerobic conditions.
- Diagrammatic flow (textual): Nitrogen gas in the atmosphere is fixed by soil bacteria and root-nodule bacteria in legumes to ammonia, which is further processed to nitrite and nitrate by nitrifying bacteria; plants assimilate nitrates and ammonium; decomposers release ammonium via ammonification; denitrifying bacteria release N2 back to the atmosphere.
- Key soil-plant interactions: legume nodules host nitrogen-fixing bacteria; soil bacteria contribute to soil fertility; nitrogen cycling is essential for ecosystems and agriculture.
- Visual cue: The nitrogen cycle involves multiple microbial players and transformations across aerobic and anaerobic environments.
Plant-like photosynthesis and chloroplast ancestry
- Plant-like photosynthesis is carried out by cyanobacteria, which are photosynthetic prokaryotes that contributed to the oxygenation of the Earth.
- Endosymbiotic origin of chloroplasts is analogous to mitochondria's origin; chloroplasts arose from a photosynthetic endosymbiont, with a parallel endosymbiotic narrative to mitochondria.
- Cyanobacteria serve as a key example of specialized prokaryotes capable of nitrogen fixation in certain cells (heterocysts) and photosynthesis.
- Anabaena: an example illustrating specialization and division of labor within a prokaryotic colony.
Cyanobacteria and the Oxygen Revolution
- For the first ~2.3 billion years, Earth had little to no free molecular oxygen (O2).
- Cyanobacteria were the first to perform oxygenic photosynthesis, releasing O2 to the atmosphere and oceans.
- The rise of oxygen dramatically changed Earth’s atmosphere and allowed aerobic respiration to become widespread, enabling higher-energy-yield pathways and the emergence of more complex life.
The Oxygen Revolution: energetic implications
- Oxygen is a highly electronegative and efficient electron acceptor.
- Electron transport chains with oxygen as the final acceptor yield more energy than other acceptors, making aerobic respiration highly advantageous.
- The availability of oxygen was a key driver in the evolution of eukaryotes by enabling more efficient energy production.
- Overall ecological and evolutionary impact: sets stage for diversification and complexity in life forms.
Oxygen timeline (conceptual overview):
- Early Earth had low atmospheric O2; later, oxygenation events increased O2 levels.
- The appearance of aerobic bacteria and eukaryotes followed the rise in oxygen, enabling more complex biological processes.
- A rough schematic of historical oxygen levels vs. major life events:
- First life → early Earth with minimal O2
- First photosynthetic bacteria → rise in O2 production
- First eukaryotes → correlate with sustained oxygen availability
- Present-day oxygen levels (~21%) are a culmination of long-term biological and geological processes
Eukaryotes: features that distinguish them from prokaryotes
- Eukaryotic cells possess membrane-bound organelles and a nucleus, which segregates transcription from translation (nucleus and endoplasmic reticulum).
- Sexual reproduction and life cycles:
- Fertilization and meiosis are pivotal adaptations in many eukaryotes, introducing genetic diversity and novel traits in offspring.
- Life cycles can be complex and involve alternations of generations in some lineages.
- The evolutionary path to complex cells is tightly linked to endosymbiosis and organelle acquisition.
Endosymbiosis: mitochondria and chloroplasts as evidence
- Mitochondria share key features with bacteria and support the endosymbiotic origin of organelles:
- Size similar to α-proteobacteria
- Replication by fission, like bacteria
- Double membranes
- Ribosomes and protein synthesis machinery like bacterial ribosomes
- Independent circular genome, similar to bacterial chromosomes
- Phylogenetic data support the endosymbiotic origin: mitochondrial gene sequences are more closely related to α-proteobacteria than to nuclear eukaryotic DNA
- Chloroplasts: endosymbiosis has occurred with chloroplasts; secondary endosymbiosis has occurred in some lineages, adding layers to the origins of photosynthetic organelles in protists and plants.
Connections to foundational principles and real-world relevance
- Foundational principles: cell theory, phylogenetics, endosymbiotic theory, genetics, metabolism, and ecology.
- Practical implications:
- Antibiotics target bacterial features (e.g., bacterial ribosomes, cell wall synthesis), with varying effects on archaea and eukaryotes due to differences in targets.
- Understanding nitrogen cycling informs agriculture, ecosystem management, and climate science.
- The endosymbiotic origin of mitochondria and chloroplasts deepens our understanding of eukaryotic evolution and helps interpret phylogenetic relationships.
Ethical, philosophical, and practical implications mentioned or implied
- Antibiotic resistance and prudent use of antibiotics in medicine and agriculture have ethical and public health implications.
- The endosymbiotic view reshapes our view of metabolism and cellular individuality, illustrating a collaborative origin of complex life.
- Studying microbial diversity informs environmental stewardship and biotechnology (e.g., antibiotic discovery from Streptomyces).
Quick reference to key equations and quantitative notes (LaTeX):
- Nitrogen fixation (simplified):
\mathrm{N2 + 8 H^+ + 8 e^- + 16 ATP \rightarrow 2 NH3 + H2 + 16 ADP + 16 Pi} - Nitrification (ammonium to nitrite to nitrate):
\mathrm{NH4^+ \rightarrow NO2^- \rightarrow NO_3^-} - Aerobic respiration overall (glucose oxidation):
\mathrm{C6H{12}O6 + 6\,O2 \rightarrow 6\,CO2 + 6\,H2O} - Oxygenic photosynthesis (cyanobacteria):
\mathrm{6\,CO2 + 6\,H2O \rightarrow C6H{12}O6 + 6\,O2} - Cellular dimensions used in figures: typical cell diameter ~ 1.0\,\mu\text{m}; largest cells ~ 100\,\mu\text{m}; examples: 0.3\,\mu\text{m} width (e.g., some small bacteria), 100\,\mu\text{m} diameter (e.g., Thiomargarita namibiensis)
- Nitrogen fixation (simplified):
Summary key takeaways
- Prokaryotes (Bacteria and Archaea) show immense diversity in metabolism, morphology, and ecological roles, with distinctive cellular and molecular features that separate them from Eukarya.
- Eukaryotes evolved through endosymbiosis and developed complex life cycles, organelles, and sexual reproduction, enabling greater energy throughput and complexity.
- The nitrogen cycle and photosynthesis by cyanobacteria had profound effects on Earth's atmosphere and biosphere, enabling aerobic respiration and the evolution of diverse life forms.
- Studying these groups connects fundamental biology to medicine, agriculture, ecology, and evolutionary theory.