Chapter 26: Bacteria and Archaea

Prokaryotes vs. Eukaryotes

Prokaryotes and eukaryotes are the two fundamental cell types in biology, differing in structure and complexity.

• Prokaryotes (Bacteria and Archaea): Lack a membrane-bound nucleus and organelles; DNA is found in a nucleoid region.

• Eukaryotes: Have a true nucleus enclosed by a membrane and possess membrane-bound organelles (e.g., mitochondria, chloroplasts).

• Size: Prokaryotes are generally smaller (0.5–5 μm) than eukaryotes (10–100 μm).

• Cell Division: Prokaryotes divide by binary fission; eukaryotes by mitosis and meiosis.

Distinguishing Features of Bacteria and Archaea

• Cell Wall Composition: Bacteria have peptidoglycan in their cell walls; Archaea do not.

• Membrane Lipids: Bacteria have ester-linked lipids; Archaea have ether-linked lipids.

• RNA Polymerase: Archaea's RNA polymerase is more similar to eukaryotes than to bacteria.

• Pathogenicity: Many bacteria are pathogenic; very few Archaea are known to cause disease.

Why Do Biologists Study Bacteria and Archaea?

• They are the most abundant and diverse organisms on Earth.

• They play critical roles in ecosystems (e.g., nutrient cycling, decomposition).

• Some are medically important as pathogens or beneficial microbes.

Abundance and Habitat Diversity

• Abundance: Prokaryotes are found in every environment, with estimates of 5 × 1030 cells on Earth.

• Habitat Diversity: Prokaryotes inhabit extreme environments (extremophiles), such as hot springs, salt lakes, deep-sea vents, and acidic or alkaline waters.

Medical Importance

• Germ Theory: States that infectious diseases are caused by microorganisms.

• Koch’s Four Postulates: Criteria to establish a causative relationship between a microbe and a disease.

• Disease Transmission: Diseases can spread via air, water, food, vectors, or direct contact.

• Virulence: The degree of pathogenicity of a microorganism.

• Endospores: Dormant, tough structures formed by some bacteria to survive harsh conditions.

• Antibiotics: Chemicals that kill or inhibit bacteria; resistance evolves through natural selection.

• Bioremediation: Use of microbes to clean up pollutants (e.g., oil spills).

Genetic Variation through Gene Transfer

Prokaryotes exchange genetic material by:

• Transformation: Uptake of free DNA from the environment.

• Transduction: Transfer of DNA by viruses (bacteriophages).

• Conjugation: Direct transfer of DNA between cells via a pilus.

Morphological Diversity

• Size: Range from very small (e.g., Mycoplasma) to large (e.g., Epulopiscium).

• Motility: Many move using flagella; others glide or twitch.

• Bacterial Flagellum: A helical structure used for movement, powered by a proton gradient.

• Cell Wall Composition: Gram-positive bacteria have thick peptidoglycan layers; Gram-negative have thin layers and an outer membrane.

Metabolic Diversity

Organisms must acquire energy and carbon:

• Autotrophs: Obtain carbon from CO2.

• Heterotrophs: Obtain carbon from organic molecules.

• Phototrophs: Use light as energy source.

• Chemoorganotrophs: Use organic molecules for energy.

• Chemolithotrophs: Use inorganic molecules for energy.

Combinations (see table below):

• Plants: Photoautotrophs

• Animals and Fungi: Chemoorganoheterotrophs

Cellular Respiration

• ATP (Adenosine Triphosphate): The main energy currency of the cell.

• Electron Transport Chain (ETC): Series of proteins that transfer electrons, creating a proton gradient used to produce ATP.

• ATP Synthase: Enzyme that synthesizes ATP using the proton gradient.

• Electron Acceptors: In eukaryotes, oxygen is the final electron acceptor (producing water and CO2); prokaryotes may use other acceptors (e.g., nitrate, sulfate).

• Fermentation: ATP production without an ETC; less efficient.

• Photophosphorylation: ATP production using light energy.

• Methanotrophs: Use methane as a carbon and energy source.

• Methanogens: Produce methane as a metabolic byproduct.

Ecological Diversity and Global Impacts

• The Oxygen Revolution: The rise of atmospheric oxygen due to photosynthetic cyanobacteria.

• Cyanobacteria: Photosynthetic bacteria that produce oxygen.

• Oxygen: Highly efficient electron acceptor, enabling aerobic respiration.

Nitrogen Fixation and the Nitrogen Cycle

• Nitrogen: Essential for proteins and nucleic acids.

• Nitrogen Fixation: Conversion of atmospheric N2 to ammonia (NH3) by certain prokaryotes.

• Nitrite (NO2-) and Nitrate (NO3-): Important intermediates in the nitrogen cycle.

• Nitrate Pollution: Excess nitrate from fertilizers can cause environmental problems (eutrophication).

Chapter 27: Diversification of Eukaryotes

Introduction to Eukaryotic Cells and Protists

• Eukaryotic Cells: Defined by a nucleus and membrane-bound organelles.

• Protists: Diverse group of mostly unicellular eukaryotes; live in aquatic or moist environments.

Medical and Ecological Importance of Protists

• Irish Potato Famine: Caused by the protist Phytophthora infestans.

• Malaria: Caused by Plasmodium species (protists).

• Harmful Algal Blooms: Caused by rapid growth of certain protists (e.g., dinoflagellates).

• Plankton: Small organisms that drift in water; protists are key components and primary producers.

• Global Carbon Cycle: Protists contribute to carbon fixation and cycling.

Evolutionary Importance

• Unikonta: Eukaryotes with a single flagellum (includes animals, fungi).

• Opisthokonta: Subgroup of Unikonta; includes animals and fungi.

• Bikonta: Eukaryotes with two flagella.

Morphological Innovations in Protists

• Earliest Eukaryotes: Likely unicellular, with mitochondria and a nucleus.

Endosymbiosis and the Origin of Organelles

• Mitochondria: Organelles for aerobic respiration; originated via endosymbiosis of a proteobacterium.

• Evidence: Mitochondria have their own DNA, double membranes, and replicate independently.

• Chloroplasts: Organelles for photosynthesis; originated via endosymbiosis of a cyanobacterium.

• Secondary Endosymbiosis: Occurs when a eukaryote engulfs another eukaryotic cell that already contains chloroplasts.

Nucleus and Endomembrane System

• Nucleus: Membrane-bound compartment containing DNA.

• Evolution: Likely arose from infolding of the plasma membrane.

Flagella and Locomotion

• Flagellum: Whip-like structure for movement.

• Eukaryotic vs. Prokaryotic Flagella: Eukaryotic flagella are covered by the plasma membrane and have a 9+2 arrangement of microtubules; prokaryotic flagella are simpler and not membrane-bound.

Support, Protection, and Multicellularity

• Rigid Structures: Some protists have cell walls, shells, or pellicles for support.

• Multicellularity: Evolved multiple times in eukaryotes; allows for specialized cells and larger body size.

Nutrition and Feeding

• Phagocytosis: Engulfing food particles using pseudopodia (extensions of the cell membrane).

• Absorptive Feeding: Uptake of nutrients directly from the environment.

Movement

• Amoeboid Motion: Movement by extending pseudopodia.

• Other Structures: Some protists use cilia or flagella for locomotion.

Reproduction in Protists

• Haploid: One set of chromosomes.

• Diploid: Two sets of chromosomes.

• Asexual Reproduction: Offspring are genetically identical to parent.

• Sexual Reproduction: Involves gametes and meiosis; increases genetic diversity.

• Gametes: Haploid reproductive cells.

• Meiosis: Cell division that reduces chromosome number by half.

Life Cycles

• Life Cycle: Sequence of events from one generation to the next.

• Haploid-Dominated: Most of the life cycle is spent as haploid cells.

• Diploid-Dominated: Most of the life cycle is spent as diploid cells.

• Alternation of Generations: Life cycle alternates between multicellular haploid (gametophyte) and diploid (sporophyte) stages.

• Gametophyte: Produces gametes.

• Sporophyte: Produces spores.

• Spores: Haploid cells that can develop into a new organism.

Chapter 28: Green Algae and Land Plants

The Viridiplantae

• Includes green algae and land plants.

Ecosystem Services of Plants

• Produce oxygen via photosynthesis.

• Build soil and prevent erosion.

• Moderate climate and provide food, fuel, and medicines.

Phylogeny and Similarities

• Green Algae: Aquatic, photosynthetic organisms closely related to land plants.

• Share chlorophylls a and b, and store starch.

Nonvascular and Vascular Plants

• Nonvascular Plants: Lack vascular tissue; small, live in moist environments (e.g., mosses).

• Vascular Plants: Have specialized tissues (xylem and phloem) for transport of water and nutrients.

• Seedless Vascular Plants: Reproduce via spores (e.g., ferns).

• Seed Plants: Include gymnosperms (naked seeds) and angiosperms (flowering plants).

Evolution of Land Plants

• Five major intervals in the fossil record show the evolution from green algae to complex land plants.

Adaptations to Land

• Cuticle: Waxy layer that prevents water loss.

• Stomata: Pores that regulate gas exchange.

• Upright Growth: Allowed plants to access more sunlight; evolution of water-conducting cells (tracheids, vessel elements).

Plant Body Organization

• Roots: Anchor plant, absorb water and nutrients.

• Shoots: Stems and leaves; support and photosynthesis.

• Surface Area to Volume Ratio: Important for efficient absorption and transport.

• Leaves: Main site of photosynthesis; can be modified for storage, protection, or reproduction.

Plant Cells and Tissues

• Unique Features: Cell wall, large central vacuole, chloroplasts, plasmodesmata (channels between cells).

• Tissue: Group of cells with a common function.

• Simple Tissues: One cell type; Complex Tissues: Multiple cell types.

Reproduction on Land

• Three innovations: Protective reproductive organs, retention of embryo, alternation of generations.

• Gametangium: Structure where gametes are produced.

• Antheridium: Male gametangium; Archegonium: Female gametangium.

• Embryo: Retained and nourished by parent tissue.

Alternation of Generations

• Gametophyte-Dominant: Nonvascular plants; gametophyte is the main life stage.

• Sporophyte-Dominant: Vascular plants; sporophyte is the main life stage.

• Sequence: Sporophyte (2n) → meiosis → spores (n) → gametophyte (n) → gametes → fertilization → zygote (2n) → sporophyte.

• Homospory: One type of spore; Heterospory: Two types (microspores and megaspores).

• Microsporangia: Produce microspores (male); megasporangia: produce megaspores (female).

Reproduction in Angiosperms

• Asexual Reproduction: Via runners, tubers, or plantlets.

• Flowers: Contain male (stamens) and female (carpels) parts; sepals and petals protect and attract pollinators.

• Pollen: Male gametophyte; Pollination: Transfer of pollen to stigma.

• Sporopollenin: Tough polymer in pollen wall.

• Mutualism: Pollination often involves mutualistic relationships with animals.

• Double Fertilization: One sperm fertilizes egg, another fuses with two nuclei to form endosperm.

• Seeds: Protect and nourish embryo; allow dormancy and dispersal.

• Fruits: Develop from ovary; aid in seed dispersal. Types: simple, aggregate, multiple.

• Angiosperm Radiation: Rapid diversification due to flowers, fruits, and vessel elements.

• Monocots vs. Dicots:

Chapter 29: Fungi

What are Fungi?

• Eukaryotic, heterotrophic organisms with cell walls made of chitin.

Economic and Ecological Impacts

• Fungi are important as food (e.g., mushrooms, yeast), pests, and decomposers.

• Mycorrhizal Fungi: Form mutualistic associations with plant roots, aiding nutrient uptake.

• Saprophytic Fungi: Decompose dead organic matter, accelerating the carbon cycle.

Fungal Morphology

• Yeasts: Single-celled fungi.

• Mycelia: Multicellular, filamentous structures composed of hyphae.

• Hyphae: Thread-like filaments; may be divided by septa with pores or be coenocytic (no septa).

Reproductive Structures

• Swimming Gametes and Spores: Motile reproductive cells (chytrids).

• Zygosporangia: Thick-walled structures formed by fusion of hyphae (zygomycetes).

• Basidia: Club-shaped cells where meiosis occurs (basidiomycetes).

• Asci: Sac-like cells where meiosis occurs (ascomycetes).

Fungi and Animals: Evolutionary Relationships

• Both store glycogen, have chitin in cell walls (fungi) or exoskeletons (animals), and use similar flagella in some groups.

Major Fungal Groups

• Aquatic Basal Groups

• Chytrids

• Zygomycetes

• Glomeromycota

• Ascomycota (monophyletic)

• Basidiomycota (monophyletic)

Symbioses Involving Fungi

• Mycorrhizae: Symbiotic associations with plant roots; can be ectomycorrhizal (outside root cells) or arbuscular (inside root cells).

• Endophytes: Fungi living inside plant tissues.

• Lichens: Symbiosis between fungi and photosynthetic organisms (algae or cyanobacteria).

• "Zombie" Fungi: Parasitic fungi that manipulate host behavior.

Fungi as Decomposers

• Saprophytic: Feed on dead organic matter.

• Extracellular Digestion: Secrete enzymes to break down complex molecules outside the cell.

• Break down cellulose and lignin in plant tissue.

Variation in Fungal Reproduction

• Spore: Fundamental reproductive cell in fungi.

• Spore germinates to form mycelium.

• Mating Types: Genetically distinct forms that must pair for sexual reproduction.

Fertilization in Fungi

• Chytrids: Fertilization involves fusion of gametes.

• Other Fungi: Fertilization occurs in two steps: plasmogamy (fusion of cytoplasm) and karyogamy (fusion of nuclei).

• Heterokaryotic Hyphae: Hyphae with two or more genetically distinct nuclei.

• Dikaryotic Hyphae: Hyphae with two nuclei per cell.

Fungal Life Cycles

• Both asexual and sexual reproduction occur.

• Plasmogamy: Fusion of cytoplasm from two parent mycelia.

• Karyogamy: Fusion of nuclei to form diploid zygote.

• Four major types of life cycles correspond to the four reproductive structures.

• Basidiomycete Life Cycle: Multicellular reproductive structure is often a mushroom.

Example: The bread mold Rhizopus (a zygomycete) forms zygosporangia during sexual reproduction, while the common mushroom (Agaricus) is a basidiomycete with a prominent fruiting body.