Chapter 26: Bacteria & Archaea

Domain Differences

Bacteria and Archaea are two of the three domains of life, distinguished by key structural and biochemical features.

• Bacteria: Cell walls contain peptidoglycan; membrane lipids are unbranched fatty acids linked by ester bonds.

• Archaea: Cell walls lack peptidoglycan; membrane lipids are branched hydrocarbons linked by ether bonds; unique RNA polymerase and ribosomal proteins.

Gram Staining & Antibiotics

Gram staining differentiates bacteria based on cell wall structure, which also affects antibiotic susceptibility.

• Gram-positive: Thick peptidoglycan layer; stains purple; generally more susceptible to antibiotics targeting cell wall synthesis.

• Gram-negative: Thin peptidoglycan layer plus outer membrane; stains pink; often more resistant to antibiotics.

Research Methods

• Enrichment Cultures: Grow specific microbes under selective conditions to study their physiology.

• Metagenomics/Environmental Sequencing: Analyze genetic material recovered directly from environmental samples, allowing study of unculturable microbes.

Pathogenesis & Survival

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

• Steps include: (1) Microbe present in diseased, not healthy, organisms; (2) Isolate and culture microbe; (3) Cause disease in healthy host; (4) Re-isolate same microbe.

Horizontal Gene Transfer

• Transformation: Uptake of free DNA from environment.

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

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

Metabolic Diversity

Prokaryotes display diverse metabolic strategies, classified by energy and carbon sources.

• Energy Sources: Light (phototrophs), organic molecules (chemoorganotrophs), inorganic molecules (chemolithotrophs).

• Carbon Sources: CO2 (autotrophs), organic compounds (heterotrophs).

Six Feeding Strategies: Combine energy and carbon sources (e.g., photoautotroph, chemoheterotroph, etc.).

• Oxygenic vs. Anoxygenic Photosynthesis: Oxygenic (produces O2, e.g., cyanobacteria); anoxygenic (does not produce O2).

• Cyanobacteria: Major contributors to atmospheric oxygen and nutrient cycling.

Chapter 27: Diversification of Eukaryotes (Protists)

Eukaryotic Synapomorphies & Paraphyly

Eukaryotes are defined by several unique features:

• Nuclear envelope

• Membrane-bound organelles (e.g., mitochondria, chloroplasts)

• Linear chromosomes

• Cytoskeleton

Protists are a paraphyletic group, meaning they include some but not all descendants of their most recent common ancestor.

Endosymbiotic Theory

• Primary Endosymbiosis: Origin of mitochondria and chloroplasts from engulfed bacteria.

• Secondary Endosymbiosis: Eukaryote engulfs another eukaryote that already contains endosymbionts.

Nuclear Envelope Origin

• Formed by infoldings of the plasma membrane, separating transcription from translation and enabling alternative splicing.

Medical & Ecological Significance

• Plasmodium: Causes malaria (disease vector).

• Dinoflagellates: Produce toxins causing red tides.

• Phytophthora: Responsible for potato famine.

• Marine phytoplankton: Major carbon sink, important in global carbon cycling.

Seven Eukaryotic Lineages

• Amoebozoa: Amoeboid movement, lack cell walls.

• Opisthokonta: Includes animals and fungi; single posterior flagellum.

• Excavata: Feeding groove, often lack typical mitochondria.

• Plantae: Includes green algae and land plants; chloroplasts with double membranes.

• Rhizaria: Threadlike pseudopodia.

• Alveolata: Sub-membrane alveoli (flattened vesicles).

• Stramenopiles: "Hairy" flagella.

Chapter 28: Green Algae & Land Plants

Synapomorphies

• Chlorophyll a and b

• Cellulose cell walls

• Starch storage

Terrestrial Adaptations

• Cuticle: Waxy layer preventing water loss.

• Stomata: Pores regulated by guard cells, balancing water retention and gas exchange.

• UV Protection: Flavonoid pigments act as internal sunscreen.

• Structural Support & Transport: Evolution from simple water-conducting cells to lignified tracheids and vessel elements for efficient water transport.

Life Cycle Evolution

• Transition from gametophyte-dominated (bryophytes) to sporophyte-dominated (vascular plants) life cycles.

Reproductive Innovations

• Protected gametangia and embryo retention

• Heterospory vs. Homospory: Heterospory produces microspores (male) and megaspores (female), leading to pollen and seeds.

• Pollen Grains: Male gametophytes with sporopollenin coat, enabling fertilization without water.

• Seed Architecture: Embryo, nutritive tissue (endosperm/gametophyte), and protective seed coat.

• Angiosperm Features: Flowers, double fertilization, and fruits.

Chapter 29: Fungi

Fungal Body Plans

• Yeasts: Single-celled fungi.

• Mycelia: Multicellular, composed of hyphae (filamentous structures).

High surface-area-to-volume ratio maximizes absorption but increases risk of desiccation.

Clade Opisthokonta

• Fungi share a common ancestor with animals.

Extracellular Digestion

• Lignin Peroxidase: Breaks down lignin in wood, exposing cellulose (does not yield ATP directly).

• Cellulases: Hydrolyze cellulose into glucose.

Symbiotic Associations

• Ectomycorrhizal Fungi (EMF): Form sheaths around roots, transfer nitrogen (temperate/boreal forests).

• Arbuscular Mycorrhizal Fungi (AMF): Penetrate root cell walls, transfer phosphorus (tropical/grasslands).

• Lichens: Symbiosis between ascomycete fungus and photosynthetic alga/cyanobacteria.

• Endophytes: Fungi living inside plant tissues.

Fertilization Mechanics

• Plasmogamy: Fusion of cytoplasm from two parent mycelia.

• Karyogamy: Fusion of nuclei, producing diploid cells.

• Often results in a prolonged heterokaryotic (n+n) or dikaryotic state.

Life Cycle Groups

• Chytrids: Flagellated spores.

• Zygomycetes: Zygosporangia for sexual reproduction.

• Basidiomycota: Club fungi (mushrooms), basidia produce spores.

• Ascomycota: Sac fungi, asci produce spores.

Chapter 30: Introduction to Animals

Animal Synapomorphies

• Multicellularity

• Lack of cell walls

• Extracellular matrix (collagen)

• Motility

• Ingestion of food

• Nerve and muscle cells

Origin of Multicellularity

• Sponges-first hypothesis: Choanocytes in sponges resemble choanoflagellates (closest unicellular relatives).

• Ctenophores-first hypothesis: Alternative view based on molecular data.

Germ Layers & Nervous Systems

• Diploblasts: Two germ layers (ectoderm, endoderm); radial symmetry; diffuse nerve net.

• Triploblasts: Three germ layers (ectoderm, mesoderm, endoderm); bilateral symmetry; cephalization; central nervous system.

Body Cavity Architecture

• Coelomate: True body cavity lined with mesoderm.

• Acoelomate: No body cavity.

• Pseudocoelomate: Body cavity partially lined with mesoderm.

• Body cavities function as hydrostatic skeletons.

Protostome vs. Deuterostome Development

• Protostomes: Spiral cleavage; blastopore becomes mouth; coelom forms by splitting (schizocoely).

• Deuterostomes: Radial cleavage; blastopore becomes anus; coelom forms by outpocketing (enterocoely).

Developmental Genes

• Homology of the Distal-less (Dll) gene in appendage development across bilaterians.

Chapter 31: Protostome Animals

Water-to-Land Adaptation

• Evolution of cuticles, internal respiratory structures (lungs/tracheae), and desiccation-resistant eggs enabled terrestrial life.

Clade Lophotrochozoa

• Defined by lophophore (feeding structure), trochophore larva, and spiral cleavage.

• Platyhelminthes: Flatworms; acoelomate; rely on diffusion for gas exchange.

• Annelida: Segmented worms; internal septa, chaetae, parapodia.

• Mollusca: Foot, visceral mass, mantle (secretes shell); radula; hemocoel.

Clade Ecdysozoa

• Grow by molting (ecdysis) outer cuticle/exoskeleton.

• Nematoda: Unsegmented, pseudocoelomate, elastic cuticle, hydrostatic skeleton.

• Arthropoda: Segmentation (tagmatization), chitinous/calcium exoskeleton, jointed appendages, Hox gene homology.

Insect Metamorphosis

• Complete metamorphosis: Distinct larval and adult stages; reduces competition.

• Incomplete metamorphosis: Juveniles resemble adults.

Chapter 32: Deuterostome Animals

Phylum Echinodermata

• Pentaradial adult symmetry

• Calcium carbonate endoskeleton

• Water vascular system with tube feet

• Sea stars as keystone predators

Four Chordate Synapomorphies

• Notochord

• Dorsal hollow nerve cord

• Pharyngeal gill slits/pouches

• Muscular post-anal tail

Invertebrate Chordates

• Cephalochordata (lancelets)

• Urochordata (tunicates)

Vertebrate Innovations

• Cranium and vertebral column

• Jaws evolved from modified gill arches

• Ray-finned fish: swim bladders, pharyngeal jaws

Tetrapod Evolution

• Lobe-finned fish as ancestors of tetrapods

• Amphibians: rely on water for gas exchange and reproduction

Amniota Clade

• Amniotic egg: Four extraembryonic membranes (amnion, yolk sac, allantois, chorion) for terrestrial reproduction

• Placental viviparity, lactation, hair, scales, feathers, endothermy

Supplemental Readings & Big Picture Topics

Symbioses and Endosymbiosis

• Endosymbiotic origins of mitochondria and chloroplasts in Eukarya

• Mycorrhizal fungi and plant symbiosis

• Lichens as mutualistic associations

• Microbiome concept (Yong): Importance of microbial communities in animal health

Solving Terrestrial Challenges

• Multicellular eukaryotes (plants, fungi, animals) evolved unique adaptations for life on land, such as cuticles, vascular tissues, internal fertilization, and desiccation-resistant structures.

Are Viruses Alive?

• Villareal’s article challenges the definition of life, considering viruses’ roles in evolution and ecology.

Learning the Grammar of Animacy

• Kimmerer’s work encourages rethinking categories and relationships in biology, emphasizing interconnectedness and the agency of non-human life forms.

Table: Comparison of Major Lineages

Additional info: Where the original notes were brief, academic context and definitions have been added for clarity and completeness.