Chapter 26: Bacteria & Archaea

Domain Differences

Bacteria and Archaea are two of the three domains of life, each with unique structural and biochemical characteristics.

• Bacteria: Cell walls contain peptidoglycan; membrane lipids are unbranched fatty acids; sensitive to antibiotics like penicillin.

• Archaea: Cell walls lack peptidoglycan; membrane lipids have branched isoprenoid chains; often extremophiles; insensitive to most antibiotics targeting bacteria.

Gram Staining & Antibiotics

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

• Gram-positive bacteria: Thick peptidoglycan layer; stain purple; generally more sensitive to antibiotics targeting cell wall synthesis.

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

Research Methods: Enrichment Cultures vs. Metagenomics

• Enrichment cultures: Grow specific microbes under controlled conditions to study their physiology.

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

Pathogenesis & Survival: Koch’s Postulates

Koch’s Postulates are criteria to establish a causative relationship between a microbe and a disease:

1. Microbe must be present in diseased individuals, absent in healthy ones.

2. Microbe must be isolated and grown in pure culture.

3. Pure culture must cause disease when introduced to a healthy host.

4. Microbe must be re-isolated from the experimentally infected host.

Horizontal Gene Transfer

Prokaryotes exchange genetic material via:

• Transformation: Uptake of free DNA from the environment.

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

• Conjugation: Direct transfer of DNA through cell-to-cell contact (e.g., via a pilus).

Metabolic Diversity

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

• Phototrophs: Use light as energy source.

• Chemolithotrophs: Use inorganic molecules (e.g., H2, NH3) as energy source.

• Chemoorganotrophs: Use organic molecules as energy source.

• Autotrophs: Use CO2 as carbon source.

• Heterotrophs: Use organic compounds as carbon source.

Combining these yields six major feeding strategies (e.g., photoautotroph, chemoorganoheterotroph, etc.).

• Oxygenic photosynthesis: Produces O2 (e.g., cyanobacteria).

• Anoxygenic photosynthesis: Does not produce O2.

• Cyanobacteria: Crucial for atmospheric oxygen and nutrient cycling.

Chapter 27: Diversification of Eukaryotes (Protists)

Eukaryotic Synapomorphies & Paraphyly

Eukaryotes are defined by several key features:

• Nuclear envelope surrounding DNA

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

• Linear chromosomes

• Cytoskeleton for structural support and movement

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

Endosymbiotic Theory

• Primary endosymbiosis: Eukaryotic cell engulfs a prokaryote (e.g., origin of mitochondria and chloroplasts).

• Secondary endosymbiosis: Eukaryote engulfs another eukaryote that already contains an endosymbiont.

Nuclear Envelope Origin

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

Medical & Ecological Significance

• Plasmodium: Protist causing malaria (disease vector).

• Dinoflagellates: Cause red tides, produce toxins.

• Phytophthora: Caused the Irish potato famine.

• Marine phytoplankton: Major carbon sink, crucial for global carbon cycling.

Seven Eukaryotic Lineages

Chapter 28: Green Algae & Land Plants

Synapomorphies

• Chlorophyll a and b

• Cellulose cell walls

• Starch as storage molecule

Terrestrial Adaptations

• Cuticle: Waxy layer preventing water loss.

• Stomata: Pores with guard cells regulating gas exchange and water loss.

• Flavonoids: Pigments protecting against UV radiation.

• Water-conducting cells: Evolution from simple cells to lignified tracheids and vessel elements for structural support and efficient transport.

Life Cycle Evolution

Transition from gametophyte-dominated (haploid) to sporophyte-dominated (diploid) life cycles in land plants.

Reproductive Innovations

• Protected gametangia: Structures protecting gametes from desiccation.

• Embryo retention: Zygote develops within parent tissue.

• Heterospory: Production of 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 or gametophyte), and protective seed coat.

• Angiosperms: Flowers, double fertilization, and fruits for seed dispersal.

Chapter 29: Fungi

Fungal Body Plans

• Yeasts: Single-celled fungi.

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

Surface-Area Trade-Off

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

Clade Opisthokonta

Fungi share a common ancestor with animals, both in the Opisthokonta clade.

Extracellular Digestion

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

• Cellulases: Enzymes hydrolyzing 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, form arbuscules, transfer phosphorus (tropical/grasslands).

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

• Fungal endophytes: Fungi living inside plant tissues, often mutualistic.

Fertilization Mechanics

• Plasmogamy: Fusion of cytoplasm from two parent mycelia.

• Karyogamy: Fusion of nuclei, producing diploid cells.

• Heterokaryotic/dikaryotic state: Cells contain two genetically distinct nuclei for extended periods.

Life Cycle Groups

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: Suggests ctenophores may be the earliest animal lineage.

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 for movement.

Protostome vs. Deuterostome Development

Developmental Genes

Homology of the Distal-less (Dll) gene in appendage outgrowth across bilaterian animals.

Chapter 31: Protostome Animals

Water-to-Land Adaptation

• Development of cuticles to prevent desiccation

• Internal respiratory structures (lungs, tracheae)

• Desiccation-resistant eggs

Clade Lophotrochozoa

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

• Platyhelminthes: Acoelomate flatworms; gas exchange by diffusion.

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

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

Clade Ecdysozoa

• Growth by ecdysis (molting) of cuticle/exoskeleton.

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

• Arthropoda: Tagmatization, chitinous/calcium exoskeleton, jointed appendages, Hox gene serial homology.

Insect Metamorphosis

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

• Incomplete metamorphosis: Juveniles resemble adults; gradual development.

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 cartilaginous 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

Roles of Symbioses

• Endosymbiotic origins: Mitochondria and chloroplasts in Eukarya

• Mycorrhizal fungi: Plant-fungi mutualisms

• Lichens: Fungi and photosynthetic partners

• Microbiome concept: Diverse microbial communities in and on multicellular organisms (see Yong's "I Contain Multitudes")

Solving Challenges of Life on Land

• Multicellular lineages (plants, fungi, animals) evolved unique adaptations for water retention, support, reproduction, and nutrient acquisition.

• Examples: Plant cuticle and vascular tissue; fungal hyphae and spores; animal exoskeletons and amniotic eggs.

Supplemental Readings

• "Are Viruses Alive?" (Villareal): Challenges the definition of life and the placement of viruses in the tree of life.

• "I Contain Multitudes" (Yong): Explores the importance of symbiotic microbes in animal biology.

• "Learning the Grammar of Animacy" (Kimmerer): Discusses the language and perception of living things, challenging traditional biological categories.