Biology 101: Exploring the Diversity of Life
1. Bacteria & Archaea
Classifications
Three Domains (Woese: small subunit rRNA): Bacteria, Archaea, Eukarya. Comparison of three domains, relationships; ‘Prokaryotes’ (=Monera) paraphyletic. [Monophyletic vs. paraphyletic – know the meaning of these terms]
Prokaryotic Cell Structure
Bacterial cell wall with peptidoglycan, Gram +/– difference, cell shape, capsule, flagellum, plasmid, endospores; archaeal cell membrane branched isoprene chains.
Reproduction & Genetic Novelties
Binary fission, mutations, transformation, transduction, horizontal gene transfer.
Medical Importance
Germ theory, pathogens, Koch’s postulates – purpose & steps.
Methods
Enrichment culture, metagenomics/direct sequencing.
Diversity of Bacteria & Archaea
Habitat, metabolic, phylogenetic.
Habitat Diversity
Very wide, includes extreme environments (extremophiles: thermophiles, halophiles, etc), not only Archaea; use in bioremediation.
Metabolic Diversity
Three energy sources for making ATP & two sources of C-C bonds (auto-/hetero) give six possibilities, all six seen in Bacteria & Archaea, only two in eukaryotes (photoautotrophs & chemoorganoheterotrophs); fermentation vs. chemiosmosis; variation in photosynthesis – bacteriorhodopsin vs. chlorophyll etc, oxygenic (water electron source, O2 released) vs. anoxygenic.
2. Viruses
Viruses vs. Cellular Organisms
Very small, incapable of protein synthesis, metabolism & replication, need to infect cells to replicate.
Virus Structure & Diversity
Protein capsid & DNA or RNA genome, with/without envelope, genomic variation – DNA, RNA, single-/double-stranded, etc.
Replication of Viral Genome
By DNA polymerase (DNA viruses), RNA replicase (some RNA viruses), reverse transcriptase (RNA retroviruses).
Infection & Propagation
Replicative infection (lytic cycle) vs. dormant infection (lysogenic infection).
Lytic Cycle (All Viruses)
Six steps incl. attachment/uncoating, destroys host cell on exit, multiply fast.
Lysogenic Cycle (Some Viruses)
Viral genome inserted in host DNA (provirus/prophage) & passed on to host cell progeny.
Human Immunodeficiency Virus (HIV) (A Retrovirus)
Infects human immune system cells with CD4 receptor & co-receptors CXCR4 or CCR5 (helper T lymphocytes), transmission by body fluids.
Roles of reverse transcriptase and protease, how anti HIV drugs like AZT & protease inhibitors work.
Acquired Immunodeficiency Syndrome (AIDS)
Depressed immune system, patient succumbs to opportunistic infections & cancers.
3. Protists
Protist Diversity
Eukarya phylogeny, “protists” as paraphyletic assemblage of eukaryotes that are not plants, animals or fungi!
Traditional classification: ‘Protozoa’ (heterotrophs) & ‘Algae’ (autotrophs) not valid.
Major lineages currently thought to fall into two groups – Unikonta (amebas, slime molds, fungi, animals) & Bikonta (very diverse, includes algae & plants, ciliates, euglenids, etc).
Endosymbiotic Origin
Origin of mitochondria & chloroplast from cyanobacteria & alpha proteobacteria, evidence supporting this theory.
Ecological Importance
Mostly aquatic, photosynthetic forms (‘algae’) major primary producers, also remove atmospheric CO2; many mutualists or parasites of other organisms.
Locomotion
By flagella, cilia or pseudopodia.
Reproduction
Asexual vs. sexual.
Protists & Human Health
Examples e.g. malaria parasite.
4. Fungi
Structure & Characteristics
Multicellular heterotrophic eukaryotes that obtain nutrition by absorption; hyphae (coenocytic/septate), mycelium, unicellular=yeasts.
Classification
Four main phyla: Chytridiomycota (flagellate gametes/spores), Zygomycota, Basidiomycota (basidium), Ascomycota (ascus); some classifications split the Chytridiomycota and Zygomycota (e.g. Glomeromycota formerly part of Zygomycota).
Life Cycles
Sexual key points – mating types, haploid hyphae, plasmogamy, heterokaryotic/dikaryotic hyphae, karyogamy, zygote (2n), meiosis & spore formation; characteristics of each group – flagellate gametes & spores in Chytridiomycota, zygosporangium in Zygomycota, ascocarp & asci in Ascomycota, basidiocarp & basidia in Basidiomycota; sporangia & conidia represent asexual reproduction.
Nutritional Diversity & Ecology
Decomposers (saprophytes), importance in breaking down wood/lignin, enzymes lignin peroxidase & cellulases; mutualists (mycorrhizae, lichens, insects), parasites.
Mycorrhizae (Fungus & Plant Roots)
Two types: ectomycorrhizal fungi (EMF) (mainly Basidiomycota) & arbuscular mycorrhizal fungi (AMF) (mainly involve Glomeromycota) – make nutrients (N and/or P) in soil available to plant roots.
Lichen
Mutualistic association between fungus (Acomycota) & unicellular photosynthetic organism; may also be mutualistic with insects.
Parasites
Many fungal diseases of plants & animals, human diseases e.g. tinea (athletes’ foot, ringworm).
Human Use
Ethanol fermentation, bread making (CO2), yeasts as model organism, edible mushrooms, sources of antibiotics (e.g. penicillin from Penicillium) & other drugs.
5. Land Plants
[Details of algae may be omitted but note closest relatives of land plants are a group of green algae (e.g. Coleochaetophyceae or Charophyceae) within the Eukaryote lineage Bikonta.]
Features Shared by Green Algae & Land Plants
Chlorophyll a & b, cellulose cell walls, starch storage.
Characteristics of Land Plants & Adaptations for Life on Land
E.g. cuticle, gametes form within gametangia, embryo retained within female structures & nourished, pores/stomata, vascular tissue in most plants.
Pros & Cons of Living on Water/Land
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Alternation of Generations
Multicellular haploid stage (gametophyte, produces gametes) alternates with multicellular diploid stage (sporophyte, produces spores); trend in plant evolution towards a sporophyte-dominated life cycle.
Land Plants – Three Main Categories
Nonvascular plants (e.g. mosses & liverworts), Seedless vascular plants (e.g. ferns), Seed plants (includes Gymnosperms e.g. pine & Angiosperms flowering plants).
Life Cycles of Each Type and Essential Features of Life Cycles
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Nonvascular Plants & Seedless Vascular Plants are Homosporous
One type of spore.
Seed Plants are Heterosporous
Two kinds of spores (megaspores & microspores): Megaspore mother cell → megaspore (only one survives) → female gametophyte. Microspore mother cell →microspore →male gametophyte (=pollen).
Ovule (Initially Megasporangium), Seed (Embryo, Food Store & Seed Coat)
Pollination, fertilization, dispersal.
Gymnosperms (Conifers etc): Pine Life Cycle & Angiosperms (Flowering Plants): Flowering Plant Life Cycle
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Angiosperms (Monocots & Dicots)
Structure of flower & functions of parts, double fertilization – zygote & endosperm, flower to fruit (ovary → fruit, ovule → seed), modes of seed dispersal.
Monocots vs. Dicots
E.g. leaf venation, arrangement of vascular tissue in stem, flower parts.
6. Plant Form and Function
Functions of Shoot System & Root Systems & Relation to Plant Lifestyle/Function (Esp. Photosynthesis)
Shoot – leaf variation, stem adaptations; root – variations/adaptations; also phenotypic plasticity.
Three Types of Plant Tissues & Their Functions
Dermal/epidermis (& waxy cuticle), ground tissue (parenchyma, collenchyma, sclerenchyma) & vascular tissue: xylem (tracheids & vessel elements; dead) & phloem (sieve tube members & companion cells).
Main Ground Tissue Parenchyma
May be specialized for photosynthesis (leaves), storage of starch (roots); also collenchyma & sclerenchyma.
Meristem Tissue & Plant Growth
Apical meristem (tips) & primary meristem (protoderm, ground meristem, procambium).
Primary Growth (Increase in Length) vs. Secondary Growth (Increase in Width/Girth)
Lateral meristem = cambium (vascular cambium & cork cambium).
Secondary Growth & Wood Formation
Annual growth rings; wood is mostly secondary xylem.
7. Water & Sugar Transport in Plants
Movement of Water (In Xylem) & Translocation of Sugars (In Phloem)
Water potential = pressure potential + solute potential: Ψ = Ψp + Ψs; pure water has high water potential, solutes decrease water potential.
Water flows from an area of high water potential to an area of low water potential.
Movement of Water
Root pressure, capillary action, cohesion-tension theory: transpirational pull, gradient of water potential from soil/root (high) to leaves/air (low).
Root Pressure, Guttation, Role of Endodermis & Casparian Strip
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Photosynthesis-Transpiration Compromise, Adaptation to Reduce Water Loss
Structural & physiological (e.g. CAM & C4).
Translocation of Sugars
Pressure-flow hypothesis; sources & sinks; proton pumps (active transport) & sugar loading at source phloem, water flows from xylem to phloem, high pressure, sugar unloading at sink, water outflow from phloem to xylem, low pressure; sugar unloading in sinks due to passive diffusion – consumption or storage (due to active processes in sink cells using/storing sugar).
8. Plant Nutrition
What is a Nutrient? What Nutrients Do Plants Need?
Essential nutrients & deficiency symptoms; C, H, O; other nutrients.
Soil
Source of water & nutrient elements (as ions); soil formation; soil texture (particle size) & soil composition (nutrients).
Negative Ions (Anions) & Positive Ions (Cations)
Difference in behavior in soil (+ ions bind to clay & organic matter, so less available); leaching by rain.
Effect of pH on Mineral Ion Availability
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Root Structure
Root hairs increase surface area for absorption, root hair plasma membrane – phospholipid bilayer.
Proton Pumps Pump H+ Ions Out, Electrochemical Gradient (Concentration & Charge Inside/Outside Cell)
Positive ions (cations) enter via channels, negative ions (anions) use proton-dependent cotransporters.
Mycorrhizae (Plant Root/Fungi Mutualism)
EMF & nitrogen, AMF & phosphorus.
Salt Exclusion (E.g. in Salty Soils or Soils with High Metal Ions)
Passive exclusion (e.g. have fewer channels) or active exclusion (metallothioneins; proton pumps & antiporters in tonoplast (central vacuole stores harmful ions).
Nitrogen Fixation (N2 → 2NH3)
Rhizobium bacteria in root nodules of legumes (pea/bean family), role of flavonoids.
Nutritional Adaptations – Epiphytes
Only attached to host plant, don’t derive nutrition from host.
Parasitic Plants (Get at Least Some Nutrients from Host Plant)
E.g. mistletoe, dodder (Cuscuta).
Carnivorous Plants (Adapted to Living in Nitrogen-Deficient Soil of Bogs, Get Nitrogen from Animal Protein [Carnivorous Plants Photosynthesize Just Like Other Plants, They Are Not Heterotrophic!])
E.g. Venus’s flytrap, sundew, pitcher plants.
9. Sensory Systems in Plants
Need to Detect and Respond to Stimuli; General Pattern of Such Information Processing
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Types of Stimuli
E.g. light (blue, red/far red), gravity, touch, attack by pathogens, herbivorous insects, etc.
Phototropism (Light-Directional Growth)
Stimulus blue light, receptors phototropins (membrane proteins). Shoots are positively phototropic, roots negatively phototropic. Role of auxin in cell elongation on shade side of shoot (auxin redistribution) – acid growth hypothesis – auxin binds to membrane protein (auxin-binding protein) causing increase of proton-pumping which lowers pH which triggers expansins (enzymes) to loosen cellulose cell wall structure, proton pumping also leads to inflow of +ve ions into cell followed by water (osmosis), causes cell elongation.
Photoperiodism (Day/Night Length Dependence, E.g. Flowering at Certain Times of Year) & Seed Germination
Both involve perceiving red light (means sufficient light) & far-red light (means shade/dark): receptor molecule phytochrome has two shapes that are photoreversible (Pr ↔ Pfr) & functions as a red/far-red activated ‘switch’- each shape is named for the wavelength it absorbs but light of that wavelength will cause it to switch to the other.
Gravitropism (Gravity-Directional Growth: Roots Positively Gravitropic)
Sensed in root cap cells, amyloplasts & statolith hypothesis.
Touch/Friction Response (Thigmotropism)
Involve electrical signaling – resting membrane potential due to proton pumps, stimulus causes depolarization, action potential; e.g. Venus flytrap – trigger hairs, action potential & trap closing mechanism.
10. Plant Chemical Signals
Plant Hormones
Chemical signals released from one area, transported to another & bind to receptors on target cells to cause a response.
Auxin (Indole Acetic Acid)
Made in shoot apical meristem & young leaves, transported down (polar transport) – many effects including role in phototropism (see Lecture 12). Auxin & apical dominance (inhibition of lateral bud growth) – so cutting off shoot tip causes lateral bud growth (“bushy”).
Cytokinins
Promote cell division by regulating cell cycle, with cytokinins present cells don’t stop at G2 checkpoint & move to M phase e.g. zeatin.
Gibberellins (E.g. Gibberellic Acid GA)
Stimulates growth & development & ABA (abscisic acid) inhibits growth & development (promotes dormancy), role of GA in seed germination – e.g. in corn, seed absorbs water causing release of GA from embryo, GA stimulates aleurone layer to release α-amylase which digests starch store for seed germination; ABA inhibits this.
ABA & Stomata Closing
Dry conditions in soil detected by roots, ABA acts as messenger between roots & leaves – stomata close. Stomata open in response to blue light, close in response to ABA – both involve changes in H+ pumping & osmosis – turgidity of guard cells (more turgid stomata open, less turgid stomata close).
Brassinosteroids (BRs)
Steroid hormones that promote growth & regulate size; more hydrophilic than animal steroid hormones so cannot pass through plasma membrane & need cell surface receptor.
Ethylene & Senescence (Aging)
Including fruit ripening, leaf abscission (leaf fall), etc; for leaf abscission decrease in auxin from leaf makes abscission zone more sensitive to ethylene (Note – unlike most other plant hormones ethylene is a gas).
Plant Protection Against Pathogens & Herbivore Insects
Pathogens
Hypersensitive response (HR): infected cells commit suicide, protects rest of plant, HR also causes systemic acquired resistance (SAR) gives long-term protection.
Insect Herbivores
Proteinase inhibitors – make animals that eat them “sick”, so herbivores learn to avoid such plants; wound response hormone systemin released by damaged tissue travels to other parts & stimulates proteinase inhibitor production via jasmonic acid.
Pheromones
Released by plants under attack by caterpillars attract parasitoid wasps that lay eggs in caterpillars, so plants get protection (“The enemy of my enemy is my friend!”).
11. Plant Reproduction
Alternation of Generations
Life cycle with haploid gamete-producing gametophyte alternating with diploid spore-producing sporophyte, plus variation in main plant groups (nonvascular, seedless vascular, seed plants incl. flowering plants).
Asexual Reproduction (E.g. Rhizomes, Corms, Plantlets, Apomixis, Cuttings) vs. Sexual Reproduction
Advantages & disadvantages of asexual/sexual reproduction.
Sexual Reproduction in Angiosperms, Parts of Flower & Their Function
(See details), meaning of perfect & imperfect with reference to flowers; meaning of monoecious & dioecious (in plants).
Ovule (In Ovary)
Initially represents megasporangium within which megasporocyte (megaspore mother cell) (2n) undergoes meiosis → four megaspores (only one survives), surviving megaspore (n) undergoes mitosis → female gametophyte (embryo sac) – seven cells (three cells at each end, one large central cell with two nuclei).
Anther – Pollen Sac Represents Microsporangium
Inside which microsporocytes (microspore mother cells) (2n) undergo meiosis → four microspores, each microspore undergoes mitosis → male gametophyte (pollen grain with tube cell & generative cell plus resistant outer coat of sporopollenin), generative cell later divides to give two sperm nuclei.
Pollination
Cross pollination & out-crossing vs. self-pollination & selfing (pros & cons); methods to reduce selfing – temporal avoidance (stamens & carpels mature at different times), spatial avoidance (stamens & carpels far apart), molecular matching (pollen landing on stigma of same plant won’t work).
Methods of Pollination & Pollination Syndromes
Wind, animals (e.g. insects); mutualism & co-evolution of plants & animal pollinators e.g. pollinators get nectar from plant.
Fertilization
Double fertilization in angiosperms, zygote (2n) & endosperm (3n) (nutritive tissue unique to angiosperms).
Seed with Embryo, Food Store (Endosperm/Cotyledons) & Seed Coat
Formation of three embryonic tissues, main features in embryogenesis, shoot-root axis.
Function of Fruit
Protection of seeds & dispersal of seeds.
Ovary Wall is Pericarp of Fruit, Surrounds Seed
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Methods of Dispersal
Wind, animals (edible or attached to fur), water.
Dormancy & Seed Germination
Dormancy broken by conditions favorable for germination.
12. Animals (Metazoa)
Phylogenetic Position & Key Features
In Opisthokonta lineage within Eukarya, close to Choanoflagellates; multicellular heterotrophic eukaryotes with extracellular matrix (ECM), obtain nutrition by ingestion, move by muscle tissue and have nerve cells with synaptic transmission (some of these don’t apply to Porifera/sponges).
Key Innovations
Symmetry (asymmetry, radial, bilateral); tissue layers (none, diploblastic, triploblastic); body cavity (coelomate, acoelomate, pseudocoelomate); early development in bilaterians (protostome, deuterostome); nervous systems (none, nerve net, centralized nervous system); segmentation (e.g. in Annelida & Arthropoda); note triploblastic animals basically bilaterally symmetrical, bilateral symmetry correlated with central nervous system & cephalization (tendency to develop a head).
Feeding Diversity
Detrivores, herbivores & carnivores, omnivores; predators vs. parasites; suspension (filter), deposit, fluid & mass feeders.
Animal Phyla & Their Relationships (Phylogeny) Based on Molecular Evidence
According to the current molecular phylogeny most bilaterally symmetrical triploblastic animals can be grouped into two clades, Protostomia and Deuterostomia.
Protostomes Represent Two Major Clades
Lophotrochozoa (e.g. Platyhelminthes, Annelida, Mollusca) and Ecdysozoa (e.g. Nematoda, Arthropoda). One morphological feature that unites Nematodes & Arthropods is the tough cuticle or exoskeleton that needs to be shed by molting for growth.
Deuterostomes Include the Phyla Echinodermata and Chordata
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Review Basic Features of Each Phylum and Position on Morphological and Molecular Phylogenetic Trees
See separate handout on animal phyla given in lab.
List of Animal Phyla You Should Be Familiar With
Porifera, Cnidaria, Platyhelminthes, Annelida, Mollusca, Nematoda, Arthropoda (largest animal phylum), Echinodermata, Chordata. Within Chordata three subphyla – Cephalochordata, Urochordata, Vertebrata (Craniata) (see Powerpoint for main points about each phylum).
Vertebrata
Primitive vertebrates lack jaws (e.g. lamprey), jaws evolved from anterior gill arches & gave rise to two main groups (all have paired fins): cartilaginous fish (e.g. sharks) & bony fish. Bony fish have swim bladder or “lung” & evolved into two main groups: ray-finned fish (most diverse today) & lobe-finned fish (coelacanth, lung fish & ancestors of land vertebrates); land vertebrates Tetrapoda (four-legged), one lineage evolved dehydration-proof amniotic egg – Amniotes. Amniotes gave rise to two main lineages – reptiles (plus birds) & mammals.