Abiogenesis and Early life

Abiogenesis and Early Life

• Abiogenesis is the process by which life arose from non-living matter.
• The first cell-like structures were aggregations of molecules called proteinoid microspheres.
• Stromatolites are fossilized microbial mats of microorganisms and trapped sediment.
• Heterotrophs obtain energy by consuming organic compounds from external sources.
• Autotrophs make their own food, with photosynthesis being the most successful method.
• Photosynthesis involves splitting water molecules and releasing oxygen.
• Oxygen formed the ozone layer, protecting plants, and enabled respiration.
• Aerobic organisms require oxygen, while anaerobic organisms do not.
• Prokaryotic cells are simple, lacking a nuclear envelope and complex chromosomes.
• Eukaryotic cells have a nuclear envelope.

Evolution of Eukaryotes: Endosymbiotic Theory

• Eukaryotes evolved through endosymbiosis, where an ancestral prokaryote engulfed other prokaryotes.
• Evidence includes similarities between mitochondria/chloroplasts and prokaryotes in size, shape, DNA structure, membranes, and reproduction by binary fission.
• Mitochondria and chloroplasts have their own circular DNA similar to prokaryotes.
• They have double membranes; the outer one has similarities to eukaryotic cell membranes.
• They reproduce via binary fission similar to prokaryotes, unlike eukaryotic cells that reproduce via mitosis.

Colonization of Land by Plants

• Ocean shores offered richer nutrients and biodiversity.
• Multicellular photosynthetic organisms developed organs to colonize land.
• Roots anchor plants and collect water and nutrients.
• Stems support photosynthetic organs.
• Leaves conduct most of the photosynthesis.

Adaptations for Terrestrial Life

• Epidermis are outer 'skin' cells with thick walls.
• Cuticle is a wax layer preventing water loss; stomata allow for gas exchange.
• Stomata are pores surrounded by guard cells.
• Xylem transports water upward, while phloem transports organic molecules throughout the plant.
• Meristems are embryonic tissues capable of indefinite cell division.
• Apical meristems extend the plant body through primary growth.
• Secondary growth thickens stems and roots via the vascular cambium and cork cambium.
• Plants absorb water from soil and release it into the air.
• Plant roots increase soil porosity, aiding water infiltration and animal burrowing further enhances this.
• Abiotic earth would have little or no soil.
• Photosynthesis requires water, light, CO2, oxygen, and minerals.
• Annuals have a one-year lifespan related to photosynthesis.
• Perennials have thickened, cork-covered stems with a cuticle-covered epidermis.

Plant Secondary Compounds

• Primary metabolites are essential compounds found in all plant cells, like sugars, amino acids, proteins, and nucleic acids.
• Secondary compounds facilitate plant adaptation to their environment and have restricted distribution.
• These compounds involved in seed germination control, allelopathy (chemical inhibition), herbivore defense, pathogen defense and symbiosis regulation.
• Alkaloids are alkaline nitrogenous compounds with pharmacological effects.
• Terpenoids are made of isoprene units, are fat-soluble, and can be defensive or allelopathic.
• Phenolics include flavonoids, tannins, lignins, and salicylic acid (aspirin).
• Antimicrobial hypothesis: Positive correlation exists between average annual temperatures and the use of strongly inhibitory spices in recipes.

Plant Cell Characteristics

• Plant cells are eukaryotic with cell walls, chloroplasts, and vacuoles.
• Plastids, cell walls, and vacuoles characterize plant cells.
• Plastids include chloroplasts, chromoplasts, and leucoplasts with a double membrane.
• Chloroplasts are sites of photosynthesis with chlorophyll and carotenoids with 40-50 chloroplasts per mesophyll leaf cell.
• Chloroplasts are semi-autonomous with circular DNA in nucleoids.
• They use light energy and CO2 to form carbohydrates and are also involved in amino acid and fatty acid synthesis
• In bright light, chloroplasts move to cell walls minimizing light absorption.
• Photosystem I and ATP synthase are mainly in the stroma thylakoids.
• Photosystem II is mainly in the grana thylakoids.
• Chromoplasts contain pigments other than chlorophyll that synthesize and retain carotenoids giving yellow/orange/red colors and may aid in pollination and seed dispersal.
• Light reactions occur in the thylakoids.
• Calvin Cycle ('dark reaction') occurs in the stroma.

Photosynthesis

• Photosynthetically Active Radiation (PAR) is radiation between 400-700 nm (visible light) being 45% of total solar radiation and measured as photon flux density.
• Chlorophyll is the primary photosynthetic pigment and accessory pigments broaden light absorption.
• Chlorophyll a is present in all photosynthetic eukaryotes and cyanobacteria, making up 75% of total chlorophyll in most plants.
• Chlorophyll and pigments are in thylakoid membranes in photosystems which include an antenna complex and a reaction center with chlorophyll.
• PSI has P700 chlorophyll at the reaction center.
• PSII has P680 chlorophyll at the reaction center.
• PSII and PSI are connected by an electron transport chain (ETC).
• PS II in the grana thylakoids, PS I is in the stroma thylakoids and at grana edges.
• PSI can operate independently, generating only ATP via cyclic photophosphorylation.

Cyclic vs Non-Cyclic Photophosphorylation

• Non-cyclical photophosphorylation involves P680 electrons being occupied by P700 without reverting to P680.
• Cyclic photophosphorylation uses chlorophyll P700 and generates ATP.
• Light-dependent reactions convert light energy and split water into ATP, NADPH, H, and oxygen in the grana.
• Carbon-fixation reactions convert CO2 and H to sugar in the stroma using ATP and NADPH from the light-dependent reactions.
• Calvin cycle (C3 photosynthesis) begins and ends with ribulose bisphosphate (RuBP).
• RuBP carboxylase/oxygenase or rubisco catalyzes the first reaction and can act as both a carboxylase and oxygenase.
• Plants open stomata to acquire CO2, causing increased water loss.
• Closing stomata under dry conditions causes issues for photosynthesis.

C3, C4, and CAM Plants

• C3 plants perform photosynthesis only in mesophyll cells, but close stomata in hot, dry weather.
• C3 plants thrive in moderate temperatures with sufficient water.
• C4 plants have an extra set of reactions to concentrate CO2, requiring spatial separation in mesophyll and bundle sheath cells.
• C4 photosynthesis is more efficient in hot, dry environments.
• CAM plants (Crassulacean Acid Metabolism) minimize water loss by opening stomata at night.
• CAM plants perform reactions in mesophyll cells only at night to avoid photorespiration.

Systematics and Taxonomy

• Systematics studies biological diversity and its evolutionary history.
• Taxonomy classifies and names species.
• Linnaeus created Latin nomenclature.
• Taxonomic classification is based on shared morphological traits.
• Binomial nomenclature was introduced by Carl Linnaeus in 1753 using a Latin sentence limited to 12 words
• KPCOFGS: kingdom, phylum, class, order, family, genus, species
• Linnaeus recognized 3 kingdoms: plant, animal, and mineral.
• Today, there are 5 kingdoms: animal, plant, fungi, protist, and monera.

Phylogeny and Cladistics

• Phylogeny studies relationships among organisms and evolutionary development.
• Phylogenetic tree diagrams depict evolutionary relationships with branching order and branch length.
• Cladograms represent evolutionary relationships and common ancestors but do not consider time.
• A monophyletic clade includes a common ancestor and all its descendants.
• Polyphyletic taxa include members from multiple ancestral lines.
• Paraphyletic taxa include a common ancestor but not all descendants.
• Cladistics classifies organisms via shared traits (synapomorphies) and ignores evolutionary time to identify monophyletic groups or clades.
• Character states of an outgroup are ancestral; those present in the ingroup but absent in outgroups are derived.
• Parsimony helps to create cladograms reflecting shared characteristics.

Phylogenetics and Domains of Life

• Phylogenetics is driven by genomics today.
• Nucleic acid sequencing underpins three domains of life: Archaea, Bacteria, and Eukarya.
• Archaea and Eukarya share a common evolutionary pathway independent of Bacteria.
• True Bacteria differ from ancient bacteria based on ribosomal RNA sequencing.
• Systematists classified all living organisms into Animal or Plant Kingdoms up to the 1970s.
• Eukaryotes, Bacteria and Archaea domains are based on microscopy & biochemistry and sequencing small subunit ribosomal RNAs
• There are fundamental differences between Prokaryotes and Eukaryotes and also between the two distinct lines of Prokaryotes - Bacteria and Archaea
• Bacteria lack chloroplasts, their thylakoids are not membrane-bound, and they do not have their own DNA.
• Archea are single-cell prokaryotes that generally live in anaerobic environments.
• Eukarya show complexity: chloroplasts and nucleus and size (larger) compared to the previous two cells.

Eukaryotic Kingdoms and Life Cycles

• There are 4 eukaryotic kingdoms with less clear relationships.
• Animalia are multicellular ingesters and Plantae are multicellular photosynthesizers.
• Fungi are multicellular, non-motile absorbers and Protista are a heterogeneous, paraphyletic group.
• The first eukaryotes were probably haploid (n) and asexual.
• Haploid, diploid and alternation of generations life cycle are common.

Evolution and Natural Selection

• Charles Darwin proposed natural selection, and that all species have descended from a common ancestor
• Natural selection occurs similar to artificial selection (the latter is used in crop domestication).
• Natural selection comes from the natural environment acting on individuals, resulting in different offspring numbers.
• Fitness is the number of surviving offspring of a genotype compared to others in a population.
• Individuals with the highest fitness are best adapted and reproduce more, increasing allele numbers.
• Population is a localized group of individuals and species can interbreed in nature.
• Gene pool is the total alleles of all genes of all individuals.
• Usually there are at least two alleles for a given gene, present in different frequencies.
• Major patterns in speciation: phyletic gradualism and punctuated equilibria.
• Phyletic gradualism involved slow, constant change such that species characteristics change significantly.
• Punctuated equilibria has branching events with morphological variation and stasis.
• Macroevolution is the change of one species into an entirely new species encompassing grand trends such as the origin of mammals where as microevolution a change in allele frequencies over short time.

Evolutionary Mechanisms

• Genetic drift is random allele frequency fluctuations.
• Bottleneck effect: A sudden population reduction can lead to loss of alleles.
• Founder effect: A new population with limited diversity is established by a few individuals.
• Gene flow: Exchange of genes between populations, reducing differences.
• Mutation: Change in DNA sequence that can alter the gene pool
• Non-random mating is mate choice based on traits
• Inbreeding occurs when nearby individuals mate causing genotype frequency changes.
• Assortative mating occurs when individuals select mates that look like themselves.
• Natural selection is differential reproduction success leading to differential allele success.
• Adaptation is the process of adjusting traits to better match their environment.

Bryophytes: Non-Vascular Plants

• Bryophytes include Marchantiophyta (liverworts), Bryophyta (mosses), and Anthocerotophyta (hornworts).
• They lack flowers and seeds, and reproduce via spores.
• They grow in shady, moist environments and are short in stature.
• They lack xylem and phloem and have non-lignified cell walls.
• They have heteromorphic generations: gametophyte (haploid) and sporophyte (diploid).
• The gametophyte is larger and free-living; the sporophyte is smaller and dependent.
• Antheridia (male) and archegonia (female) reside on the gametophyte, surrounded by a sterile jacket layer.
• The zygote and sporophyte are retained within the female gametophyte.

Bryophyte Sporophyte and Spores

• The sporophyte is anchored to the gametophyte by the foot.
• A seta supports the capsule (sporangium) where meiosis occurs to produce spores.
• A multicellular sporophyte increases the number of meioses and spores.
• Spores are protected by sporopollenin a durable polymer.
• Sporangia have a sterile jacket layer and sporogenous tissue.
• Some bryophytes have hadrom for water transport with hydroids, leptoids for food conduction and parenchyma for photosynthesis.
• Rhizoids anchor the plant but do not absorb water or nutrients.
• Mosses have multicellular rhizoids.
• Liverworts/Hornworts have unicellular rhizoids.
• In bryophytes that gametophyte is the larger, free-living stage while,the sporophyte is dependent on the gametophyte for nutrition.
• There are alternating generations with the gametophyte being dominant and the sporophyte dependent.
• Meiosis in the sporophyte produces haploid meiospores that grow into the gametophyte.

Vascular Plants - Evolution and Features

• Vascular tissue allowed plants to solve the challenge of water and food transport.
• Cooksonia, a vascular plant from 408–414 million years ago, had a branching, leafless aerial stem and stems ended in sporangia (spore-producing structures), marking one of the first vascular plant forms.
• Vascular plants have a sporophyte dominant life cycle.
• Lignin allowed plants to grow tall.
• Apical meristems allow for branching and multiple sporangia.

Vascular Plants - Lifecycle and Spores

• Selaginella has a sporophyte-dominant life stage.
• Water is necessary for sperm motility.
• Homosporous plants produce one spore type that develops into a bisexual gametophyte.
• Heterosporous plants produce microspores (male) and megaspores (female).
• Sporophylls are specialized leaves containing spore-producing structures.
• Eusporangia develop from a group of initial cells and produce many spores.
• Leptosporangia Develop from a single initial cell and produce a small number of spores leading to dehiscence via an annulus.

Angiosperm Reproduction - Flowers and Pollen

• Carpel includes stigma, style and ovary and the gynoecium is one or more carpels.
• A complete flower has a gynoecium and androecium.
• An incomplete flower is carpellate (female) or staminate (male).
• A monoecious plant has male and female flowers on the same plant while a dioecious plant has them on separate plants.
• Microsporogenesis produces microspores and microgametogenesis produces pollen grain (microgametophyte).
• Pollen consists of a vegetative cell (tube cell) and a generative cell (two sperm cells).
• Tapetum provides nutrition to microspores.
• Megasporogenesis produces megaspores and megagametogenesis forms the megagametophyte (female gametophyte consisting of two polar nuclei, one egg cell, three synergids, three antipodal cells.
• Pollination is pollen grain germination on the stigma and formation of a pollen tube to the ovary.
• One sperm cell fertilizes the egg cell, making the zygote, and the second sperm cell fuses with the polar nuclei in the embryo sac to form triploid primary endosperm nucleus.
• Endosperm provides food for the developing embryo, forming a vital nutrient source during seed development.

Plant Development - Embryogenesis and Germination

• Meristems allow for continuous plant growth.
• Plants can initiate post-embryonic organ formation with differential resources.
• Seed dormancy halts development due to impermeable seed coat or chemical inhibition and that ensures survival, germination under optimal conditions and long-distance dispersal.
• During germination, seeds absorb water via imbibition, enzymes are activated, and then the radicle emerges.
• In monocots, the coleoptile protects the shoot.
• In eudicots, the cotyledons protect the growing point.

Plant Development - Factors and Hormones

• Plants sense and respond to day length.
• Photoreceptors and hormones mediate responses.
• Development is regulated by the plant’s genome encoding essential proteins and enzymes
• Hormones act at low concentrations.
• Auxins promote cell elongation, phototropism, and gravitropism.
• Gibberellins control germination, stem elongation, and flowering while stimulating fruit development.
• Arabidopsis thaliana is a model organism for studying signal transduction pathways to indentify the gene.

Plant Hormones - Types and Interactions

• Hormones regulate physiological processes in plants through both stimulatory and inhibitory activities.
• Auxin regulates growth, cytokinin regulates cell division, and ethylene regulates fruit ripening.
• Gibberellins regulate seed germination and abscisic acid regulates stress response.
• Brassinosteroids promote cell elongation and division.
• Auxin promotes cell elongation and apical dominance, and is involved in phototropism and gravitropism.
• Cytokinin promotes cell division and delays leaf senescence.
• Ethylene accelerates fruit ripening and leaf abscission.
• Abscisic acid promotes stress responses and seed dormancy.
• Gibberellins stimulate seed germination and fruit development.

Plant Tissues - Meristems and Systems

• Meristems are populations of cells that retain the potential to divide.
• Primary meristems form the protoderm, procambium, and ground meristem.
• Secondary meristems are responsible for lateral growth.
• There are three tissue systems these are the dermal tissue that protects, the vascular tissue that transports and the ground tissue that performs photosynthesis.

Plant Responses - Environmental Cues

• Biological clocks synchronize processes with the light-dark cycle impacting, growth/ development, and metabolic processes.
• Photoperiodism is response to day and night length.
• Phytochrome exists in PR (red light) and PFR (far-red light) forms.
• Short-day plants flower when day length is shorter, and long-day plants flower when day length is longer.
• Shade-avoidance response entails growth taller to avoid shade responding to low red-to-far-red (R:FR) light ratio signaling
• Vernalization requires cold exposure for flowering in the spring.
• Heat exchange involves radiation, conduction, convection, and latent heat transfer.
• Temperature affects plant growth, as plants in hot climates use transpiration to regulate; alpine plants hug ground to avoid heat loss due to winds.
• Energy input and output balance impacts plant temperature and survival.

Plant Nutrition - Essential Nutrients

• Essential elements are necessary for the plant life cycle with common macro (carbon, oxygen and nitrogen) and micro nutrients (chlorine, copper, iron etc).
• Soil has layers with topsoil containing minerals, organisms, and humus.
• Soil texture are classified into sand, silt and clay.
• After rainfall, smaller particles retain water as field capacity.
• Cations adhere to negatively charged soil particles.
• Humus helps retain water and improves soil's ability to exchange cations providing a mineral nutrient reservoir from biotic relationships (mutualistic) between fungi/ bacteria etc.
• Deficiency symptoms depend on nutrient mobility where as common deficiencies include nitrogen, potassium, and phosphorus.

Plant Nutrition - Nitrogen Cycle

• Nitrogen fixation is the conversion of nitrogen to ammonia from atmospheric N2, essential for plants.
• Nitrification converts ammonia to nitrate.
• Plants absorb nitrogen as nitrate and ammonium.
• Symbiotic nitrogen fixation: rhizobium bacteria in legume root nodules fix nitrogen in exchange for sugars.
• Crop rotation with legumes restores soil nitrogen.
• Soil bacteria play a critical role in nutrient cycling, especially in the nitrogen cycle.
• Plants rely on these bacteria to break down organic compounds or fix nitrogen from the atmosphere into forms that they can absorb.

Plant Transport - Water

• Water makes up a significant portion of a plant’s mass.
• Water is the medium for molecular movement and biochemical reactions.
• Transpiration is water evaporation from plant parts through stomata releasing cooling effects and nutrient uptake from soil.
• Water evaporates from both non-living and living plant tissues however transpiration involves that of living tissue.
• Root hairs help water uptake occurring through osmosis.
• Water continues through cortex to endodermis and enters xylem.

Plant Transport - Xylem and Water Potential

• Xylem has dead, open tubes and forms continuous pathways from roots to leaves transporting most of water while walls are reinforced with lignin.
• Capillary action occurs which allows to move water up against gravity due to surface tension and related properties.
• The cohesion-tension mechanism includes transpiration creating tension that pulls water up from roots.
• Ψ is water potential which is higher to lower and solute potential (ψS) and pressure potential (ψP influences the water potential.
• Gradient has water moving relying on a gradient, from soil through roots, stems and leaves, to the atmosphere.
• Root pressure helps push water up as it occurs when roots absorb ions, creating positive hydrostatic pressure but less significant than transpiration.

Plant Transport - Transpiration

• Humidity causes lower humidity increases transpiration.
• Temperature causes Higher temperatures increase transpiration rates.
• Wind Velocity causes Increased wind speeds promote faster evaporation.
• Light causes Higher atmospheric pressure reduces the rate of transpiration.
• Up to 98% of water absorbed by the plant is lost through transpiration.
• Transpiration is passive requiring no ATP as the energy comes from water potential difference between soil and atmosphere.

Agriculture - History

• Neolithic Revolution around 12,000 years ago saw humans transition to settled farming and led to a rapid increase in population.
• Archaeological finds, such as fossils and copprolites show the shift from gather lifestyles to cultivation.
• Coprolites (fossilized dung), soil pollen, and other remains provide evidence of early plant domestication.
• The need for food storage due food gathering requirements led to basket-making and pottery.
• The discovery of metal tools around 4000 BC enhanced agricultural efficiency
• The annual flooding of the Nile deposited rich silt on fields and provides the region of ancient Egypt with naturally fertile land.
• Early agriculture led to village growth and a diverse social stratus and hierarchies.
• Agricultural practices have led to increased soil erosion and hypoxic zones for marine life.

Agriculture - GMOs

• Genetically Modified Organisms (GMOs) have altered genes imparting desirable traits
• There are potential risks such gene flow/ resistance/ unintended effects to GMOs however GMOs have the promise of disease and pest resistance.
• Selective breeding involves traditional crosses, strategic crosses and culminating in the green revolution of today.
• Since 1973 recombinant DNA allows for the insertion of genes.
• Traditional Plant Breeding and genetic engineering allows specific gene manipulation to achieve desired traits, such as pest resistance or increased nutritional value.
• Insect Tolerance, Disease Resistance, and Tolerance Stresses such as lack of water have allowed more diverse climates to engage in agricultural business.
• Improved Storage qualities include nutritional improvements like Golden Rice.
• Bt Corn produces insecticidal proteins from Bacillus thuringiensis which reducing the need for chemical insecticides.
• Roundup Ready Crops which are resistant to glyphosate, a widely used herbicide led to reduce losses, better adaptability to climate change.
• Golden Rice was designed to provide a reliable source of vitamin A where vitamin A deficiency is common.

Climate Change Basics

• There were Canada temperature increases from 1948 to 2022.
• Global temperatures have shown significant rise since late 1800s.
• Long-term climate change occurs over millions of years and short-term change occurs over thousands of years.
• Changes are accelerated by human based on atmospheric gas increases.
• A Pleistocene Ice Age had massive ice sheets about 20,000 years ago.
• Post glaciation boreal forests and tundra expanded southward in North America where as elevational shifts are also shown.
• Species migration and competition can be expected however plants can't migrate quickly enough compared to animals and humans pose barriers.

Climate Change - Effects and Adaptation

• Extinction can effect the food chain through both mortality of plants and organisms relying of those species.
• Adaptation can be seen in faster reproduction with higher rates of change.
• Evolutionary rescue concept occurs when genetic adaptation saves a population reducing genetic variation.
• Extinction risks occurs when plants cannot adapt or move.
• Extirpation refers to local extinction.
• The Himalayan plant studies show specie movement to higher elevations due temperature changes which can impact species evenness.
• Phenology records the timing of life cycle events with plant phenology for climate indicators showing shifts based on warmer temperatures.
• Mismatches with pollinators and migration cause reduced reproduction and synchrony.