Biodiversity, Phylogeny, and Tree of Life (Ch 1-10 Biol 211) PDF

Biodiversity, Phylogeny, and Tree of Life ​ What is biological diversity? ​ How do biologists classify and name organisms? ​ How are phylogenies used to show evolutionary relationships ​ There is a large variety of life on earth ​ Biodiversity:...

Biodiversity, Phylogeny, and Tree of Life ​ What is biological diversity? ​ How do biologists classify and name organisms? ​ How are phylogenies used to show evolutionary relationships ​ There is a large variety of life on earth ​ Biodiversity: The variety of life in all of its forms, levels, and combinations including ecosystem diversity, species diversity, and genetic diversity. ​ Biodiversities encompass microorganisms, plants, animals, and entire ecosystems like forests, oceans, and deserts. ​ It is shaped by evolution, climate, and geographical conditions ​ Importance of Biodiversity: ​ Ecosystem balance: maintains food chains, nutrient cycles, and ecological processes like pollination and water purification. ​ Human resources: provides food, medicine, and raw materials ​ Supports adaptation: shows how species evolve uniquely to survive in diverse environments. ​ Variety of Life: ​ Diverse habitats: species thrive in rainforests, oceans, deserts, and other environments, each requiring unique adaptations. ​ Rare and unique species: many species remain undiscovered, contributing to Earth’s vast biological richness ​ Current state: scientists estimate about 8.7 million species exist, but many are yet to be studied or documented. ​ How many species are there on Earth? ​ Scientists estimate there are about 8.7 million species on earth ​ Around 1.2 million species have been identified, mostly animals ​ The majority of species(e.g insects, microbes) remain undiscovered ​ It is difficult to count because many species live in inaccessible environments (e.g. deep oceans, dense rainforests) ​ Microorganisms and small species are harder to detect and classify ​ Phylogenetic Tree of All Life on Earth: ​ A phylogenetic tree is a branching diagram that represents the evolutionary relationship among species based on common ancestry ​ Circular phylogenetic tree: displays the diversity of life in a circular format, with all species branching out from a common origin ​ Three Domains: Divides life into Bacteria, Archaea, and Eukarya (organisms switch complex cells) ​ Shows how all living organisms are related through evolution ​ The phylogenetic tree helps scientists understand how species evolve over time ​ Demonstrates shared ancestry and genetic connections between all life forms ​ Where do humans fit into the diversity of life on earth? ​ Humans belong to the domain Eukarya, which includes all organisms with complex cells. ​ Within eukarya, humans are part of the kingdom animalia(animals), the phylum Chordata(vertebrates), and the class Mammalia(mammals) ​ Our species, Homo sapiens, is a branch in the primates order, closely related to other great apes like chimpanzees, gorillas, and orangutans. ​ Humans have advanced cognitive abilities, complex language, and tools that set us apart from other species. ​ Despite our uniqueness, we share 98-99% of our DNA with chimpanzees, highlighting our evolutionary connection. ​ Humans are both a part of biodiversity and a major influence on it ​ We impact ecosystems through urbanization, agriculture, and resource use often leading to species extinction and habitat loss ​ On the positive side, humans contribute to conservation efforts, protecting endangered species and restoring ecosystems ​ What is biological diversity? ​ Biodiversity is an important component of life on Earth, encompassing the variety of species, genetic information, and ecosystems. ​ It highlights the interconnectedness of all living organisms ​ All life on earth shares a common genetic code (DNA), which links all organisms through evolution ​ DNA similarities reveal how species are related and trace back to a common ancestor ​ How do biologists show this connection? ​ Phylogenetic tree: ​ Visual diagrams that map evolutionary relationships based on genetic similarities ​ Show how species diverged from common ancestors over time ​ DNA Sequencing: ​ Analyzing genetic material to compare and classify an organism ​ Helps identify shared genes and evolutionary traits ​ Molecular Clocks: ​ Using DNA mutation rates to estimate when species split from a common ancestor ​ How do biologists distinguish and categorize the millions of species on Earth? ​ Taxonomy: ​ The scientific discipline of classifying organisms based on shared characteristics and evolutionary relationships ​ Founded by Carl Linnaeus, who developed the binomial nomenclature system (e.g. Homo sapiens for humans) ​ Levels of Classification: ​ Biologists group organisms into a hierarchical system: ​ Domain( eukarya) ​ Kingdom (Animalia) ​ Phylum (Chordata) ​ Class (Mammalia) ​ Order (primates) ​ Family (Hominidae) ​ Genus(Homo) ​ Species(sapiens) ​ Genus + Species = Scientific name ​ How do biologists represent the relationship between the millions of species on earth? ​ Phylogenetic trees are branching diagrams that depict evolutionary relationships between species, showing how they are connected through common ancestors. ​ The base (root) represents the common ancestor of all species ​ The branches represent evolutionary lines or clades, with each branch point (node) indicating a common ancestry ​ A cladogram is a phylogenetic tree that shows the relationship between species based on shared characteristics ​ Clades are groups of species that share a common ancestor. Cladograms group species into these clades based on shared traits, like physical features or genetic markers ​ How are phylogenies used to show evolutionary relationships? ​ A phylogeny is the evolutionary history and relationships of organisms, often represented in the form of a phylogenetic tree or cladogram. ​ Phylogenies show how species or groups of species are related to one another based on common ancestry. ​ How Phylogenies Reveal Evolutionary Relationships: ​ Common Ancestors: ​ Phylogenetic trees trace the evolutionary lineage of species back to their common ancestors, highlighting how species have evolved from a shared origin. ​ Each branching point (node) in a phylogeny represents a common ancestor from which two or more descendant species evolved. ​ Branching Patterns: ​ The way branches split on a tree reflects how species diverged from one another over evolutionary time. ​ The closer two species are on the tree, the more recently they shared a common ancestor and are genetically similar. ​ Clades: ​ A clade is a group of organisms that includes a common ancestor and all its descendants. ​ Phylogenies show how different species are grouped into clades, which helps understand evolutionary patterns and traits shared by species within the clade. ​  Phylogeny and Homologous Traits ​ How are phylogenies used to show evolutionary relationships? ​ How and why do we use homologous structures in phylogenies? ​ How do we describe phylogenetic groups? ​ What is homology? ​ Homology is the similarity in characteristics or traits between two or more species resulting from shared ancestry. ​ Related species have common traits that are similar but function differently. ​ Arms, forelegs, flippers, and wings are homologous structures ​ Mammalian forelimbs have the same arrangement of bones, but different functions ​ Humans use arms for lifting, cats use them for walking, whales use them for swimming and bats use them for flying. ​ Types of homology: ​ Morphological homology: similarities in the physical features (structures) of organisms. Some bones have the same underlying bone structures despite being adapted for different functions ​ Molecular homology: similarities in genetic material (DNA or protein sequences) that indicate common ancestry. (EX: chimpanzees and humans share a high percentage of DNA) ​ Homology VS Analogy: ​ Homology is traits that are similar due to shared ancestry. ​ Analogy refers to traits that are similar due to similar environmental pressures or functions, not common ancestry (e.g. the wings of birds and insects). This is known as convergent evolution. ​ Homology is used in phylogeny as it shows the evolutionary relationship between species. The more homologstraits two species share, the more closely related they are, indicating that they evolved from a common ancestor. ​ How do we describe phylogenetic groups? ​ Monophyletic (clade): ancestors and all descendants ​ Polyphyletic: grouping without an immediate common ancestor ​ Paraphyletic: ancestor and only some descendants ​ What are the different types of derived traits? What do they look like on phylogenetic trees? ​ Monophyletic groups are supported by shared derived traits ​ Derived traits: new traits and lineage ​ Shared derived traits: traits shared by taxa in the monophyletic group and the most recent common ancestor ​ Shared ancestral traits: traits shared by taxa and their shared ancestry Bacteria and Archaea ​ What was early life on Earth like? ​ How did early life modify conditions on Earth for later life? ​ What traits define the diversity of prokaryotes on Earth today ​ What was early life like? ​ Early life on earth was simple and microscopic. Life began with single-celled organisms, specifically prokaryotes (cells without a nucleus). These early life forms were likely anaerobic (did not need oxygen) and could survive in harsh conditions ​ Chemoautotrophs produces their own food from inorganic substances like sulfur or methane ​ Heterotrophs relied on consuming organic molecules from the environment ​ These organisms were likely Extremophiles which adapted to survive in extreme conditions, such as high heart, pressure, and the lack of oxygen ​ What were conditions like on earth 3.8 billion years ago ? ​ Earth was still in its early stages of formation and the atmosphere was very different. There was no oxygen in the atmosphere. Volcanic activity was widespread causing frequent eruptions and releasing gasses like carbon dioxide (CO2), methane(CH4), ammonia (NH3), and water vapor (H2O). ​ Earth still was cooling after being hit by manu asteroids and meteorites. The planet had highly acidic oceans with little protection for harmful ultraviolet (UV) radiation due to the lack of an ozone layer. ​ Early earth's atmosphere was mainly composed of greenhouse gasses, which led to a hotter surface ​ What conditions on early earth made the origin of life possible? ​ Chemically rich environments had the necessities for life to form including carbon, nitrogen, oxygen, and hydrogen. The oceans were rich in inorganic molecules like methane and ammonia, which could have been used in chemical reactions that formed organic molecules (amino acids, sugars) ​ Energy sources were needed to fuel chemical reactions. These were the heat and chemicals released by volcanic activity. Lighting, UV radiation, hydrothermal vents in the ocean floor that re;eased heat and chemicals. Water was essential for lids on earth. WHile early oceans were harsh, they still provided a stable environment for chemical reactions to take place. ​ WHat organisms lived on early earth? ​ Microfossil and white smoker, alkaline hydrothermal vents. ​ Prokaryotes were the first organism and were simple single celled organisms that lack a nucleus. They are the ancestors of all life one earth ​ These early organisms were anaerobic (not requiring oxygen). chemoautotrophic (using chemicals like hydrogen sulfide to produce energy) or heterotrophic (consume organic material from their environment) ​ Cyanobacteria was also an organism in early life about 3.5 billion years ago. It evolved the ability to photosynthesize using sunlight to produce energy and releasing oxygen as a byproduct. Led to the great oxygenation event and rise of oxygen dependent organism ​ Extermophiles were early organism like thermophiles (heat loving) and halophiles(slat loving) and were able to survive in earth's extreme early environments ​ Domains of life on earth ​ Bacteria, Archaea, Euakrya ​ Archaea and bacteria are prokaryotes ​ Bacteria: singles celled organisms that are prokaryotic (lack a nucleus and membrane bound organelles) ​ Cell walls are made of peptidoglycan, a unique polymer ​ Found in nearly every environment on earth including soil, water, and within other organisms ​ Reproduce asexually and through binary fission. Can exchange genetic criteria via horizontal gene transfer ​ Archaea: ​ Also prokaryotic, but genetically distinct from bacteria ​ Cell walls lack peptidoglycan and instead contain unique compounds like pseudopeptidoglycan ​ Found in extreme environments (extremophiles). They are thermophiles(thrive in hot temperatures like hot springs), halophiles (live in high salt environments like salt flats) and methanogens (produce methane in anaerobic conditions like wetlands and animals guts) ​ Archaea plays an important role in nutrients cycling ​ Eukarya: ​ Organisms with eukaryotic cells (have a nucleus and membrane bound organelles like mitochondria and chloroplasts ​ Include both unicellular and multicellular organisms ​ Major groups(kingdoms within eukarya): ​ Protists are a diverse group of mostly unicellular organisms like algae and amoebas. They can be autotrophic or heterotrophic ​ Fungi are decomposers that break down organic material like mushrooms and yeast ​ Plants are multicellular autotrophs that perform photosynthesis like trees and flowers ​ Animals are multicellular heterotrophs that rely on consuming other organisms for energy like mammals, birds and insects. ​ Reproduction: ​ Can reproduce sexually or asexually ​ A generic cell ​ Has DNA which is the genetic material of the cell ​ Ribosomes which synthesize proteins ​ An enclosing plasma membrane which separates cells interior form their environment ​ Cytoplasm in which other components of the cell are found ​ Prokaryote: ​ Lack membrane enclosed nucleus that protect DNA ​ Lack organelles ​ DNA is localized in a region called nucleoid ​ Eukaryote: ​ Have a nucleus that separates DNA from cytoplasm ​ Have membrane bound organelles ​ How do prokaryotes reproduce? ​ Binary fission (asexual reproduction) ​ Replication, the circular dna is copied ​ Elongation, the cell grows then separates the DNA copies ​ Division, the cell membrane pinch upwards, splitting the cell into two identical daughter cells ​ How Early Life Modified Conditions on Earth for Later Life and the Evolution of Glycolysis ​ Oxygenation of the Atmosphere and the Evolution of Glycolysis ​ Cyanobacteria, through photosynthesis, began producing oxygen around 2.4 billion years ago, leading to the Great Oxygenation Event. This increase in oxygen allowed for the evolution of aerobic respiration in later life forms, which generates much more ATP than anaerobic processes. ​ However, before oxygen was abundant, early life had to rely on anaerobic processes for energy production. Glycolysis, an ancient metabolic pathway, likely evolved as one of the first ways to generate energy without oxygen. It remains central in all forms of life today, both anaerobic and aerobic, as the first step in energy production. ​ Formation of the Ozone Layer and Energy Production Pathways ​ As oxygen levels rose, it formed the ozone layer, which protected the Earth’s surface from harmful UV radiation. This made the surface more hospitable for the development of eukaryotic cells and complex life forms. ​ In early life forms, glycolysis provided a crucial means of energy production in the absence of oxygen. This pathway is simple and efficient, breaking down glucose into pyruvate and yielding ATP without needing oxygen, which made it well-suited for early, anaerobic organisms. ​ Climate Regulation, Nitrogen Fixation, and Glycolysis in Early Life ​ Early life forms contributed to regulating Earth’s climate by reducing levels of carbon dioxide (CO₂), which helped cool the planet. ​ The role of early photosynthesizers, including cyanobacteria, also led to nitrogen fixation, which provided essential nutrients for life. These organisms were able to use solar energy and carbon dioxide to create organic compounds, setting the foundation for complex ecosystems. ​ Glycolysis allowed these early organisms to generate energy while also contributing to the carbon cycle by utilizing glucose. It was a crucial pathway in an environment where oxygen was absent and energy needed to be produced in simpler forms. ​ Evolution Toward Aerobic Respiration and the Continued Importance of Glycolysis ​ The rise of oxygen eventually led to the evolution of aerobic respiration, where oxygen is used to generate a significantly larger amount of energy in the form of ATP through processes like the citric acid cycle and oxidative phosphorylation in the mitochondria. ​ Despite the development of these more complex processes, glycolysis remains essential in both aerobic and anaerobic organisms, as it provides the initial energy needed for further processes. It is an ancient pathway found in all living organisms today, suggesting its deep evolutionary roots. ​ Creation of Ecosystem Interactions and Glycolysis in Modern Cells ​ Early life forms also set the stage for the development of ecosystem interactions such as predation, symbiosis, and competition. These interactions paved the way for more complex ecological systems. ​ In modern organisms, glycolysis is still used in the initial step of cellular respiration to generate ATP. In aerobic organisms, glycolysis is followed by aerobic respiration, producing much more ATP. In anaerobic conditions, organisms can rely on fermentation following glycolysis to continue producing energy. ​ Summary ​ Early life on Earth, through processes like photosynthesis, oxygen production, and the evolution of glycolysis, transformed the planet’s environment, making it more suitable for complex life. ​ Glycolysis, an ancient and universal metabolic pathway, allowed early organisms to generate energy in an oxygen-free environment. ​ As oxygen increased in the atmosphere, more efficient metabolic pathways like aerobic respiration evolved, but glycolysis remained foundational. These processes contributed to the development of ecosystems and the eventual rise of more complex life forms.  “Introduction to Eukaryotes and the Protists” ​ Who Are the Eukaryotes? ​ Eukaryotes are organisms whose cells contain membrane-bound organelles, including a nucleus that houses their genetic material. ​ They can be unicellular (like protists) or multicellular (like plants, fungi, and animals). ​ The Three Domains of Life ​ Bacteria: Single-celled prokaryotes, lack a nucleus. ​ Archaea: Single-celled prokaryotes, genetically distinct from bacteria, often found in extreme environments. ​ Eukarya: Organisms with eukaryotic cells, including protists, fungi, plants, and animals. ​ How the Evolution of Chloroplast- and Mitochondria-like Prokaryotes Influenced the Evolutionary History of Life on Earth ​ The endosymbiotic theory suggests that mitochondria and chloroplasts were once free-living prokaryotes that were engulfed by an ancestral eukaryotic cell. Over time, these engulfed prokaryotes became essential components of eukaryotic cells, evolving into mitochondria (in animals) and chloroplasts (in plants and algae). ​ Eukaryotic vs. Prokaryotic Cells ​ Eukaryotic cells: Have a nucleus, membrane-bound organelles, and complex structures (e.g., mitochondria, endoplasmic reticulum). ​ Prokaryotic cells: Lack a nucleus and membrane-bound organelles, are generally smaller, and have simpler structures (e.g., bacteria and archaea). ​ How Did Eukaryotes Evolve from Prokaryotes? ​ Endosymbiosis: The theory that eukaryotes evolved from prokaryotes through the engulfment of prokaryotic cells that became symbiotic within a host cell. ​ What Organisms Are in the Eukarya Domain? ​ The Eukarya domain includes: ​ Protists: Unicellular eukaryotes. ​ Fungi: Eukaryotes like molds, yeasts, and mushrooms. ​ Plants: Multicellular organisms that conduct photosynthesis. ​ Animals: Multicellular organisms with complex structures and functions. ​ How Did the Prokaryotic Cell Membrane Give Rise to Eukaryotic Nucleolus and Organelles? ​ The prokaryotic cell membrane likely played a key role in the formation of the endoplasmic reticulum (ER) and nucleolus through invaginations (folds) of the membrane. This allowed for compartmentalization, which is essential for eukaryotic cellular functions. ​ What Is Endosymbiosis? ​ Endosymbiosis is a symbiotic relationship where one organism lives inside the cells of another. This concept is central to the evolution of eukaryotic organelles like mitochondria and chloroplasts. ​ How Did Eukaryotic Cells Acquire Mitochondria and Chloroplasts? ​ According to the endosymbiotic theory, eukaryotic cells acquired mitochondria and chloroplasts by engulfing free-living prokaryotes (bacteria or cyanobacteria), which provided the host cell with additional functions, like energy production (mitochondria) and photosynthesis (chloroplasts). ​ Serial Endosymbiosis Theory ​ The Serial Endosymbiosis Theory suggests that mitochondria and chloroplasts evolved through a series of symbiotic events. Early eukaryotes engulfed prokaryotes, which became increasingly integrated over time, leading to the modern eukaryotic cells with mitochondria and chloroplasts. ​ What Evidence Supports the Autogenic Hypothesis and Endosymbiosis Theory? ​ Endosymbiosis theory: ​ Mitochondria and chloroplasts share similarities with certain prokaryotes, like: ​ Their own circular DNA. ​ Double membranes. ​ Ribosomes similar to those in prokaryotes. ​ Genetic sequencing of mitochondria and chloroplasts is closely related to certain prokaryotic groups (e.g., mitochondria to alpha-proteobacteria, chloroplasts to cyanobacteria). ​ Autogenic hypothesis: ​ Suggests that eukaryotic organelles (like the nucleus and mitochondria) evolved from the folding and compartmentalization of the prokaryotic membrane. ​ Evidence for this includes the presence of membrane-bound organelles in eukaryotes and their ability to compartmentalize various functions. ​ Who Are the Protists? ​ Protists are diverse eukaryotic organisms, primarily unicellular, but some are multicellular. They can be: ​ Autotrophic (e.g., algae, which perform photosynthesis). ​ Heterotrophic (e.g., amoebas and ciliates, which consume other organisms). ​ Why Are Protists Important to Our Everyday Lives? ​ Protists are crucial to ecosystems, contributing to: ​ The oxygen cycle (e.g., algae perform photosynthesis, releasing oxygen). ​ Decomposition (e.g., slime molds). ​ Food chains (as primary producers or consumers). ​ They also impact human health, acting as both pathogens and beneficial organisms. ​ How Do We Interact with Ciliates in Our Everyday Lives? ​ Ciliates (e.g., Paramecium) are common in aquatic environments. Some can be used in scientific research, and others are important in food webs, particularly in aquatic ecosystems. ​ Human interactions: Ciliates play a role in freshwater ecosystems, but some species (like Balantidium coli) can cause infections. ​ How Do We Interact with Slime Molds in Our Everyday Lives? ​ Slime molds are important decomposers in ecosystems, breaking down organic matter. ​ Some slime molds have been studied for their unique behavior and ability to form networks, which has inspired research into problem-solving and optimization algorithms. ​ How Do We Interact with Algae in Our Everyday Lives? ​ Algae are key sources of oxygen and are used in various industries: ​ Food: Seaweed and algae are consumed in various cultures (e.g., sushi). ​ Biofuels: Some algae are used to produce biofuels as a sustainable energy source. ​ Pharmaceuticals: Algae are used in the production of certain drugs and supplements.  Plant Structure and Function ​ Why are plants important to our lives? ​ What is the evolutionary history of plants? ​ How do plants acquire energy? Why Are Plants Important to Our Lives? ​ Essential for Life: ○​ Oxygen production: Plants produce oxygen via photosynthesis, which is essential for respiration in most living organisms. ○​ Food source: Plants form the base of the food chain as primary producers, providing energy for herbivores and omnivores. ○​ Medicinal uses: Many medicines are derived from plant compounds. ○​ Ecosystem services: ​ Climate regulation. ​ Soil stabilization. ​ Water cycle maintenance. ​ Economic Importance: ○​ Source of raw materials (e.g., wood, fibers, rubber). ○​ Agricultural crops sustain human populations. What Is the Evolutionary History of Plants? ​ Origin: Plants evolved from green algae, specifically charophytes. ​ Major Evolutionary Transitions: ○​ Transition from aquatic to terrestrial environments (~500 million years ago). ○​ Development of vascular tissue (~420 million years ago). ○​ Evolution of seeds (~360 million years ago). ○​ Flowering plants (angiosperms) appeared ~140 million years ago. ​ Challenges in Moving to Land: ○​ Desiccation: Risk of drying out. ○​ UV Radiation: Increased exposure to harmful light. ○​ Gravity: Lack of water buoyancy required structural support. ○​ Gas Exchange: Need for new mechanisms to absorb CO₂ and release O₂. ○​ Nutrient and Water Transport: Required efficient systems for resource distribution. How Do Plants Acquire Energy? ​ Photosynthesis: ○​ Plants convert light energy into chemical energy in the form of glucose.  ○​ Occurs in the chloroplasts, specifically in the thylakoid membranes. ○​ Equation: 1.​ Inputs: 6CO₂ + 6H₂O + light energy. 2.​ Outputs: C₆H₁₂O₆ (glucose) + 6O₂. ○​ Stages: 1.​ Light-dependent reactions: Occur in thylakoids; convert light energy into ATP and NADPH. 2.​ Calvin cycle: Occurs in the stroma; uses ATP and NADPH to fix CO₂ into glucose. How Do We Interact With Plants in Everyday Life? ​ Food and Nutrition: Plants provide fruits, vegetables, grains, and other essential food items. ​ Shelter and Materials: Wood for construction and fibers for textiles. ​ Aesthetic and Cultural Value: Gardens, parks, and plant-based rituals. ​ Air Quality: Plants filter pollutants and produce oxygen. The Three Domains of Life on Earth 1.​ Bacteria: Prokaryotes with simple cell structures. 2.​ Archaea: Prokaryotes often found in extreme environments. 3.​ Eukarya: Includes protists, fungi, plants, and animals. Who Are Plants? ​ Definition: ○​ Multicellular, eukaryotic organisms. ○​ Primarily autotrophic, using photosynthesis to produce energy. ​ Distinct Features: ○​ Cell walls made of cellulose. ○​ Chloroplasts containing chlorophyll a and b. ○​ Alternation of generations (sporophyte and gametophyte phases). What Traits Do Plants and Algae Share? ​ Common Features: ○​ Both are photosynthetic autotrophs. ○​ Contain cell walls made of cellulose (in some algae). ○​ Use chloroplasts for photosynthesis. ​ Differences: ○​ Algae are predominantly aquatic and lack specialized land adaptations.  ○​ Plants have structures for terrestrial life (roots, vascular tissue). How Did Green Algae Adapt to Move to Land? ​ Environmental Challenges on Land: ○​ Dry conditions and UV exposure. ○​ Lack of buoyancy to counteract gravity. ○​ Limited access to water and nutrients. ​ Key Adaptations: ○​ Cuticle: Waxy layer to prevent water loss. ○​ Stomata: Pores for gas exchange and water regulation. ○​ Vascular Tissue: Xylem (transports water) and phloem (transports nutrients). ○​ Roots: Anchor plants and absorb water and minerals. How Do Photosynthetic Organisms Deal With Gravity? ​ Algae: ○​ Use structures like pneumatocysts (air-filled sacs) to stay afloat. ​ Land Plants: ○​ Develop rigid cell walls, stems, and wood for support. ○​ Roots stabilize plants and help them grow upright. How Do Photosynthetic Organisms Deal With Light Energy? ​ Underwater: Limited light penetration; photosynthesis restricted to surface layers. ​ On Land: ○​ Overexposure can damage tissues; plants evolved pigments and other protective mechanisms. ○​ Adaptations like broad leaves maximize light capture. How Do Plants Exchange Gases? ​ Stomata: ○​ Open during the day to absorb CO₂ and release O₂. ○​ Close to prevent water loss during drought. ​ Cuticle: Prevents desiccation. ​ Prediction for Closed Stomata: ○​ CO₂ levels decrease, limiting photosynthesis. ○​ O₂ levels decrease, reducing respiration efficiency. What Structures Enable Plants to Thrive on Land? ​ Root System: ○​ Anchors plants and absorbs water and nutrients. ○​ Components: Taproot and lateral roots. ​ Shoot System: ○​ Includes stems, leaves, flowers, and fruits. ○​ Key for photosynthesis, reproduction, and nutrient transport. ​ Key Innovations: ○​ Apical Meristems: Regions of active growth. ○​ Vascular Tissues: Allow efficient transport of water and nutrients. Photosynthesis: Inputs and Outputs ​ Limiting Factors: ○​ Availability of CO₂, H₂O, and light. ○​ Nutrient availability in the soil. ​ Processes: ○​ Light-dependent reactions capture light energy. ○​ Light-independent reactions (Calvin cycle) convert it into glucose. 1. How Do Plants Acquire Energy? ​ Plants acquire energy through photosynthesis, a process that converts light energy into chemical energy stored in sugars. ​ Inputs (Reactants): ○​ Carbon dioxide (CO₂) ○​ Water (H₂O) ​ Outputs (Products): ○​ Glucose (C₆H₁₂O₆): Used for energy and growth. ○​ Oxygen (O₂): Released as a by-product. ​ Overall reaction: ○​ 6CO₂ + 6H₂O → C₆H₁₂O₆ + 6O₂ 2. What Were Early Land Plants on Earth Like? ​ Early land plants were simple and small, relying heavily on water for survival and reproduction.  ​ Characteristics of early land plants: ○​ Lack of vascular tissue (no xylem or phloem for transport). ○​ No true roots, leaves, or seeds. ○​ Dependent on moist environments to prevent desiccation (drying out). 3. How Do Plants Convert Light Energy Into Chemical Energy? ​ Photosynthesis Process: ○​ Plants use light energy to convert CO₂ and H₂O into glucose and oxygen. ○​ Light energy is absorbed by chlorophyll in the chloroplasts. ○​ Glucose is used to build biomass, including: ​ Metabolism: Immediate energy needs. ​ Starch: Long-term energy storage. ​ Cellulose and lignin: Structural support for plant growth. ​ Limiting factors of photosynthesis: ○​ Carbon dioxide (CO₂) availability. ○​ Water supply. ○​ Nutrient availability (e.g., nitrogen, phosphorus). 4. How Do Plants Exchange Gases? ​ Gas exchange occurs through stomata (tiny pores on leaf surfaces). ○​ Open stomata: ​ Allow CO₂ to enter for photosynthesis. ​ O₂ and water vapor exit. ○​ Closed stomata: ​ Prevent water loss but stop gas exchange. ​ Prediction if stomata close: ○​ CO₂ levels: Decrease, as it cannot enter the leaf. ○​ O₂ levels: Increase, as it cannot leave the leaf. 5. How Do Plants Gain Biomass? ​ Biomass is created by converting CO₂ into sugars during photosynthesis. ​ Glucose is converted into structural components (e.g., cellulose) or stored as starch. ​ Trade-offs:  ○​ On hot, dry days, stomata close to conserve water. ​ Consequence: ​ Reduced CO₂ intake limits photosynthesis. ​ O₂ builds up, leading to photorespiration (wasteful process). 6. How Is Photosynthesis Impacted by Warmer Temperatures? ​ High temperatures affect photosynthesis efficiency differently in plants: ○​ Plant A: Maintains photosynthesis efficiency under warmer conditions. ○​ Plant B: Photosynthesis efficiency decreases with rising temperatures. ​ Hot, dry conditions favor photorespiration: ○​ Stomata close to conserve water. ○​ CO₂ availability decreases. ○​ O₂ builds up inside the leaf, interfering with photosynthesis. 7. Do Plants Respire? ​ Yes, plants respire through cellular respiration, which provides energy for cellular activities. ​ Reactions involved: ○​ Photosynthesis: ​ CO₂ + H₂O → O₂ + Glucose (Fixes energy). ○​ Respiration: ​ O₂ + Glucose → CO₂ + H₂O (Releases energy). ​ Day vs. night: ○​ Daytime: Photosynthesis (produces oxygen) and respiration (uses oxygen) occur simultaneously. ○​ Nighttime: Only respiration occurs (oxygen is consumed, CO₂ is released). 8. How Is Photosynthesis Different During the Day vs. Night? ​ Daytime: ○​ Photosynthesis produces O₂ and consumes CO₂. ○​ Respiration continues but is overshadowed by photosynthesis. ○​ O₂ concentration: Increases. ○​ CO₂ concentration: Decreases.  ​ Nighttime: ○​ Photosynthesis stops (no light). ○​ Respiration consumes O₂ and releases CO₂. ○​ O₂ concentration: Decreases. ○​ CO₂ concentration: Increases. 9. Plant Evolution ​ Plants evolved in stages, adapting to life on land: 1.​ Nonvascular plants (Bryophytes): ​ Examples: Mosses, liverworts, hornworts. ​ Lack of vascular tissue for transport. ​ Require moist environments. 2.​ Vascular plants without seeds: ​ Examples: Club mosses, ferns. ​ Have vascular tissue (xylem and phloem) for transport. ​ Reproduce via spores. 3.​ Vascular plants with naked seeds (Gymnosperms): ​ Examples: Conifers, ginkgos, cycads. ​ Seeds not enclosed in a fruit. 4.​ Vascular plants with enclosed seeds (Angiosperms): ​ Examples: Flowering plants. ​ Seeds enclosed within a fruit. 10. Non-Vascular Plants ​ Characteristics: ○​ Lack of vascular tissue, true roots, leaves, seeds, and flowers. ○​ Use rhizoids for anchorage instead of roots. ○​ Small, low-growing, and prefer moist environments. ​ Life cycle: ○​ Dominant gametophyte stage (haploid, n). ○​ Sporophyte (diploid, 2n) is inconspicuous and dependent on the gametophyte. ○​ Reproduction requires water for fertilization (male gametes swim to eggs).  Plant Evolution 1. Evolutionary History of Vascular Plants with Seeds ​ Vascular plants evolved in stages, beginning with seedless plants and later developing seeds. ​ Key evolutionary steps: 1.​ Non-vascular plants: ​ Examples: Mosses, liverworts, hornworts. ​ Lack vascular tissue; reproduce via spores. 2.​ Seedless vascular plants: ​ Examples: Club mosses (lycophytes), ferns, horsetails (monilophytes). ​ Traits: ​ Vascular tissue for water and nutrient transport (xylem, phloem). ​ True leaves, stems, and roots. ​ Lignin in cell walls for structural support, enabling taller growth. ​ Sporophyte (2n) is the dominant life stage. ​ Reproduce via spores, not seeds. ​ Gametophyte (n) produces sperm and eggs, requiring water for fertilization. 2. How Do Plants Acquire Water and Nutrients? ​ Vascular plants acquire water and nutrients using specialized structures: ○​ Roots: ​ Anchor the plant to the ground. ​ Absorb water and nutrients for photosynthesis and maintenance. ​ Form mutualistic relationships with fungi (mycorrhizae) to enhance water and nutrient uptake. ○​ Stems: ​ Provide structural support. ​ Transport nutrients to the leaves (main photosynthetic organ). ○​ Leaves: ​ Primary site of photosynthesis. 3. Major Limiting Factors for Land Plants Plants must overcome several challenges to survive, grow, and reproduce on land:  1.​ Gravity: ○​ Requires structural support to prevent collapse. 2.​ Light energy: ○​ Necessary for photosynthesis but limited in shaded environments. 3.​ Gas exchange: ○​ CO₂ for photosynthesis and O₂ for respiration. 4.​ Water: ○​ Essential for photosynthesis, transport, and reproduction. ○​ Limited in dry environments. 5.​ Nutrients: ○​ Absorbed from the soil for growth and metabolic processes. 4. Key Structures of Vascular Plants ​ Roots: ○​ Absorb water and nutrients. ○​ Store food. ​ Stem: ○​ Provides structural support. ○​ Transports water, nutrients, and sugars. ​ Leaves: ○​ Main photosynthetic organ. ​ Vascular System: ○​ Xylem: Transports water and minerals in a one-way flow from roots to shoots. ○​ Phloem: Transports sugars, amino acids, and photosynthetic products in a two-way flow throughout the plant. 5. How Plants Grow ​ Growth types: 1.​ Primary growth: ​ Occurs at apical meristems (localized areas of cell division at the tips of roots and shoots). ​ Increases plant length. 2.​ Secondary growth: ​ Occurs at lateral meristems (along the length of roots and shoots). ​ Increases plant thickness. ​ Growth occurs continuously throughout a plant's life. 6. How Roots Revolutionized Land Plants ​ Roots provided stability and efficiency in acquiring water and nutrients, essential for survival on land. ​ Mutualistic relationships with fungi further enhanced nutrient absorption. 7. How Do Plants Transport Water and Photosynthetic Products? ​ Water and mineral transport: ○​ Xylem uses a water potential gradient to move water upward: ​ High water potential in moist soils → Low water potential in dry air. ​ Negative pressure (created by transpiration) pulls water up from the roots to the leaves. ​ Photosynthesis product transport: ○​ Phloem moves sugars and amino acids in a two-way flow: ​ From leaves (sources) to other plant parts (sinks). 1. What is the evolutionary history of vascular plants with seeds? The evolution of vascular plants with seeds can be broken down into the following stages: ​ Non-vascular plants: The earliest plants (e.g., mosses, liverworts, and hornworts) lacked vascular tissue and seeds. These plants still rely on water for reproduction (e.g., sperm must swim to fertilize eggs). ​ Vascular plants without seeds: Vascular plants like club mosses (lycophytes) and ferns (monilophytes) emerged. These plants had vascular tissue (xylem and phloem) for transporting water and nutrients but still reproduce via spores. ​ Vascular plants with naked seeds (Gymnosperms): This group includes plants like conifers (pine trees), cycads, and ginkgoes. They developed seeds, but these seeds were not enclosed by an ovary, making them "naked." Gymnosperms also produce cones for reproduction. ​ Vascular plants with protected seeds (Angiosperms): Angiosperms (flowering plants) evolved seeds that are enclosed within a fruit (derived from the ovary). They are the most diverse and abundant group of plants today, with species like roses (dicots) and bamboo (monocots). 2. How do seed plants reproduce? Seed plants reproduce sexually, with the following processes: ​ Gymnosperms: Reproduction occurs in cones. Male cones produce pollen (the male gametophyte), while female cones contain ovules (the female gametophyte). Pollen is transferred to the female cone, fertilizing the egg inside the ovule, resulting in the development of a seed. ​ Angiosperms: Reproduction occurs through flowers, which have male parts (anthers that produce pollen) and female parts (carpels containing ovules). Pollination occurs when pollen from the anther is transferred to the stigma of the carpel. Fertilization happens when the pollen travels down the style to fertilize the egg in the ovule, forming a seed. The ovary of the flower develops into a fruit, which contains seeds. 3. What are the traits of vascular plants with naked seeds? Gymnosperms are vascular plants with naked seeds and have the following traits: ​ Naked seeds: Seeds are not enclosed in an ovary (as in angiosperms) but are exposed on the surface of cone scales. ​ Cones: The reproductive structures that produce seeds. Male cones produce pollen, while female cones hold ovules. ​ Woody, tall plants: Most gymnosperms are large, woody trees adapted to cold climates (e.g., conifers like pines and spruces). ​ Wind pollination: Many gymnosperms are pollinated by wind rather than animals. ​ Dominant sporophyte: The dominant life stage in gymnosperms is the sporophyte (2n), which is the mature plant. 4. What is the evolutionary history of seeds? Seeds evolved as a way for plants to reproduce more efficiently on land. Key points in their evolution include: ​ Seed Evolution: Seeds provide a protective coat for the developing embryo, allow for dormancy (enabling survival during harsh conditions), and can disperse over long distances. ​ Heterospory: Seed plants are heterosporous, meaning they produce two types of spores—megaspores (female) and microspores (male). The megaspore develops into a  female gametophyte (ovule), and the microspore develops into a male gametophyte (pollen). ​ Advantages of seeds: Seeds protect the embryo, provide food for the developing plant, and allow for dormancy, which enables seeds to survive until conditions are right for germination. 5. What are the traits of vascular plants with protected seeds? Angiosperms are vascular plants with protected seeds and have the following traits: ​ Protected seeds: Seeds are enclosed within a fruit, which develops from the ovary of the flower. ​ Flowers: The reproductive organs of angiosperms. Flowers contain male (anthers) and female (carpels) reproductive parts. ​ Pollination and fertilization: Pollination involves the transfer of pollen from the anther to the stigma of the carpel. Fertilization occurs when pollen reaches the ovule inside the ovary. ​ Diverse growth forms: Angiosperms include herbs, shrubs, trees, and vines. ​ Dominant sporophyte: Like gymnosperms, the dominant life stage in angiosperms is the sporophyte (2n). 6. What are the differences between monocots and dicots? Monocots and dicots are two major groups of angiosperms that differ in several ways: ​ Cotyledons: Monocots have one cotyledon (seed leaf), while dicots have two. ​ Leaf venation: Monocots typically have parallel-veined leaves, while dicots have net-like venation. ​ Flower parts: Monocots typically have flower parts in multiples of three (e.g., three petals), while dicots usually have flower parts in multiples of four or five. ​ Vascular tissue: In monocots, vascular tissue is scattered throughout the stem, while in dicots, vascular tissue is arranged in a ring. 7. How do plants reproduce sexually? In seed plants, sexual reproduction involves the fusion of male and female gametes to form a zygote:  ​ Male gametophyte (pollen): Pollen is produced in the anther and contains sperm cells. ​ Female gametophyte (ovule): The ovule is located in the carpel of the flower and contains egg cells. ​ Pollination: Pollination is the transfer of pollen from the anther to the stigma of the flower. This can occur through wind, insects, birds, or other pollinators. ​ Fertilization: After pollination, the sperm travels down the style to the ovule for fertilization, resulting in the formation of a seed. 8. What are the evolutionary advantages and disadvantages of plant sexual reproduction (pollination)? Advantages: ​ Genetic variation: Sexual reproduction creates genetic diversity, which can help populations adapt to changing environments. ​ Long-distance dispersal: Pollination allows plants to reproduce over large distances. Disadvantages: ​ Dependence on pollinators: Many plants rely on animals or wind for pollination, which can be unreliable. ​ Energy costs: Attracting pollinators requires significant energy, including producing flowers, nectar, and fragrances. 9. How are fruits involved in plant reproduction? Fruits develop from the ovary of a flower after fertilization. They contain seeds and play a crucial role in seed dispersal. The different types of fruits (e.g., fleshy fruits like apples or dry fruits like nuts) attract different animals, which help spread seeds over wide areas. 10. How is pollen distributed? Pollen is distributed by several methods, including: ​ Wind: Some plants, especially gymnosperms, rely on wind to disperse their pollen. ​ Insects: Many angiosperms rely on insects (e.g., bees) to transfer pollen between flowers. ​ Bats: Bats are important pollinators for some plants, particularly in tropical regions.  ​ Birds: Birds also pollinate certain plants, especially those with large, brightly colored flowers. 11. How do the dominant life stages change across the four groups of land plants? The dominant life stage differs across plant groups: ​ Bryophytes: The dominant stage is the gametophyte (n), which is the plant we typically see. ​ Seedless vascular plants: The dominant stage is the sporophyte (2n), but the gametophyte is still visible during reproduction. ​ Gymnosperms and angiosperms: The dominant stage is the sporophyte (2n), which is the mature plant that produces seeds. Turgor Pressure ​ Definition: Turgor pressure is the pressure exerted by the cell membrane against the cell wall due to water entering the cell. It is a critical component of plant cell structure and function. ​ Mechanism: When water enters a plant cell through osmosis, it fills the central vacuole and creates internal pressure. This pressure pushes the cell membrane against the cell wall, keeping the plant rigid and helping it maintain its shape. ​ Importance: ○​ Support: Turgor pressure helps maintain the structural integrity of the plant and supports non-woody tissues. ○​ Growth: It contributes to the expansion of plant cells and is vital for the growth of plant tissues. ○​ Transport: Turgor pressure also aids in the transport of water and nutrients through the plant’s vascular system, particularly in the xylem. ​ Related Processes: Turgor pressure is influenced by the plant's ability to retain water and the state of the vacuole. If the plant loses too much water (e.g., during drought), turgor pressure decreases, leading to wilting.  The Fungi 1. Importance of Fungi in Our Lives ​ Decomposers: Fungi play a critical role in breaking down organic matter, returning nutrients like nitrogen (N), phosphorus (P), and minerals (K, Mg, Fe) back into the ecosystem. This helps in the recycling of nutrients, which plants can take up again. ​ Carbon Cycle: Fungi are an important part of the carbon cycle, as they decompose organic matter and release carbon dioxide (CO2) back into the atmosphere. ​ Medical Uses: Fungi have applications in medicine, such as the production of antibiotics like penicillin. ​ Food Industry: Some fungi are essential in the production of foods (e.g., yeast in bread, mushrooms as food). 2. Who Are Fungi? Kingdom Fungi ​ Fungi have their own kingdom due to distinct characteristics that set them apart from other organisms. ​ Heterotrophic: Fungi are heterotrophs, meaning they obtain food by absorbing nutrients from outside their body, unlike plants, which are autotrophic. ​ Cell Wall Composition: Their cell walls are made of chitin (not cellulose like plants). ​ Multicellular and Unicellular Forms: Most fungi are multicellular (e.g., molds, mushrooms), but some are unicellular (e.g., yeasts). ​ Body Structure: Fungi have a body structure called mycelium, which is a network of thread-like hyphae. ​ Nutrient Absorption: Fungi secrete hydrolytic enzymes into their environment, which break down organic matter so it can be absorbed as nutrients. 3. How Fungi Interact with Their Environment ​ Decomposers: Fungi are essential decomposers in ecosystems. They break down dead organic material, including plants and animals, releasing nutrients and carbon back into the soil, which supports plant growth. ​ Symbiosis: Fungi engage in mutualistic relationships with other organisms, such as plants and animals. An example of this is mycorrhizal fungi, which have mutualistic relationships with plant roots. 4. How Fungi Interact with Plants Mycorrhizal Fungi ​ Mutualistic Relationship with Plants: ○​ Mycorrhizae fungi colonize plant roots and form a symbiotic relationship where they expand the root surface area for nutrient absorption. ○​ In return, the plant provides sugars produced via photosynthesis to the fungi. ​ Types of Mycorrhizae: ○​ Ectomycorrhizae: Form a sheath around the root. ○​ Arbuscular Mycorrhizae: Penetrate plant root cells. ​ Benefits: ○​ Increase surface area for nutrient absorption, especially for phosphorus (P) and nitrogen (N). ○​ Help plants communicate through a network of fungi (mycelium), known as the "Wood Wide Web." Disruption of Symbiosis: ​ The mutualism may break down under certain conditions, such as: ○​ Excessive nutrient availability: Plants may no longer require fungal assistance if they can obtain nutrients directly from the soil. ○​ Poor plant health: When a plant is unhealthy, the relationship might become parasitic, where the fungi harm the plant by taking more resources than it gives. 5. Fungi and Their Roles in Ecosystem Health Decomposition and Nutrient Recycling ​ Fungi release nitrogen (N), phosphorus (P), and other minerals back into the soil, making them available for plant uptake. ​ Without fungi decomposers, ecosystems would have lower levels of biologically available nitrogen and phosphorus, significantly affecting plant growth and ecosystem health. Fungi as Parasites ​ Some fungi are parasitic and live off a host, often causing harm to the host organism. Examples include:  ○​ Panama Disease: A fungal disease affecting banana plants, reducing their ability to absorb water and nutrients. ○​ Batrachochytrium dendrobatidis (Bd): A fungal pathogen that infects amphibians, particularly frogs, causing skin lesions and death, which has contributed to the decline in amphibian populations. 6. Fungi's Importance in Agriculture ​ Fungal Diseases: Fungi can harm crops, such as bananas being threatened by Panama disease. This fungal infection attacks the roots of banana plants, preventing them from absorbing essential nutrients and water. ​ Monoculture Farming: The widespread cultivation of a single crop (monoculture) increases the vulnerability of plants to fungal diseases. 7. Fungi and Other Organisms ​ Fungi-Insect Relationships: ○​ Leafcutter Ants: These ants collect leaves, which they use to cultivate fungus for food. The fungus breaks down the leaves, and the ants feed on the fungus. ​ Fungi in the Food Chain: Fungi can be a food source for animals, and some animals help spread fungal spores, promoting fungal reproduction. 8. Fungal Reproduction ​ Fungi reproduce via spores, which can be produced both sexually and asexually. ​ Asexual Reproduction: Spores are produced without fusion of gametes, allowing for rapid spread. ​ Sexual Reproduction: Involves the fusion of specialized fungal cells (gametes) to create genetically diverse offspring. Spore Germination: ​ When fungal spores land in a suitable environment, they germinate and form mycelium, which further develops into the reproductive fruiting bodies that release new spores.