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Viborg Hurley Biology Lecture Notes *Driving Questions indicate discussion / problem driven units. Unit 1: Introductory to Biology Time: 2.5 weeks Driving Question Part 1: How can the process of science determine what may be killing bat populations?What is science?Deals with the natural world, which can be detected, observed, and measured. Based on evidence that can be demonstrated through observations or experiments. Subject to independent validation and peer review. Open to challenge by anyone at any time on the basis of evidence. Self-correcting enterprise. Process of Science (formerly known as the scientific method)Observe and ask questions (Is the fungus living?) Suggest a hypothesis Falsifiable Can be supported but not proven Generate predictionsDesign tests by observing (descriptive or analytical) or experiments. Independent vs dependent vs constant Control vs Experimental Analyze results Communicate Accept, reject, or modify hypothesis Scientific fact (direct and repeatable observation) Scientific theory (group of related hypotheses that have received substantial confirmation through many lines of investigations by many different people)Living Organism Characteristics Composed of one or more cellsReproduce autonomously using DNA. Obtain energy from the environment to support metabolism. Sense the environment and respond to it. Maintain constant internal environment (homeostasis). *Cell Virtual Lab (Bookmarked)Pathways depend on feedback loops. Negative feedback: reduces the output of a process. (sweating)Positive feedback: increases the output of a process until an endpoint is reached. (blood clotting or birth) Can evolve as groups. What are the consequences of bats dying? Examination of the levels of organization Atoms MoleculesCellsTissues Organs Organ Systems Organism Population Community Ecosystem BiomesBiosphere **Discuss Q8 on pg. 18 (blue biology textbook)Driving Question Part 2: Why is vaccine safety being questioned?Viruses: What are they and are they living?Viruses are small, microscopic no cellular particles that can cause a number of health related issues. Lack key characteristics of life: not made of cells (protein coat with DNA), lack the ability to maintain homeostasis, reproduce, and undergo metabolismUse the host’s cells to reproduce copies of itself. Classified via:DNA or RNA Shape and structure Type of organisms they infect Disease they produce. Viral strains are variant forms of a virus that arise due to evolution. R naught If R0 is less than 1, each existing infection would cause less than one new infection. Indicates the disease will decline and die out. If it equals 1, then each infection causes one new infection. Disease stays alive and is stable, but there won’t be outbreaks or epidemics. If it is greater than 1, each existing infection causes more than one new infection. Transmitted between people and can lead to an epidemic. Ex: R18 would cause 18 infections. Covid-19’s value is 5.7. Assume no one is vaccinated, no one has had it before, and no one is taking precautions against the virus. Vaccines Injection of a material, typically inactivated and harmless infectious organism or parts of an organism, that stimulates the immune system to protect against future exposure to that pathogen. Body recognizes the inactivated organism as an invader and attacks it. Evaluating Claims (How can you make the right choice about vaccinations?)Scientific claims are statements about how the world works that can be tested using the scientific method. Exposed to hundreds daily. (many untrue)Advertisements Special interest groups or organizations Scientific Literacy An understanding of the basics of science and the scientific process. Enables us to make informed decisions about the world around us. (voting or making decisions about your own life)Credentials Background to assess the strength of a person’s scientific claim. What level of a degree do they have? Is it in the filed they are making a claim on? Identify bias Prejudice or opinion for or against something. Ideological, political, or religious beliefs Ex: Blind trials (Grey’s Anatomy)Types of Research Basic research: intended to expand the fundamental knowledge base of science. Funded by taxpayers Applied research: scientific knowledge is applied to human issues and often commercial applications. Normally bias results in this research. Types of Literature Secondary Literature (typically first source we go to when evaluating a claim)Summarizes and synthesizes an area of research Textbooks, review articles, Internet searches, and popular science magazines. Websites affiliated with respected institutions are best. Primary Literature Scientific research is first published. Technical reports, conference proceedings, dissertations, and peer-reviewed journals. Correlation vs Causation (Vaccines and autism) Correlation Two or more aspects of the natural world behave in an interrelated manner. (if one shows a particular value, we can predict the value of the other) Causation A change in one aspect causes a change in another. Correlation DOES NOT establish causation. Example: Autism and Vaccines AND Autism and Organic Food Sales (Handout with discussion) **Q5 Blue book (also on E-book) Discuss this question.Real or Pseudoscience?Pseudoscience is characterized by scientific sounding statements, beliefs, or practices that are not actually based on the scientific method. Asking these sets of questions can help you establish what is real and what is fakeIs there an initial observation based on observable and quantifiable phenomena?Has the observation given rise to a clear and measurable hypothesis?Has the hypothesis generated testable and falsifiable predictions?Is there a carefully designed, reproducible experiment with sufficient sample sizes, clearly identified experimental variables, and control groups?Did scientific conclusions logically follow from analysis of the experimental results to support or fail to support the hypothesis?Have the results undergone review from practicing scientists and been published in an established scientific journal?Fears versus Facts Must consider nonscientific aspects of your decisions. Values, ethical stances, and religious beliefs How it affects others (not vaccinating can impact the entire community)Not vaccinating can put those who are unable to get vaccines at a big risk. Herd immunity: spread of disease is contained due to a large portion of the population being vaccinated. (keeps the virus out of circulation) Ongoing process Even if a Coronavirus vaccine is created it will continuously be evaluated. Discuss Q7 Chapter 2 in blue book as a class. (E-book ch. 24)Assessment: Team Learning – Assessment Review Questions Unit 2: Chemistry of Life Time: 2.5 weeks Driving Questions: How can a model of the primitive Earth provide new insights into why life is carbon-based?Chemistry Concept Review (Lecture discussion prior to introduction of Driving Question)Matter: Anything that has mass and takes up space. Element: Pure substance that has distinct physical and chemical properties that cannot be broken down. 98 natural and 20 synthetic. Atom: smallest unit of an element that retains the element’s distinct properties. Nucleus, protons, electrons, and neutrons. Atomic Number: number of protons Mass Number: number of protons + neutrons / Isotopes: same element with varying numbers of neutrons. Covalent Bond: chemical bond where electrons are shared to form molecules. Organic molecules include Carbon. How did life begin?All life is carbon based. Stanley Miller and Harold Urey were the first to propose a hypothesis about how life started from Earth’s early atmosphere. Urey proposed that Earth’s early atmosphere contained the chemical compounds: Methane, Ammonia, Hydrogen, and Water Vapor. Miller proposed the Miller-Urey ExperimentFour gases were mixed in a large, sealed glass apparatus. Then zapped the four gases with a spark to simulate lightning. (Chemical reaction: reactants and products) Why need lightning? What would the reactants and products be?After just one week, a red liquid pooled in the bottom of the apparatus: contained five amino acids. Amino acids: building blocks of proteins (20) 3 of the 5 they found are in the 20. Miller continued to vary different variables in the experiment but never published results. Ex: injected hot steam instead of the spark. In 2008 new technology was used to test original samples and they found 14 amino acids and 22 in the unpublished steam example. Why so much for the steam?World of Water Water has unique qualities:Polar molecule: unequal sharing of electrons when forming a compound. Hydrogen bonds: weak electrical charges between a hydrogen atom with a partial positive charge and another with a partial negative charge. Both bonds allow water to break apart the compounds in the experiment (Ammonia). Ex: soaking dirty dishes in soapy water. Ammonia was soluble. (mix completely with water)Universal Solvent: substance that dissolves a solute or substance. Hydrophillic: molecules that are soluble in water Hydrophobic: molecules (fats and oils) that don’t dissolve in water because they are nonpolar or uncharged. Steam allowed for more amino acids because it allowed more chemical reactions to occur due to solubility and its polar nature. Exists in all three phases (solid, liquid, gas)Decreases in density as a solid vs a liquid High heat of vaporization Volcanic Eruptions and the Miller-Urey Experiment 2011 scientists discovered that an additional experiment was carried out with Hydrogen Sulfide added to the gas mixture. Identified 22 amino acidsMethionine: initiates the construction of all proteins in cells Supported hypothesis that volcanoes played a key role in the creation biologically crucial molecules. Extra Terrestrial Theory of the Origin of Life Many believe amino acids could have originated from meteorites that hit the surface of early Earth. 90 amino acids identified on meteorites. One characteristic of amino acids supports this theory:Left-handed amino acids are produced by living organisms on Earth Right-handed amino acids are produced only in labs. The pH scale and the Miller Urey Experiment (Inquiry learning via soil lab)pH scale is a measure of the increase or decrease of hydrogen ion concentration in a solution. 1-6 is acidic (High H+ concentration), 7 is neutral, and 8-14 is basic (low H+ ion concentration)Calculations pH = -log [H+] pH + pOH = 14 pOH = -log [OH-]Later evidence suggested that carbon dioxide and nitrogen gas were present in early atmosphere. Miller retested with these but found that resulting solution was acidic and broke down amino acids. Added calcium carbonate (base) to counteract acid and it worked. Life’s Building Blocks Biomolecules or Organic Molecules Carbohydrates, Lipids, Proteins, and Nucleic Acids All rely on the versatile Carbon atom. All but lipids are polymers (long chains)Proteins Most abundant organic compound in the body. Monomers are amino acids. Consists of enzymes, structural proteins, receptor proteins, transport proteins, etc. Carbohydrates Simple sugars (monosaccharides), disaccharides, or polysaccharides. Cell’s fuel to make ATP (energy for cells to function), store energy (glycogen and starch), structural support (cellulose or fiber, chitin)Nucleic Acids DNA and RNA Form the basis of life. Monomers are nucleotides. Provides long term, stable genetic information. Lipids Includes fats, oils, and steroids. Don’t contain monomers and are not polymers. Made of hydrocarbons, fatty acids, or glycerol. Store energy or serve as insulation**Lesson Analysis: Select Chapter Review Questions Origin of Life Documentary Assessment: Exam Unit 3: Biodiversity Time: 5 weeks Driving Question: What is the importance of biodiversity?Life’s Beginning All life shares a set of common properties (discussed in Unit 1). Indicates that all life arose from a common ancestor called a universal ancestor. Base of the tree of life. Biodiversity The variety of all the world’s living things (species)Genetic biodiversity Ecosystem biodiversity Functional biodiversity Organizing Biodiversity Domains (highest, broadest level) Sketch a tree! Bacteria *First appear about 3.7 billion years ago. Microscopic and single-celled (prokaryotes)Reproduce asexually by splitting in twoArchaea **Adaptations to extreme environments (prokaryotes)Microscopic and single celledReproduce asexually by splitting in two Eukarya Larger cells size and presence of nucleus and other organelles. Multicellular Reproduce sexually First appear about 2.1 billion years ago after a group of bacteria developed the ability to undergo photosynthesis. (Why is that important?)Evolutionary Trees and Tracking Biodiversity Lineages Lines of descent (birds to dinosaurs)Ex: Birds were closely related to theropodsTheropods were fast moving dinosaurs on two legs with hollow, thin-walled bones (like birds)Evolutionary Tree Models of evolutionary relationships (phylogeny)Based on similarities and differences in DNA, physical features, biochemical characteristics, or a combination of those. Maps the relationships between ancestral groups and descendants. Cladistics / Nodes Clades are branches on an evolutionary tree that include an ancestor and all its descendants. Made using cladistics. Can be broken down into cladograms which use shared derived characteristics. Unique features common to all members of a group and the ancestor. Not found in groups that are not direct descendants of that ancestor. Sketch an example. Nodes are the moments in time when an ancestral group split into two separate lineages. (on an evolutionary tree)Represents the most recent common ancestor of the two lineages. History of Life On Earth Biological Classification Developed by Carolus Linnaeus (Linnaean hierarchy)System of biological classification that organized all life from broad categories to most specific categories. Ensures that all scientists have the same classification system. Hierarchy: Domain (discussed earlier)Kingdoms ProtistaPlantaeFungiAnimaliaBacteria Archaea Phylum Class Order Family Genus Species (Subspecies) Naming Rules for Species NameScientific name is a two-word Latin name that consists of the genus name and the species name. Always in italics or underlines. Genus name is capitalized, species is lower case. Subspecies have three parts. Geologic Timeline of Life (Calendar modification)Precambrian (4.6 bya to 540 mya)Origin of life took place. Photosynthesis evolved and increased oxygen content. First eukaryotes evolve. All took place in the water. Cambrian (540 – 480 mya)Cambrian explosion occurs Large and sudden increase in the diversity of animal life. (primarily in ocean)First vertebrates appearTransition to land life beginsOrdovician (480 to 445 mya) Plants and fungi begin to colonize land. Developed support, movement, reproduction, and regulation of heat in order to survive. First extinction event occurs (discuss later) Silurian (445 to 415 mya)Fish diversity increasesLand colonization occurs by insects and other invertebratesDevonian (415 – 360 mya)Diversity of land plants increasesAge of Fishes First amphibians appear and move to land. (evolved from lobe-finned fish)Mass extinction event occurs. Carboniferous (360-300 mya)Extensive forests, amphibians dominate life on land. Insect diversity takes place. (largest they have ever reached)Highest atmospheric oxygen content (35%)First reptiles appearEvolved the amniotic age which removed the need for a water source to reproduce. **Major event! Permian (300-250 mya)Age of reptiles begins Continents form PangeaMass extinction occurs Triassic (250 – 200 mya)Early dinosaurs appear. First mammals appear. Mass extinction occurs Jurassic (200-145 mya)Continents begin to separate Diversity of dinosaurs increases (mostly plant-eating) First birds appearFirst flowering plants Cretaceous (145 -65 mya)Flowering plants dominate life on land. K-T Extinction (meteor) occurs at the end. Last non-avian dinosaurs go extinct. Paleogene / Neogene (65-2.6 mya)Continents are near current positions Flowering plants, birds, mammals, and pollinating insects increase in diversity. Ice age begins. Quaternary (2.6 mya to current) Repeated advance and retreat of glaciers Evolution of humans Extinction of large mammals and birds Beginning of 6th mass extinction Mass Extinction Events Causes include climate change, massive volcanic eruptions, meteor impacts, changes in marine and atmospheric gas composition, sea level changes, and human-related activities. Six Mass Extinctions Ordovician Extinction: 50% of animal families died. Devonian Extinction: 30% of animal families died. (mainly fish)Permian Extinction: 60% of animal families died including marine species, insects, amphibians, and all remaining trilobites. (Biggest extinction to date) Great Dying. Triassic Extinction: 35% of animal families died including many reptiles. Cretaceous (K-T) Extinction: 50% of animal families died including non-avian dinosaurs and marine species. Meteor – Chixculub Crater Holocene Extinction (6th Extinction)100 to 1,000 times faster than natural ratesNumerous families of mammals, birds, amphibians, reptiles, insects, coral reefs, and plants have went extinct. Number of species known to be extinct since 1500 Arachnids: 9Crustaceans: 12Reptiles: 22Amphibians: 36Insects: 58Fishes: 71Mammals: 79Plants: 134Birds: 145Mollusks: 324Mass Extinctions alter biodiversity in two ways:Entire groups of organisms perish. Provides new opportunities for groups that previously were of minor importance. Adaptive radiation (expand to take new ecological roles an form new species) Kingdoms of Life Bacteria and Archaea Make up more than 2/3rds of the species on Earth. Bodies contain 39 trillion microbes (microscopic organisms)Found in guts, eyelashes, belly button, skin, mouth, etc. Structure (Lab-petri dishes)Shape varies from rods to spheres to spirals to corkscrew to comma. Wrapped in a cell wall and capsule. Capsule acts like an invisibility coat to avoid immune system. Pilli: hair-like projections that allow for attachment to surfaces. Flagella: whip-like projection to help bacteria and archaea move. No nucleus Archaea Groups Thermophiles (exist at locations of extremely high temperatures)Halophiles (exist in very salty, high-sodium environments) How Bacteria and Archean Feed ChemoheterotrophicConsumes organic molecules to get energy and carbon. Photoheterotrophic Acquire carbon from organic sources but their energy is from sunlight. Photoautotrophic Absorb energy of sunlight and take in carbon dioxide to conduct photosynthesis. Chemoautotrophic Get their energy from inorganic chemicals in their environment (iron ore, hydrogen sulfide, or ammonia)Benefits of Bacteria and Archean Nitrogen Fixation Help plants by taking nitrogen from the atmosphere and converting it to ammonia so plants can use it. Nutrient Cycling Decomposers break down dead organisms or waste and release chemical elements to the environment. Protista What Mr. Groenke terms the “Misfit Kingdom”All eukaryotes that are not plants, animals, or fungi are in this kingdom. Eukaryotes allow for sending messages, producting energy, or cleaning up waste via organelles. Broken down into two categories Protozoans (nonphotosynthetic and motile)Algae (photosynthetic and either motile or not) Photosynthesis occurs and CO2 is absorbed throughout the entire organism. Water and minerals are absorbed by the whole organism Water supports the whole organism Dehydration is not an issue Plants Multicellular autotrophs that are mostly terrestrial. Evolved from Green Algae (both use chloroplasts for photosynthesis) Photosynthesis occurs and CO2 is absorbed primarily in the leaves via stomata. Roots absorb water and minerals from soil. Roots anchor and support the plant within the ground. Lignin and vascular tissues support the plant aboveground. Cellulose also helps. Waxy cuticle holds moisture in to prevent dehydration. Benefits Food source Soil stability Soil health Recycle CO2 and produce oxygen Groups Bryophytes (liverworts and mosses)Thin bodies (few cells thick)Lack a vascular systemFerns First land plants with a vascular system were ancestors to ferns. First to evolve lignin as well. Allows for plants to grow tall. Gymnosperms First plants to evolve pollen and the seed. Produce naked seeds that are unwrapped. Conifer trees. Angiosperms Flowering plants, younger than gymnosperms. Almost all agricultural crops are angiosperms. Key evolutionary development was the flower (structures that enhance sexual reproduction via scent, shape, and color attraction of pollinators)Seed is enclosed in a fruit wall. (ovary) Fungi Absorptive heterotrophs that digest organic material outside the body and absorb the breakdown products. Three major groups Zygomycetes (molds)Ascomycetes (sac fungi)Basidiomycetes (club fingi)Evolutionary Innovation of Fungi Multicellular except yeasts (single-celled)Heterotrophy Network of fine, colorless hair-like threads called hyphae that absorb nutrients. Mycorrhizal fungi are fungi associated with plant root systems. Form a mat of hyphae which draws in more water and nutrients for the plant. (Inquiry lab?)Fruiting body (mushroom): structures that release sexual spores for mating via sexual reproduction (can do both)Spores can survive for long periods of time in dormant states. Wait for favorable conditions. Kingdom Animalia Multicellular digestive heterotrophsPhyla within Animalia **Shape of Life Videos Diagram **pg. 303Sponges Cnidarians Flatworms Mollusks (Dissection)Annelids (Dissection)NematodesArthropods (crustaceans, spiders, and insects)Echinoderms (Dissection)Chordates (fish, birds, reptiles, amphibians (Dissection), and mammals)Diagram cladogram pg. 304Characteristics of Animals Presences of a notochord enclosed in a vertebrae (bone or cartilage) Body plan Exhibit symmetry Asymmetrical (sponges)Radial symmetry (cnidarians)Bilateral symmetry (chordates) Paired arrangement of limbs Locomotion Segmentation Repeated units known as segments. Mammals Body hair, sweat glands, and milk produced via mammary glands. Three categories Eutherians Offspring are nourished inside the mother’s body via the placenta. (95% of mammals)Marsupials Simple placenta that results in offspring being born early and complete development in an external pouch. Found primarily in Australia and New Zealand. MonotremesEgg laying mammals that lack a placenta. Includes Platypus and Echidna species. **Remainder of Ch. 17 (pg. 307 and on will be addressed in Evolution Unit) Assessment: Designing a preserve / zoo – Diversity Project (Beginning ) and Exam Unit 4: Ecology Time: 6 weeks Unit 2: Ecology Section 1: Biosphere and Ecosystems Case Study: Biosphere (watch video as well)Ecology Biosphere: Includes all parts of Earth in which life exists. Ecology: Study of interactions among organisms, populations, and communities and their interactions with their environment. Think-Pair-Share: Why study ecology?Biotic and Abiotic Factors Biotic: Any living part of the environment with which an organism might interact. Abiotic: Any nonliving part of the environment, such as sunlight, heat, precipitation, humidity, wind or water currents, and soil type. Environments represent a mix of these factors. Modeling Global Systems Models allow us to show systems, the processes that operate within each system, and ways those systems and processes interact. Biosphere Atmosphere HydrosphereGeosphere Climate, Weather, and LifeClimate: patterns and averages of temperature, precipitation, clouds, and wind over many years. (30+) *More predictable Weather: Consists of short-term changes in temperature, precipitation, clouds, and wind from day to day or minute to minute. Global Climate System (4 parts)Solar Energy and the Greenhouse Effect Earth’s average temperature is determined by the balance between the amount of heat that stays in the atmosphere and the amount of heat lost to space. Atmosphere (greenhouse gases) absorbs sunlight that bounces off Earth’s surface. Gases include: Carbon dioxide, methane, and water vapor. Without greenhouse effect, Earth’s temp would be 30 degrees Celsius cooler. Latitude and Solar Energy Earth is tilted at 23.5 degrees, so certain regions have specific climate zones. Tropical zone: most direct 0 to 23.5 degrees N and STemperate zone: Less direct 23.5 to 66.5 degrees N and SPolar zone: Least direct up to 90 degrees N and SLab: Can Earth’s Surface also impact temperature?Differential heating and Global Winds Unequal heating creates wind and ocean currents. Warm air rises at equators and spreads north and south losing heat. As air cools, it becomes dense and sinks at poles creating convection cells. Ocean Currents Driven and shaped by patterns of warming and cooling by winds and location of continents. Surface currents, such as the Gulf Stream and California Current, can impact coastal climates by influencing water temperature and salinity. Deep ocean currents rise and sink via upwelling and are influenced by El Nino. Regional Climates Influenced by latitude, transport of heat and moisture by winds and ocean currents, and by geographic features such as mountain ranges, large bodies of water, and ocean currents. Ex: Colorado or Oregon Rain shadow EffectChanges in Climate Includes changes in temperature, clouds, winds, pattern and amount of precipitation, and the frequency and severity of extreme weather events. Nonhuman causes: Solar energy, Earth’s orbit (varies every 100,000 years), meteorite impacts, changes in continents and oceans, mountain building, volcanic activity. Human causes: Deforestation, pollution HWK: Climate Change WorksheetsChanges that occur too quickly = mass extinction 5 have occurred and 6th is happening now. Ecological Footprints Total area of healthy land and water ecosystems needed to provide the resources you use. Include use of energy, food, water, and shelter, and your production of wastes. The average American has an ecological footprint more than four times larger than the global average. 2x more than England and Japan6x more than China Age of Humans The Great Acceleration Began around the 1950s: Burned more fossil fuels, farmed more land enriched with fertilizers, caught more fish, death rates fell dramatically, birth rates stayed high, energy use increased. What are the cause and effects of this?Anthropocene Age of humans is the period during which human activity has become the major cause of global change. Altered ? of all land, increased greenhouse gas levels, disrupted the nitrogen cycle. 6th mass extinction () Human Causes of Global Change Changing Atmosphere and Climate (climate change and global warming)Causes organisms to adapt, move, or go extinct. Climate change and global warmingAcid rainOcean acidification (coral reefs, shellfish dying) *Demo egg in vinegarNitrogen enrichment and algal blooms Changes in Land UseDeforestation can affect water quality and soil erosion. Monoculture: growing large areas of a single, highly productive crop but requires a lot of fertilizers and pesticides. Changes and degrades soil structure. Reforestation Development and Urbanization Habitat loss, fragmentation (decreases biodiversity), and restoration. Hunting and fishing (overhunting and overfishing / poaching)Introduction of invasive speciesPollution Harmful materials created as a result of human activity and released to environment. Includes:CFCs destroy the ozone layer (absorbs UV radiation)Smog (ozone at ground level) Biological magnification (pollutants are concentrated as they pass through trophic levels) Ex: DDT and bald eagle population **Image. PCBs or polychlorinated biphenyls Heavy metals such as cadmium, lead, mercury, and zinc. Biomes Described in terms of abiotic and biotic factors that are summarized in climate diagrams. Vary by region. **Print off Pages!!!Terrestrial Biomes (Planet Earth Episode 1)Tropical Rain Forest Tropical Grassland/SavannahDesert (hot and cold)Temperate GrasslandChaparral Temperate Forest Boreal Forest / TaigaTundra Polar Regions (frozen sea ice up to 5 km thick)Aquatic Biomes Marine Ecosystems Described by salinity, depth, temperature, flow rate, and concentrations of dissolved nutrients. Water Depth influences life Photic zone: sunlit zone that ranges from few meters to 200 meters. Aphotic zone: Area in which sunlight doesn’t reach. Most food chains are based on phytoplankton. Regions of Marine Ecosystems Intertidal ZoneCoastal Ocean Open Ocean Photic Open Ocean Aphotic Freshwater Ecosystems 3% of Earth’s surface Regions Rivers and StreamsLakes and PondsWetlands (bogs, marshes, and swamps)What is the difference? Think-Pair-ShareEstuariesWetland formed when the river meets the ocean. Mixture of salt and freshwater. Spawning and nursery for many fish and shellfish including bluefish, striped bass, shrimp, and crabs. Mangrove swamps = Florida Everglades = tropical estuaries. Case Study Wrap-up: In Class Discussion Ecosystems Energy, Producers, and Consumers Primary Producers: First producers of energy rich compounds that be can be used by other organisms. Autotrophs = make own food. Photosynthesis (Carbon dioxide + water = sugar + oxygen + energy)Without light organism undergo chemosynthesis (carbon dioxide + oxygen + hydrogen sulfide + chemical energy = carbohydrates + sulfur compounds)Consumers Heterotrophs = obtain food from other organismsTypesHerbivoresCarnivoresScavengersOmnivoresDecomposersDetritivores Lesson Check: Where does energy flow from a nonliving source to a herbivore? Analyzing data graphs. Energy Flow in Ecosystems Food Chains Series of organisms in which energy is transferred from one organism to another. Food WebsNetwork of feed interactions through which both energy and matter move. HWK: Food Webs and Disturbance: How does your invasive species disturb the natural food web? Ecological Pyramids Utilized to show the relative amount of energy or matter contained with each trophic level (step in food chain) 10% rule: About 10% of energy is passed on to the next trophic level and 90% is lost as heat via metabolic heat. Example: Producer 100%, first level consumer 10%, second level 1%, 0.1% third level. Lesson Check: Imagine you have a five-step food chain. If 100% of the energy is available at the first trophic level, what percentage of energy is available at the highest trophic level? Cycles of Matter Matter and Energy are never created or destroyed in an environment, they are recycled via biogeochemical cycles. Driven by:Biological processes Geological processes Physical and chemical processes Human activities Types of Cycles Water Cycle Carbon Cycle Carbon source vs sinkNitrogen CycleNitrogen fixation and denitrification Phosphorus Cycle Sulfur Cycle Nutrient Limitation Net Primary Productivity describes an environment’s rate at which primary producers create new organic material. Can be limited by availability of nutrients such as geological processes. (land = nitrogen, aquatic = nitrogen)HWK: Nutrient Cycling Questions Part B: Populations and Communities How do populations grow?PBL connection: How do you invasive species grow in their new environment? Example: Lion Fish Describing populations Geographic range (natural vs new range-connection to invasive species)Growth rate (increase, decrease, stay the same – connection to invasives)Density and distribution Number of individuals found per unit area = population density Describes way individuals are spaced out across their range. Random, clumped, or uniform. Age structure (age and sex of individuals: Why is this important?)Population Growth Factors that can impact population growthBirth and death rates (Hunting connection) Emigration and Immigration Estimating Population Size Grid method Mark and Recapture Random Sampling HWK/Lab: Estimating Population Size Worksheet Types of Population Growth Exponential Growth Under ideal conditions with unlimited resources, a population will increase exponentially. Larger the population gets = faster it grows. Ex: Human population. Graphing results in a J curve. Occurs with organisms that reproduce fast (bacteria) and slow (elephants) and with organisms in new environments (invasive species). Logistic Growth Occurs when a population’s growth slows and then stops, following a period of exponential growth. Phase 1: Population grows rapidlyPhase 2: Growth slows down (Why?)Phase 3: Growth stops (Why?)Results in an S-shaped curve**In Class: Interpreting Ecological Data Carrying Capacity Maximum number of individuals of a particular species that an environment can support. What factors would impact this?If it falls low enough, populations are wiped out leading to mass extinction. HWK: Khababi Case Study Limits to Population Growth Limiting factor: Any factor that controls the growth of a population and can be abiotic or biotic. Determine the carrying capacity. Types of Limiting Factors Density-Dependent Operate strongly based on population density. Includes: competition, stress from overcrowding, parasitism, disease, predation, and herbivory. Predator-Prey Relationships Cyclical fluctuations In Class Activity: Deer PopulationDensity-Independent Affecting all populations regardless of population size or density. Includes: Environmental extremes such as hurricanes, droughts, or floods, natural disasters such as wildfires. In some cases, density independent factors are not truly density independent. Controlling Invasive Species Lesson Check: What kinds of limiting factors could help control a population of invasive species? Section Assessment: Cicada Lab Communities and Ecosystem Dynamics **Introduce with Yellowstone Case Study Habitats, Niches, and Special Interactions Communities are defined as an assemblage of populations in the same area and the interactions that occur during. Habitat: an area with a particular combination of physical and biological environmental factors that affect which organisms can live within it. What determines a habitat? Tolerance: variety of environmental conditions within which it can survive and reproduce. Allows organisms food, energy, growth, and reproduction or simply to maintain homeostasis. Graph pg. 176. What happens when conditions change? Polar Bears Example. NichesDescribes where an organisms lives and what it does via its interactions with biotic and abiotic factors. Set types of resources. Resource partitioning: division of limited resources by species to help avoid competition in an ecological niche. Lesson Check: In Class Activity: Niche and Resource Partitioning Activity!Competition Intraspecific (same species) and Interspecific competition (different species)Competitive Exclusion Principle States that no two species can occupy exactly the same niche in exactly the same habitat at exactly the same time. If so, one species will exclude the other species or one species must change their lifestyle to coexist. (Resource partitioning)Competitive RelationshipsPredator-PreyHerbivore-PlantKeystone Species ( ) Introduce Concept with a Video (19 minutes)Plays a vital and unique role in maintaining structure, stability, and diversity in an ecosystem. Ex: Otters on the Pacific coast, Sea Stars, etc. **Based on the Case Study would you consider wolves in Yellowstone to be a keystone species?Symbioses Interdependent relationship between two species. Three main types:Commensalism (whale and barnacles)Mutualism (sea anemone and clownfish)Parasitism (tapeworms and humans)*In class activity: What type of relationship is this? Handout. SuccessionEngagement: In 1883 Krakatau erupted and left behind a tiny, barren island. By 1929, a forest with 300 plant species along with birds, lizards, bats, and insects was on the island. What changed the island? Ecological SuccessionA series of somewhat predictable events that occur in a community over time. Primary successionSuccession that begins on newly formed rock or other areas that have no remnants of an older community. Pioneer species: first species to colonize barren areas. Ex: Lichen and Mosses = broad tolerance Secondary succession Process that occurs after a disturbance affects an existing community but does not completely destroy it. Faster than primary succession. Pg. 183 diagram**Occurs after wildfires, hurricanes, volcanic eruptions, farming, logging, etc. Climax Communities Communities that are mature and unchanging are climax communities. Described via species richness and abundance. Succession after natural disturbances generally reproduce identical climax communities, but that is not the case following human caused disturbances. Why?Assessment: Designing a wildlife preserve project assessment. Unit 5: Cells Time: 4 weeks Driving Question: To create a synthetic cell, which approach is best, and why – start by making the DNA or the cell membrane?Cells: smallest and most basic unit of lifeMicroscopic, self-contained units enclosed by a protective membrane. Human body is composed of approximately 100 trillion cells. Building blocks of cells Genome: complete genetic informationDNA: large and complex molecule that acts as a set of instructions for building an organism.Structured like a twisted ladder…..a double helix. Genes: segments of DNA that code for distinct genetic characteristics. Synthetic Biology Field that aims to design and construct new biological entities with useful functions. Algae that can digest trash and produce energy, bacteria that can produce new antibiotics. Sheds light on the origin of life and how cells play a role. Cell Theory Every living thing is composed of one or more cells. Smallest unit of living things. All cells come from preexisting cells. Which statement does synthetic biology challenge?The Outside of the Cell Scientists suspect that one of the first events at the start of life was the formation of a plasma (cell) membrane. Barrier separating a cell from its external environment. Composed of two layers of phospholipids (phospholipid bilayer)Bilayer contains a hydrophilic head and a hydrophobic tail. Semipermeable Cell Transport: Through the Barrier Cell membrane contains numerous transport proteins. Gates, channels, and pumps that allow molecules to move into and out of the cell. Selective permeability: some substances can cross the membrane while others are excluded. 2 classes Carrier Protein: bind to specific molecules in order to move across the membrane. AKA receptor proteins. Channel Protein: form pores that extend across the bilayer and allow specific solutes to pass through the membrane. Types of Transport Active Transport Movement of a substance that requires an input of energy. (ATP)Regions of low concentration to regions of high concentration. Types Sodium-Potassium Pump: uses energy to pump sodium and potassium ions in and out of the cell. Exocytosis: Substances are packaged into vesicles and exported from the cell by fusing with the cell membrane. Endocytosis: section of the plasma membrane bulges inward to form a vesicle to the contents move into the cell. Receptor mediated: receptor proteins recognize specific characteristics of substances to be taken into the cell. Ex: cells taking in cholesterol. Phagocytosis: “cell eating” that engulfs very large biomolecules. Ex: immune system attacks bacteriaPinocytosis: “cell drinking” that engulfs fluids and is non-specific. Passive Transport Movement of a substance that requires no energy. Regions of high concentration to regions of low concentration. Types Diffusion (movement of small, uncharged molecules such as oxygen and carbon dioxide, from high to lower concentration)Faster = higher temperatures and large gradientOsmosis (movement of water from high to low concentration)Critical as cells are 70% water. Types of Osmotic Solutions (IV solutions)Isotonic: concentration is the same inside and outside of the cell. Hypertonic: Extracellular environment has a higher solute concentration so water flows out of the cell and the cell shrivels. Hypotonic: Extracellular environment has a lower solute concentration so water flows into the cell and the cell swells. Facilitated Diffusion (diffusion that requires transport proteins)Hydrophilic substances such as sodium and hydrogen ions and larger molecules like sugars and amino acids. Hydrophobic substances can pass easily as they mix with the central hydrophobic area. Prokaryotes vs Eukaryotes 2 types of living organisms depending on their cellular structure Prokaryotes Lack organelles or a nucleus. Smaller in shape Common in bacteria Eukaryotes Larger in shapeContain a nucleus and membraned-bound organelles Common in plants and animals. What’s in a cell? (Case Study)Nucleus Control center of the cell that contains most of the cell’s DNA Takes up 10% of the space in a cells. Contains a nuclear envelope and nuclear pores. Regulates what messages can come in and out of the nucleus. Endoplasmic Reticulum Interconnected network of sacs that are smooth or rough. Smooth ER manufacture lipids and hormones via enzymes and break down toxic compounds. Rough ER manufacture proteins via ribosomes which are attached to its surface. Golgi Apparatus Resembles a pile of flattened pancakes. Acts as a packaging and direction center. Sends proteins, lipids, and hormones to their final destination via a transport vesicle. Adds a chemical tag to each molecule it sends out. Lysosomes Organelles that act as a garbage and recycling center. Contain enzymes that degrade and break down organic molecules. Vacuoles Only found in plant cells. Act mainly as water storage in plants and can store noxious compounds that prevent animals from eating plants. MitochondriaPowerhouse of the cellMade of a double membrane and use chemical reactions to transform the energy of food into ATP (adenosine triphosphate). Site of cellular respirationChloroplasts Only found in plants. Capture energy from the sun and use it to manufacture food via photosynthesis. Contain the green pigment, chlorophyll. Cytoskeleton Protein cylinders and filaments that give the cell a framework. Gives the cell structure and movement. Allows cells to change shape. Cytoplasm or Cytosol Jelly-like fluid of the cell that contains the organelles. Ribosomes Non-membrane structures that are the site of protein synthesis. Chapter 5: How Cells Work All organisms require energy Used for growth, reproduction, defense, and to manufacture the chemical compounds that make up living cells. Obtain energy from the living or nonliving components of their environment. At the core of making or storing energy is the transfer of electrons. Cells cannot create energy from nothing so they utilize one form of energy and change it to another. Living organisms can’t get this “electricity” due to cell membrane so they get it via attached molecules. Metabolism All the chemical reactions that occur inside living cells, including those that store or release energy. Done by transferring electronsMetabolic pathways Chain of linked events in metabolism that produce chemical building blocks such as amino acids and nucleotides. Main types of metabolism Anabolism: metabolic pathways that create complex molecules from simpler forms. Require energy. Ex: Photosynthesis…..any process that makes proteins, lipids, carbs, or nucleic acids. Catabolism: metabolic pathways that release chemical energy Ex: Cellular respiration Review QuestionsWhat source of energy would plans use for anabolic reactions? Would an animal use the same kind of energy?What source of energy would plants release in catabolic reactions? Would animals release the same kind of energy?Energy carriers Carriers that deliver usable forms of energy to carry out metabolic reactions. Cells use ATP (adenosine triphosphate): small, energy rich organic molecule that powers the movement of molecules and ions in and out of the cell, sending nerve impulses, triggering muscle contractions, and moving organelles. Also fuel enzymatic reactions. No ATP = cell deathEnergy is release when ATP loses a phosphate group and breaks down into ADP. Requires energy to make it back to ATP. Other energy carriers include: NADPH, NADH, and FADH. ATP carriers the most energy. Major metabolic pathways of life Photosynthesis: organisms capture energy from the sun and use it to create sugars from carbon dioxide and water. Light energy transforms to chemical energy. Cellular respiration: cell breaks down sugars into usable energy. Review Questions Why is photosynthesis called “primary production”?How does animal life depend on photosynthesis?Explain how photosynthesis and cellular respiration are complementary processes.Photosynthesis Takes place in the chloroplast and relies on chlorophyll which is concentrated in the thylakoids. Two stagesLight reactionsChlorophyll molecules (Photosystem II) absorb energy from sunlight and use that energy to split water via energized electrons. Splitting water produces oxygen that is released into the atmosphere. Produces electrons and protons (H+) ions which move along the electron transport chain (ETC). A proton pump then moves hydrogen ions across the cell membrane using energy via electrons. Light energizes electrons in PS I and fuels synthesis of NADPH. Hydrogen ions build up and move through ATP synthase to generate ATP for dark reactions. Light independent reactions AKA Calvin Cycle Converts carbon dioxide (taken from atmosphere) into sugar using energy from the light reactions. Rubisco, the most abundant enzyme on the planet, catalyzes the first reaction in a process called carbon fixation. Takes in CO2, ATP, and NADPH to convert carbon dioxide into a sugar (glucose). Review Questions What is the source of the carbon dioxide used for photosynthesis?Which products of the light reactions of photosynthesis does the Calvin cycle use?What are the two major products of photosynthesis?Enzymes Biological catalysts (molecules that speed up chemical reactions) that drive all metabolic reactions. Most are proteinsLife would not exist. How they work?Position substrates (molecules that will react to form new products) in a way that favors the making or breaking of chemical bonds. Molecules bind to the enzyme at its active site and triggers induced fit, which is the process where an enzyme changes shape to fit the molecule. Enzyme facilitates the reaction and releases the new product. Enzyme recycles after reaction. Factors that affect enzyme activity Temperature, pH, and salt concentration. Review Questions Why is it important that enzymes are not permanently altered when they bind with substrate molecules?How would a higher temperature or higher salt concentration make it more difficult for an enzyme to function effectively?If a cell was unable to produce a particular enzyme necessary for a metabolic pathway, describe how the absence of that enzyme would affect the cell. Cellular Respiration Takes place in the mitochondria and cytoplasm of a cell. Obtain energy by converting sugars into energy via catabolism. Carbon-carbon bonds in glucose are broken and released into the environment via carbon dioxide and water . 3 stages Glycolysis Takes place in the cytoplasm of the cell. Glucose is split to make a 3-carbon compound called pyruvate (2). Produces 2 molecules of ATP and 2 molecules of NADH. Earliest means of producing ATP in evolutionary terms. Anaerobic process (no oxygen)Used in cancer cells or muscle cells during intense exercise. Krebs Cycle AKA Citric acid cycle Pyruvate is moved into the mitochondria and is broken down via enzymes to release carbon dioxide. Enzyme is called acetyl-CoA. By-product produced in addition to carbon dioxide is citric acid. Produces a large amount of energy carriers including ATP, NADH, and FADH2. Goes through the cycle 2x. Aerobic processProduces4 ATP10 NADH2 FADH2Oxidative phosphorylation Occurs in the inner mitochondrial membrane and is an aerobic process. Generates the most ATP. Electrons and hydrogen atoms are removed from NADH and FADH2 and handed over to molecular oxygen via the electron transport chain creating water. Hydrogen ions build up and move through ATP synthase forming ATP synthesis. Generates 30 ATP. Review Questions What are the products of cellular respiration?Considering the inputs and products of each process, why is cellular respiration considered the reciprocal process to photosynthesis?Which of the three stages of cellular respiration could organisms have used 4 billion years ago, before photosynthesis by cyanobacteria released oxygen into the atmosphere?Fermentation Anaerobic process. Glycolysis still occurs as long as the cell contains NAD+ supplies and breaks down glucose to pyruvate. Two routes following glycolysis:Alcoholic fermentationUses NADH to break down pyruvate into ethanol (alcohol) and carbon dioxide. Common in yeasts and is used to make alcohols. Lactic Acid FermentationUses NADH to break down pyruvate into Lactic acid. Occurs in muscle cells and is directly responsible for muscle soreness. Both produce about two ATP. Review Questions Which product released by fermentation accounts for the bubbles in beer?Bakers yeast breads rely on fermentation, allowing bread to rise before baking. Describe what is occurring with the yeast as the bread rises. Explain in your own words by lactic acid builds up in your muscles during strenuous physical activity. Chapter 6: Cellular Division Driving Question: What evidence is there that some chemicals in plastics can impact cell division? Cell Cycle Sequence of events that make up the life of a typical eukaryotic cell. Time it takes depends on the organism, the type of cell, and the life stage of the organism. Ex: Humans take 24 hours. 2 main stages Interphase Longest stage where cells spend 90% of their life span. Cells take in nutrients, manufacture proteins, expand in size, and conduct special functions. 3 intervals G1 phase: first phase of life where cells grow and ready for replication. S phase: Cell prepares for replication and copies its DNA. G2 phase: Checks are made to ensure that conditions are suitable for cell division to take place. G0 phase: non dividing phase where many cells reside for a few days or permanently (nervous system cells). Cell Division Last stage in the cell cycle of an individual cell. Contains 2x the DNA in order to reproduce new cells OR to grow and repair a multicellular organism. Complete mitosis or meiosis. Asexual reproduction Generates clones which are offspring that are genetically identical to the parent. Binary fission: cell copies the circular chromosome and each daughter cell receives one copy of the DNA loop. Results in two identical cells. Mitosis is also asexual. Sexual reproduction Production of egg and sperm cells. Meiosis Produces offspring that contain half of their genetic information from mom and half from dad. Mitosis Type of cell division that generates two genetically identical daughter cells from a single parent cells. Steps Interphase: Chromosomes are replicated during the S phase before mitosis begins. Prophase: Chromosomes condense and attach to the mitotic spindle (cytoskeleton proteins). Nuclear envelope breaks down. Metaphase: Mitotic spindle aligns the replicated chromosomes (sister chromatids) at the center of the cell. Anaphase: Sister chromatids are separated and become individual chromosomes. Move toward opposite poles of the cell. Telophase: New chromosomes reach poles and the nuclear envelope reforms. Chromatin decondenses. Cytokinesis: Cytoplasm divides and the cell physically separates into two, diploid cells or somatic cells. Meiosis Specialized type of cell division that kicks off sexual reproduction and produces four haploid cells or gametes. Fertilization: fusion of two gametes to form a single cell called a zygote which forms a diploid set of information (homologous pair). Steps of Meiosis Meiosis I: Reduces the chromosome number to haploid by separating one of each homologous pair into two different daughter cells. Very similar to mitosis. Separates maternal and paternal chromosomes. Meiosis II: separates each sister chromatid into two different daughter cells. Provides segregation of chromosomes. Produces four haploid daughter cells. Creates genetic diversity in two ways Crossing over: physical exchange of identical chromosomal segments between nonsister chromatids. Undergo genetic recombination and create diversity and variation. Independent assortment: random distribution of the homologous chromosomes into daughter cells during meiosis. Cancer and the Cell Cycle Runaway cell division due to damaged or non-functioning cell cycle regulatory proteins. Creates a tumor (cell mass) Benign: remained confined to one site, not life threatening. Malignant: tumors that spread or metastasize to other areas. Undergo angiogenesis: formation of new blood vessels. Carcinogens Cancer causing materials that damage the DNA of a cell. Ex: cigarettes, BPA in plastic, radiationAssessment: Exam Unit 6: Genetics and Heredity Time: 6 weeks Driving Question 1: What can variation in dogs teach us about heredity or inheritance of traits? Traits: any inherited characteristic of an organism that can be observed or detected in some manner. Invariant traits: Same in all individuals of the species. Variant traits: Different variations of traits within a group. Types of traits (variant or invariant)Physical traits: traits relating to physical structure. (shape, color, height, etc.)Biochemical traits: traits relating to specific chemical processes of an individual Behavioral traits: traits relating to specific behaviors. Getting to the Genes Genes determine genetic traits. Basic units of information that consist of a stretch of DNA located on a chromosome. Chromosomes are located in the nucleus. Genes code for proteins and the proteins construct given traits. Alleles Different versions of a given gene. (Tall vs short)Arise due to mutations = random changes in the DNA that makes a gene. Genetic diversity is due to many different alleles. Ex: Dogs are the same species but we have thousands of breeds. Genotypes and Phenotypes Genotypes are the genetic makeup of an organism made up of combinations of alleles. Typically represented by letters. Ex: BbPhenotypes are the physical expressions of the genetic makeup. Which alleles determine the expressed trait?Two types of alleles Dominant: one allele prevents a second allele from affecting the phenotype when two alleles are paired together. Represented by a capital letter. Ex: Black fur is dominant (B)Recessive: an allele that has no effect on the phenotype when paired with a dominant allele. Represented by a lower case letter. Ex: Brown fur is recessive (b)Combinations of Alleles Homozygous Carries two copies of the same allele. AKA purebreds. Can be dominant (BB) or recessive (bb). Heterozygous Carries two different alleles for a given phenotype. Usually will show the dominant trait. (Bb)Review Questions Which might you observe directly: the genotype or the phenotype?Which poodle could be heterozygous: black coat or brown coat?Can you identify with certainty the genotype of a black poodle? A brown poodle?History of Genetics Father of Genetics Gregor Mendel (Austrian monk and mathematician)Studied pea plants in the mid-1800s and discovered patterns of inheritance. Established how genes were passed on to offspring and how we could use the parental genotypes to predict offspring genotypes. Mendel’s Experiment Carried out genetic crosses Controlled mating experiment performed to examine how a particular trait is inherited. GenerationsP generation: Organisms involved in the first cross in a series of crosses. (Parental)Mendel investigated flower color by crossing true purple flowers (PP) with true white flowers (pp). F1 generation: First generation of offspring of a genetic cross. (Filial)F2 generation: Second generation of offspring due to cross of individuals from F1 generation. Mendel allowed this generation to occur through self-fertilization. Predictions Punnett Squares Grid-like diagram that shows all possible ways that two alleles can be brought together through fertilization. Probabilities Male genotypes is written on the top and the female genotype is written on the left. *Demo Generation crosses from above!!Monohybrid Crosses (one trait crossed)Mendel’s Laws Law of Segregation States that the two alleles of a gene are separated during meiosis and end up in egg or sperm cells. (Modern version, as Mendel had no idea of DNA at the time.)Law of Independent AssortmentStates that when gametes form, the two alleles of any given gene segregate during meiosis independently of any two alleles of other genes. Ex: Seed shape and color are independent of each other. Discovered via a dihybrid cross. (Write below)Mendel’s and Today’s Genetics Mendelian Traits Traits controlled by a single gene and unaffected by environmental conditions. Chromosome Theory of Inheritance Genes are located on chromosomes and these chromosomes are the basis for all inheritance. Describes the mechanisms of Mendel’s laws by identifying that chromosomes are the paired factors. Mendel’s original laws made no mention of genes or chromosomes as they were not discovered at the time. Unique Combinations of Genetics Genomes Complete genetic sequences of an organism. Helpful in identifying traits that are specific to certain groups of organisms via unique circumstances. Questions Boxers are far more inbred than poodles. Why does that inbreeding make the former a better target for genetic studies of disease than the latter?Explain why a geneticist interested in finding a gene linked to cancer would want to look at the DNA of golden retrievers with and without cancer?Special Circumstances Incomplete Dominance A situation in which neither allele is able to exert its full effect, so a heterozygous individual will exhibit an intermediate phenotype. Demo with a Punnett Square Large dogs (II) and small dogs (BB)Codominance Situation in which the effect of the two alleles is equally visible in the phenotype of the heterozygote. Ex: Roan coat in horses or cattle, Dog gums (pink with black spots), Blood type (AB) *Demo Punnett Square Complex Traits Complex Traits are genetic traits whose pattern of inheritance cannot be predicted by Mendel’s laws of inheritance. 20,000 of 24,000 genes are complex. Ex: body weight, intelligence, athleticism, and musical talent. Inheritance involving complex traits PleiotropySingle gene influences a number of different traits. Ex: One gene controls multiple skeletal traits in dogs such as shape of the skull and shape of the limbs. Polygenic Traits Single traits are controlled by more than one gene. Ex: eye, skin color, running speed, blood pressure, body size, and chronic diseases. Epistasis Occurs when phenotypic effects a gene’s allele depend on the presence of alleles for another, independently inherited gene. Example: Labs and coat color: Coat color is black (B) or brown (b), but another gene for expression (E or e) determines if pigment is deposited. Black labs: BB, EE or Bb, EeBrown labs: bb, EE or bb, EeYellow labs: ee (no pigment is deposited)Environmental Effects Body temperature, carbon dioxide levels in the blood, external temperature, and amount of sunlight can impact the expression of genes. Ex: Siamese cats: have a gene that codes for melanin. Melanin is not produced at warmer areas, so Siamese cats have melanin only in their paws, tail, nose, and ears. Chromosomes and Human Genetics Genetic Disorders Diseases that are caused by inherited mutations passed down from a parent to a child. Can track and identify, but cannot intervene. Pedigrees (Family Pedigree Project)A chart similar to a family tree that shows genetic relationships among family members over two or more generations. Analyze information in order to learn about inheritance of particular traits or disorders. Symbols and rules for constructing pedigreesRoman numerals identify different generationsCircles represent females; squares represent malesOpen symbols represent unaffected individuals; filed symbols represent affected individuals. Numbers listed below the symbols ID individuals of a given generation. Chromosomes and Disorders All species have a characteristic number of chromosomes. (Humans = 46 chromosomes, 23 pairs)Sex chromosomes: one pair that determines if an organism is male or female. X or Y. Autosomes: all other chromosomes and are homologous (identical in length, shape, and genes they carry)Karyotypes A photograph of a cell’s chromosomes during mitosis and pair up each set of homologous chromosomes. Questions Is the karyotype in your book that of a male or female?How would the karyotype of a person with Down syndrome differ from this karyotype? *Hint: Down syndrome is called Tisomy-21. The size of a chromosome correlates roughly with the number of genes residing on it. Why are an extra copy of chromosome 21 and a missing Y chromosome two of the least damaging chromosomal abnormalities?Chromosomal Abnormalities Any change in the chromosome number or structure, compared to a typical number for a species. Changes in overall number Changes in chromosome structure Review Questions What are the odds that a given egg cell will contain an X chromosome? A Y chromosome? What are those odds for a sperm cell?If a couple has two daughters, does that mean their next two children are more likely to be sons?Sisters share the same X chromosome inherited from their father, but they may inherit different X chromosomes from their mother. What is the probability that brothers share the same Y chromosome? What is the probability that brothers hare the same X chromosome?Chromosome Structure and Traits Sex Chromosomes are Different 1,240 of 20,000 genes are found on the sex chromosomes and 1,180 are found on the X chromosome. Sex-Linked Genes X or Y linked. Genetic Crosses with Punnett SquaresSRY Gene Sex-determining region on the Y chromosome. Master sex switchGene is absent = female Intersex Disorder XY chromosomal makeup, but a nonfunctioning SRY gene. Genetically male, but phenotypically female. Types of Chromosomal Abnormalities Deletion: a segment of the chromosome breaks off and is lost. Inversion: a segment breaks off and is reattached in reverse order. Translocation: a segment breaks off one chromosome and becomes attached to a different nonhomologous chromosome. Duplication: chromosome becomes longer after acquiring an extra copy of one of its chromosome segments. X-Linked Disorders Genetic carriers Individuals who have only one copy of a recessive allele. Don’t express the disorder but carry and can pass on the gene for the disorder. Women are normally carries, while males are directly impacted by X-linked disorders. Ex: red-green color blindness, hemophilia, muscular dystrophy. Ex: Demo hemophilia with Punnett Square Review Questions No known genetic disorders are encoded on the Y chromosome. Why do you think this is?Explain why most single-gene disorders are recessive rather than dominant. Recessive and Dominant Genetic Disorders Recessive Genetic Disorders Both sexes are equally likely to be affected by recessive genetic disorders on autosomes. Vary in severityEx: Cystic fibrosis, sickle-cell, Tay-sachs, lactose intolerance. QuestionsTwo carrier parents of cystic fibrosis are having a baby. What are the odds they will be unaffected? Carriers? Affected?Dominant Genetic Disorder Caused by an autosomal dominant allele. Allele that causes disorder can not hide. Rare because a dominant disorder often produces serious negative effects immediately after birth and rarely live long enough to reproduce. More commonly caused by mutations. Ex: Achondroplasia and Huntington disease Questions A noncarrier mother and an affected father have a baby. What are the chances the baby will inherit the genetic disorder? Be unaffected?Screening and Treatment of Genetic Disorders Prenatal Screening AmniocentesisA needle is inserted through the abdomen into the uterus to extract a small amount of amniotic fluid to examine fetal cells. Chorionic villus sampling (CVS)Physician uses ultrasound to guide a narrow tube through the vagina and into her uterus to extract a cluster of cells (villi) via suction to examine. Risks Vaginal cramping, miscarriage, and premature birth (All very rare.)Treatment Gene Therapy Method of genetic engineering (permanent introduction of one or more genes into a cell, tissue, or organism.)Steps Cells are removed from the patient. A virus is altered in the lab so that it is no longer disease causing. A healthy copy of the patient’s missing or damaged gene is inserted into the virus. The virus is mixed with patient cells. The cells integrate the new gene into their genomes. The genetically altered cells are injected back into the patient. The new gene causes cells to produce desired protein. Risks Develop side effects of virus Chapters 9/10 DNA and Genes DNA Structure (KINEX Activity) DNA (Deoxyribonucleic acid): the genetic code of life. Structure is built from two parallel strands of repeating units called nucleotides. Discovered by James Watson and Francis Crick with the help of Rosalind Franklin and Maurice Wilkins. Nucleotides consist of a sugar deoxyribose, a phosphate group, and one of four bases. Bases: Adenine, Cytosine, Guanine, and Thymine. Nucleotides are connected by covalent bonds between each nucleotide and the sugar. DNA strands are connected by hydrogen bonds. The strands twist to form a double helix shape. Base pairing rules for nucleotides Adenine pairs with Thymine Cytosine pairs with Guanine Genomes contain millions of nucleotides. Ex: Humans contain 3.2 billion base pairs, Tomato has 900 million base pairs, and a pig has 3 billion base pairs. Differences in DNA result in different species and different phenotypes within a species. More similar the strand = more closely related the organisms. RNA Structure Single stranded molecules consisting of a ribose sugar and four nucleotide bases. Nucleotide bases include Adenine, Guanine, Cytosine, and Uracil. Base pairing: Adenine and Uracil, Cytosine and Guanine. Found in prokaryotic organisms. DNA Duplication Replication of a DNA molecule. Reason why viral DNA remains in our genomes today. Occurs prior to a cell entering mitosis. Takes about 8 hours in humans. Three Steps DNA molecule unwinds through special proteins called helicase enzymes that bind at origins of replication and break hydrogen bonds. Each strand is used as a template for the construction of a new strand of DNA. DNA polymerase (an enzyme) is used to build two new strands starting from primers and pairs complimentary nucleotides. Construction completes and there are two, identical copies of the original DNA molecule. DNA polymerase proofreads the strand to check and fix errors and DNA ligase seals up the fragments. Known as a semiconservative replicationOld strands are saved and reused as templates for new strands. Genetic Technology and DNA Replication Polymerase Chain Reaction (PCR)Technique that produces millions of copies of a targeted DNA sequence. PCR relies on heat to unwind DNA strands. Primers are added to target and start the replication process. DNA polymerase and loose nucleotides are added to produce new, complimentary strands. Process repeated 25-40 times to replicate millions of copies of DNA. CRISPRComposed of two RNA molecules and two Cas9 proteins. Acts like a delete key and Cas9 proteins cut through both strands of the target DNA. The DNA sequence between the cut sites is removed and the remaining DNA is relinked. What is the benefit of this technology?Gel Electrophoresis and DNA Fingerprinting DNA Mutations Mutations: Change to the sequence of nucleotides in an organism’s DNA. Types Point mutation: change in a single base pair. Substitution: One nucleotide is substituted for another in the DNA sequence. Insertion/Deletion: Nucleotides are inserted into or deleted from a DNA sequence. Can cause a frameshift mutation, which results in a change to the entire strand. Also can be silent mutations, ones that have no effect on the resulting protein. DNA Repair Repair proteins detect and tag the damaged DNA strand. Repair enzymes (DNA polymerase) cut the DNA on both sides of the damage. Damaged segment of DNA is removed and degraded. A repair DNA polymerase fills the gap in the DNA with correct sequence. 99% effective. Gene Expression Process in which genes are transcribed into RNA and then translated to make proteins. Used extensively in biopharming. Developing vaccines in plants instead of animals. (Discuss process via pg. 175)Two-Step Dance of Gene Expression Transcription: DNA to RNARNA Polymerase binds to a segment of DNA near the beginning of the gene called a promotor. Takes place in the nucleus. RNA polymerase unzips DNA double helix, separating a short portion of the two strands. One strand is used as a template strand. RNA polymerase moves down the template strand and constructs a messenger RNA (mRNA) molecule. Follows the RNA base pairing rules. Transcription stops when the RNA polymerase reads a special sequence of bases called a terminator. mRNA strand undergoes chemical modifications and undergoes RNA splicing as it prepares to leave the nucleus. RNA splicing snips out introns (stretches of sequences that don’t code for anything). Splices exons (stretches that code for building proteins) together. Translation: RNA to Protein Process by which ribosomes convert the information in mRNA into proteins. Ribosomes read the mRNA in sets of three bases at a time called a codon. 64 possible codons specify amino acids. Start codon (AUG) is the ribosome’s starting point and it will end at three possible stop codons (UAA, UAG, and UGA). Codons contain information for the genetic code. Steps mRNA molecules must first bind to a ribosome. Ribosome scans through the mRNA until it finds a start codon. Ribosome recruits transfer RNA (tRNA) one by one to attach amino acids together. Each tRNA contains an anticodon which is the complimentary pair to the codon on the mRNA. Ribosomal RNA (rRNA) creates covalent bonds to hold amino acids together. Ribosome reaches a stop codon, the mRNA strand and amino acid chain separate from the ribosome. The new protein folds into its specific 3D shape. mRNA strands are read to determine the amino acid using the amino acid chart. Unit 7: Evolution Time: 6 weeks Driving Question 1: What evidence is there that modern-day whales evolved from terrestrial ancestors?Evolution Change in the inherited characteristics of a group of organisms over generations. Whales evolved from four-legged land living animals. Evidence of evolution consists of:Features from existing organisms (Fossils)Shared characteristicsEmbryological evidenceDNA evidence Geographic evidence Artificial selection Artificial to Natural Dogs are an example of evolution that we can directly observe. Evolved from wolves and began 16,000 years ago. Bred for desired qualities. Artificial Selection Use of selective breeding to allow individuals with certain inherited characteristics to mate. Used for dogs, domesticated organisms, ornamental flowers, pet birds, and food crops. Natural Selection (Teach using Simulation) Process by which individuals with advantageous inherited characteristics for a particular environment survive and reproduce at a higher rate than do individuals with other, less useful characteristics. “Survival of the fittest.”Organisms that produces more offspring causes those characteristics to become more common in the next generations. Based on adaptations. Evolutionary process by which a population becomes better matched to its environment over time. Example: Darwin and his finches. Fossil Secrets Fossils are the mineralized remains of formerly living organisms or the impressions of formerly living organisms. Preserved in amber Preserved imprints (tracks, nests, burrows)Completely mineralized bone and wood. Fossil record enables biologists to reconstruct the history of life. Depth from the surface of Earth indicates its order in the fossil record. Older = deeper. Evolutionary biologists look for transitional fossils. Evidence of species with some similarities to the ancestral group and some similarities to the descendant groups. Example: A fossil that contains land-living mammal characteristics AND whale characteristics. Adaptive traits Features that give an individual improved function in a competitive environment. Examples: Early land-living whale ancestors had thicker bone structure to float in water. Bats have echolocation, and stick insects mimicking plants. The Ultimate Family Tree Common ancestors and common descent Common ancestor refers to the organism from which many species have evolved. If a groups of organisms share a common ancestor they have common descent. Multiple species that split from one species, show homologous traits. Similar features due to common descent. Mammals share a common limb bone pattern of one bone, two bones, many bones, phalanges. (Human arm, bat wing, whale fin)Vestigial traits Another type of trait that many organisms have because of a common ancestor. Key features of the evolutionary past, but are no longer used. Appear reduced or degenerated. Examples Whales have a femur and muscles for external ears. Snakes have reduced hind legs. Humans have the appendix and wisdom teeth. Clues in the CodeDNA Sequence Similarity (Whale DNA Activity) Measure of how closely related two DNA molecules are to each other. Closer the relatedness, the more recent a common ancestor that we have. Human and Chimpanzee insulin genes are 98% similar. Human and Mice insulin genes are 83% similar. Human and Chicken insulin genes are 72% similar. Birthplace of Wales: Biogeogrpahic evidence for Evolution Plate Tectonics Earth’s continents are on tectonic plates that slowly move over time via continental drift. Pangea was a massive, single continent that formed 250 million years ago and began to split apart 200 million years ago. Biogeography Geographic locations where fossils will be found for related species. Example: Fully aquatic whale ancestors are found in Pakistan and Canada. Growing Together Embryonic development Study of developing embryos and observing shared patterns. Caused by descent from a common ancestor. 413385024193500Manner at which an embryo develops mirrors ancestral forms. Examples:Fish, reptiles, birds, and humansMechanisms of Evolution Driving Question 2: How do bacteria develop resistance?Macro vs Micro Evolution Macroevolution Large scale evolution that takes place over thousands and millions of years. Examples: Humans, dogs, etc. Microevolution Small scale evolution that is observable. Takes place over hours, days or years. Examples: Bacteria and Viruses Natural selection results in resistance to antibiotics and vaccines. Concept Questions What is natural selection selecting for when bacteria and viruses evolve from year to year?Why do bacteria that are not genetically resistant to antibiotics die out when exposed to antibiotics?Why would an antibiotic be similar to a strainer?Allele Frequencies Charles Darwin and Alfred Wallace came to the conclusion that species descend with modification from ancestor species and new species arise. Allele frequencies in a population change over time and that drives evolution. As allele frequencies change, the phenotypes of a population change as well. Populations evolve, individuals do not. Hardy Weinberg Equilibrium Principle that states that genetic variation in a population will remain constant from generation to generation in the absence of disturbing factors. Mating is random in large populations. Four mechanisms of evolution act as disturbing factors Natural Selection (acts on the phenotype, not the genotype)Mutation Gene Flow Genetic Drift Hardy-Weinberg EquationP2 + 2pq + q2 = 1P2: frequency of homozygous dominant trait. (AA)2pq: frequency of heterozygous trait (Aa)q2: frequency of homozygous recessive trait (aa). Rising Resistance with Patterns of Selection We observe three common patters of natural selection. All share this in common: Individuals with a certain form of an inherited trait have better survival rates and produce more offspring. Directional Selection (Moth Lab)Most common pattern of natural selection. Individual at one extreme of an inherited phenotypic trait have an advantage over other individuals in the population. Example: Peppered moth. Pollution = darker tree bark = large population of dark moths. Clean air = lighter tree bark = large population of light moths. Stabilizing Selection Individuals with intermediate values of an inherited phenotypic trait have an advantage over other individuals in the population. Example: Humans and Birth Weight Light or heavy babies did not survive as well as babies of average weight. Disruptive Selection Individuals with either extreme of an inherited trait have an advantage over individuals with an intermediate phenotype. Least commonly observed in nature. Example: Beak size within a population of birds called African seed crackers During a dry season, birds with large beaks survived on hard seeds and small beaks survived on soft seeds, but intermediate sized beaks fed inefficiently and died. Convergent Evolution Any of the above patterns cause distantly related organisms to evolve similar structures because they survive and reproduce under similar environmental pressures. Convergent EvolutionOrganisms that appear very much alike despite vastly dissimilar genetics. Example: Sharks and dolphins share common characteristics, but are very distantly related. Share analogous traits, which are characteristics due to convergent evolution. Ex: streamlined bodies of sharks and dolphins. Coevolution Two or more organisms that evolve together because they depend on a relationship with each other. Example: Bees and flowers.Mutations and Gene Flow Mutations Change in the sequence of any segment of DNA in an organism and is the only way in which new alleles are generated. Create new alleles at random. All evolutionary change depends on mutation. Only mutations formed in the cells that create egg and sperm can contribute to evolution. If an organism is asexual (bacteria and viruses) it undergoes horizontal gene transfer. Process by which bacteria pass genes to one another in a structure called a plasmid. Viruses hijack cell’s reproduction mechanisms to duplicate versions of the viral proteins, which are released by causing the host cell to break open. Gene Flow Exchange of alleles between populations. Same species or different species. Occurs when gametes move from one population to another. Can be two-way gene flow can occur and counteracts the effects of the other mechanisms such as mutation. Let’s Talk About Sexual Selection Sexual Selection Nature selects a trait that increases an individual’s chance of mating even if that trait decreases the individual’s chance of survival. Most species exhibit sexual dimorphism. Species whose males and females are different in appearance.Ex: peacocks lions, ducks, humans. Females often choose whether to mate. Certain traits increase an individual’s chance of mating while decreasing their chance of survival. Ex: Male tungara frogs have complex mating calls called “chucks”, but frog eating bats use that same call to locate prey. Genetic Drift Change in allele frequencies caused by random differences in survival and reproduction among the individuals in a population. Occurs by chance and is more likely to cause evolution in a small population. Two factors can cause strong genetic drift Genetic Bottleneck Drop in the size of a population, for at least one generation, that causes a loss of genetic variation. Ex: Florida panther population plummeted in the 1970s due to hunting and habitat destruction. Led to a severe drop in genetic variation and a severe inbreeding among individuals left. Resulted in low sperm counts and abnormally shaped sperm. Gene flow was used to help improve genetic variation in the 1990s. (Cheetahs face the same issue.)Founder Effect Occurs when a small group of individuals establishes a new population isolated from its original, larger population. Ex: South Africa has a population of people called Afrikaners descended from a few Dutch colonists. Afrikaner population has an unusually high frequency of the allele that causes Huntington disease. Speciation and Adaptation Driving Question 3: What events created new species of island-dwelling lizards and sea fan corals?Leaping Lizards In 1971, biologist Eviatar Nevo captured 10 lizards on a small, rocky island of the coast of Croatia. His team released the lizards on a nearby island 3 miles away separated by a deep ocean gulf. He was interested to see what would happen, because there were already two other lizard species on the new island. Team returned in 2004. What do you think happened to the lizard species?Adaptive Traits Specific inherited characteristics that enable a species to survive and reproduce successfully in their environment. Can include:Structural features Biochemical traits Behaviors Example (lizards): fast with long legs to catch insects, territorialAdaptation Trait that is advantageous to an individual or a population. Evolutionary process of natural selection that enables a good match between a population of organisms and their environment. Natural selection does not always result in a perfect match.Extinct species represent a failure to adapt in the face of adversity. Example (lizards): They would need to adapt in order to survive. New environment was smaller and included a large supply of plants. Researchers discovered that the only species of lizard on the new island was the species that was moved there in the 1970s. Discovered, after many tests, that the new lizard was a new species that was a descendant of the original species. New traits included: larger and different shaped head, stronger bite, unique digestive tract structure, muscles to slow down food digestion. Behaviors changed as well: less territorial and more mating. Occurred in just 33 years. What makes a species?Species Members of a group that can mate with one another and produce fertile offspring. Species Concepts Biological Species Concept States that a species is a group of natural populations that can interbreed to produce fertile offspring and cannot breed with other such groups. Reproductively isolated from other populations. Doesn’t work for species who reproduce asexually. Morphological Species Concept States that a species is a group of natural populations that have similar physical characteristics and DNA sequence similarity. Doesn’t work for species who look similar, but are still separate species. Why Sex?The definition of a species is dependent on sexual reproduction. Costs of Sex Time and energy invested to find or attract mates. Parents pass on only 50% of their genetic materials to offspring. Gene combinations that have benefited parents maybe shuffled and broken apart during meiosis. Benefits of SexGenetic diversity is critical for adaptation to new environments. Sexual reproduction can help a population eliminate detrimental alleles and generate beneficial alleles. Rapid genetic change can help a population evolve resistance to parasitic infections. Speciation Process by which one species splits to form two or more species. Occurs due to genetic divergence. Accumulation of differences in the DNA sequences of genes in two or more populations of organisms over time. Two types of speciation Allopatric Speciation Occurs due to geographic isolation due to a geographic barrier such as a river, canyon, or a mountain chain. Blocks gene flow between populations. Mutations, natural selection, and genetic drift can more easily cause populations to diverge from one another. Ex: Squirrels and the Grand CanyonSympatric Speciation Occurs to ecological isolation due to reproductive isolation caused by slight differences in habitat. No geographic barrier is present. Species are similar enough to interbreed, but they become specialized in their respective habitats. Ex: Corals in the oceanReproductive Barriers Barriers that cause two species to become reproductively isolated. Two categories:Prezygotic Barriers Act before the zygote exists. Ecological isolation prevents mating. Behavioral isolation prevents mating. Mechanical isolation prevents mating. Gametic isolation prevents fertilization. Postzygotic Barriers Barriers that prevent zygote from developing and act after the zygote forms. Zygote death prevents offspring from being produced. Hybrid sterility prevents offspring from being produced. Hybrid performance causes hybrids to not be successful at mating. On the Diversity of Species 8.74 million eukaryotic species on Earth. Estimate that 86% of land species and 91% of aquatic species have not been discovered. Numbers of known species Insects: 1 millionBirds: 10,000Fish: 31,200Millipedes and centipedes: 16,100Crustaceans: 47,000Segmented worms: 16,800Fungi: 99,000Flatworms: 20,000Arachnids: 102,200Roundworms: 25,000 Plants: 310,100Mammals: 5,500Sponges: 6,000Amphibians: 6,500Reptiles: 8,700Jellyfish and Corals: 9,800Human Evolution Driving Question 4: What evidence is there that humans and Neanderthals interbred?Our Place in Mammals We are placed in class Mammalia. Humans and Neanderthals are in the order of Primates. Flexible shoulder and elbow joints5 functional fingers and toesOpposable thumbsFlat nails Brains that are large in relation to body size. Humans and Neanderthals also belong to the family of hominids (apes)Share characteristics with other apesUse of tools Capacity for symbolic language Performance of acts of deceptionFrom there we split to the hominin branch (human branch) Characteristics Thick tooth enamelUpright posture (fossilized footprints) Loss of opposable toes Split from apes about 5-7 mya99% similar to Neanderthals, 96% similar to Chimpanzees Human Evolutionary Process Split in the Hominin group Homo lineage Braincase is largerSkull and teeth depart from other apes structurally Australopithecus lineage Braincase is relatively smallSkull and teeth resemble other apes, not humansTracking DNA via Hominin Relatives Mitochondrial DNA Passed down unchanged from mother to child. Can be tracked via material lines through many generations. No mtDNA has been found in modern humans. Nuclear DNA Passed down from mother and father to child. Can also be tracked. We do have Neanderthal nuclear DNA. (1-4%)What does this mean?Hominins United Modern humans diverged from Neanderthals about 550,000 years ago. The Homo lineage Based on fossil fragments, scientists believe the earliest members originated 2-3 mya in Africa. The more complete fossils come from a species called Homo habilis Anatomically is more similar to the Australopithecus lineage but has a more rounded skull. Represents the shift from ancestral hominins to more recent species. (1.9 to 1.6 mya)Shift to more recent species including:Homo erectus (believe to be the common ancestor to modern humans and Neanderthals) 1.5 mya to 500,000 years ago (estimate)Homo floresiensis Homo heidelbergensis Homo sapiens (modern humans originating 200,000 years ago)Neanderthal DNA introduced into our genome only 90,000 to 40,000 years ago. (If Neanderthals were our common ancestor it would be much older…10x) Out of Africa Hypothesis Anatomically modern humans first evolved in Africa around 195,000 to 200,000 years ago. Migrated throughout the continents. Fossil records indicate we overlapped in time with both Homo erectus and Neanderthals, but remained distinct from them. Migrated to Europe about 40,000 years ago and coexisted with Neanderthals for 10,000 to 80,000 years before replacing all other Homo populations. Migrated to North America 18,000 years ago. Still unknown what relationships were like. Fossil evidence was found that produced a hybrid human-Neanderthal skeleton (still being studied)Suggests interbreeding took place. Assessment: Test ................
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