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B5G4 Damien Taylor (Big Idea 1 (Hardy Weinberg Equation (5 Critical values…

- - - - study of geographic distribution between extinct and extant species
        
        observe extant (living) animals traits
        
        study fossil records of extinct animals
        
        find climate during time when extinct species was alive
        
        find past biodiversity (the variety of living organisms)
    - - science of physical properties on Earth
        
        how rocks formed and changed overtime
        
        explains how Pangaea formed
        
        300 million years ago, all landmasses were connected (supercontinent)
        
        meaning that animals could migrate by land
        
        examples
        
        fossil record says mesosaurus lived in South America and Africa
        
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        marsupial animals
        
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        tectonic uplift
        
        asteroid bombardment
      - influences climate + pressures on species to migrate/ adapt/ extinct
    - - definition: study of similarities and differences in physical structures of organisms
        
        Different Ways/ Types to Compare Evolution
        
        Organization
        
        Genetic Homology
        
        comparison of organisms based on similarities in DNA/ protein sequences
        
        more reliable than comparative anatomy; analogous structures that look similar may lead to incorrect grouping on phylogenetic tree
        
        can be expressed using cladogram
        
        Taxomony
        
        classifying organisms based on morphological similarities; also not reliable
        
        can be used to organize organisms by protein/ DNA sequence. Or derived traits
        
        Comparative Embryology
        
        early stages of development of morphology can be compared between two or more different species; used for grouping evolutionary relationship
        
        Fossil Record
        
        gives record of species that lived millions of years ago, shows how extinct species disappeared, and how extant species evolved
        
        Using Transitoinal Fossils
        
        used to find missing links between two species, one that evolved form the other
        
        show sequential adaptations from one species (usually extinct) to another (that's more recent)
        
        Fossil Dating
        
        Relative Dating
        
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        Absolute Dating
        
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      - convergence
        
        example: fish, penguin, whale are distantly related, belong to different phylum. But their fins, wings, flippers serve same purpose
        
        distantly related species evolve with similar analogous structures that share a similar function
      - divergence
        
        example: whale flipper vs human hand. Both evolved to serve different functions, but anatomically consist of the same bone parts
        
        closely related species, evolve to have different homologous structures. Appear different but are the same anatomically
        
        homologous structures can lose function through evolution, become vestigial organs. (Ex: human appendix)
        
        because of this, classification based on morphology is not reliable because it's possible to group the wrong species together based on appearance (ex: flying phalanger (marsupial) and squirrel (mammal))
  - - - observable traits of a population
      - phenotype frequency
    - - genotype frequency
        
        each gene has two alleles
        
        dominant allele
        
        recessive allele
        
        Homozygous dominant AA
        
        Heterozygous Aa
        
        homozygous recessive aa
    - - P is the frequency of dominant alleles
      - Q is the frequency of recessive alleles
      - P^2 is the frequency of homozygous dominant genotype frequency
      - Q^2 is the frequency of homozygous recessive genotype frequency
      - 2pq is the frequency of heterozygous genotype frequency
      - The equation: P^2 + 2pg + Q^2
    - - no mutations because they can affect the frequencies
      - must be random mating because sex selection can cause some alleles to be higher than others
      - no natural selection
      - must be a large population so genetic drift does not impact the frequencies
      - must be a closed population
  - - - Definition: a diagram of different species'
        lineages and how they relate to one another
        
        Example
        
        primate family: hominid and lemurid vs cat family
        
        hominid and lemurid species
        
        more closely related than cat family
        
        both diverged from more recent common ancestor
        
        cat family
        
        outgroup
        
        meaning: furthest group, most unrelated species
        
        cats are the least related to the primate family
      - Structure of phylogenetic trees
        
        Representation
        
        3 primary branches= 3 domains of life
        
        archaea
        
        single-celled organisms
        
        eukaryote
        
        multicellular organisms (and unicellular) with nucleus in cells
        
        bacteria
        
        prokaryotic organisms
        
        trunk= first prokaryote
        
        unicellular cells; no membrane-bound organelles
        
        branches split into later lineages
        
        kingdom
        
        phyla
        
        classes
        
        orders
        
        families
        
        genera
        
        extinct/ extant species
        
        Features of phylogenetic diagrams
        
        taxa
        
        includes single population, entire species, genus, other level of biological classification
        
        outgroups
        
        furthest group; most unrelated species in a cladogram
        
        nodes
        
        indicates evolutionary divergence
        
        sister groups
        
        closest relative of the species focusing on
        
        common ancestors
        
        species that two groups (or more) of other species descend from
        
        clade
        
        What's a clade?
        
        analogy: collection of terminal branches, makes up other branches
        
        contains 2 or more taxa, share a node
        
        minimum: 1 clade, 1 outgoup, at least two sister groups
        
        sister groups share a derived trait
        
        cladograms vary in size, depending on # of taxa
        
        How to Construct a Cladogram
        
        Step 1: Get group of different organisms
        
        Step 2: identify derived characteristics
        
        shared traits between organisms
        
        examples
        
        nails, claws, four limbs, egg, live birth
        
        Step 3: Comparison chart of organisms and derived traits
        
        Step 4: mark organisms with same trait
        
        Step 5: make a venn diagram based on marked organsisms
        
        Step 6: construct the cladogram
        
        What is a cladogram?
        
        Example
        
        Evolution of heart chambers
        
        compares evolution between the 5 phylum chordate
        
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        based on heart morphology; each phylum= different amount of chambers
        
        Defintion
        
        diagram; shows relationship between species
  - - - Permian Event (250 million years ago)
        
        volcanism
        
        oceans becomes acidic
        
        global warming
      - Triassic Event (200 million years ago)
        
        global warming
        
        volcanism
        
        CO2 spike
      - Devonian Event (360 million years ago)
        
        terrestrial plants
        
        CO2 sequestration
        
        global cooling
      - Cretaceous Event (65 million years ago)
        
        climate change
        
        global warming
        
        meteor impact
      - Ordovician Event (443 million years ago)
        
        geologic uplift
        
        glaciation
        
        global cooling
      - Will cause:
        many global changes through Earth's history leads to bottleneck effect (many species die out) and a change in geography
      - How to find when events occurred: dating the events
        
        Absolute dating of fossils using radioisotopes
        
        molecular clock hypothesis
        
        used to find when species diverged by genetic homology analysis (sequence)
        
        How to use the molecular clock hypothesis
        
        1) find mutations in genetic homology; the number of genetic differences show when species diverged
        
        2) use genetic homology analysis to find how related other species are to each other
        
        Relative dating of fossils by biostratigraphy and fluorine dating
      - 6th Major Extinction Event
        
        Fossil Fuel Burning and Climate Change
        
        green house gases are re;eased and trapped in the atmosphere, raising average global temperature as heat= absorbed in water
        
        Human Expansion
        
        cutting down forests leads to species losing habitats
    - - two types of divergences
        
        gradualism; divergence goes through slow process of a species changing over time.
        
        punctuated equilibrium: species go through evolution at a steady rate until a sudden change in the environment occurs, causing divergence from ancestor species.
        
        How Divergence Occurs: divergence from ancestral specie/ evolution occurs by mutations accumulated in a gene pool. Sources of mutation include:
        
        Exposure to DNA alternating environment
        
        radiation
        
        chemicals can damage DNA (carcinogens)
        
        Error in internal processes, DNA altered
        
        DNA replication error
        
        DNA repair mistakes
      - Divergence and Evolution in Plants by Polyploidy
        
        self-fertilizing plants can have more than 2 copies of each chromosome from parents, unlike humans (which are diploid)
        
        Plants can become reproductively isolated when duplicating the genome; must be founder of new population to survive
        
        triploid
        
        tetraploid
        
        Types of Polyploids:
        
        autopolyploidy
        
        1 parent specie gives rise to new species (chromosomal doubling, ex: 2n=6 to 4n=12). Self-fertilization
        
        alloploiddy
        
        2 different individuals (ex: 2n=4 and 2n=6 produce hybrid 2n=10). Undergoes gamete fusion, mitotic nondisjunction, self-fertilization)
        
        ex: evolution of modern wheat bread
        
        1) einkorn (2N=14), AA, 11,000 yrs. ago x wild wheat (2N = 14), BB
        
        2) sterile hybrid, self-fertilize, 2N=14, AB
        
        -> Wilder memmer (2N=28), AA BB, 8,000 yrs. ago x wild wheat relative (2N=14), DD
        
        -> Common wheat (2N=42) AA BB DD, 8,000 yrs. ago
    - - 2) the separate populations (subpopulations) develop own gene pool
      - 3) subpopulations accumulate their own mutations
      - 1) original populations splits to two separate populations, causes post-zygotic barriers
        
        can happen when populations become isolated
        
        peripatric speciation (major genetic drift, small subgroup separated by main population)
        
        allopatric speciation (minor genetic drift, geographic barrier like river)
        
        or when populations share their geographic area
        
        sympatric speciation (niche specialization, coexisting populations)
        
        parapatric speciation (populations occupy area, no geographic barrier. Adjacent populations may be able to reproduce; distant subgroups= too isolated!)
      - 4) subpopulations will not be able to reproduce with one another over time (reproductive isolation)
        
        pre-zygotic barriers (prevent zygote formation)
        
        temporal isolation (different mating times)
        
        behavioral isolation (different mating habits)
        
        habitat isolation (geographic isolation)
        
        mechanical isolation (impossible to fertilize egg)
        
        post-zygotic barriers
        
        reduced hybrid viability (hybrid development fails)
        
        reduced hybrid fertility (sterile hybrid, ex: mule won't reproduce)
        
        gamete isolation (fertilization fails)
        
        hybrid breakdown (infertility in later generations)
    - - hypothesis for source of variation:
        
        2) medium beaked finches are hybrids of small beaked and large beaked birds
        
        3) variation in beak sizes are from natural selection and allopatric speciation
        
        1) variation from genetic drift
      - for 30 yrs, captured birds, studied traits, keeping account of phentoype+babies+deaths and climate. Had 5 conditions for area:
        
        population large enough for accurate data
        
        can easily account for all newborns
        
        closed population, no gene flow
        
        strong pressures from environment
        
        small population, easier to keep track
      - Most influential factor: size of available food
        
        directional selection from small to large beaked birds depending on weather
  - - - a process of change in the observable characteristics of a population over
        time.
      - challenged traditional views such as religions, etc
      - fossil record supports evolution
        
        strata, the layers of sedimentary rocks
        
        contains fossils
        
        compare fossils using morphology, time period
        
        able to map out the evolutionary history
        
        catastrophism
        
        explains why one strata is very different from the next
        
        mass extinctions events
        
        abrupt environmental change
        
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      - Lamark's Hypothesis of evolution
        
        principle of use and disuse
        
        idea that organisms change in response to their environment
        
        increased use meant the trait is kept and refined while decreased use meant the trait will slowly lose functionality and eventually disappear
        
        principle of transmission of acquired traits
        
        traits that organisms acquire in their life time can be directly given to their offspring
        
        Example: A giraffe acquires a long neck in its lifetime by training to eat leaves from a tall tree and its offspring will also acquire the long neck.
      - Darwin's theory of evolution
        
        5 key observations
        
        species tend to produce more offspring than the environment can carry
        
        natural population are stable
        
        each environment has limited resources
        
        individual variation within the population
        
        observable traits are passes down by inheritance
        
        3 key inferences
        
        superfecundity and a stable population keeps competition high
        
        individuals with traits better adapted in the environment out compete others
        
        the unequal survival rate will eventually lead to accumulation of the better trait
      - Natural Selection
        
        genes: carry genetic information
        
        phenotype
        
        physiology
        
        the function of living tissue
        
        Example: The function of a dog's tail is to wag
        
        morphology
        
        the study of organisms' structures
        
        innate behavior
        
        behaviors that are innate; not learned
        
        Example: dogs will drool the first time they see food and every time after
        
        these 3 factors affects
        
        fitness
        
        fecundity
        
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        ecological performance
        
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        Natural selection vs artificial selection
        
        artificial selection
        
        environment pressure is whatever the breeder wants
        
        natural selection
        
        pressure is form nature; survival
        
        both can cause a less diverse population
        
        causes punctuated equilibriums
        
        extinction
        
        adaptive radiation
  - - - Necessary for evolution
      - Mutations
        
        creates new alleles/ traits in the population
        
        Positive mutation
        
        Negative mutation
        
        Genetic shuffling to randomize the alleles
        
        sexual reproduction
        
        meiotic crossover
        
        fertilization
      - preservance of genetic variation
        
        diploidy
        
        exists in most eukaryotes; when the organism has two copies of each gene
        
        example: humans eyebrows; dominant two seperate, recessive: unibrow
        
        heterozygote advantage
        
        when heterozygous has highest fitness, which keeps both alleles in the population
        
        example: sickle cell anemia; dominant: normal blood, recessive: blood cell is deformed and carry less oxygen and can cause blood clots easily; heterozygous: has enough normal blood cells and also deformed cells that are not affected by malaria
        
        frequency dependent selection
        
        as the frequency of one allele reach a certain point, selection starts favoring the other allele
        
        example: non camouflage rabbit vs camouflage rabbit the non camoflage rabbit was hunted by dogs until the population of it was low and camoflage rabbits were easier to find so the selection switches from non camo to camo
        
        neutral variation
        
        having no selective advantage or disadvantage
    - - Phenotypic
        
        environmental
        
        Natural selection
        
        directional selection
        
        when the frequency of either homozygous dominant or recessive increases
        
        disruptive selection
        
        when the frequency of heterozygous decreases in a population
        
        stabilizing selection
        
        when the frequency of heterozygous increases in a population
        
        sex selection
        
        intersex selection
        
        when one sex chooses the other to mate( usually female)
        
        sexual dimorphism
        
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        intrasex selection
        
        male showiness
        
        agonostic behavior
        
        territorial behavior
        
        breeder's choice
        
        artificial selection
        
        taste
        
        texture
        
        visual appeal
        
        example: farmer( selector) only plant tomatoes that taste good, looks good and are big
      - non Phenotypic
        
        chance events
        
        genetic drift(within population)
        
        founder's effect: new population
        
        example: when 2 recessive white birds emigrate from their black dominant population and start a new population, the new population's gene pool will be very different
        
        bottleneck effect: catastrophic event
        
        accidental death
        
        gene flow (between populations)
        
        immigration
        
        emmigration
        
        introduces new alleles or lose current alleles
  - - - Milankovitch Cycles - cyclical changes in the Earth's circumnavigation of the sun that happen because of changes in eccentricity, axial tilt, and precesion
        
        Eccentricity is the change of the orbit's shape. It affects season lengths and can cause cool/ warm periods.
        
        Obliquity(axial tilt) is the change of the Earth's pole tilt which will change the location of the equator
        
        Procession cycles is when the earth's pole turn counter clockwise and affects season lengths and intensity
    - - Spontaneous Generation - the idea that living organism can appear from thin air
        
        Jan Baptista van Helmont's recipe: The person that wrote about the idea of spontaneous generation.
      - Pasteur's experiment
        
        Hypothesis: previously unspoiled broth left in an open container would become contaminated with microbes in the air
        
        Experimental design: contain the unspoiled broth in a goose neck flask that only allows air and traps microbes in the bend of the neck; after a year, the broth will be unspoiled; after breaking the neck, the broth quickly became cloudy from contamination
        
        the experiment disproves spontaneous generation
      - The theory on how earth was formed.
        
        Earth formed 4.5 billion years ago
        
        Excess free energy from the sun but molten earth crust was too hot for life
        
        Earth started cooling down and that allowed prebiotic chemistry to create early molecules of complex molecules such as nucleotides to form the early primordial soup
        
        primordial soup hypothesis
        
        miller urey experiment
        
        they mimicked early earth environment in a lab
        
        electric sparks: mimicks free energy
        
        gas in the early earth atmosphere
        
        water: as the soup
        
        heat source to boil water
        
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        The early primordial soup suggests that the environment's selective pressure back then was structural stability, ability to replicate itself, and to retain information, and biochemical functionalities
        
        RNA world hypothesis: RNA evolved before DNA and protein and the first cell was RNA protocell
        
        The with the wanted traits was favored by natural selection
        
        The monomers then formed the first RNA protocell
        
        After the world cooled, the first RNA monomers formed
        
        Why was DNA not the original genetic molecule?
        
        Although DNA is more stable and also able to store information, but it couldn't replicate just by itself and also lacks biochemical functionalities
        
        Why was protein not the original genetic molecule?
        
        It was structurally unstable and could not self replicate
        
        Post RNA world
        
        Deep Sea Geothermal vents
        
        Takes in inorganic material to use as energy to form the first organic molecules
        
        We know it happened in water because it is the best place for reactions to occur since water is a solvent and it helps molecules move to each other.
        
        Different types of systems
        
        Open system
        
        nothing is restricted
        
        Isolated system
        
        nothing is let in or out
        
        Closed system
        
        only let energy in and out
        
        The early earth timeline
        
        Earth forms 4.5 Billion years ago
        
        stable hydrosphere prebiotic chemistry begins 4.2-4.3 billion years ago
        
        pre RNA world 4 billion years ago
        
        RNA world and protobiont 3.7-3.8 billion
        
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  - - - 1) Kwang Jeon's amoeba colony got infected by bacteria
      - 2) some amoeba got sick and died
      - 3) survivors reproduced healthy amoebas that had the bacteria in their cytoplasm
      - 4) antibiotics killed the bacteria and amoebae
      - amoeba and bacteria developed a symbiotic relationship; evidence of endosymbiosis
        
        Different types of symbiosis
        
        commensalism; one specie benefits, other is neither helped nor harmed
        
        parasitism; one specie is benefited, the other harmed
        
        mutualism; both species benefits
      - In Eukaryotic Evolution
        
        Hypothetical Theory on How Eukaryotic Cells Evolved
        
        2) endomembrane system formed. Now has nuclear membrane, golgi apparatus, endoplasmic reticulum, vesicles.
        
        3) Eukaryote engulfs aerobic prokaryote; symbiotic relationship (mutualism) takes place. Host gives protection + nutrients, prokaryote produces ATP energy
        
        1) precursor prokaryotic cell increases in size; undergoes invagination (pinches) to increase surface area to volume ratio for nutrient uptake
        
        4) Aerobic eukaryote engulfs cyanobacterium, now a modern chloroplast
      - Evidence for Endosymbiosis
        
        1) mitochondria+chloroplast have inner and outer membrane. Shows successful endosymbiosis that preserved membranes of previous endosymbiont
        
        2) outer membranes of mitochondria and chloroplasts have transport proteins also found in bacteria membrane
        
        3) chloroplasts and mitochondria= similar size to other prokaryotes
        
        4) ribosomes of mitochondria and chloroplasts are more related to bacteria cell ribosomes than cytoplasmic eukaryotes'
        
        5) Mitochondria and chloroplasts reproduce like bacteria. (Parent cell -> 2 daughter cells)
- - - - lipid molecules
        
        hydrophobic substance
        
        non-polar molecules due to symmetric distribution of electronegativity in atom formation, repel water molecules
        
        When substance is more hydrophobic, less adhesion
        
        Some Substances are Both Hydrophillic and Hydrophobic
        
        Amphiphilic substances
        
        soap
        
        hydrophobic tail (symmetric distribution of hydrogen atoms)
        
        asymmetrical body (hydrophilic) because COO- head
        
        phospholipids
        
        synthesized through dehydration reaction, combines:
        
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        has major role in cell membrane formation, 3 classes
        
        phospholipids; form lipid bilayer of cell membrane
        
        fats, synthesized by dehydration reaction; used for energy reactions, insulate body
        
        steroids
        
        builds steroid hormones
        
        stabilizes membrane, restrict phospholipid movements
        
        balanced amount of saturated and unsaturated lipids so membrane is stable w/ effective cell communication
      - carbohydrate molecules
      - protein molecules
        
        may have both hydrophillic and hydrophobic regions, AKA integral membrane proteins/ transmembrane proteins
      - water molecules
        
        some things attracted (cohesion) to these water molecules (hydrophillic)
        
        attraction by Van der Waals forces by dipoles (partially negative/ partially positive atoms) of water molecules
        
        When substance is more hydrophillic, more adhesion
        
        asymmetrical distribution of electronegativity
      - diffusion is movement of molecules from high concentration to low concentration. Some things that can pass phospholipid bilayer by diffusion: (ONLY)
        
        because only specific molecules can diffuse, other structures are needed to fix challenge that only specific molecules can diffuse, using membrane proteins:
        
        glycolipids and glycoproteins help in cell recognition
        
        structural lipids- support membrane
        
        enzymatic proteins: involved in cell communication; help produce ATP
        
        ligand receptors; send signals from outside environment
        
        protein pumps- move particles against concentration gradient
        
        transport proteins facilitate movement of large charged molecules
        
        small, uncharged molecules
        
        small hydrophobic molecules
        
        Simple dffusion is one of the passive transports (no energy required), along with:
        
        osmosis- water diffusion (low concentration of particles to high concentration of particles)
        
        hypotonic= low concentration of particles
        
        plant placed in hypotonic solution, no change ; cell wall protects plant cell form burst
        
        animal cell placed in hypotonic solution, will burst due to increase in volume.
        
        hypertonic solution= high concentration of particles
        
        isotonic= solutions are at equilibrium; osmosis will occur until this is reached
        
        facilitated diffusion; uses membrane proteins to move molecules that can't transport by simple diffusion
        
        However, active transport uses energy to transport molecules of low concentration of water to high concentration of water
        
        endocytosis- import by phagocytosis (cell eating) or pincytosis (cell drinking), pinching off phospholipid bilayer
        
        exocytosis- export mechanisms by fusing with phospholipid bilayer
  - - - enable transport efficiency and reaction rates in small cells.
        Small cells had greater advantage during early Earth because of this.
        
        example: Metabolic reaction rates in chloroplasts (thylakoid membrane absorbs energy from light. Membrane surface area= high SA:V ratio, so reaction= faster.
      - as volume of cell decreases, surface-area-to-volume ratio increases
    - - surroundings: anything outside of cell (example: Earth)
      - Barrier: cell membrane
      - Inside the system, Compartmentalization
        
        Positive effects: forms endomembrane system to separate organelles, system derives from eukaryotes and results from invagination before endosymbiosis. Organelles in endomembrane system:
        
        endoplasmic reticulum
        
        Rough ER (has attached ribosomes)
        
        folds polypeptide
        
        builds the membranes
        
        modifies protein and phospholipids
        
        communicates with smooth ER
        
        receives synthesized polypeptides from ribsomes
        
        Smooth ER (no attached ribosomes)
        
        synthesizes lipids
        
        breaks down glycogen
        
        sends vesicles to golgi apparatus
        
        detoxifies poisons and drugs (would see a lot of this in poisoned cell)
        
        golgi apparatus
        
        receives proteins
        
        synthesizes and modifies carbohydrates
        
        proteins -> glycoproteins
        
        secretory vesicles to cell membrane
        
        nuclear envelope
        
        separates nucleus's tasks from cytoplasm
        
        has all genomic DNA
        
        double bilayer membrane
        
        controls cell's activity
        
        vesicles
        
        are small lipid bilayer copartments
        
        transports material between organelles; to and from cell membrane
        
        vacuole
        
        largest organelle in plant cells
        
        stores nutrients, wastes, pigments
        
        regulate water pressure and pH of cell
        
        lysosomes
        
        has hydrolytic enzymes
        
        digests + recycles used cell parts
        
        apoptosis
        
        phagocytized vacuole, digest food + phagocytized bacteria+ infected cells
        
        Negative effects of metabollic processes:
        
        lytic enzymes (digest food particles) in lysosomes
        
        protect cell from bacteria by killing engulfed cells to keep them from spreading
        
        but if content of lysosomes releases to cell cytoplasm, whole cell dies, so use apoptosis (self-destruction)
  - - - water cycle
        
        water getting heat up by sun turn into water vapor, then it forms cloud and come back down to the ground by rain
        
        resorvoirs
        
        oceans
        
        lakes
        
        underground water
      - carbon cycle
        
        photosynthesis(plants): uses CO2 and light to make glucose
        
        respiration(plants and animals): uses glucose and oxygen to make ATP, CO2 and H2O
      - nitrogen cycle
        
        plants need nitrogen but it can not get it directly from the air
        
        legumes: type of plants symbiotic relationship with nitrogen fixing bacteria
        
        other plants get nitrogen from soil that has nitrogen from nitrogen fixing bacteria
        
        denitrifying bacteria puts nitrogen back in the atmosphere
    - - Polar properties
        
        hydrogen bonds; oxygen end is negative end and hydrogen ends are positive because of electronegativity that affects the electrons
      - Cohesive and adhesive properties
        
        the polar properties allow water form hydrogen bonds with other molecules
        
        van der waals interaction
        
        intermolecular interactions between hydrogen atoms of water with nitrogen, oxygen, or fluorine of other polar molecules
        
        cohesion: attraction between water molecules
        
        adhesion: attraction of water molecules with other molecules
      - universal solvency
        
        water can dissolve anything that is polar
      - capillary action
        
        uses cohesion between water molecules and adhesion of water to the surface of the xylem to help water climb up xylem in plants
      - surface tension
        
        cohesion in water molecules create this effect that gives water strength
      - heat capacity
        
        water is good at retaining heat
        
        Heat of fusion: the amount of energy needed to turn water into ice
        
        Heat of vaporization: the amount of energy needed to turn water into water vapor
        
        ice is a good insulator
  - - - photosynthesis
        
        produces glucose
        
        photosynthesis action spectra
        
        photosynthesis requires absorption of light by pigments in leaves
        
        chlorophyll a transfers absorbed energy to ETC from electrons
        
        uses antenna pigments to fit absorption spectra
        
        strongest absorbance: blue, red
        
        weakest: green, yellow; green= reflected
        
        leaves change color in fall
        
        chlorophyll= chemically unstable, breaks down + resynthesizes during growing season
        
        late summer= leaves lose color, show other antenna pigments because chlorophyll production declines
        
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      - respiration
        
        turns sugar into ATP
      - primary producers
        
        ecosystem's total energy depends on it
    - - herbivore: receives energy from plants
      - carnivore: receives energy by eating other organisms
    - - gross primary productivity GPP
      - net primary productivity NPP
      - NPP = GPP - respiration
    - - every trophic level up, only 10 % of energy is kept
        
        example: light 100% to plant 10% to herbivore 1%
    - - photosynthesis: using light energy to make sugar
        
        chloroplast:organelle that does photosynthesis
        
        chlorphyll captures light
        
        chloroplast structure
        
        stroma: space inside the chloroplast
        
        chloroplast envelope
        
        intermembrane space
        
        innermembrane semi permeable
        
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        outer membrane: permeable
        
        capture and energy of Cavin Cycle has 5 key players
        
        photosystems I and II (energy absorbing protein complexes)
        
        made of:
        
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        found in thylakoid membrane
        
        absorbing wavelengths
        
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        ETC
        
        7 protein complexes:
        
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        antenna pigments (chlorophyll b, lutein, xeaxathin, b-carotene, lycopene)
        
        NADPH (electron carrying cofactor)
        
        chlorophyll a
        
        transfers energy to ETC from electrons
        
        inner membrane of chloroplast
        
        less permeable, has embedded transport proteins to facilitate selective permeability
        
        outer membrane of chloroplast
        
        permeable to most small molecules and metabolites
      - chemosynthesis: archaea bacteria use energy from inorganic molecules from hydrothermal vents in deep sea
        
        energy is passed to high trophic levels (ex: tubeworm)
    - - cellular respiration
        
        mitochondria: converts sugar into ATP using oxygen and water
        
        structure
        
        outer/inner membranes
        
        intermembrane space: contains DNA and ribosomes
        
        crista: the inner membrane is invaginated to increase surface area
        
        anaerobic respiration
        
        glycolysis
        
        stages
        
        energy investment stage 2PGALs are created and uses 2ATP
        
        electron acceptor stage: NAD+ cofactor accept 2 electrons from each PGAL to become NADH and form 2 intermediate metabolites
        
        energy harvesting stage: each PGAL is converted into pyruvate and makes 2ATP each
        
        fermentation
        
        converts NADH back to NAD+
        
        either lactic acid
        
        pyruvate=lactate (3C=2C + 1C)
        
        lactic acid build up in exercise -> oxygen debt. breathing heavy in order for fermentaion to use to replenish the NAD+ used in glycolysis. Once oxygen debt repaid, lactic acid is concerted to pyruvate (lower acid content)
        
        or ethanol (alcohol)
        
        pyruvate= ethanol + CO2
        
        Ethanol and lactic acid can be toxic to cells at high concentrations
        
        evolved in oxygen-free atmosphere; ATP= used as fuel
        
        aerobic respiration
        
        18x more ATP than anaerobic respiration
        
        structure + function of ATP:
        
        made of adenosine, attached to triphosphate side chain
        
        3 phosphate groups, linked by covalent bonds
        
        outermost group stores the most energy
        
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        produced from ADP+ phosphate during respiration; energy= released from food
        
        evolved when Earth had oxygen-rich atmosphere; result: prokaryotes became complex -> eukaryotes
        
        Reactions:
        
        KREB cycle
        
        along with glycosis, the KREB cycle is involved in catabolic and anabolic pathways
        
        catabolic pathways (energy releasing by breaking down molecules)
        
        anabolic pathways (energy absorbing by using energy to synthesize compounds)
        
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        glycosis- glucose is broken to pyruvate (catabolic) and helps to synthesize phospholipids and fats (anabolic pathway)
        
        Steps to and in KREBs Cycle
        
        3) pyruvate crosses to matrix
        
        4) pyruvate is oxidized to form acetyl-CoA and CO2. Donated electrons accepted by NAD+, reduced to NADH
        
        2) pyruvate enters intermembrane space from outer membrane
        
        5) Coenzyme A delivers acetyl to KREBs Cycle
        
        1) glucose is converted to 2 pyruvate molecules (+2 ATP , +2 NADH)
        
        6) each round of KREBs produces 2 CO2, 1 ATP, 3 NADH, 1 FADH2
        
        ETC
        
        receives 10 NADH and 2 FADH2 from KREB, fermentation, glycosis.
        
        34 ATP produced from oxidative phosphorylation
        
        releases energy from electron to ATP
        
        2 ATP per FADH2, 3 ATP per NADH produced (oxidative phosphorylation), proton gradient across inner membrane (high in intermembrane space, low in matrix); protons pass by ATP synthase
        
        NADH and FADH2= electron donors
  - - - use light energy and water as fuel to make glucose
    - - respiration
        
        glucose turns into ATP
        
        aerobic respiration
        
        anaerobic respiration
        
        fermentation
        
        glycolysis
    - - excess energy
        
        stored as fats and carbohydrates
        
        building structural and functional molecules
        
        power life sustaining processes
        
        generate heat
      - free energy
        
        population size depends on free energy in the system
        
        example:humans population is increasing because we have food, living space, everything for survival and more
    - - endotherm
        
        uses free energy to regulate body temperature
        
        allows them to do better in cold environments
        
        example:birds, humans
      - ectotherm
        
        regulated body temperature using outside sources
        
        they have to adjust behavior such as lieing in the sun when cold
        
        example: lizards
      - plants do not regulate temperature
        
        protection from cold
        
        lower freezing point
        
        removing water from cell to not get ice crystal damage
      - k strategist: low reproductive rates
        
        more parental care, more energy for each individual, take more time to mature, longer life expectancy, lower mortality rate
        
        example: humans, elephants
      - r strategist: high reproductive rates
        
        no parental care, little energy per individual, matures quickly, dies quickly, high mortality rate
        
        example: fish, frogs
    - - Whole-animal metabolic rate
        
        the bigger the mass of the organism, the more energy it uses
      - Mass-specific metabolic rate
        
        measures the efficiency of an organism, the bigger the organism the more efficient it uses energy
  - - - system
        
        open system
        
        energy and matter can enter or exit
        
        closed system
        
        energy can enter but matter can not
        
        isolated system
        
        energy and matter can not enter or exit
      - surrounding
    - - conservation of energy: energy can not be created or destroyed, it can only be changed from one form to another or from substance to substance
        
        relevance to biological systems
        
        consumers
        
        eats to get energy
        
        herbivore: eat producers
        
        cows
        
        carnivore eat other non producers
        
        wolfs
        
        lions
        
        producers (autotroph)
        
        gets its energy from inorganic material; 10% of energy is kept
        
        oxidative phosphorylation
        
        respiration
        
        trophic levels
        
        food chain; every level up only 10 percent of the current energy is kept
      - in an isolated system, entropy will naturally increase until maximum threshold
        
        relevance in biological systems
        
        living organism resist entropy
        
        barriers that resist entropy
        
        behavioral: seperate 2 population that recently diverged
        
        reproductive: seperate different species from reproducing
        
        organelle membrane: seperate for example the chloroplast from the cytoplasm
        
        physical structures
        
        DNA introns
        
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        chromosomes
        
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        geographic: seperate 2 populations by geography
        
        living organisms die at a certain point of entropy
      - the entropy of the system correlates directly with the temperature
        
        Heat: measurement of energy
        
        work: measurement of when energy is used to move matter
        
        H = G - TS
        
        T is temperature
        
        G is gibbs free energy
        
        -S is negative entropy change
        
        The energy spent to reverse entropy
        
        reactions
        
        exergonic : energy is released to surrounding
        
        endergonic: energy is absorbed from surrounding
        
        H is enthalpy