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Course Mind Map, Energy Metabolism: Respiration (Anaerobic (Glycolysis…

- - - - Well-drained soil = good oxygen
      - Flooded soil = no Oxygen = death
        
        Rice is exception
- - - - Kinases: enzymes that remove phosphate groups
      - Phosphorylases: enzymes that give phosphate groups
    - - Pyruvate --> lactate (in animals)
      - Pyruvate --> acetylaldehyde -->ethanol (in plants)
    - - Cycles through 10 different compounds
    - - ATP used for protein synthesis, nucleic acid replication, etc.
- - - - Vitis vinifera all variations of this grape
    - - Red fermented 25-30 degrees Celsius
      - White fermented 25-30 degrees Celsius
  - - - Add ethanol to make it stronger, because yeast can't survive, or distill it
        
        Distilled - heated, boiled ~78 degrees Celsius
        
        Grain based = whisky, vodka, and gin
        
        Agave based = tequila and mescal
  - - - Use S. cervisiae yeast to help ferment
- - - - FMN: flavin mononucleotide
        
        transfers electrons to quinones
        
        ubiquinone known as coenzyme Q: transfers electrons to cytochrome b
        
        cytochrome oxidase
        
        large enzyme complex with proteins and 2 copper ions
        
        copper gives electrons to form H2O to pump across matrix
        
        made of cytochromes a and a3
        
        reduces to FMNH2
        
        cofactor
      - ATP Synthesis
        
        By proton flow from crista lumen to mitochondrial matrix
        
        Adds phosphate on ADP to turn it to ATP
        
        Total: 36-38 ATP per glucose molecule
        
        #
      - occurs in mitochondrial matrix
    - - Net gain: 2 ATP
      - Same as anaerobic
      - Occurs in cytosol and plastids
    - - Occurs in mitochondrial matrix
      - Begins with pyruvate reacting with coenzyme A --> acetyl coA
        
        Cycle through 9 different compounds #
        
        Net gain: 2 ATP, 6 NADH, 2 FADH2
      - Also known as Krebs cycle or tricarboxylic acid cycle
- - - - Hydrophilic backbone (glycerol and phosphate)
      - Hydrophobic tail (fatty acid)
        
        Plus oligosaccharides: glycolipids
    - - ~60% of the membrane
      - Extrinsic: large hydrophilic regions
      - Intrinsic: large hydrophobic regions
        
        Plus oligosaccharides = glycoproteins #
  - - - More permeable to hydrophobic substances
        
        Causes need for facilitated diffusion
        
        EX: inorganic salts, sugars, amino acids
        
        Movement of charged particles
        
        Active transport: membrane protein uses energy and solute concentration to change shape and pump molecules across
- - - - Amyloplasts: store starch
      - Chromoplasts: store red or yellow pigment for flowers and fruits
      - Proplastids: young, meristematic cells
      - Leucoplasts: colorless plastids
      - Chloroplasts: chlorophyll rich, carries out photosynthesis, has own DNA #
        
        Thykaloids:photosynthetic membrane
        
        Granum: flat vesicles, staked, carry out chemiosmotic phosphorylation
    - - Aids in cell growth, larger it gets
  - - - Plasma Membrane: semipermeable membrane that surrounds protoplasm
      - Cytosol: liquid substance of protoplasm, not including organelles
      - Cytoplasm: protoplasm, includes nucleus, vacuoles, and cytoplasm
    - - Central Dogma: DNA --> RNA --> Protein
      - Nuclear Envelope: inner and outer membrane surrounding nucleus
      - Nuclear Pores: in envelope, transport materials between nucleus and cytoplasm
      - Nucleoplasm: substance inside nucleus, includes DNA, histones, RNA, enzymes, nucleic acids, and water
      - Nucleoli: synthesize ribosomal RNAs
    - - Crista: folds on inner membrane
      - Matrix: liquid in between crista and membranes
      - Has own DNA #
    - - Smooth: lipid synthesis
      - Rough: ribosomes attached, protein synthesis
- - - - Beta-tubulin: polymerize into tublin
      - Centrioles: organizes the microtubules of flagella
      - Alpha-tubulin: polymerize into tubulin
    - - Cilia: used for movement, similar to flagella, only shorter
        
        9+2 arrangement of microtubules in cilia and flagella:
      - Flagella: used for locomotion, sperm cells
        
        Basal Body: similar to centrioles #
- - - - Marks where new cell wall will attach to existing cell wall
      - Does not always create two equal-sized cells
  - - - Trap dictyosome vesicles = plate-like vesicle with 2 walls and a lamella
      - Grows outward to walls of original cell
      - Cell plate = phragmoplast, vesicle, walls
        
        Cell plate and plasma membrane fuse with original wall and membrane to form daughter cell walls and membrane
- - - - Meiosis I
        
        Anaphase I: homologous chromosomes (2 chromatids connected by centromere) move to opposite sides #
        
        Telophase I: possible uncoiling of chromosome, but usually skipped step
        
        Metaphase I: tetrads move to metaphase plate
        
        Prophase I:
        
        3: Pachytene and Crossing-Over: chromosomes shorten and thicken, paternal and maternal homologs recombinate genes allowing for genetic diversity in offspring
        
        Diplotene: paired chromosomes begin to separate from each other, except at places called "chiasmata" where they are tangled, chromatids (4) called "tetrads"
        
        Zygotene: homologous chromosomes pair up (2 chromosomes, 4 chromatids, 4 genes), align, form the synaptonemal complex, and is then called "bivalent"
        
        Diakinesis: continued separation, chiasmata move to ends of chromosomes, only connected by centromeres
        
        Leptotene: chromosomes condense and become distinguishable
      - Meiosis II #
        
        Metaphase II: chromosome lines up at metaphase plate, centromeres divide, chromosome separate into two chromasomes
        
        Anaphase II: separation of each new chromosome to opposite ends
        
        Prophase II: no stages, prepare nucleus for division if Telophase I occured
        
        Telophase II: new nuclei form. Nucleus contains one set of chromosomes with a single chromatid each. Results in 4 new haploid cells! #
- - - - Plants arose from this type of cell wall division
    - - Can be by cleavage furrow or by cell plate formation
- - - - Cytokinesis is caused by infurrowing, pinching in two
- - - - Oxidation Reaction - increases the positive charge on an atom
      - Oxidized Compounds - tend to contain a great deal of oxygen
      - Oxidation State - the number of electrons added to or removed from a molecule during a redox reaction
      - Oxidizing Agent - an electron carrier that is not carrying electrons
      - Oxidize - to raise the oxidation state of a molecule by removing an electron from it
    - - Reduced Compounds - contain a great deal of hydrogen
      - Reducing Power - The ability of an electron carrier to force electrons onto another compound
      - Reduction Reaction - reduces the positive charge on an atom
      - Reducing Agent - An electron carrier that is carrying electrons
      - Reduce - to lower the oxidation state of a molecule by adding an electron to it
- - - - this is done by the enzyme RuBP carboxylase (RUBISCO)
      - RUBISCO is one of the largest and most complex enzymes, 8 subunits making it the most abundant protein on Earth
      - Heterotrophs would starve without RUBISCO
    - - Plants use this to build sugars, fats, amino acids, and nucleic acids and convert it to RuBP
  - - - Gluconeogenesis - synthesis of glucose
        
        3-phosphoglyceraldehyde --> dihydroxyacetone phosphate* --> fructose-1,6-biphosphate -P-> fructose-6-phosphate -->glucose-6-phosphate -P->glucose
      - Steps:
      - Glucose-6-phosphate makes amylose, amylopectin, and cellulose
        
        Amylose and amylopectin make starch. Amylose has ~20,000 glucose residues, amylopectin has ~1 million. #
    - - Starch degradation: amylase in saliva helps in animals
      - Plants store starch in their chloroplasts and convert it into glucose during the night, then moved to cytosol and phloem as sucrose
  - - - Radiation can be quanta, waves, or photons #
      - Short waves = lots of energy in quanta (UV, X-ray, etc)
      - Long waves = little energy (microwaves, radio, etc)
      - Plants use visible light (350 - 760nm) for photosynthesis
        
        Photosynthetic pigments transfer absorbed light energy into electrons to be used for chemical reactions
        
        chlorophyll a absorbs red and blue light, letting most radiation pass through
        
        Absorption spectrum - shows wavelengths that are most strongly absorbed by a pigment
        
        Action spectrum - shows which wavelengths are most effective at powering photochemical processes
        
        chlorophyll b and carotenoids aid photosynthesis by broadening the action spectrum
        
        Extra pigments will transfer (resonance) their energy to chlorophyll a
    - - Plastocyanin donates an electron to chlorophyll a of photosystem I reaction center
      - Cytochrome b6/f complex donates electron to plastocyanin
      - Plastoquinone donates an electron to ctyo b6/f #
      - Q donates an electron to plastoquinone
      - Phaeophytin donates an electron to Q
      - Phaeophytin obtains an electron from chlorophyll a of photosystem II reaction center, P680
      - P680 chlorophyll a gets electrons from water
    - - P700 - chlorophyll pair at the reaction center absorbs red light, electron is excited and absorbed by Fx
      - Fx passes electron to ferredoxin located in thylakoid membrane
      - Ferredoxin passes electron to enzyme; ferredoxin-NADP+ reducatase which reduces NADP+ to NADPH
- - - - Oxygen is broken down into one molecule of 3-phosphoglycerate and one molecule of phosphoglycolate
      - Phosphoglycolate will move out of the chloropast into a perioxisome where it will be broken down into glycine, serine, and CO2
        
        Called Photorespiration, very exergonic, takes up 30% of all ATP and NADPH produced by chloroplast to break down this toxic molecule
    - - PEP carboxylase - has high affinity for CO2, never picks up oxygen
      - Acts as the iniital carboxylating enzyme
      - PEP is carboxylated, forms oxaloacetate, reduced to malate/other acids
    - - Examples: corn, sugarcane, sorghum, grasses
  - - - Stomata closed during day allows for the built up malate and acids to break down into CO2 to be used for C3 metabolism
- - - - Good at absorbing carbon dioxide, but not conserving water
    - - Small internal surface area slows water evaporation
      - Photosynthesis is slower due to slower at dissolving carbon dioxide from air
  - - - Photosynthesis is faster on brighter days, more sunlight
        
        Light Compensation Point - the level of illumination at which photosynthetic fixation of carbon dioxide matches respiratory loss
      - 1/4 - 1/2 of ordinary sunlight is all most leaves can use
      - As light intensity increases, lower leaves can photosynthesize, thus entire plant photosynthesis increases
      - Too much light = adaptations
        
        thick layer of dead trichomes, plant hairs
        
        Heavy coating of wax
    - - More light = more photosynthesis
        
        Too much light, build up of starch, plants wait until night to convert to glucose
        
        Photosynthesis can stop is plant has reached maximum photosynthesis
      - Near equator = 12 hours long per day
        
        Near poles = 24 hours long per day
      - Summer = longer days, brighter light, photosynthesis > respiration
        
        Winter = shorter days, dim light, photosynthesis about equal to respiration, rely on stored nutrients
    - - Canopy and tops of trees absorb most of the red and blue light, which is needed for chlorophyll
      - Shrubs and plants underneath the canopy or on the ground can receive less crucial red and blue light
        
        Need for accessory pigments like carotenoids and chlorophyll b #
      - Sunlight is pure white, contains entire visible spectrum
- - - - long fibers has elastic secondary walls
        
        fiber-rich bark can resist insects, fungi, and pests
        
        long fibers allow for flexibility, ex = wood. Fibers on trunk allows for strength while fibers on branches allow for swaying in the wind
      - short schlereids, cubiodal has elastic secondary walls
        
        form pit-pairs with neighboring cells to allow nutrient transport through plasmodesmata
        
        Pit-pairs
        
        strong outer walls which are brittle and inflexible that form hard, impenetrable surfaces
        
        secondary walls are impregnated with lignin, which makes it waterproof and nutrients only enter through plasmodesmata
    - - walls are elastic, so will return to shape after pressure/tension released (opposite of collenchyma)
  - - - transfer: short distance transfer using membrane pumps, have knobs, ridges and in-growths on inner surface for larger surface area
        
        phloem: conducts nutrients over long distances (opposite of transfer cells)
      - stamen and some fruits are the result of dead parenchyma cells
      - glandular: secrete nectar, fragrance, mucilage, resins, and oils, have lots of endoplasmic reticulum and dictyosomes, need high levels of sugars
      - chlorenchyma: for photosynthesis, many chloroplasts, thin walls allow for good gas exchange
  - - - help resist tip breakage, flexibility, and elongation
      - works with parenchyma cells in stems to allow rigidity and growth
- - - - can be wide, intermediate, narrow, long or short (helps with adaptation)
    - - axillary bud - mini shoot with dormant apical meristem and young leaves, covered by bud scales
- - - - 2 types of conducting sclerenchyma cells: trachieds and vessel elements
        
        scalariform thickenings - strong, secondary wall underlies most of the inner surface of the primary wall, has pits
        
        reticulate thickenings - secondary wall shape of a net
        
        helical thickenings - secondary wall exists as 1-3 helicies interior to primary wall
        
        circular bordered pits - strongest tracheary elements have these, secondary wall borders all of the primary wall, little water flow
        
        annular thickenings - small amount of secondary wall organized as a set of rings interior to primary wall, weak, lots of water flow
        
        pit membrane - trachieds, set of primary walls and middle lamella between them, friction caused as water passes though #
        
        vessel elements help reduce friction
        
        perforations = vessel elements have these on each end and line up to match adjacent cells, large holes in cell walls, lots of water passage with little friction
        
        Pits vs Perforations
    - - pith - region of parenchyma similar to cortex = in basal angiosperms and eudicots
      - collateral = all vascular bundles = xylem and phloem strands run parallel to each other
      - primary xylem = large cells, made of xylem parenchyma nd mechanical schlerenchyma that forms xylem fibers
      - primary phloem = storage parenchyma and mechanical schlerenchyma = phloem fibers
    - - 2 types of conducting parenchyma cells:
        
        Sieve Cells
        
        shaped like trachied, has sieve areas with sieve pores
        
        sieve pores = plasmodesmata grew to >1 um, align with adjacent cells, a cluster is called a Sieve Area
        
        associated with albuminous cells because nuclei degenerates in sieve cells and helps with transport of water
        
        Sieve Tube Members
        
        stacked sieve cells, has a flat end walls with sieve plates with large sieve pores
        
        associated with companion cells because nuclei degenerates in sieve tube member (sieve cells)
        
        companion cells hold lots of ribosomes and help load sugars in and out of sieve tube members
- - - - protoxylem - 1st trachieds or vessel elements to appear, has annular or helical secondary walls for stretching # #
        
        EXTERIOR CELLS: sieve cells; protophloem - live for ~1 day, has no companion cells
      - metaxylem - cells with longest time for development into tracheary elements, has any type of secondary walls
        
        EXTERIOR CELLS: sieve cells; metaphloem - differentiate fully, large sieve areas, has companion cells #
    - - pith - calls enlarge, spaces expand, all walls are thin
      - cortex - plastids develop into chlorophyll
    - - epidermis - 1st stage of trichome outgrowth in youngest internodes
- - - - Mesophyll has fibers that deposit lignin in their walls- makes them hard and resistant to decay
  - - - Stems can range in length and can have small or large scales
  - - - When tendril touches something, that side stops growing but the other side continues elongation
        
        Elongation forms a coil that grows around objects FIGURE 6-44
  - - - Cuticle is very thick, and waxes are abundant on these types of leaves
  - - - Makes mesophyll transparent allowing light to penetrate further into the leaf
  - - - Nitrogen helps build plants amino acids and nucleotides
- - - - Functions for turbulence, barriers, and abscising pathogenic leafs
      - Pinnately compound – leaflets attached individually (A)
        
        Leaflets always arranged in two rows
      - Figure 6-7
      - Palmately compound – leaflets attached at the same point (B)
      - Compound leaf has leaflets – small blades
        
        Huge range of shapes, yet none are more advantageous than the other
        
        Attached by a petiolule – extension of petiole to the rachis
  - - - Results in leaf base wrapping around the stem = sheathing leaf base
    - - Adjacent undamaged cells for a corky protective scar – leaf scar
- - - - Have coating of cutin hat helps retain water and make waterproof
    - - Guard cells and trichomes can be abundant #
    - - Not all bad because it can prevent fungi from entering leaf
    - - Can fall into epidermal cavities called crypts – helps trap water to re-enter stomata instead of blowing away
    - - Consequences – deflect excessive sunlight on upper epidermis and prevent rapid air movement on lower epidermis
      - Advantages – Make walking or chewing difficult for insects, prevent water coverage of stomata #
        
        Glandular trichomes secrete stinging compounds to prevent animals form eating the leaf
  - - - 1-4 thick layers with intercellular spaces surrounding them
  - - - Minor veins - release water from xylem and loading sugar onto phloem
        
        Sites of material exchange, have large surface area, do not contain fiber cells, have both phloem and xylem
      - Midrib and lateral veins – function is conduction
        
        Can be arranged as bundle sheaths around vascular tissue
        
        Always contain primary xylem on upper side and primary phloem on lower side
      - Larger veins can produce mucilage, tannin, or starch storage cells
        
        Have bundle sheath extension – mass of fibers above, below, or both
        
        Fibers give rigidity to blade and moves water out to mesophyll
  - - - Can be arranged into ring, plate, or many other patterns
    - - Function – protect shoot apical meristem and contribute to photosynthesis
- - - - More apical meristem cells involve with the primordium until it’s a cylinder that encircles the shoot apical meristem
        
        This cylinder becomes the lamina with inner adaxial epidermis and outer abaxial epidermis
      - Basal expansion – protoxylem and protophylem are always being stretched and disrupted in basal meristem
      - Apical meristem adjacent cells grow with primordium forming a hood-like shape
      - Vessel elements – sieve tube members differentiate rapidly so conduction is never interrupted
  - - - As grow upward increase in thickness establishes bulk of midrib
      - Row of cells growing outward of primordium becomes the lamina
        
        Now consist of two wings and midrib
        
        Cells in wings are meristematic and division expands lamina
        
        Stomata, trichomes, and vascular bundles differentiate, and petiole becomes distinct
      - Consists of leaf protoderms and leaf ground meristem, young xylem and phloem
- - - - If outer cell remains a cambium cell then the inner cell becomes secondary xylem
        
        as these daughter cells elongate they increase the diameter of the plant
        
        this increase is by the cambium cells that divide longitudinally by anticlinal walls
      - If inner cell remains a cambium cells then the outer cell becomes secondary phloem
    - - if inner cell remains cambial ray initial then outer cell becomes phloem parenchyma
      - if the outer cell remains cambial ray initial then the inner cell becomes xylem parenchyma
      - produce storage parenchyma and albuminous cells in gymnosperms
    - - ray initials are grouped in short vertical rows
        
        one cell wide - uniseriate
        
        two cells wide is biseriate
        
        many cells wide - multiseriate
        
        FIGURE 8-15
      - fusiform initials are in horizontal rows (a storied cambium) or without pattern (nonstoried cambium)
- - - - Radial Xylem Parenchyma
        
        stores carbohydrates and conduct material over short distances
        
        upright cells and procumbent cells
        
        Ray is adjacent to axial - plasmodesmata
        
        Ray adjacent to tracheid or vessel element - pits in secondary wall
    - - creates Axial Xylem Parenchyma
        
        temporary water reservoir
        
        conifers - contain only tracheids in axial system
        
        angiosperms - tracheids, vessel elements in axial system
- - - - primary cork cell walls have suberin which makes them waterproof, chemically inert and dead
- - - - outermost cells of this bundle develop fibers with thick secondary cell walls
- - - - mucigel - root cells secrete this complex polysaccharide for lubrication and help soil diffuse ions #
    - - root hairs - trichomes, increase surface area and water/mineral absorption
- - - - Water leaves cells and enters cells at the same rate – equilibrium
      - Small water potential, less pressure potential
    - - High pressure potential, low water potential #
      - Figure 12-15
      - This makes the guard cell turgid and swell which allows the opening of the stomata
  - - - Cells at these joints called motor cells
    - - When cells are shrunken it causes the plant to close up, the potassium expelled out of cells
  - - - Larger the membrane, more pumps it can hold and vice versa
    - - Plasma membrane pressed against this wrinkly cell inside wall and allows for greater surface area
- - - - Move upward most easily through tracheids
    - - Upper tracheary elements lift this weight and there is tension on these water molecules, pressure potential is a negative number
      - Vertical xylem the weight of water counteracts its tendency to rise to areas of more negative water potential
    - - This water loss is called transstomatal transpiration
    - - Cellulose, DNA, enzymes, sugars, soil, etc
      - Interact with polymers of cell walls of tracheids and vessel elements, prevents water being drawn upward
    - - Molecules above the cavitation point are drawn upward and those below rush downward
      - Tracheid or vessel element can never conduct water again
      - Water column acts like a broken cable
    - - If hits vessel element it can expand and perforate the entire vessel
      - Occasionally embolisms can be healed
      - If hits tracheid only that one will lose water
      - FIGURE 12-25
  - - - Osmotic and water potential become more negative, water diffuses into sieve elements #
        
        This build up in pressure causes the protoplasm to leak out of sieve members into the next cell, creating phloem sap
      - Phloem is loaded by the polymer trap mechanism in some species – conducting cell membranes are permeable to monosaccharides and disaccharides
      - In both, parenchyma and companion cells are important in loading the phloem
      - STM/CC complex is a conducting cell and several companion cells
      - Sugars are actively transported into sieve elements
        
        Figure 12-17
        
        As sugars are accumulated the sieve member’s protoplasm becomes concentrated
    - - Mass transfer divided by cross-sectional area of phloem = specific mass transfer
    - - P-protein gets swept into the cell center where it becomes a tangled mass and forms a P-protein plug
        
        Figure 12-18
      - Callose – precipitates into a mass and is carried to broken sieve areas which helps leaking
- - - - Certain Chemicals
        
        Nitrous Oxide: A colorless gas with a sweetish odor, prepared by heating ammonium nitrate. It produces exhilaration or anesthesia when inhaled and is used as an anesthetic and as an aerosol propellant.
        
        Reacts with Cytosine and replaces it with Uracil
      - UV light: Ultraviolet light is a form of radiation which is not visible to the human eye. It's an invisible part of the "electromagnetic spectrum."
      - X-Rays: A photographic or digital image of the internal composition of something, especially a part of the body, produced by X-rays begin passed through it and being absorbed to different degrees by different materials.
      - Radiation: Energy travelling through space.
        
        Radioactivity in Material: the amount of radioactive material is measured in Becquerel (Bq), which enables us to compare the typical radioactivity of some natural and other materials. A Becquerel is one atomic decay per second, so a household smoke detector with 30,000 Bq contains enough americium to produce that many disintegrations per second.
- - - - Parent Generation: The first set of parents crossed.
      - F1: First filial generation; or the first generation crossed from the parent generation.
        
        F2: Second filial generation; Or the first generation crossed form the first filial generation.
      - Homozygous: Refers to having two identical alleles for a particular gene or genes.
      - Heterozygous: Refers to having two diffrent alleles for a particular gene or genes.
        
        Selfing: Refers to the situation where a heterozygote crosses with themselves.
      - Incomplete Dominance: A situation in which the phenotype of both alleles of a heterozygote are expressed.
      - Microgametophyte: A gametophyte that produces microgametes, sperms, only.
      - Megagametophyte: A gametophyte that produces megegametes, eggs, only.
    - - Dominant Trait: Refers to traits that are expressed or seen when a heterozygous genotype is present.
      - Recessive Trait: Refers to traits that are not expressed or seen when a hereozygous genotype is present
    - - Complete Dominance: A situation in which the presence of one allele completely masks the presence of the homologous allele.
      - Pure-Bred Lines: A situation in which a homozygous recessive trait is kept via being selfed to be kept pure.
  - - - Recombinant Chromosome: A chromosome that results from crossing-over in meiosis, being composed of parts of the parental and maternal homologs.
      - Parental Type Chromosome: A chromosome that, after meiosis, has not undergone crossing over
      - Map Unit: A measure of the separation of genes on a chromosome; one map unit equals a 1% probability that crossing over will occur between them.
- - - - DNA polymerases can replicate a full genome, or all the alleles of an organism.
- - - - Factors that allow natural selection:
        
        The progeny must differ from each other in their types of alleles
        
        a population must produce more offspring than can possibly grow and survive to maturity in that habitat
      - Factors that don't allow natural selection:
        
        Purpose, Intention, Planning,Voluntary Decision Making
      - Does not have to be caused by external factors
      - Can only act on pre-existing alleles: does not cause mutations
    - - Selective Breeding - modifying the characteristics of living things, especially to enhance one or more desirable traits
        
        Cauliflower is an example
  - - - Pump ions- pumps ions into and out of the cell, creates concentration gradient
      - capacity to reduce nitrogen - critical limiting element for plant growth and production
      - Efficiency to produce P-protein - form a gel, forming a plug at any site of damage
- - - - Events which an organism cannot adapt, all individuals in the affected area are killed
        
        Avalanche - a mass of snow, ice, and rocks falling rapidly down a mountainside
        
        volcanic eruption: lava and gas are discharged
        
        often cause temporary food shortages and volcanic ash landslides called Lahar
        
        Infrequent floods: large amount of water beyond what's normal at infrequent intervals
        
        Droughts - a prolonged period of abnormally low rainfall, leading to a shortage of water #
        
        Hailstorms - storms accompanied by hail
      - Any change in the sequence of DNA
- - - - Wind-distributed - allows the pollen to be able to travel great distances
      - Animal- Mediated -animals tend to stay in a relatively small area, allows rapid movement of alleles
    - - Biotic - fruit that are spiny or gummy stick to the fur or feathers of animals, migratory animals can be especially important to dispersing seeds #
      - Vegetative Propagation - asexual reproduction, the new plant is genetically identical to the parent
      - Abiotic - carried by wind, floods, and stream flow
  - - - Allopatric/Geographic Speciation - Original species is physically divided
        
        Oceans - The vastness of salt water, unusable to land vegetation and mostly uncrossable by animals makes it a reproductive barrier
        
        Ultraviolet Light - reproductive barrier mainly for long distance wind dispersal of pollen
        
        Deserts - The inhospitable conditions of very little nutrient rich soil and extreme temperatures make for a reproductive barrier
        
        Rivers - prevent seed dispersal via small animals but not overall gene flow
        
        mountains - pollinators do not fly across entire mountain ranges while feeding or gathering pollen
        
        Evolutionary Changes in Pollinators - can become a reproductive barrier if the changes cause a decrease in gene flow
- - - - appropriate energy sources
      - an immense amount of time
      - An absence of oxygen in its destructive elemental form, 02
      - correct inorganic chemicals
    - - Chemicals Present in the Atmosphere
        
        Second Atmosphere - Produced by the release of gases from the rock matrix composing Earth and from heavy bombardment by meteorites
        
        Oxygen - elemental oxygen was theorized to be absent as oxygen was already combined with other elements
        
        Reducing Atmosphere - oxidation is prevented by removal of oxygen and other oxidizing gases or vapours
        
        Gases - hydrogen sulfide(H2S), ammonia(NH3), methane( CH4 ), and water(H2O)
        
        First Atmosphere - contain mostly Nitrogen, which is such a light gas that theoretically most was lost to space
  - - - UV Light and Gamma Radiation - have energetic quanta that knock electrons from atoms, creating highly reactive free radicals #
        
        Ammonia (NH3) - Some of the ammonia would have been decomposed to hydrogen and nitrogen
        
        Methane( CH4 ) - Some methane would have converted to carbon monoxide and carbon dioxide.
    - - Coalescence of Gas and Dust - As particles fell toward the center of gravity, they accelerated and then collided, converting kinetic energy to heat
      - Radioactive Decay - the process by which an unstable atomic nucleus loses energy
        
        Uranium and Radium - enough remains to keep Earth’s core molten
    - - Storms - The rain storms developed from the fall of water and the immediate evaporation of that water theoretically lasted for thousands of years
      - Lightning - triggered chemical reactions
      - Water (H2O) - Initially water was suspended in the air due to high atmospheric temperature. But when Earth cooled the water fell but evaporated due to the high temperature
- - - - Allelochemics - Chemicals given off by a species to inhibit the germination or growth of another
        
        Allelopathy - inhibition of germination or growth of one species by chemicals given off by another species
      - Uniform Distribution - evenly spaced from their neighbors
      - Clumped Distribution - spaced between plants either large or small but rarely average
      - Random Distribution - no obvious, identifiable pattern
- - - - produce many offspring
      - relatively low probability of surviving to adulthood
      - exploit less-crowded ecological niches
  - - - being relatively larger than r-selected species
      - long gestation periods lasting several months
- - - - Carbon Cycle - circulation of carbon in various forms through nature
- - - - B Horizon- the zone of deposition, which receives leached materials from the A horizon above it
      - C Horizon-The deepest soil layer, composed of parental rocks and rock fragments
      - A Horizon-The uppermost soil layer, the zone of leaching
      - Pioneers-The first plants to inhabit an area that previously had no life
      - Soil Factors: combination of all five factors normally determines the kind of soil developing in any given place
        
        climate
        
        parent material
        
        time
        
        topography and relief
        
        organisms
    - - Photoperiod-In reference to cycles of light and darkness, the length of time that uninterrupted light is present.
      - Altitude - is the height measured from sea level up to any given point
    - - fires
      - floods
      - snow avalanches
      - landslide
- - - - c - constant found from studying individual communities
      - A - area used
      - z - constant found from studying individual communities
      - S - number of species
    - - Spatial Scale
- - - - dN/dt=rN-aNP - Models the net rate of change in prey numbers as
        
        r - the intrinsic rate of increase for the prey species
        
        N - the number of individuals of prey species in the community
        
        dN/dt - the rate of change with time of the prey
        
        a - the number of prey eaten per prey per predator per unit of time( a - is prey dependant)
      - dP/dt=faNP-qP - the net rate of change of predators numbers
        
        f - a constant indicating the predators efficiency at converting prey it has eaten into new predators
        
        q - the predators per capita mortality rate which is independent of population density
        
        dP/dt - is the rate of change with time of the predator population
    - - Feed Rate - refers to how quickly a predator can find new prey
      - Handling Time - refers to how quickly a predator can consume its prey
  - - - Bracken Fern - intense competitor, takes over entire areas as its leaves catch sunlight above the shrubs and the stem spreads underground
    - - Resource - any substance or factor that can lead to increased growth rates
- - - - 2) patches can be occupied by species and others can't
      - 3) empty patches colonized by migration from occupied patches
      - 1) region of environment has many patches where species live
        
        high-quality patch is called a source habitat
        
        low-quality patch is called a sink habitat
      - 4) populations within patches have probability of going extinct within that patch
- - - - Selaginella Pilifera - nurse plant to Echinocereus Pectinatus, a small cactus
- - - - undergo alternation of generations
      - produces haploid spores that develop into a gametophyte
        
        makes gametes that fuse and grow into a sporophyte
        
        the sporophyte generation is the dominant generation
        
        FIG 20-19
      - multicellular diploid generation found in plants and algae
      - Parts:
        
        Seta - a narrow stock between the foot and the sporangium
        
        Operculum - the apex of the sporangium that differentiates as acaplike lid
        
        Capsule - a simple apical sporangium that develops from the upper cell growing by cell division and expansion
        
        Peristome teeth - two rows of teeth resulting from precise and elaborate cell breakage
        
        Foot - a small bulbous tissue developed from the basal cell
        
        Calyptra - a layer of cells derived from the neck of the archegonium
- - - - FIG 20-27
- - - - Spermatophytes - Cycads, Conifers, Angiosperms: have both vascular tissue and seeds
      - Vascular Cryptogams - Clubmosses, Scouring rushes, and Ferns: have vascular tissue but no seeds
    - - FIGURE 20-1
  - - - absorb water and minerals
      - to anchor them to the ground
    - - nonvascular plants are placed into one of 3 different divisions
        
        Bryophyta
        
        Anthocerotophyta
        
        Hepatophyta
- - - - Found in Cooksonia plants
        
        Refers to a genus of extinct plants that are among the earliest vascular plants
  - - - Contains either tracheids or vessel elements or both, as well as parenchyma, fibers, and sclereids
        
        Parenchyma - Cells with only thin primary walls, with all other features varying from type to type
        
        Tracheids - a long and tapered xylem conducting cell that never have a complete hole in the primary wall
      - Endarch Protostele - A stele that forms a solid core of xylem encased by phloem
        
        Located in the center and metaxylem differentiates on the outer edge of the xylem mass
        
        Phloem - The portion of vascular tissue involved in conducting sugars, water, minerals, and other organic compounds
      - Exarch Protostele - involves the development of protoxylem from the outermost edge of procambial cylinder.
        
        Protoxylem is found outside the metaxylem
        
        Protoxylem - The part of the primary xylem that differentiates early, while adjacent cells are still elongating
        
        Development is from outside to inside.
      - Siphonostele - A vascular cylinder that contains pith
        
        Common in stems but absent in early vascular plants
        
        Pith - refers to a spongy, central cylinder of tissue found inside the stems of most flowering plants
      - Seed Plants - Any plant that bears seeds as part of its reproductive cycle
        
        May have originated twice in evolution
        
        Concept of seed plant is a grade not a clade
        
        Grade - A level of evolution
        
        Clade - A group of closely related organisms sharing a common ancestor
      - Protostele - A vascular cylinder that has no pith
        
        Pith - refers to a spongy, central cylinder of tissue found inside the stems of most flowering plants
        
        Common in roots and early vascular plants
  - - - Their sporangia opened transversely along the top edge
      - Their xylem was an exarch protostele
      - Their sporangia were lateral, not terminal
- - - - Ligule - A small flap of tissue on the upper surface of a leaf
      - Heterosporus and the megagametophyte develops inside the megaspore wall
    - - Approximately 60 species still living today
    - - Approximately 200 living species
    - - Suggested that the 2 species of stylites are extreme forms of isoetes
- - - - Sporophyll - A leaf that bears sporangia
        
        Sporangiophore - stalked, umbrella-like structure that bears sporangia
      - Ferns - Have vascular tissue, megaphyllous leaves but do not produce seeds
      - Seed Plants - Any plant that bears seeds as part of its reproductive cycle
      - Arthrophytes - Refers to any plant belonging to the former class Arthrophyta, called horsetails
      - Euphyllophytes - Refers to plants that have megaphylls
      - Lignophtyes - Synonym for a plant that develops wood
      - Monilophytes - The clade containing ferns in a broad sense
    - - Plantation - The concept that all branching occured in one plane, resulting in a flat system
      - Webbing - The concept that the lamina originated by the production of parenchyma cells between telomes
        
        Lamina - The broad, expanded part of a leaf
        
        Parenchyma - Cells with only thin primary walls, with all other features varying from type to type
      - Telomes - In a plant with dichotomous branching, the last two twigs produced by the last bifurcation
      - Overtopping - In the evolution of unequal branching, the ability of one shoot to grow for a longer time than the other shoot that resulted from the branching
      - Overtopping, Plantation, and Webbing
  - - - The plant consists of long, hollow, narrow stem segments with miniscule, non-photosynthetic leaves
      - vascular plants that reproduce by spores in a similar fashion to ferns
  - - - Pseudomomopodial Branching - A single main trunk rather than a series of dichotomies
        
        have small lateral branches, some fertile and bearing sporangia and others sterile acting as leaves
      - Overtopping - have an unequal branching in which one stem was more vigorous
        
        so pronounced that the main stems and lateral stems can be easily identified
  - - - Having leptosporangia is a derived trait occuring only in the clade Leptosporangiate
      - This undergoes several more divisions, which result in a small set of sporogenous cells and a thin covering of sterile cells, produces only a few spores
    - - This is the fundamental type of sporangium, it exists in virtually all plants other than Leptosporangiate
      - Outer cells develop into the sporangium wall, and the inner cells proliferate into sporogenous tissue, which results in a relatively large sporangium with many spores
  - - - They have an epidermis, cortex, and a simple vascular cylinder
    - - Tmesipteris is from the Greek language, meaning a "cut fern,'' referring to the truncated leaf tips
- - - - Ferns and Fern Allies - Refers to ferns, which do not produce seeds, flowers, fruits, ect., and other plants like ferns
  - - - Sporophyte - A diploid plant that produces spores
      - Zygote - The diploid cell formed as the result of the fusion of two gametes
      - Meiosis - Reduction division, a process in which nuclear chromosomes are duplicated once but divided twice, such that the resulting nuclei have only one half as many chromosomes as the mother cell
      - Haploid - Refers to one full set of chromosomes per nucleus
    - - Evolution - The change of nucleotide sequences in a species’ DNA through natural selection, genetic drift, or accident
      - Zygote - The diploid cell formed as the result of the fusion of two gametes
      - Sporophyte - A diploid plant that produces spores
      - Sporangium - A structure that produces spores
    - - Evolution - The change of nucleotide sequences in a species’ DNA through natural selection, genetic drift, or accident
      - Sporophyte - A diploid plant that produces spores
  - - - Epidermis - The outermost layer of the plants primary body #
        
        Covering leaves, flower parts, young stems, and roots
      - Cuticle - Layer of cutin on epidermal cells
        
        Reduces water loss but also unavoidably restricts the entry of carbon dioxide
    - - In certain species gametophytes have become so small that the microgametophyte develops within the spore wall
        
        Microgametophyte - A gametophyte that produces microgametes , sperm only
      - The megagametophyte protrudes from the spore only slightly
        
        Spore - A single cell that is a means of asexual reproduction, it can grow into a new organism but cannot fuse like a gamete
        
        Megagametophyte - A gametophyte that produces gametes, eggs, only
    - - To remain on the parental sporophyte is an important step in the process of seed evolution
      - Megaspore - A large spore that grows into a megagamtophyte that produces egg cells #
      - Megagametophyte - A gametophyte that produces gametes, eggs, only
      - Megasporangium - A structure that produces megaspores
      - Sporophyte - A diploid plant that produces spores
      - Evolution - The change of nucleotide sequences in a species’ DNA through natural selection, genetic drift, or accident
- - - - spores: (1n), no syngamy, mitosis to create gametophytes (1n)
      - megagametophytes: female, created from megaspores
      - sporocytes: diploid (2n), have organs that undergo meiosis to produce spores (1n)
      - microgametophytes: male, created from microspores
    - - heteromorphic: gametophytes to not resemble sporophytes #
  - - - Stamens: all stamens = androecium #
        
        microsporocytes produce 4 microspores by meiosis
        
        tapetum = "nurse cells" for microspore development
        
        filament is the stalk
        
        pollen = broken microspore tetrad
        
        produce pollen in anther (1n)
      - Petals: all petals = corolla
        
        "leaf-like": chlorophyll and other pigments, few/no fibers, thinner
        
        attract pollinators by modifications
        
        sepals + petals = perianth
        
        petals not developed in wind-pollinated species
      - Carpels: make up the gynoecium #
        
        Ovary: inside are placentae = tissues that hold ovule
        
        Ovule: has central mass of parenchyma called the nucellus
        
        fertilized ovule = seed with surrounding ovary becoming fruit
        
        3 parts: Stigma (catches pollen grains), style (elevates stigma), ovary (megaspore production) #
        
        Nucellus: has hole at the top called the micropyle
        
        holds megasporocytes that undergo meiosis to make 4 (1 used) megaspore
      - Sepals: lowermost, outermost appendage
        
        thick, tough, waxy
        
        all sepals together = calyx
        
        modified leaves that hold immature flower parts
  - - - generative cells: divide mitotically to form 2 sperm cells (microgametes)
      - pollen tube: made when pollen lands on stigma to reach ovule
    - - embryo sac: multinucleate megagametophyte by mitosis
        
        3 small antipodal cells
        
        egg apparatus with 2 synergids and an egg (megagamete)
        
        central cell with 2 polar nuclei
  - - - (2n) zygote as the result
  - - - Pericarp: entire fruit wall
        
        mesocarp: inner fleshy layer
        
        endocarp: stones or thin
        
        exocarp: outer layer, skin or peel
- - - - chemical reactions between pollen and carpal that prevents pollen grain growth
      - test pollen tube and pollen grain surface for proteins produced by gene #
        
        inhibit if gene matches incompatibility gene
  - - - imperfect flower: lacks one or both
      - perfect flower: has both
  - - - also with birds and bats
- - - - Types: raceme, spike, umbel, head
- - - - dehiscent fruits: break open and release seeds
      - indehiscent fruits: doesn't break open, fleshy
      - Fruit Types
- - - - megaphyllous leaves, vascular cambium (secondary xylem, phloem), true woody trees, no seeds
        
        Aneurophytales
        
        vascular cambium #
        
        primary xylem was protostele like
        
        shrubs to large trees
        
        webbing between branches, not actually leaves
        
        relictual progymnosperms
        
        Archaeopteridales
        
        abundant wood and secondary phloem
        
        stems had siphonostele - pith surrounded by primary xylem
        
        average height of 8.4m
        
        leaflets = spirally arranged simple leaves
        
        had full megaphylls
- - - - rays were many cells wide and very tall
      - wood was manoxylic #
    - - inner cortex had secretory ducts
      - stem cells made into parenchyma, not trachieds
    - - integument attached at base and was vascularized
  - - - each on separate plants, dioecious #
      - pollen cones = spirally microsporangia
        
        pollen tubes and large multifagellated sperm
      - seed cones - relictual, large, loose pinnately compound megasporophylls
      - 6-8 ovules at base
    - - rays massive
      - old stems have only small amount of wood
      - trachieds long and wide
      - pith with secretory canals
- - - - several parallel veins in scale leaves
    - - transfusion parenchyma cells and transfusion trachieds
        
        trachieds = cuboidal with circular pits
        
        parenchyma make 3D platform that help transfer materials between vascular and mesophyll tissues
  - - - rays thin, tall have parenchyma and trachieds
      - resin canals = vertically in trachieds, horizontal in rays
        
        sticky pitch
      - no axial parenchyma
      - phloem = sieve tube members and albuminous cells with tall, narrow rays
      - cork cambium = thick, good protection from fires #
  - - - leaves = thick cuticle, sunken stomata, cylindrical shape
  - - - one cells becomes generative
  - - - no sporophylls
      - each bracts has axillary bud
        
        bud bears megasporophylls
        
        megasporophylls fuse laterally to form ovuliferous scale
    - - retained insde and grows into a large multinucleate megagametophyte
        
        FIGURE 22-24
    - - pollen tube digests its way towards megagametophyte as egg forms
      - only 1 zygote develops from the 2-3 eggs fertilized
        
        zygote
        
        1st cells elongate = suspensor that pushes deep into megagametophyte
        
        "other cells" = proembryo, develop into embryo
        
        no double fertilization
- - - - thick, fleshy scales
      - microsporophylls below mega and curled upward to surround the megasporophyll
      - megasporangium surrounded by integument with long micropyle
      - microsporophyll = cup shaped with lots of microsporangia
      - each ovule had a stalk
  - - - ovules in pairs a the end of the stalk
        
        large with 3-layered seed coat
  - - - leaves scale-like
      - deserts like in Mexico
    - - short, wide stem
      - 2 perennial leaves only from basal meristem
      - Africa
    - - broad leaves
      - Asia, Africa, Amazon Basin
    - - pollen cones are compound and have small bracts #
      - seed cones compound with extra tissue surrounding ovules
      - have vessels in wood
      - pollen spindle-shaped with narrow ridges
      - thought to be sister clade to flowering plants