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Course Mind map, Chapter 11, Chapter 9, Chapter 5, Chapter 15, Chapter 16,…

- - - - Strict Aerobes
  - - - Glycolosis
    - - Obligate Anaerobes
  - - - Fatty Acids
        
        Phospholipids
        
        Triglycerides or glycerol Phosphate
        
        Further broken down (β-oxidation)
        
        Acetyl CoA
      - Gylcerol
  - - - dont pump protons
      - no ATP produced
      - NADH energy into heat
  - - - Ribulose-1,5-Biphosphate
        
        3-phosphoglycolate, 1 phosphoglycolate
      - not carbon dioxide
  - - - Transforms glucose
        
        Four-carbon Sugars(Erythrose)
        
        Five-carbon sugars (ribose)
        
        Shunted into nucleic Acid Metabolism
        
        Forms basis of DNA
        
        Forms basis of RNA
    - - oxidations produce NADPH
      - Gives carbon dioxide
- - - - 40% fatty acid into ATP
  - - - 2 NADHS transported
        
        forms 2-3 ATP
        
        to mitachontria
        
        electrons power mitachondria
      - Conversion pryruvate to acetyl CoA
        
        Yields 1 NADH
      - 2 pryruvate per initial glucose
        
        6 per glucose
        
        ATP created
      - Yeilds 2 ATP
    - - each original glucose yields
        
        6 NADH
        
        2 FADH2
        
        2 ATP
        
        Total of 24 ATP
  - - - Per every glucose fermented
    - - depends on substrate
      - glucose or glucose-6-phosphate
    - - H+
      - NADH+
- - - - lower respiration rate
  - - - seed becomes dormant
        
        metabolic inhibitors
        
        no respiration occurs
      - burst of respiration
      - then sudden decrease in resp.
      - endogenous hormones
- - - - higher amounts of oxygen
- - - - want <20%
        
        stronger alcohol can be added
        
        alcohol condenses
        
        must be distilled
        
        alcohol evaporates
        
        proof is double percent
        
        solution is heated
        
        stops at 95.6%
      - Ethanol boils before water
      - once 20% yeast die
  - - - Pinot
      - Merlot
      - Noir
      - Cabernet Sauvignon
      - Chardonnay
    - - Glucose and fructose
      - sugar content 20-30%
      - washed then crushed
  - - - Barley
        
        hops
        
        dried carpellate inflorescences
        
        bitter taste
        
        related to cannabis
        
        added to beer
        
        prevents sweetness
        
        converts starch to sugar faster
        
        malt
        
        sprouted grain
        
        dry
        
        most common beer
        
        in order to brew
        
        mixture called mash
        
        malt mixed w/ water
        
        more cheap starch added
        
        cheaper beer
        
        less flavor
        
        greatest number of enzymes
      - Corn
      - Rice
        
        Sake
        
        Rice wine
      - before grain can ferment
        
        Allow to germinate
        
        embryo secretes enzymes
        
        break down starch
        
        convert starch to glucose
      - Wheat
        
        Specified as Wheat beer
      - seedlings shows roots
        
        sprouting is done
        
        prevents enzymatic reactions
        
        grains are dried
    - - yeast to ferment for 1-12 weeks
        
        aged 2-3 weeks
        
        the filtered
        
        pasteurized to stop fermentation
      - for ales, bitters or stouts
        
        Saccharomyces Cerevisiae is used
      - for lagers and pilsners
        
        add S. Uvarum
  - - - red wine in particular
      - 2 drinks lowers heart disease
    - - driving under the influence
        
        kills innocent people
        
        5th leading cause of death
      - ethanol affects fetuses
- - - - penetrate closed stomata
      - diffuses into plant
    - - Potato
    - - large gas bubbles
      - Depleted after rain
    - - https://www.google.com/imgres?imgurl=https%3A%2F%2Fih1.redbubble.net%2Fimage.615194266.7356%2Fmwo%2Cx1000%2Cipad_2_snap-pad%2C750x1000%2Cf8f8f8.u1.jpg&imgrefurl=https%3A%2F%2Fwww.redbubble.com%2Fpeople%2Fkranman%2Fworks%2F33147356-dwight-schrute-beets%3Fp%3Dipad-case&docid=at2BzLllGhZJYM&tbnid=s_M_Zoszc5N1NM%3A&vet=10ahUKEwi266n346LnAhXaK80KHXQ9C9YQMwhlKAIwAg..i&w=750&h=1000&bih=655&biw=1366&q=dwight%20schrute%20beets&ved=0ahUKEwi266n346LnAhXaK80KHXQ9C9YQMwhlKAIwAg&iact=mrc&uact=8
      - Carrots
  - - - Above 40C
        
        Enzyme damage,
        
        Disruption of organelle membranes
      - Below 5C Respiration decreases
      - increase 10C between 5C and 25C
        
        Doubles respiration rate
      - influences plant growth
      - Affects Shoots more than roots
- - - - pollinized by pollen of same flower
      - or by different flower on same plant
  - - - exposed pollen lives only briefly
      - once stigma matures, no pollen is left
    - - older flowers can be pollinated by younger ones
      - this is a poor method of ensuring cross polination
  - - - Chemical reactions between pollen and carpels
      - prevent pollen growth
    - - Critical proteins deposited on outer surface
      - Incompatibility genes look for match in proteins produced
      - Any proteins matched get blocked from pollination
  - - - individuals that produce only staminate flowers
      - others that produce only carpellate flowers
    - - condition of having staminate flowers
      - located on the same plant as the carpellate flowers
- - - - called sporophyte phase
      - or sporophyte generation
    - - gametes can fuse with other gametes
      - process called syngamy or fertilization
  - - - Sepal
        
        lowermost and outermost of the 4
        
        modified leaves
        
        surround and enclose maturing flower parts
        
        always protects flower bud
        
        keeps bacterial/fungal spores away
        
        protects from nectar robbing
        
        thickest, toughest and waxiest of the 4
        
        all the sepals are called the calyx
      - Petal #
        
        above sepals
        
        sepal and petals together make up perianth
        
        petals together make up corolla
        
        leaf like except for
        
        petals have pigments beside chlorophyll
        
        petals have fewer to no fibers
        
        thinner than leaves
        
        petals importance
        
        attracts pollinators
        
        petals absorb UV light
        
        help pollinators recognize flowers
      - Stamen #
        
        above petals
        
        collectively known as androecium
        
        two parts to a stamen
        
        filament
        
        its stalk
        
        supports anther
        
        anther
        
        produces pollen
        
        composed of diploid cells
      - Carpels
        
        constitute gynoecium
        
        highest level on the receptacle
        
        3 main parts
        
        Stigma
        
        catches pollen grains
        
        female reproductive organ
        
        style
        
        elevates stigma
        
        puts it in a more useful position
        
        ovary
        
        megaspores produced here
        
        contain ovules
        
        ovules develop into seeds if fertilized
      - complete flowers have all 4
  - - - microspores develop into microgametophytes
      - pollen tube
        
        how pollen grains germinate
        
        tube penetrates into tissues of stigma
    - - what surviving megaspores develop into
      - nuclei migrate through cytoplasm
        
        pulled by microtubules
        
        3 nuclei lie at each end and 2 in the center
        
        becomes a megagametophyte w/ 7 cells
        
        1 large central wall w/ 2 polar nuclei
        
        3 small antipodal cells
        
        1 egg apparatus w/ 2 synergids and an egg
- - - - most cases this is ovary wall
      - but in some species the receptacle tissues are involved
    - - develops from single ovary
      - develops from fused ovary from 1 flower
  - - - dry isn't typically eaten by natural seed dispersing animals
      - fleshy is eaten during natural seed dispersal
    - - dehiscent breakopen and disperse seeds
      - indehiscent do not
- - - - limited potential for growth
      - apex is converted into a flower, ending growth
      - terminal flowers typically open first
    - - lower flowers open first
      - new flowers are still initiated at apex
      - main axis is thick and fleshy with minute flowers embedded in
- - - - individual parts become self sufficient
        
        by establishing advantageous roots
        
        modifications improve fragmentation
        
        in cacti, branches are poorly attached. helping fragmentation
        
        saxifrage, pineapple, have plantlets where flowers should be
        
        willows have shoot buds on roots that form individual plants
      - if middle part of plant dies, ends become self sufficient
- - - - allows light in
      - allows CO2 in
  - - - long fibers
      - short sclerids
      - elastic secondary walls
    - - tracheids
      - vessel elements
- - - - leaves 1 per node
    - - 2 per node
    - - 4 rows
    - - 3+ per node
    - - not aligned
    - - leaves in 2 rows
- - - - conducts water #
      - conducts minerals
      - travels through dead cells
      - conducting cells
        
        tracheids #
        
        vessel elements
        
        Tracheary elements
        
        enter cell cycle arrest
        
        stops dividing
        
        becomes long and narrow
        
        deposits secondary wall
    - - distributes sugars
      - distributes minerals
      - living
      - 2 conducting cells
        
        sieve cells #
        
        sieve tube members
      - parenchyma cells
      - remains alive
  - - - runs parrallel
    - - eudicots they are a ring
      - monocots are scattered
- - - - reformation of double helix
      - by cooling a solution of single stranded DNA's
      - Single strand DNA solution
      - AKA reannealing
    - - AKA DNA denaturation
      - separation that produces a single stranded DNA solution
  - - - run opposite of restriction endonuclease
      - present in both strands
      - can read forward or backward
  - - - DNA fragments are used to study DNA evolution
      - Restriction map
        
        made by staining
        
        used to see fragments
      - Restriction fragment length polymorphism
        
        a variation in the length of restriction fragments
        
        produced by a given restriction enzyme in DNA
        
        used in forensic investigations.
        
        and to map hereditary disease
    - - used if any cell forms a lot of protein
      - reverse transcriptase
        
        virus enzyme
        
        synthesizes DNA using RNA
        
        complementary DNA
        
        complementary to the exons
        
        exons of a gene
        
        synthesized using fluorescent nucleotides
      - expression profile
        
        uses cDNA's to examine gene expression
        
        compare development in species
  - - - short, circular piece of DNA
      - occurs in bacteria
      - acts like tiny bacterial chromosome
    - - carriers
      - plasmid genetically modified to be ideal
  - - - DNA is first cloned
      - divided into 4 batches
      - each batch has enzymes added
      - dideoxynucleotide can be added to growing DNA
      - DNA acts as a template, replication begins
    - - DNA added to all enzyme solution
      - single nucleotide is added
      - flash of light
      - Open reading frame
        
        region w/ gene like features
        
        regions searched for
        
        promoters
        
        enhancer
        
        TATA boxes
        
        AUG sites
- - - - Indirect protein synthesis
        
        mRNA carries info from DNA
        
        DNA uses a messenger molecule mRNA
        
        info goes to protein synthesis site
      - stored in nucleus
        
        protected from cytoplasm
        
        protected by nuclear envelope
        
        protected from cytosol enzymes
      - histone proteins
        
        holds nuclear DNA
        
        done in inert, resistant forms
    - - spherical structure
      - histones form aggregates
      - DNA wraps around them
      - forming nuclesomes
  - - - used in reading nucleotides
      - used in groups of three
      - 64 possible triplets
    - - UAG, UAA, UGA
      - signals ribosomes stop protein synthesis
    - - AUG
      - signals where to begin
    - - multiple codes exist for amino acids
      - degeneracy protects DNA
  - - - genes are composed of this
      - codes for amino acid sequence
      - codes for a promoter
        
        promoter is a controlling region
        
        regulates the synthesis of mRNA
        
        mRNA from the structural region
        
        promoter upstream from structural region
        
        promoter region
        
        intracellular messenger binds to this
        
        or binds with other things who act with this
    - - short sequence
      - about 6-8 pairs long
      - rich in A and T
      - If damaged, RNA polymerase 2 wont mind
    - - other promoter sequence
      - located even farther upstream
      - in eukaryotic genes
    - - introns
        
        sequence of nucleotide not expressed
        
        intervene between exons
      - exons
        
        sequence of nucleotides
        
        codons are eventually expressed
        
        expressed in sequence of amino acids in protein
    - - when RNA is created
      - DNA strands seperate
      - ribonucleotides diffuse into area
      - transcription proceeds rapidly
      - DNA nucleotides that are self complimentary
        
        RNA transcribed from them can double back
        
        hydrogen bonds to itself
        
        results in a small kink
        
        kink named hairpin loop.
        
        affects RNA polymerase
  - - - ribosomes in cytoplasm of eukaryotes
      - means they are dense
    - - ribosomes of plastids, mitochondria, and prokaryotes
      - smaller, lighter
- - - - greatest number of known virus
      - contain single strand RNA
      - source of reverse transcriptates
    - - many plant viruses
      - not all nucleic acid packaged together
      - consists of 2 different particles
      - both transmitted to new host cell
  - - - viruses that attack bacteria
      - AKA phages
      - extremely specific virus
    - - multiplies quickly
      - dominates the cell
      - symptoms:
        
        Chlorosis
        
        necrosis
        
        leaf curling
- - - - sequence fits into large groove of double helix
      - recognizing specific sequence of nucleotide basees
    - - come from somewhere else
      - binds to DNA
    - - Promoters, enhancers, TATA boxes
      - part of the gene itself
- - - - chemicals
        
        mostly man made
        
        increasing drastically in environments
      - x-rays
      - UV light
      - Radiation
    - - caused in several ways
        
        self-complementary sequence
        
        DNA unwinds ahead of DNA polymerase
        
        self-complementary sequence may form loop
        
        DNA polymerase pass through loop
        
        DNA molecule gets shorter than it should
      - transposable elements
    - - variety of enzymes repair DNA
      - transposable elements
        
        most useful causes of insertion
        
        Pieces of dna
        
        Change position between chromosomes
        
        two basic forms
        
        insertion sequence
        
        few thousand base pairs long
        
        contain genes that code for enzymes
        
        enzymes involved in cutting and splicing
        
        transposons
        
        like insertion sequence except for
        
        may be much longer
        
        carries genes tha code
        
        genes code for proteins
        
        proteins not associated with transposition
        
        insertion mutations caused may vary
        
        element inserted into spacer DNA is ok
        
        insertion in gene causes disruption
        
        may be viruses
        
        plants have mechanisms to fight
        
        but most nuclei contain transposable elements
  - - - If mutations are in spacers, there's no effect
      - insertion/deletion in introns are unimportant
      - in exons small mutations wont matter if amino acid is same
      - some codon mutations can disrupt proteins
      - an insertion can cause improper folding
      - mutations in promoter area can inactivate genes
    - - enzymes are 300-400 amino acids long
      - trillions of proteins can exist
      - Mutations in tRNA and rRNA can be less useful
  - - - in blackberries, alder, and prickly pear cactus
      - if it affects rise in vegetative offshoot
      - mutation could affect a flowers sex cells
  - - - loops
      - base mismatches
      - other problems
    - - may make an error 1 in 1million nucleotides
      - genomes can be several billion base pairs long
      - this means numerous errors
- - - - needs exact same genotype
      - results in 3 types of F1's
  - - - they may carry recessive trait
      - only way to know is to show it
    - - all gametes produced carry recessive
      - unable to mask homologous alle
      - if question plats is homo dominant, all show dominant trait
      - if hetero, show half and half
    - - dominant homo, selfed is always dom homo
      - useful in expirements
- - - - genes on different chromosomes
      - alleles of 1 gene move independently
- - - - cells closest to root meristem
      - forming files of cells
      - cells undergoing cell division
  - - - central area is inactive
      - inactive area is called Quiescent center
        
        cells more resistant to radiation
        
        reserve of healthy cells
        
        can create apical meristems
  - - - differentiate into epidermis
    - - develop into primary xylem
      - develop into primary phloem
  - - - increases water absorption
      - increases minerals
  - - - causes water absorption to decrease
      - water absorption doesn't stop entirely
      - endodermis cells don't change
    - - called passage cells
      - slow to develop
    - - root pressure
      - when roots keep water in
- - - - grows straight down
    - - lateral roots grow more lateral roots
      - results in highly ramified set
      - lateral roots can swell
    - - what taproots develop from
      - AKA embryonic roots
      - present in the seed
      - grows after germinization
  - - - formed by root primordia
      - root primordia grows from radicle
      - adventitious roots
        
        increase absorptive transport
        
        no radicles
        
        don't arise on pre-existing roots
    - - perinneal
      - secondary growth
        
        functional wood in roots
        
        functional wood in trunk
        
        causes increase in leaves
        
        increases # of roots
    - - no secondary growth
      - after stem forms-
        
        set # of vascular bundles
        
        Set # of tracheary elements
        
        Set # if sieve tubes
        
        cant increase conducting capacity
        
        extra leaves cant get water
      - increase size by stolons or rhizomes
        
        horizontal roots produce adventitious roots
        
        roots in new stem tissue
        
        transports water into shoot
        
        they can produce more roots this way
  - - - where growth occurs
      - growth by discrete apical meristem
      - localized growth
      - root cap
        
        thick layer of cells
        
        protects root apical meristem
        
        constantly worn away
        
        always rejuvenating
        
        mucigel
        
        root cap secretion
        
        allows lubricated passage
        
        makes soil release ions
        
        rich in amino acid
        
        rich in carbohydrates
    - - behind the root cap and apical meristem
      - only a few millimeters long
      - cells undergo division and expansion
    - - behind zone of elongation
      - epidermal cells extend into trichomes
- - - - roots are the only permanent part
      - most stem dies in autumn
      - carbs stored create new shoot
  - - - meaning living attached to trees
      - roots dangle from branches
- - - - AKA palisade mesophyll
      - main photosynthetic tissue
      - lots of intercellular space
    - - lower portion of leaf
      - open loose aerenchyma
      - allows CO2 diffusion
  - - - AKA midvein
      - lateral vein emerge
        
        branch into narrow minor vein
        
        realesing water from xylem
        
        loading sugar in phloem
        
        primary xylem
  - - - palms
      - rhubarb
      - celery
      - water lillies
- - - - mutations will disrupt development
      - these mutations become advantageous
      - disruptive mutations outnumber constructive
- - - - 1 species becomes so changed its considered different
      - millions of years to evolve #
      - new beneficial allele has to spread to entire population
      - gene flow is physical movement of alleles
      - pollen transfer
        
        all alleles are present in plants pollen grain
        
        pollen grains carry 1 full haploid genome
        
        new alleles can travel to distant plants
        
        possible rapid allele movement
      - seed dispersal
        
        some plants drop fruit/seeds close by
        
        some plants have long-distance dispersal mechanisms
        
        seeds can be dispersed by weather
        
        carried by wind
        
        flood dispersal
        
        stream flow
        
        spiny and gummy stick to creatures
        
        migratory animals can carry seeds far
      - vegetative propagation
        
        plants can produce small mobile peices
        
        these pieces reproduce vegetatively
    - - species splits and half evolve into 2nd species
      - occurs when species don't stay homogeneous
      - reproductively isolated
        
        happens to species in 2 separate regions
        
        if alleles arise in one region but not other
        
        start reproducing differently
      - abiological reproductive barriers
        
        any physical, nonliving feature
        
        prevents two populations from exchanging genes
        
        original species physically divided into 2
        
        if speciation results, its called either
        
        allopatric
        
        geographic speciation
        
        example of barriers
        
        mountain rages
        
        rivers
        
        deserts
        
        oceans
        
        valleys
      - biological reproductive barriers
        
        any biological phenomenon
        
        preventing successful gene flow
        
        discriminating pollenator
        
        very picky about what it chooses to pollinate
        
        reasons- flower color, shape, or fragrance
        
        muatations
        
        can cause pollinators to be confused
        
        could cause recognition issues
        
        timing of flower
        
        flowers open at night vs day
        
        cant interbreed with flowers opening other times
        
        when plant decides to flower
        
        sympatric speciation
        
        two groups growing together
        
        become reproductively isolated anyways
        
        prezygotic internal isolation mechanisms
        
        they act before zygotes are formed
        
        reproductive barriers preventing pollen from moving
        
        postzygotic internal isolation barriers
        
        genomes being too different
        
        hybrid sterility
        
        earliest postzygotic barrier to arise
        
        species allowed to breed
        
        offsprings seeds are sterilized
  - - - normally due to new habitat
      - no competition existing
      - no environmental stress
    - - first species
      - if only 1 founder, there's small gene pool
    - - small gene pool means easy influence
      - small populations subject to more accidents
      - gene pool can change rapidly and erratically
- - - - 2 parents with 2 different gene patterns
      - crossing over causes variation
      - variation causes genetic diversity
    - - created by different individuals
      - all alleles in individuals sex cells
    - - Mutations
        
        all genomes subjected to mutagenic factors
        
        mutation causes new alleles
        
        significance depends on population size
      - Accidents
        
        accidents are unadaptable situations
        
        phenomena qualify as accidents
        
        can wipe out area of mutation
        
        could wipe out entire alleles
        
        impacts future generations
      - Artificial Selection
        
        humans purposely change allele frequency
        
        selective breeding
        
        influences gene pool
        
        used to create perfect plants/clones
      - Natural Selection
        
        most important factor changing gene pool
        
        survival of the fittest
        
        individuals most adapted survive
        
        2 conditions before natural selection occurs
        
        offspring
        
        population must produce offspring
        
        must have too many offspring for all to live
        
        offspring then compete for space/resources
        
        progeny
        
        progeny must differ from each other
        
        alleles must be different
        
        that way fungus cant wipe all out
        
        if all are same, natural selection wont occur
      - factors not part of natural selection
        
        purpose, intention, planning
        
        voluntary decision making
        
        plants don't make decisions. natural selection does
        
        situations in which natural selection does not operate-
        
        if which individuals are same
        
        impossible to adapt
        
        survival being universal
- - - - earth condensed from gas and dust
      - atmosphere mostly hydrogen 4.6 bil. years ago
        
        hydrogen is light, most lost in universe
        
        replaced by a second atmosphere
        
        second atmosphere released from rock matrix
        
        provided hydrogen sulfide, water, ammonia,
        
        methane
        
        all found in volcanic gases
        
        found in meteorites
        
        rock matrix was composing earth
        
        heavy bombardment by meteorites
        
        second atmosphere was a reducing atmosphere
        
        due to lack of molecular oxygen
        
        presence of powerful reducing agents
    - - early 2nd atmosphere exposed to powerful energy
      - intense UV and gamma radiation from sun
        
        these radiations have energetic quanta
        
        energetic quanta knock electrons from atoms
        
        creating highly reactive free radicals
      - heat powered reactions
        
        coalescence of gas and dust was a heat source
        
        2nd heat source radioactive decay
    - - time available for chemosynthetic origin had no imits
      - due to lack of free molecule oxygen
      - without oxygen, nothing to breakdown chemicals
- - - - differ from each other structurally
      - sporophyte
        
        tiny in nonvascular
        
        temporary
        
        inconspicuous
        
        never independent of gametophyte
      - gametophyte
        
        larger
        
        more prominent generation
        
        any familiar green moss
        
        photosynthetic, perennial, and rapid asexual production
- - - - they are all over the world
      - in almost every environment
      - they are perennial
    - - gametophores
        
        leafy stems
        
        grow close together
        
        tightly appressed and forming dense mounds
      - cuticle
        
        only occurs on the upper surface
        
        underside in uncutinized
        
        lack of cuticle
        
        no protection from desiccation
        
        when microhabitat dries, so do leaves
    - - hydroids
        
        in primarily the polytrichaceae family
        
        composes the innermost cortex
        
        conducts water
        
        dissolves minerals
      - leptoids
        
        if they have hydroids they probably have leptoids
        
        resemble sieve cells
        
        prominent interconnection
        
        lack nuclei at maturity
      - majority of mosses lack hydroids and leptoids
        
        water is conducted on the outside of stems
        
        use capillary action
        
        leaves and stems form small channels
      - rhizoids
        
        at base of stem
        
        small,multicellular trichome-like
        
        only anchor the stem
        
        they don't absorb water
        
        they don't dissolve minerals
        
        lack chloroplast
    - - growth of a gametophore
        
        begins when a spore germinates
        
        sends out a long, slender chlorophyllous cell
        
        cell undergoes mitosis
        
        produces a branched system of similar cells
        
        this network is a protonema
        
        superficially resembles a green alga
        
        distinguished by many chloroplast in each cell
      - protonema
        
        perennial
        
        can grow extensively
        
        can produce many buds
        
        filamentous cells
        
        usually break when mosses are collected
        
        tuft of gametophytes may appear
        
        all arisen from a single protonema
    - - gametophyte produce gametangia
      - mosses are oogamous
        
        meaning they have small sperm cells
        
        they also have large nonmotile egg cells
      - antheridia
        
        microgametangia
        
        where sperm is produced
        
        consists of a short stalk
        
        outermost layer of sterile cells
        
        inner mass of cells that turn to sperm
      - archegonia
        
        megagametangia where eggs occur
        
        shaped like a vase with a long neck
        
        neck is hollow at maturity
        
        single egg is located at the base
  - - - bulbous tissue
      - interface with the gametophore
        
        absorbs sugars, minerals, and water
        
        its cells are transfer cells
    - - simple apical sporangium
      - outer layer of sterile cells
      - inner column of sterile cells
    - - narrow stalk
      - between the foot and sporangium
    - - cap like lid
      - separates from the rest of the sporangium
      - cells torn apart
    - - caused by cell breakage
      - exquisitely complex
      - respond to humidity
      - trapping spores when humid
- - - - divided into 2 groups
        
        thallose liverworts
        
        less resemblance to mosses
        
        not leafy at all
        
        instead are flat
        
        occasionally ribbon like
        
        bilateral symmetry
        
        thallus
        
        what the body is referred to
        
        no root,stem, or leaves
        
        thicker than those of leafy liverworts or moss
        
        leafy liverworts
        
        no midrib
        
        no conducting tissue
        
        gametophyte resembles that of moss
      - air pores
- - - - important in measuring diversity
      - how big an area
      - larger areas will be more diverse
    - - relationship between area and species richness
      - S=cA^z
        
        s= number of species
        
        A= area
        
        c and z are unknown constants
    - - plotting # of species in each abundance class
      - reflects a species individuals
      - doesnt reflect all individuals as equal
  - - - oldest and most commonly taught theory
        
        tropical regions near equator have benign environments
        
        short occasional dryness
        
        always warm
        
        constant rains
        
        those at higher lat. have more severe conditions
        
        have to adapt to freezing or water stress
        
        bitter temperatures
        
        permafrost
        
        brief and cool growing periods
      - geographical and geological theory
        
        high altitude in southern hemisphere
        
        very low diversity
        
        partially due to no ice free land
        
        tropical regions
        
        more land available for plants
        
        more land for all other organisms due to food sources
      - evolution
        
        50 million years ago earth climate started to change
        
        it got colder
        
        the land was still morphing
        
        continents still were shifting
        
        weather started getting cooler
        
        in order for plants to survive 12mya they had to evolve
        
        plants didnt have much time to adapt
        
        so fewer plants are adapted to cold dry weather
        
        causing diversity # changes in latitudes
        
        plants in temperate climates needed different structures
        
        needed to use day length to detect winter
        
        well-protected resting buds are needed
        
        doormant vascular cambium in winter
        
        storage organs
- - - - helps us understand how we should harvest
      - we harvest various preys- fish, deer, lumber, etc.
    - - predators feeding rate
        
        hunting time
        
        how fast they find prey individuals
      - handling time
        
        amount of time needed
        
        consuming prey
    - - functional response depends on prey density
      - feeding rate increases when prey increases
      - dN/dt = rN- aNP
    - - line indicating population stability
      - if pred. is sparser than line, prey increases
      - if pred. line is above line, prey is below
    - - may be an important factor
        
        could explain the loss of species diversity
        
        in an "improved" habitat
      - improving conditions for prey
        
        may lead to predator to over-exploit prey
        
        causing loss of both species
  - - - 3 factors are initially important
        
        probability of encounter
        
        rare species will be consumed less
        
        finding a specific individual
        
        camoflage and size are factors
        
        decision by predator
        
        decision to attack an individual once encountered
        
        is the prey poisonous or spiny?
        
        is it too small? or worth the trouble
        
        probability of being eaten
        
        is the fruit hard to crack open?
        
        optimal foraging
        
        examine interactions of these factors
        
        understand why predators eat what they do
        
        optimal diet model
        
        produced from optimal foraging
        
        model makes 4 predictions
        
        predators prefer higher energy prey
        
        will include lower energy prey if more abundant
        
        some prey will always be eaten others wont, regardless
        
        probability of one plant being eaten depends on other species factors
        
        is the prey hard to digest?
      - predators choice of prey
  - - - occurs when organisms consume shared resource
      - makes it less available for other organisms
    - - one organism restricts another organisms access to a resource
      - even though the first organism might not be using it
    - - when a species can increase from low population to high
      - even with the competitors present
    - - any substance/factor that can increase growth rates
      - as availability is increased
      - and that is consumed by an organism
- - - - alter small area of habitat immediately below them
      - more favorable soil for other species seedlings
- - - - a region of the enviro. is composed of discrete patched species live
      - some patches are occupied while others arent
      - empty patches will be occupied by migration from other patches
      - population in patches have a probability of going extinct
  - - - high quality patch
      - high emmigration rates
- - - - animals that move have several
      - they have summer, winter, and route habitats
      - sort of life a vacation home
      - plants
        
        plants dont migrate
        
        parts of plants to though
        
        seeds, pollen, spores, fruit
    - - the aspects that directly affect a plant
      - doesnt include what we dont know
  - - - critically important to organisms
      - most species are restricted to regions
      - many components to climate
        
        temperature
        
        average temp not as important
        
        the extreme temps are what really matters
        
        rainfall
        
        inches per year doesnt matter as much
        
        you need to know how often it rains
        
        need to know how hard it rains
        
        if there is a flood season
        
        relative humidity
        
        winds, etc.
      - tolerance range
        
        between low and high extremes
        
        some species have broad tolerance ranges
        
        other are super sensitive and dont
    - - soil is broken down rock
      - all young soil is deficient in nitrogen
      - pioneers
        
        first plants to invade new soil
        
        tolerate severe conditions
        
        sandy/rocky soil
        
        harsh winds due to exposure
        
        soil doesnt retain water
        
        lack of nutrients in soil
        
        pioneers change soil drastically
        
        co2 from roots produce carbonic acid
        
        accelerate chemical weathering
        
        dead plant parts become substrate
        
        decay creates humus
        
        after many years, you get a thick soil layer
        
        the thick layer has a soil profile
        
        soil profiles have 3 horizon layers
        
        A horizon
        
        uppermost layer
        
        sometimes called zone of leeching
        
        consists of litter and debris
        
        2 more items...
        
        B horizon
        
        Zone of deposition
        
        rich in nutriets
        
        contains both hummus and clay
        
        C horizon
        
        mostly parent rock
        
        lots of rock fragments
        
        no roots in this layer normally
    - - latitude
        
        contributes a lot to abiotic factors
        
        at equator, days are 12 hours long
        
        determines seasons
        
        farther north or south latitudes have longer days/nights
        
        intermediate latitude has distinct seasons
      - altitude
        
        high altitudes
        
        high winds
        
        poor soil
        
        much or all year is cold
        
        short growing season
        
        low altitudes
        
        subject to flooding
        
        standing water could stay year round
        
        if isnt inland, then raising ocean levels
  - - - plants modify their habitats by existing
      - they can modify it to help, do nothing, or harn
    - - multiple species existing in the same area
      - creates possibility of interaction among species
      - types of interaction
        
        mutualism
        
        benificial for both animals
        
        doesnt cause harm
        
        competition
        
        disadvantageius
        
        fighting for the same resource
        
        competitive exclusion
        
        result of competition
        
        whatever species is less adapted gets excluded from ecosystem
    - - space an organisms fills in the food web or ecosystem
      - set of conditions an organism adapts to
      - their habitat and food source is part of their niche
- - - - limiting factor
        
        one factor that determines the outcome
        
        happens at any given time or locality
        
        applies to all aspects of interaction
      - biotic factors #
        
        some plants dont thrive because of location, its due to competition
        
        a cactus cant compete with other plants
        
        some plants need animals to thrive
        
        soil #
        
        soil factors produce abrupt boundaries
        
        mineral composition and soil texture matter
    - - individuals have 1-3 types of local distribution
        
        random
        
        no obvious, identifiable pattern
        
        no predictive value
        
        some may seem random, but may be too complex to see
        
        clumped
        
        spaces between plants are either small or large
        
        rarely average though
        
        birds can eat many seeds, and deposit them in same place
        
        uniform
        
        occur in orchards and tree plantations
        
        evenly spaced from neighbors
        
        not very common in natural populations
        
        if it does occur, its due to intraspecies competition
        
        roots of one individual could create a no-grow zone
        
        zones could be created by chemicals
        
        the chemicals are called allelochemics
        
        the inhibition is called allelopathy
  - - - generation time
        
        length of time from birth of 1 individual
        
        to the birth of first offspring
      - intrinsic rate of natural increase
        
        AKA biotic potential
        
        number of offspring produced by an individual
        
        but have to live long enough to reproduce
    - - r-Selection
        
        disturbance usually produces r conditions
        
        r is biotic potential
        
        r-selected species
        
        typically annuals
        
        small or shrubby perennials
        
        pioneer species
      - K- Selection
        
        K is carrying capacity
        
        species that live long to occupy a site longest
        
        K-selected species
        
        Redwoods
        
        Douglas firs
        
        bristle-cone pines
        
        face severe competition
- - - - Life form is means of surviving stress
      - therophytes
        
        Annual life span
        
        survives stress as seeds
      - geophytes
        
        buds are underground
        
        on rhizomes, bulbs, corms
      - Hemicryptophytes
        
        buds are at surface of soil
        
        protected by leaf ans stem base
        
        many grasses and rosette plants
      - Chamaephytes
        
        buds are above ground
        
        low enough to not deal with winds
        
        small shrubs
      - Phanerophytes
        
        buds are located high
        
        25-30cm high
        
        trees and large shrubs
- - - - encompasses gramma rays, X-rays, UV light, Infrared light, etc.
      - radiation referred to by quanta/protons or waves
      - types of radiation have different wavelengths
      - short wavelengths have large amounts of energy
      - long wavelengths have relatively little energy
      - light is a small segment of the electromagnetic radiation spectrum
    - - pigment is a distinctive color from absorbtion of wavelengths
      - some pigments absorb light to protect
      - pigments can attract mates, pollinators, or hiding
      - photosynthetic pigments
        
        transfer absorbed light energy
        
        transfers to electrons that enter chemical reactions
      - Chlorophyll A
        
        critical pigment
        
        only absorbs some red and blue light
        
        high energy quanta has too much energy
        
        electrons are activated by visible light
        
        activated means raised to an higher level orbital
        
        electron goes from ground state to excited state
      - the release of a light by a pigment is called fluorescence
  - - - pair pf chlorophylls
      - in photosystem 1 reaction center
      - absorb red light of 700nm
      - energy excites electron of p700
        
        ferredoxin
        
        located in thylakoid membrane
        
        small protein
        
        active site with 2 iron atoms
        
        iron atoms bound to sulfur atoms
  - - - plastocyanin is now oxidized
      - plastocyanin must require lost electron
      - receives new electron from a complex of cytochrome
        
        this is called cytochrome b6/f complex
        
        in turn gets molecule from plastoquinone
        
        plastoquinone gets molecule from Q
        
        Q is a molecule of Quinone
        
        receives electrons from phaeophytin
        
        phaeophytin becomes oxidized as it donates to Q
  - - - more specific name- Chemiosmotic phosphorylation
      - involved in the chloroplast
        
        chloroplasts make thylakoids
        
        thylakoids come from inner membrane
        
        thylakoids can swell, becoming vesicles
        
        all vesicles occur in the same spot
        
        this is called grana
  - - - mediated by enzymes
      - enzymes aren't bound to thylakoid membranes
    - - accepter molecule reacts with CO2
      - product of 6 carbons
      - new molecule immediately breaks apart
      - stable bonding orbitals cant form
        
        orbitals rearrange
        
        2 identical molecules are formed
        
        molecule- 3-phosphoglycerate
      - carboxylation only
    - - electrons and energy added
      - ATP donates a high-energy phosphate group
      - this converts to 1.3-diphosphoglycerate
        
        this is reduced by NADPH
        
        reduced to 3-phosphogyceraldehyde
        
        phosphate comes off this step
        
        carbon is now reduced & reenergized
    - - some 3-phosphoglyceraldehyde gets taken out
        
        used to build anything the plant needs
        
        the rest stays for more reactions
- - - - first theory
        
        allow pigments to enter every reaction
        
        energized pigments are large
        
        pigments move slowly
        
        pigments never cross membranes
        
        pigments are too energetic
        
        energetic pigments are hard to control
      - second theory
        
        allow pigments to make smaller intermediates
        
        less energetic
        
        photosynthetic reactions:ATP
        
        guanosine triphosphate
    - - 3 methods
        
        substrate-level phosphorylation
        
        animals, fungi, and nonchlorophyllous plants
        
        respire high energy compounds
        
        compounds with high energy phosphate groups are made
        
        force phosphate onto ADP making ATP
        
        photophosphorylation
        
        only occurs in chloroplasts in light
        
        based off photosythesis
        
        only occurs in plants with chloroplast
        
        oxidative phosphorylation
        
        last stages of respiration
        
        occurs in distinct sites in cell
  - - - atom does not carry as many electrons as it can
      - oxidation state increases the positive charge
      - oxidized compounds contain a lot of oxygen
      - oxidizing agents take away electrons
    - - electrons added to atom
      - reduction reaction reduce positive atom charges
      - reduced compounds contain hydrogen
      - reducing power
        
        ability to force electrons onto ompounds
      - reducing agents place electrons onto molecules
  - - - small proteins
      - contain a cofactor heme
      - heme holds an iron atom
      - iron carries electrons
      - intrinsic membrane proteins
      - integral part of chloroplasts thylakoid
    - - transport electrons over short distances
      - pick up two electrons
      - bind two protons
      - hydrocarbon tails make them hydrophobic
      - dissolve easily into lipid component
    - - small protein that carries electrons on a metal atom
      - metal atom being copper
      - loosely associated with chloroplast
      - moves short distance along the surface
      - does not travel far
- - - - one of the meristems
      - produces the secondary plant body
    - - the cells never undergo cell cycle arrest
      - they continue to divide instead of maturing
      - constitute fascicular cambium
    - - mature parenchyma cells between vascular bundles
      - cells come out of cell cycle arrest, resume mitosis
      - forms interfascicular cambium
      - connects on each side w/ fascicular cambium
    - - one of 2 types of cells in vascular cambium
      - second cell type is ray initials
  - - - parallel to the circumference of the cambium
      - fusiform initial uses this to undergo longitudinal cell division
    - - perpendicular to cambiums surface
      - vascular cambium cells divide longitudinally to this
  - - - shorter though
      - less cuboidal
    - - w/ 1 daughter remaining a cambial ray initial
      - the other differentiating xylem or phloem
    - - mostly just storage parenchyma
      - in gymnosperms, albuminous cells
  - - - ray initials are grouped
        
        short vertical rows
        
        may be one cell, two cell, or many cells wide
      - fusiform may occur in horizontal rows
        
        storied cambium
        
        or may be irregular, nonstoried cambium
    - - if fusiform are side by side
        
        one undergoes transverse division
        
        transformed into a set of ray initials
      - if rays are side by side
        
        one or several may elongate
        
        gets converted into a fusiform initial
- - - - derived from fusiform initials
      - radial system develops from ray initials
    - - large amount of fibers
      - strong, tough, and useful for construction
      - eudicots, even soft ones like balsa
      - wood of all basal angiosperms
    - - wood from conifers
      - few or no fibers
      - even though sometimes this wood is harder than hardwood
    - - upright cells
      - procumbent cells
- - - - both branches of equal size
      - equal in vigor
    - - central walls are sporogenous
      - sporangium must open to release spores
      - no separate microspores or mega spores
      - epidermis with cuticle
    - - protostele
        
        solid mass of xylem
        
        no pith
        
        in the direct center
      - endarch protostele
        
        protoxylem is in the center
        
        metaxylem differentiates on the outer edge
      - exarch Protostele
        
        present in early vascular plants
        
        metaxylem located in middle
        
        protoxylem on the edges
        
        clumped in several groups
        
        next to the phloem
      - siphonostele
        
        didn't evolve until later
        
        pith is in center
        
        occurs in stem of ferns and seed plants
  - - - sporangia were lateral
      - sporangia opened transversely along top edge
      - xylem was an exarch protostele