Introduction--Nature of Biology
A. Organization of Life
    1. molecular component -> organelles -> cell -> tissue -> organs ->
       organ systems -> individual -> population -> ecosystem -> biosphere
    2. emergent properties - each level has properties not relevant to the
       other levels
B. What is life -- Characteristics
    1. composed of cells - membrane selects what goes in & out of cells, genetic materials
        a. eukaryotic - chromosomes, nucleus, membrane - bound orgganelle
        b. prokaryotic - genetic material circle, no membrane boundd organelles
    2. DNA - genetic material
    3. metabolism - obtain energy & use it to run the body (feed back mechanism)
    4. reproduce
    5. interacts w/ environment
    6. evolves
C. Science -- Method of Reasoning
    1. deductive reasoning - from basic laws or assumptions- deduce what's happening in
        a particular case (general to specific)
    2. inductive reasoning - make observations of specific cases, induce (conclude) general
        laws that explain them (specific to general)
    3. hypotetico deductive reasoning - Karl Popper found flaws in inductive
        a. specific observations
        b. conclude hypothesis (must be testable)
        c. if hypothesis is true, then expect ___
        d. if no ___, then hypothesis is false, if ___, then hypothesis supported, but not
            proven, must test again
        e. hypothess passing many tests is a theory

Ecology - study if interactions that determine the distribution and abundance of organisms
A. Interactions
    1. biotic - interactions w/ other organisms
    2. abiotic - interactions w/ physical and chemical parts of the environment
B. Types
    1. population - all members of a species that live in a particular enviornment
    2. community - all the populations in an environment
    3. ecosystem - communities & abiotic factors
    4. biosphere (landscape) - all the ecosystems
C. Biosphere
    1. energy flow - sun --light/energy--> primary producers (plants, algae, bacteria, protists)
        use photosythesis (CO2 + H20 --> C6H12O6 + O2) to convert into chemical energy
        (1%-2% light used) some used by producer for growth and respiration --> primary
        consumers (herbivores) eat primary prducers, less consumers than producers, some
        used for growth & respiration --> secondary consumers (carnivores) less than primary
        consumers, not enough energy left for another level ----> decomposers use undigested
        dead material, bacteria & fungi (eaten by consumers), called trophic (feeding) levels
    2. Carbon cycle - CO2 in atmosphere used by photosynthetic organisms to form C6H12O6
        used as fuel thru trophic levels, break down of glucose yields CO2
    3. Nitrogen cycle - N2 in atmosphere -> converted by bacteria in soil to NO3- andd NH4+
        plants (legumes) keep nitrate from bacteria in roots --> food for consumers (food web)
        --> waste goes back into soil
        a. nitorgen poor soils - plant eating animals, fungi (mychorrizae) -->lose is fire
    4. phosphorus, sulfur, sodium cycles
D. Ecosytems (communities & physical factors)
    1. important : what physical factors affect primary producticity
        a. light intensity - more productivity at equator & less at poles, aquatic increase shallow
        b. temperature - metabolism = chemical reactions => optimall temp
        c. water - metabolism in soln
        d. inorganic nutrients C,N, etc
    2. most productive -- rainforests, reefs, estuaries
    3. Biomes - different ecosystems (ex. deserts, tundra...) pg. 1034 - 1042
E. Communities
    1. amount of food & other resources
    2. interactions btw differnet populatios
    3. physical disturbance
    4. adaptations populationshave allowing them to survive (evolution)
    FOOD & RESOURCES AVAILABLE:
- each population has a niche -- biotic & abiotic resources a pop needs
- fundamental niche --> theoretical resources a pop can use
-realized niche -- what a population is constrained to use
    INTERACTIONS
-struggle for existence btw & within trophic levels
    -within level => competition    result 1.) Gauss Principle - competitive exclusion
        2 or more speicies needing same resources will not survive in exactly
        the same area  2.)resource partitioning -- coexisit by using resources differently,
        at different times, or divide resources => character displacement - features
        become different to use resources differently
    -btw trohpic levels  results 1.) extinction of one population   2.) coevolution- when
        changes in one speicies affect evolution of another => arms race
        1.) predator/prey    2.) symbiosis   parasite/host  => cycling of population
    -symbiosis cooperations - mutualisms - both populations benefit
    DISTERBANCE
-ecological succession - change in community sturcture over time until new stable
    community produced
    1.) 1st primary succession -> pioneer species live in harsh conditions, doesnt compete
        well, form soil, hol soil together (lichens)
    2.) Seconday succession -> more species move in (push pioneers out)
    3.) Best competitors finally take over, stabilizes ==> climax community
    ADAPTATION OF POPULATION
-adaptation- features that allow an organism to win resouces & survive

EVOLUTIONARY THEORY--
1.) Aristotle - student of Plato - essentialism (differnce dont matter, focus on "essence"
    species dont change, scale of Nature  (imperfect (pond scum) ---> perfect (human))
2.) Carlous Linnaeus - attributed nature to God, life organized heirachically, created
    categories:  Kingdom -> Pylum -> Class -> Order -> Family -> Genus -> speccies
    name: Genus species , used Latin
3.) Catastrophism - fossils are remnants of extinct life that dies in a horrible event
    (earth is young)
4.) Uniformatarianism - the earth is constantly changing due to forces we see every
    day (earth is old)
5.) Lamark - life changes as Earth changes, organisms have force that lets them adapt,
    aquired characteristics inherited, did not think one species turned into another
6.) Darwin - 1831 Voyage of the Beagle, Earth changes constantly, organisms change
    adapt with it
    observed - organisms are adapted to their environments, resemble other organisms
    that live near by or in the fossil record nearby, not organisms similar but distinct
    environments, dont produce as many offspring as capable of, populations tend to
    stay same size, offspring resembled their parents in specific features they have,
    environments constantly changed
    conclusions - organisms struggle to win limited resources, reproduction isnt random
    => organisms w/advantageous features win more resources, so leave more
    offspring, offspring inherit favorable feature & poulation has more indivual w/
    features, over time populations characteristics have changed, because environment
    keeps changeing favorable characterisitcs keeps changing (process doesnt stop) ==>
    NaTuRaL SeLeCtIon
7.) Natural Selection - individual w/heritable features that allow them to win resources
    leave more offspring which, in turn, inherit the favorable feature, over generations,
    pop changes & becomes better adapted
8.) Two types of selection
-Density dependent - # individuals in population, ex food - getting will depend on #
    present, limiting factor -  those forces/resources that limit sucess
-Density independent - not dependent on #s, ususally physical forces
9.) Patterns of Natural Selection
-Directional selection - most common, one type selected against, another type for
-Stabilizing selection -extremes removed, middle stays, results in no big change
    "living fossils"
-Diversifying selection - mean selected against, extreme selected for, results in
    polymorphism (2 or more major forms in population)
10.) Sexual selection - natural selection w/ emphasis on what allows organism to
    reproduce, secondary sexual features--result in differnces btw males/females
11.) Darwin's other contribution: one species transformed into another
12.) If evolution occurs, expect 1.) transitory fossils & further back in time more diff

Genetics -- study of inheritance
Mendel: garden peas breeding true - all offspring, exactly like parents, clear cut features
    in one of two forms, expect blending, got phenotypes
Law of Segregation:   1.) each feature (gene) consistes of two alleles (forms)
    2.) each individual gets one allel from each parent
    3.) which one gets passed on is totally random
    4.) alleles dont blend - but remain distinct
    5.) alleles have dominant/recessive relationship (dominant expressed when present,
        recessive shown if dominant not there)
Hardy-Weinberg: under certain conditions, the proportion of dominant to recessive alleles
    doesnt change from one generation to the next
    assumption 1.) all offspring grow up and mate (no natural selection)
    2.) no change in alleles (no mutations)
    3.) random mating  (no mate choice)
    4.) no change events (genetic drifts)
    5.) no one leaves or comes into gene pool (migration)
Speciation - process by which one species transforms into another
species- one or more populations that interbreed (or could) & produce viable offspring
    and are reproductively isolated from other such groups
reproductive isolation - 2 pop become seperated & cant interbreed, change in two groups
    independent & different, due to different NS, mutations, drift, migration, mate selection,
    eventually 2 isolated sep species
Types of reproductive isolation:
    1.) prezygotic - prevent successful fertilization (ex behavioral differences)
    2.) postzygotic - fertilization, but offspring not viable (die or sterile)
Conditions:
    1.) allopatric speciation - geographic barrier
    2.) phyletic speciation - time

SYSTEMATICS: study of evolutionary relationships among organisms
Goals: 1.) reconstructs phylogeny - pattern ancestor dependents
            2.) organize all the info about organisms in heriarchical systems
            3.) apply Linaeus categories to evolutionary lineages - naming all branches
                on tree of life
Data to do this: anatomy, development, molecular biology (gene sequences, biological
    pathway), fossil record (life from past)
Reconstruct evolution: 2 reasons for similarity  1.) homology - similar due to common
    ancestor    2.) homoplasy - similar due to convergent evolution (occurs when 2 unrelated
    organisms adapt to the same environment with the same "solution" ->structure, etc
Homology vs Hemoplasy    1.) similar in detail    2.) similar in position    3.) similar genetic
    controls    final test=congruence of all the characteristics
overall homology? no. 2 kinds: 1.) homology from ancient ancestor (doesnt tell closest
    relative)--plesiomorphy    2.) homology from recent ancestor - apomorphy
    (synapomorphy -shared advanced or recent homology)
outgroup comparison -- not in group of interest
phylogenetic tree -- related animals, characteristics
Tree of Life:
original-- 2 kingdoms: plants (photoautotrophic, not motile), animals (heteroauto, motile)
Cladistics - method of systemization by apomorphy, result in a phylogeny, an information
    framework, system can be named
Hagel-- 3 kingdoms    Protists Kingdom - everything that is unicellular, trash can group-
    used for stuff that didnt fit anywhere else
To recognize difference btw prokaryotes & eukaryotes -> Monera for prokaryotes
Fungi - eukaryotes, multicellular, heterotrophic, saprotrophic (secrete digestive enzymes
    & then absorb molecules), Animals- ingest
2 Types of Prokaryotes based on molecular biology (diff biochem pathways, fundamentally
    different genes) - Archea, eubacteria ---- higher rank than kingdoms -> created Doomain
    above kingdom (Archea, Eubacteria, Eukaryotes)
3.8 Billion Years Ago (1st life forms) -- Earth is 4.5 Billion years

History of Earth -- 4 time periods
1.) precambraim - 4.5bya - 590 million years ago - porkaryotes evolved, 1st eukarotes appear
    (mostly "protista") end: 1st plants, animals, fungi
2.) plaeozoic - 590 mya - 248 mya -- animals, plants, fungi went onto land
Major extinction -- 90% life lost
3.) Mesozoic - 248 mya - 60 mya - Dinosaurs, 1st birds, 1st mammals, 1st flowering plants
Major extinction -- 60% life lost due to meteor
4.) cenozoic - 60mya- present -- humans, grass

Origin of Life
Inorganic chemistry - in early earth's oceans --> complex organic chemisty--> molecules of
life (proteins, lipids, carbohydrates) --> assemble to form life
    - chemicals present => CO2, CH4, NH3, H2O => no O2 in early Earth
    -electricity, UV light
    -amino acids (protein), nucleic acid (DNA), sugars (carbohydrates) => found
1.) Prokarotes - first forms of life (formerly kingdom Monera)
    -cell structure- cell membrane (selective barrier), cell wall (protective, nonliving)
        cytoplasm (liquid), DNA, ribosome (where proteins are made), no membrane bound
        organelles, chromosomes, microtubules, structurally simple, metabolically complex
    a.) Archae - 1st type, evidence - live today in environments similar to thosse of early earth
        (very hot, salty, no free oxygen), chemoautotrophs (make energy & nutrients from just
        carbon) H2S, Fe+, CO2, oxide to make glucose, not sensitive to antibiotics, all DNA
        has some coding gene & some junk DNA (noncoding parts) --Archae & eubakaryotes
        have the same pattern of junk interspersed in coding regions, way amino acids are used
        is eukaryotic like
    b.) true eubacteria - more complex, glycocalyns (surface coat of sticky carbohydrate),
        flagella - for locomotion, but not like flagella in pprotists, cell wall sensitive to antibiotics
        distinctive shapes: cocci (spheres), bacilli (rods), spirilli (screw, spirochetes), 3 types of
        nutrition 1.) chemoautotrophs - no mouth/ingesting, pull chemicals into cell through
        transport systems (pores in wall & membranes)    2.) photoheterotrophs - use light in
        photosynthesis to make glucose but they have to ingest carbon from an organismal source
        (ex purple sulfur bacteria)
    c.) photoautotrophic - cyanobacteria, CO2 + H2O --> C6H12O6 + O2, dominant life in
        midprecambrium, transform atmosphere to O2 rich atmosphere --BAD, bacteria that
        can take O2 and use to make ATP energy
Bacteria Odds & Ends--
    disease causing- 2 mechanisms :  exotoxins (secreted posions), endotoxins (poisons
        embedded in cell membrane)
    reproduction: cell fission --
        asexual reproduction- no exchange of genes
        sexual reproduction- exchange of genes through plasmids
        plasmids- small circles of DNA

everything else is eukaryotic
-cells more complex, membrane bound organelles, endoplasmic reticulum, golgi-protein
    packaged, mitochondria, chloroplaasts, microtubules- small tubes of proteins that are used
    for transport & movement, make flagella & cillia, move chromosome in cell divison
    (meiosis & mitosis)
-endosymbiosis- theory of eukaryotic evolution, probably symbiosis of several diff
    bacteria cells

Steps in the Origins of Eukaryotes--
1. ancestral prokaryote that loses its cell wall (protects against osmotic shock- water moves
    into cell & cause it to swell & burst) - so had to happen in ocean
2. cell membrane infolds (convolution) to make bigger cell (more surface area)
3. fold can give endoplasmic reticulum & nuclear membrane
4. mitochondria, cholorplasts, & eukarotes are similar
    a. similar size & shape
    b. m & c have 2 membrane systems (as if pulled into cell by eukaryotic cell)
    c. m & c have divide by fission (like eubacteria)
    d. m & c have DNA in circular loop
~~conclusion: eukaryotic cell arose through symbiosis/cooperation of different organisms

Adaptations of Unicellular Life --
1. small size - no organ systems, every life process done inside a single cell, restricted in
    volume because of necessary surface area
2. osmotic shock- excess H20 moves into cell, contractile vacuole-pump H20 out
3. nutrition-- a. photoautotrophs - photosynthetic
    b. heterotrophs- ingulf food (bring into food vacuole--infolds of cell surface--digest inside
        vacuole) or saprotrophic (secrete digestive enzymes & absorb macromolecules)-
        parasitic protists
4. sensation- sense environment stimuli, no nervous system, but cells have same organelles
    as in nerve cells
5. locomotion systems-- flagella & cillia => microtubules in 9 + 2 arrangement
    (9 pairs outside, 2 in center), walk up side of one tube then slide against each other
    --pseudopodial movement -"false foot"- cytoplasm very thick (ectoplasm, semisold), just
        under cell membrane, in middle of cell more liquid thin (endoplasm), actin filaments-
        cause ectoplams to get thin in an area, endoplasm rushes into area & creates bulge
        (pseudopod), actin filaments squeeze cytoplasm into pseudpod
6. reproduction - 2 types
    asexual - cell divison, no exchange of genetic material (mitosis)
    sexual - exchange of genetic information
        gametic- cells divide by meiosis to make egg & sperm
        conjugation- ciliated protists only, 2 kinds of nuclei: macronucleus-runs cell,
            mircronucleus- exchanged during conjucation

Parasitic Protists--
many serious diseases (Leishmaniasis, sleeping sickness, malaria)
cell surface coats -- 200 to 5000 different ones
Malaria--caused by Plasmodium
    primary host (mosquito)-> gametocytes egg & sperm -> fertilization in female mosquito
    -> zygote developes into ovocysts -> divides to make hundereds of sporazoans --> in
    salavary glands of mosquitos -> goes into human when mosquito bites -> sporazoans in
    human liver -> merizoite breaks out -> goes into red blood cell -> red blood cell full of
    divided merizoites -> bursts -> goes into more red blood cells ->mosquito picks
    up -> carries -> cycle starts again

Multicellular Life---
Why be multicellular?
1. Division of Labor
2. Larger Body Size (cells can not get large - they would choke on their own waste and be
    unable to exchange gasses; But an organisms made of many small cells could be very big)

What are the multicellular groups:
1. Red Algae
2. Brown Algae
3. Fungi
4. Plants
5. Animals

What are animals?
1. Multicellular Eukaryotes
2. Heterotrophic organisms that engulf food
3. Develope from a fertilized egg (zygote)(see figure 32.1 in text)
    a. Cells divide until they form a blastula
    b. In almost all, the blastula forms a gastrula
    c. In the gastrula, three embryonic tissues form
        - endoderm
        - mesoderm
        - ectoderm

General Organization of the Animal Body
The unicellular protists are complete organisms and carry on all the functions of higher
    organisms within the confines of a single cell.
The animals, on the other hand, have cells organized into groups (called tissues) that are
    specialized for specific functions.
In general, structural complexity has increased in the evolution of animals so that there is
    considerable specialization and division of labor within body tissues.

I. Grades of Organization
organisms are composed of many units organized into successive units: Molecules are the
    units of organelles, Organelles are the units that make up cells, Cells are the units that
    make up tissues, Tissues are the units that make up organs, and Organs make up
    organ systems
Each level is more structurally complex than the one before and, as a general rule, a more
    recent evolutionary product.
A. All life functions are confined within the boundaries of a single cell. Within the cell, the
    protoplasm is differentiated into organelles capable of carrying out specialized functions.
B. Cellular organization is an aggregation of cells that are functionally differentiated. A
    division of labor is evident, so that some cells are concerned with, for example,
    reproduction, others with nutrition. Such cells do not become organized into true tissues
    but may form definite patterns or layers.
C. Cells all of one type begin to function in a unified way to accomplish a task. Cnidarians
    are usually considered to be at this level of organization.
D. The aggregation of different kinds of tissues into organs is a further advancement in the
    evolution of animals. Organs appear first in the flatworms.
E. Organ Systems form. When organs work together to perform some function (circulation,
    respiration, reproduction, digestion, etc.) we have the grade of organization seen in all
    animals that evolved after the flatworms.

II. Increased Complexity of Development
Embryology is the study of the progressive growth and differentiation that occurs during
    the transformation of a fertilized egg to a new individual. A brief summary of
    development is necessary for understanding the early evolution of animals.
A. General Pattern of Development
    1. Fertilization - In all animals, germ cells produce by meiosis eggs or sperm. The fusion
        of an egg or sperm to form a zygote is called fertilization. This is the starting point
        for development.
    2. Cleavage - The division of the zygote into smaller and smaller cells.
    3. Blastulation - cleavage eventually gives rise to a hollow ball of tiny cells called a blastula.
    4. Gastrulation - The sorting out of cells of the blastula into layers (ectoderm, mesoderm,
        endoderm) that become committed to the formation of future body organs.
    5. Differentiation - the formation of body tissues and organs. The basic body plan of the
        animal is established.
B. Constraints on Animals
    1. Size - small animals can carry out gas exchange, remove wastes, and circulate nutrients
        within their body by diffusion (substances seep in and out of the cells); larger animals
        need a circulatory system and perhaps even organ systems to carry out these functions.
    2. Habitat - animals that live in marine water have the same salt concentration in their cells
        as the surrounding water - so they have no problems; animals that live in freshwater must
        have a system of eliminating the water that leaks into their body by osmosis (they have
        an internal concentration of salt higher than the surounding environment); terrestrial
        animals must cope with drying conditions.

Terrestrial animals must:
a. Have an outer protective covering that prevents water loss (e.g., skin)
b. The respiratory surface must be kept wet but it can't be allowed to cause loss of too much
    water, therefore it is kept inside the body (e.g., lungs).
c. Water is more dense that air, so that gravity feels stronger. Need a support or skeletal
    system on land.
d. Need to protect embryos and gametes from drying (internal fertilization, and embryos
    inside the body or in a shelled egg).
e. Waste from digesting proteins includes an ammonia molecule. Aquatic animals can
    eliminate this by flushing it out with water. Terrestrial animals can't afford to lose that
    much water - so they convert it to a nontoxic form (urea or urine) so that less water can
    be used to get rid of it.
3. Speed of locomotion - slow moving animals must be aware of potential predators or prey
    moving in on any side, so they are often radial or bi-radial in symmetry; rapidly moving
    animals must be more concerned about the environment that they are moving into, so they
    often have bilateral symmetry and cephalization.(see figure 32.4 in textbook)

Major Animal Groups (Phyla)--
Porifera- multiple cells, no true tissues (cells acting in coordinated manner to carry out funt)
    ex. Sponges
    blastula is last embryo stage -> settles to bottom of ocean where 4 kinds of cells appear
        1. pinocytes - outer layer of cells
        2. porocytes - hole that goes right through them that alllows H20 into cells
        3. chanocytes - brings in food, have flagellum pushing H200 out of cell & sucking more
            in through proocytes, collar - around flagellum that filters food into vacuoles
        4. amoebocyte - move btw cells to deliver food vacuoles, ssecrete spongin
            protein (thickness and shape)

Cnidaria - have tissues but no organs
    ex. jellyfish, sea anemones, coral
    very sucessful because of unique feature - nematocyst - helps in survival, can effect structural
        damage, emit chemical posion, or entangle prey (hunting)
    polyp (tenticle up) and medusa (swimming) forms
    outer tissue layer (epidermis), inner layer (gastrodermis)- digests food), in btw is jelly,
        non-cell layer (mesoglea)
    sac like digestive system - only one opening (mouth/anus)
    no true muscles- cells w/actin & myosin contract -> locomotion, mesoglea is skeleton

Platyhelminthese- organs but no organ systems
    ex. flatworms
    three tissues-- epidermis, gastrodermis, mesodermis
    more efficient for locomotion b/c there are true muscles & more rigid mesoderm for
        muscle contraction => develop head end
    sac like digestion - one opening
    solid body contrustion- no room for organs to grow (crush adjacent organs) & no
        room for eggs or embryo, hard to move material through body by diffusion alone
        **solution: get body cavities w/fluid for circulation, can give better "skeleton" for
        locomotion (hydroskeleton- fluid filled sac acting as non-compressible lever for loco)

** 3 Major Groups w/ Body Cavities Appear--Pseudocoelomates, Protostomes, Duetrostomes**

Pseudocoelomates-
    ex. nematodes
    body cavity = coelom , left over space from inside of blastula
    coplete digestive tract w/ mouth and separate anus
    mesoderm becomes muscle (contracts -> animal bends)
    bigger b/c fluid can circulate gas & waste

****
True coelom- mesoderm (therefore muscle) around digestive tract
1.) Schizocoelom- split in mesoderm
    a. determinant cell division (fate determined early)
    b. spiral cell division (to one side)
    c. 1st indentation in gastrula becomes mouth, 2nd anus
    d. Protostomes -- annelids, molluscs, arthropods
2.) Eterocoelom- pocket in gastroderm
    a. indeterminate cell division (cell fate determined late)
    b. radial cell division (right on top)
    c. 1st indentation in gastrula becomes anus, 2nd mouth
    d. Deuterostomes -- echinoderms, chordates
****

Mollusca--
ex, Snails, Clams, Octopods, Squid
1.) mantle- flap of epidermis that secretes CaCO3 shell
2.) radula- feeding structure, many teeth
3.) large muscular foot- used in locomotion
4.) ventral nerve cord

Annelida--
ex. Segmented worms, Earthworms, leeches
1.) ventral nerve cord
2.) body segmented (except gut, nerves)
3.) each segment moves independently (efficient locomotion), fine control for burrow behavior
    (seperate muscles to move each segment)
4.) protect skin- secrete thin cuticle

Arthropoda--
ex. crayfish, insects
1.) cuticle- much thicker & forms exoskeletom (provides protection against physical injury,
    chemicals, drying)--allowed movement onto land
2.) jointed exoskeleton- thin flexible cuticle at meeting of joints inside- musles tend to bend
    body at joints --> allows flight
    -noncompressible lever (efficent motion)
3.) to grow- exoskeleton must be periodically shed (molted) & resecreted (constrains size)

Echinodermata--

Chordata--
ex. vertebrates, sea squirts (urochordates), lacets (cephalochordates)
1.) notochord- flexible rod for muscle attachment, replaced by vertebrae in vertebrates
2.) tail
3.) nerve cord
4.) pharygeal gill slits- feeding, gas exchanged, developed into jaws

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Phylum Chordata
characteristics- notochord, pharyangeal gill slits
-Subphylum Urochordata -- tail, ex. sea squirts
-Subphylum Cephalochordata-- notochord goes all the way to head
-Subphylum Vertebratae -- vertebrae
    -Class Agnatha -- jawless fish, (ex. lamprey, hagfish), jaws evolved from gill slits
  **jaws evilve from gill slits**
    -Class Chonrichthyes -- cartilage fishes (ex. sharks, skates, rays, sawfish)
    -Class Osteichthyes -- bony fishes
 **4 legs evolve from rays (tetrapod)**
    -Class Amphibia -- time in both H20 and land, (ex. frogs, toads, salamanders)
 **aminotic egg - tough cell to have reproduction away from aqueous environment**
    -Class Reptile -- scaly covering to prevent desication (drying), (ex. snakes),
        poikilothermy-animal cannot maintain constant body temp (cold blooded)
 **homeothermy-warm blooded, metabolically maintain constant body temp**
    -Class Aves- fly, feathers, (ex. birds)
    -Class Mammilia- mammary glands, nourish young, hair
        monotremes- egg layers (ex. duck billed platapus, spiny anteater)
        marsupials-pouches, young born very underdeveloped
        placental/eutherian-placenta, young born at advanced stage

Cell Division
somatics cells- body cells (2N)        germ cells- sex cells (N), egg & sperm
mitosis, meiosis
DNA (genes, in nucleus) ---> mRNA (transcription) ---> protein (goes to cytoplasm, translationn)
    protein- chain of amino acids joined by peptide bonds, structural, enzymes, receptors, other
cell membrane- plasma membrane, composed of phosopholipids w/ polar head & nonpolar tail
    protein has mobility within membrane lateraly, but cannot flip thru membrane
    interaction of substance w/protein causes change in shape further in cell-->transmitor system
    conformational change- change in shape to affect inside by reacting outside
    ion channel- transmits thru protein complex w/ channel

Fertilation
zona pellucida- extracellular material that is secreted, not really membrane, digested by acrosome
    (exocytosis)
acrosome- membrane bound vessicle containing digestive enzymes
acrosome digests zona pellucida -> sperm & egg cell membranes fuse -> sperm nucleus enters egg
    --> fertilized egg
cleavage- early divisions of embryo w/o grown
blastula- hollow ball of cells, after many cleavages, cells begin to grow soon after
blastocoel- cavity of blastula
invagination occurs forming gastula (invaginated cell, primary germ layers develop)
    -ectoderm- epidermis, nervous system
    -endoderm- lining of guts & respiratory system
    -mesoderm- connective tissue, muscle, cone,blood
archenteron- primative gut
blastopore- opening of archenteron

Differentiation
unequal distribution of cytoplasmic chemicals, concentration of chemical in cell determines which
    gene is turned on (type of cell)
interaction among cells
Neural Tube Formation
homeotic=homebox=hox genes - genes that regulate other gene series
"stem cell"- percursor that can differentiate into other cells
    sources- embryonic tissue (aborted fetuses, unused embryos from invitro fertilization,
        umbilical cord blood), adult tissue (bone marrow, cadavers, brain)
    uses- cure diseases (ex. diabetes, parkinsons, alzhiemers), grown own body parts
tissue- group of cells that function together in the performance of one or more specialized tasks
organ- structure consisting of several tissues adapted to perform specific functions
organ system- several organs that perform common task
homestasis- maintainace of stable operating conditions in the body

Tissues
1. epithelial- covers, lines, rests on basement membrane, one layer-simple, more than one-stratified
    shape of outer (luminal) cell- squamous (flat), cuboidal, columnar
    a.) simple squamous epithelium- very delicate, easy diffusion (least barrier), lines all blood vessels
            & alvioli of lungs
    b.) simple cuboidal epithelium- line thyroid, kidney tubules
    c.) simple columnar epithelium- lines gallblader, active in secretion/absorbtion, lines intestine
    d.) stratified squamous epithelium- bottom layer is cuboidal, upper layers flatten out, lines
            esophagus, skin, cheek
    epidermis- protein keratin-hard, prevents drying out
2. connective- filler, support, specialized (cartilage, blood, bone)
    often abundant extracellular material including fibrous proteins
    collagen- strong but resists stretch, make up tendons & ligaments
        elastic fibers- stretchable, abundant around arteries
        serves as area for transport (passage) of nerves & blood vessels
    adipose- fat tissue, functions: 1.) storage of energy (per unit calorie fat takes less space & weighs
        less than carbohydrates or protein) 2.) protection or cushioning  3.) insolation (blubber)
    cartilage- support (ex. nose, ears, trachea-rings)
    bone- minerallized (calcified), functions- movement (limb bones), protection (skull)
    blood- liquid-plasma containing H2O, ions, urea, nutrients (glucose, amino acids), vitamins, hormone
        red blood cells- erythrocytes, carry O2, CO2, hemoglobin, human-no nucleus (possible
            advantage-more efficient O2 transfer, more flexible)
       white blood cells-leucocytes, all have nuclei
            lyphocytes- immune system
            neutrophil- "non specific" immune system
       platelets- fragments of cells, function in clotting
3. muscle- smooth, skeletal, cardiac
    smooth- actin & myosin not rigidly arranged into striations, can stretch & still contract,
        peristalisis- movement of food along gut (ex. urinary bladder, blood vessels)
    skeletal- voluntary, bwt 2 Z-lines = functional unit of muscle (sarcomere)
        sliding filament theory- myosin filament pull actins together bringing z-lines closer
        elastic element make it go back to normal
4. nervous- communication via axon
    very variable- neurons & support cells ("glia")
    neuron- nerve cell, receive & transmit information (impulses)

Body Fluids
body fluids (outside cell)- high Na, high Cl, low K, high Ca
inside cell- low Na, low Cl, low Ca, high K
1. extracellular fluid (ECF)- immediately outside cell (bathes cell)
2. blood- fluid within blood vessels
3. lymph- fluid within lymphatic vessles
4. cerebrospinal fluid (CSF)- fluid that fills spinal canal & ventricles of brain, functions- help
        cushion brain, serves as lymphatic system for central nerous system (CNS)

Circulatory System
blood- "closed system"- blood remains in vessles
heart- pump
blood vessels- arteries, veins, function- transport in plasma of O2, CO2, nutrients, hormones, vitamins,
    plasma proteins, heat
plasma proteins- ex. albumin-helps osmotic balance, clotting proteins, antibodies, cpmplement prot
cells- erythrocytes- carry O2, CO2
    leucocytes- lymphocytes, neutrophil
    platelets- clotting
pathway- blood low O2 & high CO2 enters from vena cava into right atrium w/ rate determined
    by pace maker then into right ventricle which pumps into pulminary artery (goes to lungs) &
    comes back high O2, low CO2 entering left atrium thru valve into left ventricle when contraction
    squeezes blood into aorta to systemic system (to body)
systole- ventricular (heart) contraction        diastole- rest
blood flows continuously because aorta is elastic
pulminary artery -> arterioles -> capillaries -> venules -> veins
artery- thick wall due to smooth muscle, high pressure
vein- thin walled, low pressure, have valves to prevent back flow
lung alveoli- air sacs
coranary arteries- service heart
cardiac output- how much blood can be pumped by left ventricle per minute in liters= stroke
    volume x heart rate, varies 4-5x btw rest & vigor, dependent on arterial pressure/ peripheral
    resistance
as blood flows through systemic capillaries, there is a net loss of H2O & proteins into ECF, lymphatic
    vessel takes lost H2O/protein & puts back in vena cava
lymphatic system- to drain excess H2O & protein lost from capillaries & return to circulartory system
arteriosclerosis- "hardening of arteries" less elastic, fatty deposits => decrease opening size, clots
    get blocked, vessels rupture more easily
angioplasty- opening blocked arteries
coranary bypass- use veins from shunts around block region

Body Defenses
1. skin- multilayer barrier (stratified squamous), keratin- hard, dry environment, not conducive
        to bacterial growth
2. non-specific-
    a. white blood cells (leucocytes)- ex. neutrophil
        inflammation- regulated by leucotyes, triad- reddening, heat, swells, function- wound healing
        destruction of pathogens
    b. complement system- proteins always in blood plasma (inactive)
        bacterium invades->complement protein binds to bacterium membrane-> protein A activated
        -> activates B -> activates C -> C causes holes in baterium membrane
3. specific immune system-
    antigen- mediated system thru lymphocytes
    antigen- invading, foreign substance (ex. bacteria, virus)
    self (person or identical twin) vs. non-self
        cell surface markers tell if something is non-self
    lymphocytes- in blood & connective tissue
    immune organs- areas of concentrate lymphocytes (lymph nodes)
    special about lymphocytes- each one can recognize a specific antigen molecule, in develop
        specific genes can reshuffle forming up to 1 billion possible combinations
    two classes of lymphocytes-
        -differentiated in thymus gland (t-lymph, t-cells), subtype invovled w/ cellular immunity
        -differntiated in bone marrow (B-lymph, b-cells), involved w/humoral immunity- uses blood
            to transport messages, makes antibodies
    three main lymphocytes-
        -helper t-cells- "master cell", regulates killer t-cells, b-cells via release at interleukins
        -killer t-cells ("cytotoxic")- directly attacks cell by injecting lethal chemicals into the cell
            & causes holes in cell membrane (attacks cancer, virus infected, transplanted, etc)
        -b-cells - produce antibodies (proteins), function- nneutralize toxins, tag cells for later destruc
            by phagocytic cells
        all three can produce memory cells that upon subsequent exposure to a specific antigen can
            produce a much more potent and more rapid response
        antigen presenting cell- presents antigen to t-cell, engulf antigen, digest it, present pieces of
            molecules to t-cells (b-cells can do by itself)
            ex. macrophage- very phagocytic, can serve as an antigen-presenting cell, found in conn tiss
    immunization- memory cells booster for faster more mmediate response
    allergies- immune reactions to harmless antigens, often involves inflammation
    blood types- "A" & "B" are molecules on surface of erythrocytes, Rh factore another surface antigen
    autoimmune disease- body mounts immune rxn against own cells or tissues (HIV, Kaposis sarcoma)

Cell-Cell Communication
-involves a signal molecule
1.) autocrine- cell sends signal to itself, helps cell determine how much signal is released
2.) paracrine- local effect, one cell releases signal that is detected by nearby cells
3.) nervous system- one cell (neuron) releases signal (neurotransmitter) at end of a process (axon)
        to affect target cell, very specific route
4.) endocrine system- uses blood stream as transport route, one cell (endocrine cell) releases
        signal (hormone) into blood stream, signal goes all over body, only cells w/appropriate
        receptor respond

Nervous System
anotomical division-
    central nervous system (CNS)- brain & spinal cord
    peripheral nervous system (PNS)- nerves & ganglia
Central Nervous System-
    cerebrum- complex motor patterns, concious thought, memory, sensation
    cerebellum- muscle control
    medulla oblungata- controls automatc functions (heart rate, etc)
    spincal cord- connection btw PNS & brain, reflexes
Peripheral Nervous System-
    ganglia- areas or structures containing cell body portion (where nucelus is) or neuron
    nerves- bundles of axon and /or dendrites
Physiological division-
    autonomic  nervous system- controls automatic process (ex. peristalisis, breathing, heart rate)
        parasympathetic system- at rest, dec breathing rate, dec heart rate, inc peristalisis
        sympathetic system- "fight or flight" & exercise, inc breathing, inc heart rate, dec peristalisis
ion channels- neurotransmitter receptor, allow passage along gradient (passive)
ion pumps- pump ion against gradient (active), requires ATP
resting potential- all living cells in body have, due to leakage of ions
excitable cells- transmit impulses
    threshold- voltage that must be reached for excitable cell to fire (generate action potential)
    depolarization- reversal of normal polarity (making inside more positive)
types of ion channels-
    ligand-gated - channels open only in response to neurotransmitter, graded (in dendrite)
    voltage- gated- channels open only when threshold voltage is reached, all or nothing, (in axon)
neurotransmitter- released by neuron at synapse, can be excitatory or inhibitory
excitation- neurotransmitters open ion channels that cause voltage to become more positive
inhibition- inhibatory neurotransmitters open ion channels that cause inside of cell to be
    even more negative than usual (hyperpolarization)
action potential- due to opening of Na, K channels
    action potential arrive at axon ending, causes opening of Ca channel, Ca opens cells & triggers
    exocytosis of synaptic vesicles, releasing neurtransmitter into cleft, neurotransmitter diffuses
    over target cell membrane, interaction of neurotransmitter w/ion channel to open
stop action of neurotransmitter-
    -enzymatically destroy it in synaptic cleft
    -active reuptake back into axon ending via pumps
Serotonin- iincreasing time in synaptic cleft deviates deprssion
Antidepressents-
    1. MAO inhiibitors (monoamine oxidase)- enzyme destroying serotonin, longer
        time for serotonin in synapse, many side effects, patients must avoid ceratin foods
    2. Tricyclics- inhibit reuptake protein, many side effects b/c effected other synapses
        besides serotonin
    3. SSRI's (selective serotonin reuptake inhibitor)- fewer side effects, ex. prozac,zoloft, etc..
    4. MDMA- "ecstacy"- illegal-- inhibits MAO enzyme & reuptake protein, flood synapse
        w/serotonin

Endocrine System
hormone- chemical released in the blood stream by one cell that causes effects in a cell at
    some distance
endocrine gland- "ductless" gland, uses blood stream
Maintaining relatively constant hormone levels in bloodstream (ex. homeostasis)--
    negative feedback- increase in A causes increase in B, which inhibits A release..
        less A= less B, lack of B allows more A to be released (cycle)
    Positive feedback- increase in A causes increase in B, which causes increase in A release
        (cycle), ex. ovulation, child birth
Nervous System- route: very specific via axon    time: msec
Endocrine System- route: general - uses blood stream    time: secs, min, hrs
Method of Hormone Administration-
    1. oral ingestion- small hormones (ex. steroids, thyroid hormones)
    2. inhalation- small hormones (ex. steroids, adrenyline- epinephrine)
    3. injection- large hormones (ex. insulin, growth hormone)
Mechanism of Hormone Action-
    A. Polar Hormones- ex. peptides, proteins, modified amino acids--adrenalin, melatonin)
        -cannot get through cell membrane
        -interact w/ cell via receptors
        -many work via "second messangers" - molecules formed inside the cell mediate effects
        -G-proteins- cell membrance associated proteins that mediate effect btw hormone
            receptor complex & enzyme that causes second messanger formation
        -ex. of secondary messanger is AMP (adenosine monophosphate)
        -protein kinase- can add phosphate group to other proteins
            Some effects of protein phorphorylation via protein kinase:
                1. may activate an enzyme (ex. activation of glycogen breaks down glucose)
                2. may cause smooth muscle contraction (ex. uterine smooth muscle -> birth)
                3.may be an ion channel- causes opening/closing easier (ex. neuromodulation)
                4.may activate proteins involved in gene transcription (DNA--> mRNA)
                5. may induce exocytosis (ex. GHRH- releasing hormone for growth hormone in
                    hypothalmus--> activates GH in pituitary gland ->exocytosis of GH, #4 GH)
    B. Non-Polar Hormones- ex. steroids (derived from cholesterol), thyroid hormone T3, T4
        -HR binds to DNA to make mRNA which moves to cytoplasm (gene transcription) where
            translated to protein
Endocrine Glands-
    1. Pituiary Gland (hypophysis)- makes at least 10 hormones (hypothalmus in brain issues
            releasing hormones which affect release of pituitary hormones)
        a. Growth Hormone (GH)- causes growth of bone & CT in growing children, in adult-
            causes increase in protein sythesis & decrease in fat stores
            deficiency as child- shorter stature    excess- giganticism
            excess as adult- acromegaly (excess connective tissue growth)
        b. beta-endophin- natural morphine (oplate), pain reliever, released during stress &
            excercise, may be involved w/effects of accupuncture
    2. Thyroid- in neck region, secretes hormones T3 & T4 (affects basal metabolic rate (BMR))
        hypothyroidism- sluggish    hyper- nervousness, increase b.p.
        regulated by TSH from pituitary gland, negative feed back from T3 & T4
        T3 & T4 need iodine (w/o iodine excess TSH formed b/c no- feed from no T3 & T4)
        causes enlarged thyroid- goiter
    3. Islets of Langerhorns- in pancreas (most of which manufactures digestive enzymes)
        a. insulin- decrease blood glucose
        b. glucagon- increase blood glucose
    4. Adrenals- on top of each kidney
        cortisol (cortisone)- steroid hormone released during stress & exercise, mobilizes energy
        stores from body to combat stress, inhibits immune system & inflammation, may be to
        prevent autoimmune attack on body which is morelikely when wounds occur
        long term chronic stress- increase stress, increase cortisol, decrease immune sys -->
            increase likely hood of getting sick...

Reproductive System
Early Pregnancy-
    gonads - initially indistinguishable stage
    internal ducts- all have both female and male ducts
    external genitalia- indiffernt stage
    mullerian duct- becomes Fallopian tube, uterus, vagina
    wolffian duct- becomes epididymis, vas deferens, prostate
Normal XX Female-
    indifferent gonad develops into overy
    mulerian duct develop, wolffian ducts degenerate
    external genitalia -- female pattern
Normal XY Male-
    indifferent gonad develops into testis
    testis secretes 2 hormones testosterone, anti-mullerian hormone
    testosterone- causes development of wollfian ducts
    anti-mulerian hormone- causes degeneration of mullerian ducts
    in cells of external genitalia (indifferent) , testosteron converted to
    dihydrotestosterone (dihT) to cause male pattern
Genetic Disorders-
    individual is xy male- only problem - cannot produce anti-mulerian hormone, havee
        both ducts systems
    xy male- cannot prodice testosterone (anti-mullerian ok)- inside no ducts,
        outside- female
    xy male- cannot produce dihydrotestosterone from testosterone
        inside- male    outside- female
Puberty
    girls- menstrual syles begin, estrogen secreted by ovaries, secondary sex characteristics
    boys- inc testosterone secretion, secondary sex characteristics, lower voice
Male Reproductive Organs-
    testis- seminiferous tubules, produce sperm , secrete testosterone
    epididymis- coiled tube, runs along side of testis, store sperm
    vas deferens- very muscular tube (cut in vasecomy)
    prostate- secretes basic material contributing to semen
Female Reproductive Organs
    ovaries- produce egg (follicle- egg plus surrounding cells)
    fallopian tube- egg ovulates into tube, fertilization occurs here
    uterus- embryo implants in endometrium (inner most layer), placent & baby
        develope here
    vagina- birth canal , receptacle for penis
Menstrual cycle (~28 days)
    first ~9 days-- follicular phase- period of egg maturation, ovary secretes estrogene
        -effects in ovary, prepares uterus for baby ovulation due to positive feedback
        mechanism- egg goes to fallopian tube
    second ~9 days- in ovary, old follicle becomes corpus luteum (luteal phase), secretes
        estrogen & progesterone to inhibi pituitary, further devlop uterus
    no fertilization- corpus luteum degenerates, estrogen decrease, progesterone decrease
        menstrual period ~5days, causes degeneration of outer endometrium--
        blood--menstrual flow
    positive fertilization- early embryp secretes hormone- hCG (human chronic gonadotrophin)
        similar to pituitary hormone, keeps corpus lutem functioning releasing estrogen
        & progesterone, keeps uterus devloping
Birth = Parturition- another positive feedback
    signal from baby- causes release of oxytocin (pitosin) from pituitary causes uterine
    smooth muscle to contract which causes increase in oxytocin--cycle
    strong contraction = birth