Biology Notes Test I

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					                             Bailes Brown
              Biology Notes: Exam Review
                                    7/2/10
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 Bailes Brown


Biology
   Dr. Bill
   GSSM
    2002
                                                                           Bailes Brown
                                                            Biology Notes: Exam Review
                                                                                  7/2/10
                                                                            Page 2 of 55


           Biology Notes: Test I
1. History of Biology
      a. Galileo
                i. Galileo believed in the Heliocentric theory proposed by Copernicus
               ii. This theory violated the church‟s believe, and because the teachings of
                   the church were law, he was forced to go to court
             iii. Was forced by Inquisitors to say that he “ab-jouved, cursed, and
                   detested his erroneous claim that the earth moved around the sun”
      b. Aristotelian Logic or Deductive Reasoning
                i. The church believed that only deductive reasoning was sound because
                   measurements depended on senses which could be fooled. Therefore,
                   Galileo‟s telescope measurements were wrong.
               ii. Deductive reasoning starts with basic truths and attempts to prove a
                   result by syllogism
             iii. Deductive Syllogism
                       1. Major Premise – “If”
                       2. Minor Premise – “Then”
                       3. Conclusion – “Therefore”
              iv. Examples
                       1. Birds
                               a. If all birds have wings
                               b. Then sparrows are birds
                               c. Therefore sparrows have wings
                       2. Students
                               a. If all normal people have legs
                               b. Then students are normal
                               c. Therefore students have legs
                       3. Church‟s Example
                               a. If God created perfect heavenly bodies
                               b. Then the moon is in heaven
                               c. The moon must be a perfect heavenly body
      c. After Galileo, many scientists have proved many things
      d. Taxonomy – science of classifying living things
                i. 2 million have been identified
               ii. 80% are probably still unidentified
2. Background of the Theory of Evolution
      a. Diversity (many and varied)
                i. Leads to question “Where did it all come from”
               ii. Brought clash of creation and evolution
      b. Evolution
                i. From Latin meaning “an unrolling”
               ii. Definitions
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                      1. Changes in organisms over a geological time period
                      2. Changes in the gene pool frequencies of a species
             iii. Best explanation of diversity
             iv. Unifies all of Biology
                      1. Unites Micro, Macro, etc
      c. Theodosius Dobzshaskoy – population biologist
3. Theories before Darwin
      a. Plato (427-347 BC)
               i. He believed in two worlds
                      1. The Real world, which was ideal and eternal
                      2. The Imperfect world that was perceived by senses
              ii. This theory became Idealism or Essentialism
      b. Aristotle (384-322 BC)
               i. Challenged Plato‟s two worlds
              ii. Was a Naturalist – observed world
             iii. Scala Naturae – ladder or scale of nature with each life form at a
                  specific rung. This is a rigid form of classification
             iv. Immutable – unchanging
                      1. Was a view of Aristotle‟s that said that animals do not change
                      2. Stood for 2000 years
              v. Developed/Used Aristotelian logic, not research
      c. Dark/Middle Ages where nothing really happened
      d. Roger Bacon – Said “Cease to be ruled by dogma‟s and authority! Look at
          the world!”
      e. Other scientists
               i. Sir Thomas Moore
              ii. Copernicus
             iii. Galileo
      f. Inductive Reasoning – Scientific thinking process that goes from specific to
          general concept
               i. Requires Research
      g. Carolus Linnaeus (1707 – 1778)
               i. Father of Taxonomy
              ii. Was performing duty of religion/church by classifying
             iii. Believed in immutability
             iv. His theories helped Darwin
              v. Books
                      1. Species Plantarum (1753)– about plants
                      2. Systema Naturae (1758)– about animals
             vi. Binomial Nomenclature
                      1. Established by Linnaeus
                      2. Used Greek/Latin which didn‟t change
                      3. Used for Scientific Names
                      4. Uses format
                              a. Genus species or Genus species
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                      b. The Genus is a generic name (noun), while the species
                          is a specific epithet (adjective
               5. Examples
                      a. Ursus maritimus – Polar Bear
                      b. Ursus actos horribilius – grizzly bear
                      c. Ursus americanis – American bear
h. George Cuvier (1769 – 1832)
        i. Father of Paleontology, and also a anatomist
       ii. Looked at “Paris Basin” strassa and found fossils in different levels
           (from different periods)
     iii. Did not believe in Evolution
      iv. Found extinction of species
       v. Discovered Change in species
               1. Explained it by Catastrophism
               2. Catastrophism
                      a. Natural Disasters caused extinction and opened space
                          for new animals from different regions
      vi. James Huttem (Sp)
               1. Proposed Gradualism
               2. Gradualism – Gradual change in species over geological time
     vii. Charles Lyell (1797-1875)
               1. “Most important Geologist around Darwin‟s time”
               2. Created Uniformitarianism
                      a. Geological processes are so uniform that they balance
                          out over time
                      b. The processes didn‟t change over time (Of course the
                          structures did)
               3. Darwin took these ideas and decided
                      a. If the processes of earth were slow but consistent, they
                          could make a big change over time
                      b. The Earth was much older than the church said (6,000
                          years)
    viii. Jean-Baptiste Lamarck (1744-1829)
               1. One of first to try to explain evolution
               2. Published book in 1809
               3. He ordered/arranged mollusks in order of succession and
                  realized that they progressed
               4. He decided that the more complex they were the better
               5. His mechanism for evolution
                      a. Use/Disuse of Body Parts (proved true through Nat.
                          Sel.)
                               i. Those parts used extensively by an organism get
                                  bigger
                              ii. Those parts not used become smaller
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              b. Inheritance of acquired characteristics (phenotypes)
                  were passed on to descendents (Proven wrong)
              c. Examples
                      i. Giraffes
                            1. Populations of giraffes browse for food
                            2. The need to get higher causes stretching
                                of necks
                            3. Necks grow, giraffes reproduce
                            4. Phenotype is passed down
       6. Lamarck was attacked
              a. These attacks disgraced Lamarck
       7. Major contributions to science
              a. Statement that species do change over time
              b. Invoked role of environment as a cause of change
ix. Charles Robert Darwin (1809-1882)
              a. Background
                      i. Came from a successful social family
                            1. Father (Robert, was fat) and Grandfather
                                (A-something) were both physicians
                            2. His dad was very hard pressing on
                                Charles
                     ii. Education
                            1. Darwin didn‟t like formal study because
                                he had too much inquiry and energy
                            2. His dad sent him to Edenburg Medical
                                school, where he made descent grades
                                but left after watching a surgery
                            3. His dad then sent him to Christ College
                                at Cambridge University
                                    a. He loathed Science and Math
                                    b. He graduated at age of 22
                    iii. People
                            1. He had a group of friends called the
                                “Glutton Club” that he partied with
                            2. John Henslow, his botany professor,
                                bonded with him and helped him start
                                his career
                            3. Adam Sedgewick, his geology professor
                                helped him with geology
                            4. Emma, his cousin born of his Uncle
                                Josiah, and Darwin started to get a little
                                too close for relative (bad pun) comfort
              b. Career
                      i. HMS Beagle
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             1. Henslow recommended Darwin to go on
                 the Beagle as the naturalist after he
                 himself had to turn down the position
             2. Duty of the Beagle
                     a. To gather better longitude for
                         maps. Especially in South
                         America
             3. Captain Robert FitzRoy
                     a. About the same age as Darwin
                     b. Was manic depressive
                     c. Eventually committed suicide
                     d. He wanted the naturalist to find a
                         biblical explanation for creation
             4. Darwin didn‟t get a salary
             5. Left on December 27 1831
             6. Henslow gave Darwin a copy of
                 Lywell‟s Principals of Biology to read
                 on trip
c. Darwin‟s Trek through South America
       i. Collected 1000‟s of species in South America,
          and sent them back on other ships
      ii. Rabbits
             1. He realized no rabbits were present in
                 South America
             2. Did find Patagonian Hare, or Mara, that
                 resembled rabbits but were closer to
                 rodents
     iii. Skeletons of Giants
             1. Found giant armadillo shell (animal
                 would have been 2 tons) and huge
                 ground sloth
             2. Realized similarity to modern ones
             3. Found many extinct mammals, and he
                 hypothesized that South America and
                 North America must have been once
                 united by land bridge
             4. This migration led to the Marsupials of
                 South America to be replaced by the
                 incoming aggressive placentas
             5. The migration was made possible due to
                 the isthmus of Panama
             6. This suggested to Darwin that geology
                 and biology could change over time
     iv. Andes Mountains
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               1. He discovered clam shells on mountain
                   tops
               2. Petrified forest with sea shells
               3. earthquake raise the ground
      v. Galapogas Islands
               1. Oceanic archipelago 500-600 miles from
                   Ecuador
               2. Had very few species because recently
                   formed, and no mammals except for
                   those that were dropped off by ships
               3. It was a “little world unto itself”
               4. Darwin realized that the species were
                   close to those on South America
               5. Note: Most potential colonizers die, but
                   a very few live to spread out
               6. The islands were downwind from South
                   America, and therefore could have more
                   easily gotten the drift down
               7. Animals there
                       a. Marine Iguana – herbivore, could
                            process salt
                       b. Galapogas Tortise
                       c. **Finches
     vi. Darwin‟s Finches
               1. These finches gave Darwin the
                   mechanism for “Descent with
                   Modification”…Natural selection
               2. The finches each tried to find their own
                   niche to get food…some had different
                   bills, one bird (tool using Finch) could
                   even break open bark with a twig to get
                   insects
d. Darwin‟s return
       i. 1836 arrives back in England
      ii. He went to animal breeders to better understand
          artificial selection, which would help him
          develop natural selection
               1. They breed pigeons
               2. They put two desirable phenotypes
                   together
               3. Darwin thinks that if humans can
                   (artificially) select phenotype, then they
                   can propogate offspring
               4. Therefore, the same forces could act in
                   nature
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 iii.   Wasn‟t inclined to publish b/c it would bring
        attacks
 iv.    Thomas Malthus
            1. Economist, minister
            2. 1798 wrote “Essay on the principal of
                population” where he speculated that
                populations grew and overwhelmed food
                supply
            3. Food increased arithmetically (adding, 2,
                4, 6, 8, 10)
            4. Population increases by multiples or
                geometrically (2,4,8,16,32)
            5. This gave Darwin the struggle for food
                and survival
            6. Thought that several things could effect
                food vs. Population
                    a. Famine
                    b. Disease
                    c. War
  v.    Joseph Hooker
            1. Darwin sent initial theory of Natural
                selection to Joseph Hooker
            2. Hooker was a botanist
 vi.    Darwin‟s sickness
            1. Could have been caused by being bitten
                by a Benchuga or Giant Black bug of the
                P____. These Benchugas can carry
                Chaga‟s disease.
            2. May have been psychosomatic
vii.    Natural Selection
            1. was what Darwin was initially going to
                publish
            2. Had 6 volumes
viii.   Alfred Bussel Wallace –
            1. Englishman who sent some ideas to
                Darwin for comment, all were about
                natural selection
            2. Darwin and Wallace jointly appeared at
                Royal Linnaean Society of London
 ix.    Origin of Species
            1. Full name is Origin of species by means
                of natural selection or…..
            2. Basic Premises
                    a. Evolution occurs over billions of
                         years (long geologic time)
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             b. Natural Populations have
                  variations
                       i. Certain genotypes are
                          going to have a survival
                          advantage
                      ii. This leads to greater
                          biological fitness
             c. Populations have great capacity
                  for reproduction and overproduce
                  prodigy
                       i. Natural forces will weed
                          these populations out
                      ii. Competition will help
             d. Mechanism: Natural Selection
      3. Herbert Spencer – wrote about survival
         of fittest and formed “popular” natural
         selection
x. Examples of Natural Selection
      1. Peppered Moth (Biston betularian)
             a. In England
             b. Was polymorphic
                       i. Melanistic (Darker,
                          because umelanine)
                      ii. Normal, just peppered
             c. Early 1800‟s had very few
                  melanistic
             d. As industrial revolution
                  progressed, the darker became
                  more common
             e. E.B. Ford was first to describe
                  the changes in Moths
                       i. He said that smog killed
                          the lichens on the trees,
                          making darker more
                          favorable to not being
                          eaten
             f. H.B. Kettlewell
                       i. Tested Ford‟s prediction
                      ii. Went to Dorsett (non-ind)
                          and found that Melanistic
                          were more likely to be
                          eaten
                     iii. Went to polluted area and
                          found the normal
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                                                             peppered version more
                                                             likely to be eaten.
4. Modern Synthesis
     a. After Darwin‟s Origin of Species, evolution was mainly accepted but lots of
         people didn‟t acknowledge Natural Selection because genetics had not been
         invented yet
     b. Mendel – Father of genetics
              i. Genetics helped influence the theory of evolution by reinforcing
                 Natural Selection mechanisms
             ii. People who also “discovered Natural Selection
                    1. Hugo de Vries
                    2. Carl Correns
                    3. Eric Bontshermack (sp)
            iii. Genetics
                    1. E. coli is “lab rat for genetics
                    2. Human genes are multiple
            iv. 1930 Mendelism and Darwinism begin to combine
     c. Neo-Darwinism (Modern Synthesis)
              i. Characteristics
                    1. populations are the unit of evolution, not individuals
                    2. Natural Selection
                    3. Gradualism
     d. Evidence of Evolution
              i. Presence of Fossils
                    1. remnants of life forms
                            a. Partial to total skeletons in 3D
                            b. Impressions (2D)
                    2. Problems
                            a. Where are the missing links?
                    3. Example of a horse
                            a. Performed by O.C. Marsh
                            b. Horses through the epochs
                                     i. Hyracotherym (Iohipus)
                                            1. 2nd Epoch
                                            2. Was small
                                            3. 4-toed
                                            4. broad, flat, low crowned teeth  forest
                                                plants
                                    ii. Mesehippus
                                            1. Oligosine Epoch (38M-24M years ago)
                                            2. Longer legs
                                            3. 3-toed
                                            4. Higher teeth crown
                                   iii. Myrichippus
                                            1. Miocene 24M – 5M
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                                 2. Longer neck/legs
                                 3. Higher crowns
                                 4. One big toe and 2 small ones
                       iv. Plyohippus
                                 1. Plyocene 5M-1.8M
                                 2. Hoof
                                 3. High crowns
                        v. Eques – Modern horse
                                 1. Pleistocene Epoch 1.8M – 10K
                                 2. Hoof, high crowns
                c. Punctuated Equilibrium
                         i. Some classes evolved in relatively short period
                            of time, while others evolved very slowly
                        ii. People
                                 1. Niles Eldridge
                                 2. Steven Gould
                       iii. They said
                                 1. Evolution had to be punctuated
                                    equilibrium
                                 2. Certain species existed relatively
                                    unchanged, then suddenly they
                                    disappeared and were replaced by new
                                    but similar species
                                 3. Fits and Starts
                                        a. Fits were sudden bursts of
                                            evolution
                                        b. Starts were the development of
                                            new species
                       iv. Most morphological changes happen in 1st
                            50,000 years of the species existence
                        v. Evolution accelerates as the environment
                            rapidly changes
 ii. 2nd Evidence: Biogeography
         1. Definition: distribution of living things
         2. Questions
                a. Why do isolated groups have unique species?
                         i. Ex Australian marsupials, Galapogos islands
      rd
iii. 3 Evidence: Comparative anatomy
         1. Definition: can discern relationships by look at similar animals
         2. ex – learned from mammals that vertebrates  giraffes to rats
         3. Sub Phylums
                a. Vertebrate – backbone, spinal column
         4. Principal of homology
                a. Homologous – phylogenetic history, may have different
                    function
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                               b. Examined mammals forelimbs
                                        i. Parts
                                               1. Humourous
                                               2. Radius and ulna
                                               3. Carpuls and metacarpuls
                                               4. Philanges
                                       ii. Formation
                                               1. Arise from limb buds in embryo
                               c. Analogous – same function, different phylogenetic
                                   history
                                        i. Ex bird and bee wings
                               d. Vestigial – useless structures left over from ancestral
                                   past
                                        i. Ex Whale and Python skeletons both have
                                           remnant of pelvic girth
                                       ii. Both probably related to land walking animals
                                      iii. Human structures – wisdom teeth, appendix
      e. 4th Evidence - Comparative Embryology
                      1. All vertebrate embryos have paired gill slits and post anal tail
           th
      f. 5 Evidence - Comparative Bio-Chemistry
                      1. Amino acids in hemoglobin
                      2. DNA/Genes
               ii. Taxonomy – “tree of life” – Linnaean
5. Population Evolution
                i. Variation!!
               ii. Natural populations have variation which natural selection acts upon
              iii. Define Population – group of interbreeding individuals of a single
                   species living in the same area and by interbreeding share a common
                   gene pool
              iv. Individuals do NOT evolve, populations evolve
               v. Hardy-Weinburg Law
                      1. mathematical model that is the foundation for population
                          genetics
                      2. Population genetics – the study of allelic populations
                      3. Gene – sequence of DNA that codes for a protein
                      4. Allele – an alternate form of same gene
                      5. If smooth skin is S and wrinkled is s then…
                      6. Alleles occur at homologous chromosomes
                      7. Populations can have more than one allele, though individuals
                          can only have 2.
                               a. Ex Blood Ia Ib and Io
                      8. People
                               a. J. H. Hardy – English mathematician at Cambridge
                               b. R.C. Punnitt – worked with Hardy to find HWE
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       c. William Weinberg – German, published the same thing
          as Hardy
       d. W.E. Castle – also published HWE info
9. Actions
       a. J.H. Hardy and Punnitt got together to defend Mendel
          against critics
10. Hardy-Weinberg
       a. Background
               i. Frequency – what proportion of total of alleles
                  that a specific allele is
              ii. Evolution – change in gene allele frequency
                  over time
             iii. Phenotype – something that can be seen or
                  measured
             iv. Genotype – genetic makeup
              v. Genetic Structure – a population‟s frequency of
                  alleles and genotypes
             vi. HWE give the standard to measure changes in
                  populations
       b. Assumptions
               i. No survival advantage (no Natural Selection)
              ii. Alleles transported by sperm/eggs at same
                  frequency as appear in population
       c. Conditions of Stability:
               i. Large population size (infinitely large)
                      1. Chance does not affect allelic frequency
              ii. Mutations do not occur
                      1. Or they must be in mutational
                          equilibrium
                              a. Fwd mutation = bwd mutation
             iii. No immigration or emigration
             iv. Mating must be random with respect to
                  genotypes
              v. Reproductive success must be random with
                  respect to genotype
       d. Equations
               i. P + q = 1
              ii. P2 + 2pq + q2 = 1
             iii. Proof:
                      1. A normal punnitt square would represent
                          gametes
                      2. A special punnitt square could represent
                          the frequency of each allele. By doing
                          this, you will cross the alleles and the
                          frequencies, and prove HWE
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                     e. AA example
                            i. Genotypes: AA, Aa, aa
                           ii. Frequency
                                    1. Allele: A - .9, a - .1
                                    2. Genotype: AA - .81, Aa - .18, aa - .01
                          iii. If you calculate the 2nd generation of gametes
                               and frequencies, you see that it is the same
                          iv. This proves that Evolution is not automatic
                           v. Evolution only occurs when something disturbs
                               it from genetic equilibrium
                     f. Ex.
                            i. d causes obvious disease
                           ii. dd = .04
                          iii. dd = q2  d = q = .2
                          iv. p = .8
                           v. Dd = .8*.2*2 = .32
                     g. Multiple Alleles
                            i. Just add more combinations
                           ii. For example,
                                    1. p + q + r + s = 1
                                    2. (p + q + r + s) 2 = 1
                     h. Summarize
                            i. Most useful application
                                    1. States conditions under which evolution
                                       will not occur, and those in which it is
                                       likely to occur
                           ii. Gives standard against which allelic frequencies
                               which are always occurring in natural
                               populations can be measured
b. Microevolution
       i. Define – changes in allelic frequency over time
      ii. Five Factors that cause MicroEvolution
             1. Genetic Drift
                     a. Define – gene or allelic frequencies can change in small
                         populations because of chance factors such as natural
                         disasters
                              i. Ex Field Mice in forest with new highway
                     b. Bottleneck Effect – Unselective killing (not dependent
                         on phenotype) of individuals that can change a gene
                         pool
                     c. Founder Effect
                              i. Caused by colonization, gene pool doesn‟t
                                 reflect that of parent group
             2. Gene Flow
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      a. Occurs as populations gain or lose alleles because of
          immigration/emigration (could be just gametes leaving)
3. Mutation
      a. Random changes made to genetic material
      b. Point Mutations – Individual nucleotide changes
               i. Ex. Tay Sachs disease is caused by an enzyme
                  that metabolizes fat, usually deadly
      c. Chromosomal Mutations/Aberrations
               i. Deletions
                      1. Part of chromosome breaks off ABCDE
                           ABC
              ii. Inversions
                      1. Series in wrong direction ABC  CBA
             iii. Chromosomal Translation
                      1. Reattaches to a non-homologous
                          chromosome ABC  ABC Σθ№
             iv. Note: Natural Sleection acts on variations in
                  standard phenotype. Therefore, mutations and
                  sexual recombination lead to the diversity of
                  species
4. Non-Random Mating
      a. Means: Potential for any individual to mate with any
          other of the same population, anywhere. However, it
          has been shown that proximity is key
      b. Inbreeding
               i. Means mating with closely related individuals
              ii. Starts to occur when individuals mate in
                  proximity
             iii. Leads to Homologous genes
      c. Assortative mating
               i. Ex
                      1. Lesser Snow Geese
                              a. Normal
                              b. “Blue Geese”
              ii. Shows mating with similar phenotypes because
                  Blue x Blue and White x White
5. Natural Selection
      a. Every population will have variation
               i. Examples of misunderstandings
                      1. John Vanwind said “You seen one
                          alligator, you seen em all:
                      2. Ronald Reagon said “ You seen one
                          redwood tree, you seen em all”
      b. Types of Selection
               i. Stabilizing selection
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                                               1.  
                                               2. Ex. Baby weight is usually 3-4kg
                                     ii.   Directional selection
                                               1.  
                                               2. Ex
                                                       a. Black bears in Europe are larger
                                                           because they had to survive
                                                           higher temperatures
                                                       b. Birdman‟s rule – going N to S,
                                                           species get smaller because of
                                                           heat and SA/V ratio
                                    iii.   Disruptive or Diversifying Selection
                                               1.  
                                               2. Against middle
                                               3. ex
                                                       a. Elephant seals
                                                       b. Selected for large males and
                                                           small females
                                               4. Sexual Dimorphism – when there are
                                                   noticeable differences between males
                                                   and females in the same species
                                                       a. Ex Cardinals, Ducks, Elephant
                                                           Seals
                                    iv.    Sexual Selection – Darwin proposed
                                               1. A struggle between one sex for
                                                   possession of the other (Male fight for a
                                                   mate)
                                               2. Female Choice
                                                       a. Female usually gets to choose
                                                           who she mates with
                                                                i. Ex Malty Anderson
                                                                   studied the Long Tailed
                                                                   Widow bird
                                                               ii. He cut some tails and
                                                                   attached to others
                                                              iii. Found that long tailed
                                                                   were 4 times more likely
                                                                   to mate
                                      v.   Shifts lead to Natural Selection
                                     vi.   Patchy Distribution
                                    vii.   Phylogeny – similar ancestry
                                   viii.   Convergent evolution
6. Definitions
      a. Extinct – no individuals left on the face of the earth
      b. Extant – still alive (opposite of extinct
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c.   Endemic – restricted existence in specific location
          i. Ex Venus fly traps and Kangaroos
d.   Population – group of interbreeding individuals of a single species living in
     the same area and by interbreeding share a common gene pool
e.   Fitness – relative ability of an individual to survive and produce offspring
f.   Natural Selection – The differential reproduction of various genotypes
g.   Polymorphism – two forms
h.   Biogeography - distribution of living things
i.   Comparative anatomy - can discern relationships by look at similar animals
j.   Homologous – phylogenetic history, may have different function
k.   Analogous – same function, different phylogenetic history
l.   Vestigial – useless structures left over from ancestral past
m.   Population genetics – the study of allelic populations
n.   Gene – sequence of DNA that codes for a protein
o.   Allele – an alternate form of same gene
p.   Evolution (Microevolution)– change in gene allele frequency over time
q.   Phenotype – something that can be seen or measured
r.   Genotype – genetic makeup
s.   Frequency – what proportion of total of alleles that a specific allele is
t.   Genetic Structure – a population‟s frequency of alleles and genotypes
u.   Genetic Drift - gene or allelic frequencies can change in small populations
     because of chance factors such as natural disasters
v.   Bottleneck Effect – Unselective killing (not dependent on phenotype) of
     individuals that can change a gene pool
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                  Bill Notes Test II
1. **Evolution of Species** - Microevolution
      a. Missed Notes
               i. Evolution of Species
              ii. Species – „kind‟ or „appearance‟ (from Latin)
            iii. Mayr (Harvard) – used birds as mechanism for evolution studies
                      1. 1937 – New Guinea – Arafak Mountains – wanted to study
                          birds. Natives had 137 different names for local birds.
                          Scientists found 138 different species. Humans can see these
                          differences!!
             iv. Typological species: (since Aristotle‟s time) believed in my laymen
                  and scientists. Static immutable species
              v. Morphospeices: Linnaeus. Recognized by appearance/morphology.
                  Used today more than others.
             vi. Intraspecific variation: variation within a species
            vii. Hard to do if there is i.v.  ex. Wood ducks. Thought males and
                  females were different species
           viii. 1942: Ernstan Mayr: Biological Species – genetically distinct group of
                  natural populations that share a common gene pool and are
                  reproductively isolated from all other such groups (even those very
                  similar)) **Reproductively Isolated**
             ix. Conspecific: relatedness of some species
              x. Intraspecific: event between individuals of same species
             xi. Interspecific: event between individuals of different species
            xii. Difference can be physiological, anatomical, or behavioral
           xiii. Distinct characteristics of a species partly result from reproductive
                  isolation
      b. Biological Species
               i. Biological species – genetically distinct group of a Natural Population
                  that shares a gene pool and is reproductively isolated
              ii. Other theories:
                      1. Recognition
                              a. Defines a species by its set of characteristics that
                                  maximize successful mating with members of the same
                                  population
                      2. Cohesion concept
                              a. Says that a distinctive, integrated set of adaptations has
                                  been refined in the evolutionary history
                              b. Cohesion of phenotype is the basis of species integrity
            iii. Flaws with Bio-Species
                      1. Hybridization
                              a. Examples
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                      i. Canis Lupis (Gray wolf) can mate with Alaskan
                         Husky to make Pawnee
                     ii. F African Lion x Male Siberian Tiger = Tiglon
                    iii. M Af. Lion x F Sib. Tiger = Liger
                    iv. Mallard x [insert duck here]
             b. Usually Sterile
      2. Asexual Species like Prokaryotes, Fungi, and Protists
      3. Varying across distance
             a. Ex – Deer mouse
                      i. They form a diamond shape with some corners
                         cross breading and others not. This allows some
                         gene flow between populations
iv. Mechanisms for Speciation
      1. 2 Kinds of Processes
             a. Anagenesis (Phyletic speciation)
                      i. 1 species gradually replaces another
             b. Cladogenesis (Divergent Speciation)
                      i. 1+ species branch off, parent stays
                     ii. Increases the number of diverse species
      2. 3 Modes for Speciation
             a. Aldopatric Speciation
                      i. Occurs when original species becomes
                         separated geographically and the two groups
                         evolve separately
                     ii. Examples
                             1. Layering of earth as water came/went
                                 through the Colorado River and cut
                                 squirrels into two populations that
                                 evolved into the Kaibab and Abert
                                 species
                             2. Pup Fish (Genus Cyprenonand) in Death
                                 Valley
                    iii. Splinter Population
                             1. Define: Peripheral Isolate
                             2. Gene drift, small population size leads to
                                 speciation
                             3. New environment may have new
                                 selection factors
                    iv. Adaptive Radiation
                             1. A number of Species from a common
                                 ancestor
             b. Parapatric
                      i. Boundary is usually a change in environmental
                         factors
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      ii. Populations are mostly separated
          geographically, but touch at a common border
     iii. Gene pools are fairly separate, but with some
          gene flow possible
     iv. Distance could be enough to separate
c. Sympatric
       i. (Less common form of divergent species)
      ii. New species arise from parents
     iii. Reproductive isolation without geographical
          separation
     iv. Can occur in single generation if mutations
          occur
      v. Example: nondisjunction (in meiosis)
             1. Nondisjunction is the improper
                  separation of gametes. In other words,
                  an organism would have too few or too
                  many chromosomes
             2. Could be caused by a specific gametes
                  chromosomes not splitting, therefore
                  contributing 2n instead of 1n
             3. Tetraploid – an organism with 4
                  homologous chromosomes
             4. Examples in humans – Trisomy 21 or
                  Down Syndrome
             5. This Non-Disjunction is “instant
                  evolution”
             6. Autopolyploids – a single species that
                  changes its chromosomes
             7. Allopolyploid – 2 different species that
                  contribute to gene material to form a
                  hybrid
             8. Vegetable propagation – when plants
                  asexually reproduce, making it possible
                  to spread mutations easier
             9. Examples of polyploids – potatoes, oats,
                  and bread wheat
     vi. Reason for two colors in Bead lab
             1. Cell is Eukaryotic animal cell that is the
                  PRODUCT of sexual reproduction
             2. Each mom/dad contributed 1n, so that
                  two different Chromosomes colors show
                  which parent it is from.
             3. In other words, it shows the difference
                  between the 2 homologous
                  Chromosomes
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                    4. Homologous chromosomes not exactly
                       the same, instead they are the same kind
                       of chromosome
3. Mechanisms for reproductive isolation
     a. Prezygotic Barriers or Factors
             i. Ecological Isolation
                    1. 2 species live in same geological area
                       but exist in different terrains. For
                       example some garter snakes live in the
                       marsh while others live in the dry areas
                    2. Examples
                           a. Garter Snakes – Genus
                               Harmonopis (sp)
                           b. Lungless Salamanders –
                               Plethodontidae
            ii. Temporal Isolation
                    1. Isolated by a time frame
                    2. Caused when 2 species have breeding
                       cycles that occur at different periods of
                       the day or in different seasons
                    3. Ex. Trout (Rainbow and Brown)
           iii. Behavioral Isolation
                    1. Displays – behavior to attract a mate
                    2. Visual, Olfactory, or Auditory signals
                       used to attract a mating partner
                    3. Ex – Mocking birds
                    4. Ex olfactory – pheromones  Important
           iv. Mechanical Isolation
                    1. Cannot breed because of anatomical
                       incompatibilities
                    2. Ex Key
                    3. Ex2 – Dragonflies
            v. Gametic Isolation
                    1. Ex. Mtn gorilla and zebra (made it up)
                    2. Even if you inject gametes, the sperm
                       will not be able to reach the egg
                    3. Similar concept to contraceptives
                    4. May not be able to bind to egg,
                       biochemical recognition sites
     b. Postzygotic Factors
             i. Reduced Hybrid Viability
                    1. Hybrid Zygote chromosomes are
                       genetically incompatible
                    2. Embryo will abort
            ii. Reduced Hybrid Fertility
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                                      1. Individual is born but sterile
                                      2. Ex. Mule
                             iii. Hybrid Breakdown
                                      1. First generation hybrid is fertile, but
                                          second generation is weak and/or sterile,
                                          so they can‟t continue
                       c. Introgression
                               i. Despite all these barriers, alleles can be
                                  introduced through hybrids that back-breed with
                                  a parent
                              ii. Example Teosinte x Zea Mays (Field Corn)
                                      1. Hybrid can recombine with Mays
                 4. Genetic Means of Speciation
                       a. Alan Timpletin of Washington Univ.
                       b. Adaptive Divergence
                               i. As populations are separated, they allele
                                  frequencies change because of chance, gene
                                  flow, etc.
                              ii. This divergence of species leads to reproductive
                                  barriers that cause speciation
                             iii. This is important when allopatric populations
                                  become united at a common border.
                                      1. If hybrids form, then not adequately
                                          separated to be species
                                      2. If no hybrids, then two different species
                                      3. In reality, it is usually a cross between
                                          these extremes, resulting in a few
                                          hybrids that survive but are less fit than
                                          parents. These would then be
                                          semispecies
                             iv. Adaptive Landscape – Bumpy map from book
                                      1. Sewell Wright
                                      2. Peaks represent gene pools in
                                          equilibrium where gene pool has
                                          maximum average genetic fitness.
                                      3. Valleys represent unfit places
                                      4. NS is the force that causes the “ping
                                          pong ball” to fall and change the
                                          landscape
                                      5. Once the landscape is redefined, what
                                          was once on a peak and was knocked
                                          down must climb back up to a peak or
                                          become extinct.
2. Macroevolution
     a. Background
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  i. Many major historic events in the history of living things caused
     Macro Evolution
        1. Examples
                a. Increasing cranial capacity
                b. Evolution of feathers/wings
                c. Major extinction
                         i. Dinosaurs, 65 million years ago (mya)
                        ii. Walter and Louis Alvares – Asteroid hypothesis
 ii. Ways of getting knowledge
        1. Fossils and paleontology play an essential role in piecing the
           parts together.
                a. If we imagine a clock with the earths history on it:
                         i. 2 (AM) – first rocks
                        ii. 5:15 – oldest known living fossils
                       iii. 6 – Photosynthetic stuff
                       iv. 1:15 (PM) – first free oxygen
                        v. 4:30 – first Euk. Organisms
                       vi. Multi-cellular
                      vii. Land plants
                     viii. 11:15 – Mesozoic Dinosaurs
                       ix. 11:59:30seconds – first homosapiens
                b. Notice how humans have had so much of an effect in so
                   little time
        2. Electron microscopes give good cellular view of old forms –
           40mya
iii. Geological Time Scale
        1. Artificially produced
        2. Time is hard to understand because so large
        3. Techniques to find Geological time scale
                a. Relative Dating
                         i. Can see which fossils came in which order
                        ii. Examining strata
                                1. Index fossils – same fossil organism in
                                   may different locations
                b. Absolute Dating
                         i. Uses radioactive isotopes that become part of
                            organisms when living
                        ii. Half Life – amount of time for a quantity of
                            radioactive material to decay by a factor or ½
                       iii. Carbon 14 is an isotope of Carbon 12 that has a
                            5.6K half-life
                       iv. Potassium 40 (K40) has a half life of 1.3by
                        v. Uranium 238 – 4.5by
                       vi. Plutonium 24.5K
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                     4. Discussion of Geological time period – his chart is 23.1 on pg.
                        456
                            a. Eras – big, big geological time period
                                    i. Precambrian – 1st
                                            1. no important period divisions
                                   ii. Paleozoic – “ancient animals” – Can Old
                                        Soldiers Die Carrying Packs? (From latest to
                                        earliest)
                                            1. Cambrian
                                            2. Ordovician
                                            3. Silurian
                                            4. Devonian
                                            5. Carboniferous
                                            6. Permian
                                  iii. Mesozoic – age of reptiles
                                            1. Triassic
                                            2. Jurassic
                                            3. Cretaceous
                                  iv. Cenozoic – age of mammals
                                            1. Tertiary
                                                    a. Paleocene
                                                    b. Eocene
                                                    c. Oligocene
                                                    d. Miocene
                                                    e. Pliocene
                                            2. Quaternary
                                                    a. Pleistocene
                                                    b. Recent
                                      Note: all throughout these periods different
                                      geological things happened. For example,
                                      mountains came out during all eras, and this
                                      explains why Appalachians are smaller than the
                                      Rockies, because they are older

3. Continental Drift
      a. Background
               i. People
                     1. Francis Bacon – acknowledged similarity between continents
                         fitting
                     2. Alfred Wegeder – theory of continental drift
      b. Theory of Plate Tectonics – Tectonic is Latin for cover or plate
               i. Has two parts: Continental drift and Floor spreading
              ii. Mid-Atlantic Ridge is a mountain range that is underwater and 6.5K ft
                  from top to bottom. It also has a lot of seismic activity
             iii. Quakes caused by skipping of land masses
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              iv.   Rifts – splits in land where tectonic plate shifts and quakes often occur
               v.   Sea Floor Spreading
                        1. Magma solidifies in water and becomes the new
                            crust…movement is about 2cm a year
              vi.   Parts of the Earth
                        1. Atmosphere
                        2. Crust
                        3. Lithosphere – made of 6 major and 12 minor Tectonic plates
                        4. Asthenosphere – upper layer of the Mantle
                                a. Semi-plastic because fluid and not rocky
                                b. Is what the plates move around on
             vii.   Trenches
                        1. Peru-Chile
                        2. Marianas Trench – 5 miles deep, has hydrothermal vents
                        3. Subduction zones
            viii.   CAT Scan – Computerized Axial Topography
                        1. people monitor shockwaves to watch for quakes
              ix.   4 Depictions of Land masses – pg. 466
                        1. 200-250my Pangea (All lands) and Panthalasa (all seas)
                        2. 135-180my – N and S split at about equator
                                a. N – Laurasia
                                b. S – Gondwana – much larger
                                c. Laurenchia – Ancient North America
                                d. Tithys sea – separates N/S land masses
                        3. 65my
                                a. India Migrated into Asia
                                b. North America and Europe separated at 80my
4. Origin of Life
      a. Big Bang Theory
               i. Time period
                     1. Controversy of exact time, but lets say 14by
      b. Original Earth
               i. Cold until compaction, radioactive decay, and meteorites provide heat
              ii. Minerals sorted out by density
                     1. Fe and Nickel sank towards core
                     2. Mg, Silicon, and Ox formed Mantle
                     3. O, Silicon, Al, Ca, Sod, K formed crust
      c. Origins of Life
               i. Panspermea Theory – 19th century
                     1. Initial spores of life came from the universe
              ii. Directive Panspermea
                     1. People
                             a. Francis Crick
                             b. Lesli Orger
                     2. Theory
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                       a. Said that spores of life were intentionally sent to the
                             earth by intelligent beings in the universe
      iii. Special Creation – strictly biblical
      iv. Abiogenesis – “Beginning without life”
               1. Theory
                       a. Life arose from inanimate matter
                       b. Spontaneous evolution of life occurred on a planet
                             much different from now
                       c. Energy probably came from volcanoes, not lightning
                             (that‟s what Dr. Bill said)
       v. Bio-Chemical evolution of Life
               1. People
                       a. JBS Haldane
                       b. Alexander O‟Perry – Russian
               2. Theory
                       a. Long period of biosynthesis in oceans (1-3by)
d. Tracing Origin of Life
        i. Changes in Earth
               1. Chaotic conditions
                       a. Meteorites
                       b. Volcanoes
                       c. Hot
               2. Water: There was water in the oceans, but no life!!
               3. At 4.3by conditions started to stabilize and an Hydrogen
                   (reducing) atmosphere appeared
               4. However, it didn‟t stay for long…It disappeared and later
                   appeared a second atmosphere that came from within the earth
                   itself, like volcanoes
               5. Resulting atmosphere had H20, CO, CO2, N2, CH4 (Methane),
                   and NH3 (Ammonia)
               6. As earth cools, atmosphere does too, leading to rain
       ii. First Living Organisms
               1. Anaerobic bacterial form at 3.5by (just first evidence, not
                   necessarily first true form)
               2. probably formed many times in many places
               3. Best evidence is located in Geological formations, especially
                   stromatolites
                       a. Locations: Shark Bay in Australia, South America
                       b. Stromatolites
                                  i. Oldest know evidence of life
                                 ii. If cut open, you can sea the streaks and lines
                                     that represent life form activity at 3.5by
               4. Prokaryotes
                       a. Types
                                  i. Cyanobacteria
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              1. blue green algae that has chlorophyla
                  (normal for plant) and phycocyanin,
                  which makes it blue/green
              2. (pg. 488) Lynn Margulis and Kenneth
                  Nealson collect mud and stuff with
                  modern cyanobacteria that we think
                  resemble the stromatolite fossils
b. Prokaryotic vs. Eukaryotic
       i. Change in systems
              1. Originally, a 2-Kingdom (animal/plant)
                  system existed
              2. Problems, like Euglena, which is now
                  considered a protist, had both Flagella
                  for movement and chloroplasts
              3. Robert Whitaker created the 5-Kingdom
                  system which included Animals, Plants,
                  Fungi, Protists, and Monera, which
                  include prokaryotes bacteria and
                  cyanobacteria
      ii. Prokaryotic
              1. means “before kernel”, meaning that it
                  doesn‟t have a nucleus
              2. Doesn‟t have any envelopes other than
                  outer membrane
              3. Also doesn‟t have Endoplasmic
                  reticulum, golgi apparatus, lisosomes,
                  vacuoles or mitochondria
              4. Singular circular chromosome, less
                  protein
              5. Can have ribosomes, usually smaller
              6. Escherichia Coli (found in human
                  digestive tract) are the lab rats for
                  genetic experiments
                      a. Very little protein
c. Origin of Prokaryotes (4 Steps)
       i. Abiotic Synthesis and accumulation
              1. Monomers, or basic molecules start to
                  collect
                      a. These include simple sugars,
                          amino acids, etc
                      b. This can be compared to “stacks
                          of bricks and boxes of nails”
              2. Haldane-O‟Parry
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              a. The reducing atmosphere then
                  was different from the oxidizing
                  one now
       3. Harold Urey and Stanley Miller
              a. Simulate the generation of
                  Monomers
              b. “Spark Discharge Apparatus” -
                  see page 489 or hand notes for
                  diagram
              c. In one week, they notice color
                  changes and compounds forming
                       i. Form-Aldehyde
                      ii. Carboxylic Acid
                     iii. Amino Acids – Glycine
                          and Alonine
              d. When Miller first presented it, he
                  got a bad reception, but after he
                  repeated, he was eventually
                  accepted
                       i. He put whole instrument
                          in an autoclave to kill
                          bacteria
              e. Repeated experiments have
                  found all 20 Amino Acids, ATP,
                  basic DNA parts, etc
ii. Polymerization
       1. More complex molecules form, such as
          proteins
              a. These molecules are collections
                  of monomers and are called
                  polymers
              b. “one wall of a house”
       2. Dehydration Synthesis (Condensation)–
          process by which monomer bond to form
          polymers
              a. Ex. Glucose + Glucose =
                  Matrose + H20
              b. This process is difficult to occur
                  in water because of the chemical
                  ratios
                       i. Need for Enzymes
                          (Glovular Proteins) or not
                          in water
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                c. Carl Woese suggests that life
                    began in the atmosphere, not in
                    water
        3. Dr. Sidney Fox demonstrated how amino
            acids polymerization could have taken
            place in hot, dry locations like near
            Volcanoes
                a. He found that heat vaporized the
                    water, and then polymers could
                    form
                b. Found polypeptides with 200+
                    amino acids…Called them
                    Thermal Proteinoids
                c. When he dumped them in water
                    they clumped into groups which
                    he called Proteinoid
                    Microspheres - bilayerd
iii. Protobionts – organic systems
        1. Aggregating polymers
                a. Little organic systems in water –
                    Protobiontic droplets
                b. Now the organism can respond to
                    stimuli
        2. 3 Types we know, many more out there
                a. Proteinoid Microspheres
                         i. Can reproduce for 3-4
                            generations
                        ii. Maintain controlled
                            internal environment,
                            with the semblance of a
                            plasma membrane
                b. Coacervate – minute droplets
                         i. Created by O‟ Perry (O‟
                            Perring?)
                        ii. Formed when solvent
                            containing two polymers
                            that don‟t react with each
                            other but do react with
                            the solvent combine
                       iii. Cane synthesize and
                            accumulate starch
                       iv. Can conduct
                            oxidation/reduction
                            reactions
                        v. Can photosynthesize
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                      vi. Can grow and divide
                c. Liposomes
                       i. Forms spontaneously
                      ii. Form Lipid bilayer
       3.
iv. Origin of first true cell
       1. Hereditary Mechanism becomes present
           (includes RNA and DNA)
       2. Many protobiants gather together and
           vary in many ways
                a. Chemically
                b. Relative levels of permeability
                c. Catalytic ability
                d. Metabolic capacity
                e. Ability to grow and divide
                f. Ability to interact to stimuli
                g. “Better Equipped”
       3. Some will survive and others will die 
           Competition
                a. Heterotrophic
                          i. “Other Feeders”
                         ii. First eating type, they
                             consumed other
                             organisms to survive and
                             get resources
                        iii. As food declined, other
                             Energy sources where
                             needed
                b. Autotrophic – Chemosythesis
                          i. “Self feeder”
                         ii. Examples of
                             Chemosynthesis include
                             CO2 + 4H2  CH4 +
                             2HO + Energy, and H2+S
                              h2S + Energy
                c. Autotrophic – Photosynthesis
                          i. At about 3by
                         ii.
                d. Cellular Respiration
                          i. 2.5by
                         ii. Only first step, Glycolisis
                             was possible before
                             oxygen was present in the
                             atmosphere.
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                                     iii. At 2.3by there was
                                          enough to perform
                                          aerobic respiration, which
                                          is 20 times more efficient
                              e. Richard Dawkins – The Selfish
                                  Gene
                        4. Need for replication
                              a. Today the mechanism for
                                  reproduction
                                       i. DNA transcribes into
                                          mRNA (messenger)
                                          which goes to ribosomes
                                      ii. There the tRNA (transfer)
                                          translates into a protein
                                     iii. During transcription, only
                                          exons are needed, introns
                                          are looped together and
                                          taken out. This string
                                          also begins with a primer
                                          cap
                              b. We aren‟t sure what they used
                                       i. Some say that they only
                                          used RNA with rough
                                          Amino Acids, meaning
                                          RNA preceded DNA
                              c. Thomas Cech
                                       i. Found RNA molecules
                                          functioned in modern
                                          organisms as catalysts
                                      ii. Ribozymes – group of
                                          RNA catalysts during
                                          transcription
                                     iii. These act as the editing
                                          mechanisms to pull
                                          introns out
                                     iv. RNA is also an
                                          autocatalytic for mRNA,
                                          tRNA, and rRNA
iii. First Eukaryotic
         1. 2.7by
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                Bill Notes Test III
1. Cellular Respiration
      a. Background
               i. Characteristics of Life
                      1. Growth
                      2. Reproduction
                      3. Irritability (response to stimuli)
                      4. Homeostasis is the steady state conditions relative to the
                         internal body
                      5. Metabolism – Greek for “Change”
                              a. Comes from specific interaction among molecules in a
                                  cellular environment
                              b. Is very carefully orchestrated by Enzymes which help
                                  keep Homeostasis
                                       i. Homeostasis is the steady state conditions
                                          relative to the internal body
                                      ii. Constantly changing concentrations in the fluid
                                          in the body
                              c. Two Divisions
                                       i. Catabolism or the catabolic pathway
                                              1. Energy is produced
                                              2. Complex organic molecules are
                                                  chemically degraded to simpler subunits
                                                  with the release of energy
                                              3. This energy is used to drive Anabolic
                                                  processes
                                              4. Ex. CR
                                      ii. Anabolism or the anabolic pathway
                                              1. Energy is lost
                                              2. Ex. PS (Photosynthesis), Protein
                                                  synthesis
                                              3. Steroids
                                                       a. Long Term Results: Tumors,
                                                           Death
                                                       b. Work by increasing amino acids
                                                           uptake to body cells
              ii. Summary Equations
                      1. CR: C6H1206 + 6 02  6 CO2 + 6 H2O + ATP‟s
                      2. PS: 6 CO2 + 6 H2O  (with light and Chl A)  C6H1206 + 6 02
             iii. Energy
                      1. Bio-Energetics – How organisms manage their Energy
                         resources
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       2. Matter – anything that has mass and takes up space
       3. Energy – the ability to do work (usually moving matter against
          a force)
       4. Laws of Thermal Dynamics
              a. 1st Law of Thermal Dynamics
                       i. Law of Conservation of Energy
                      ii. Says that E cannot be created or destroyed, only
                          transferred or transformed
                   nd
              b. 2 Law of Thermal Dynamics
                       i. As Entropy (useless Energy) increases, the
                          amount of useful energy decreases
       5. Living systems must use Energy to keep their system ordered
       6. Types of Energy
              a. PE – E of position or configuration. May come locked
                  in chemical bonds
                       i. Chemical: When E is absorbed, the electrons are
                          bumped out to higher levels, when E is released,
                          electrons move down energy levels
              b. KE – E of motion
              c. Generation of Heat by molecular motion
iv. Chemistry
       1. Processes of rearranging bonds
       2. In body, the molecules have KE, which lead to collisions which
          can provide the activation energy for a reaction.
       3. Free Energy – E that is available to perform work in living
          systems when temperature and pressure are constant
          throughout the system
       4. ∆G = ∆H – T∆S
              a. ∆G is Change in free energy
              b. ∆H is Change in total Energy
              c. T is temperature
              d. ∆S is Change in Entropy
       5. Exogonic (exothermic) vs. Endogonic (endothermic)
              a. Exo is a loss of Energy in the product, meaning energy
                  was released to do work…∆G is negative
              b. Endo is a gain of energy in the product, meaning energy
                  was absorbed
              c. See Hand-written copy for diagrams (4-19-02)
              d. These reactions are usually coupled, using the Exo
                  energy to drive an Endo reaction
       6. ATP
              a. ATP is the energy currency
                       i. Each ATP has 7.3 kc, and Glucose has 881 kc
              b. See handwritten copy and the book, page 97 and others
              c. Chemically
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              i. ATP is a nucleoside Triphosphate,
                    1. In DNA, you have nucleotides. This is
                        similar b/c it has a similar structure D –
                        Nit Base
                    2. usually uses Adenosine, but also can be
                        Guanosine (GTP) or Uradine (UTP)
                    3. See my copy for diagrams
             ii. ATP + H2O  Hydrolytic, ATPases  ADP +
                 P + -7.3kc (minus b/c E is given off, taken
                 form molecule)
                    1. Hydrolysis –means “splitting water”
                    2. Kinases – enzyme that phosphorylates
                            a. Phosphorylates is when a
                                  molecule picks up a P from
                                  ATP…This is Endothermic,
                                  makes the molecule more excited
                                  and less stable
            iii. ADP + Pinorganic  Energy, ATP Synthases 
                 ATP
                    1. Replenishes ATP
                    2. Human cells replenish all ATP in usually
                        one minute, that is 10 Million
                        molecules/second, every cell
7. Chemical Reactions
      a. Reactants and Products
              i. Reactants  Products
             ii. Reversibility
                    1. R   P
                    2. In vitro (in artificial systems), goes to
                        equilibrium, or completion
                    3. In vivo, (in living organisms) does not
                        go to completion
                    4. At equilibrium, ∆G=0
                    5. Equilibrium Defined: when the rates of
                        forward reactions equal the rate of
                        backward reactions
                    6. In living systems, enzymes join with
                        products which then move to the next
                        reaction, thus no equilibrium is reached
8. Enzymes
      a. They are Globular Proteins (roughly spherical)
      b. Define: biological catalysts that changes the rate of
         reaction without being affected or consumed by the
         reaction
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c.   Allow cells to do work in an organized and efficient
     manner
d.   Other catalysts, like temperature, don‟t work in living
     systems b/c they mess with the living part
e.   Cold Chemistry – the activity of enzymes in organic
     systems that reduces the activation energy for a reaction
f.   Enzymes have surface active site that binds with
     specific other substances
          i. Even isomers, similar compounds with different
             arrangements, won‟t work
g.   Substrates: Substance a specific enzyme acts on (the
     product)
          i. Enter into the active site of enzyme to form a
             enzyme-substrate complex
         ii. Enzyme-substrate complex is when the
             Substrate is bound to the enzyme
        iii. Induced fit model – when substrate bind, it
             changes enzyme, which results in causing
             substrate to complete reaction
        iv. 1000 substrates/s by 1 enzyme
h.   Substrate  with enzyme  Product
          i. Ex. Sucrose  Sucrase  Glucose and
             Fructose
         ii. Co2 + h2O  Carbonic Anhydrase  H2CO3
              H(+) + HCO3(-)
                 1. H+ make it more acidic, so we need
                     buffer
i.   3 Factors that effect enzymes
          i. Temperature (but only to a point)
                 1. Obviously, temperature will help speed
                     up reactions
                 2. At a certain point, the temperature
                     causes the enzyme to break apart, or
                     denature
                 3. Denatured – when the enzyme loses its
                     specific configuration
                 4. ex. Egg frying
         ii. pH
                 1. pH = -log [H+]
                 2. pH is measured on a scale from 1-14
                     (acidic, or more H+ is lower)
                 3. This numbers represent the
                     concentration of H+ in relation to OH-.
                 4. Each „1‟, say from 7 to 6, is a difference
                     of 10x.
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                                5. Most enzymes prefer 6 to 8, but others in
                                   the stomach prefer about 2 (like Pepsin)
                      iii. Salinity – salt concentration
               j. Enzyme Cofactors
                        i. Co factors are accessories that facilitate the
                           function of enzyme
                       ii. Inorganic: iron, zinc, copper, etc
                      iii. Organic
                                1. Are called co-enzymes, not co-factors
  v. Metabolic Control
        1. Feedback Inhibition
               a. Occurs when a particular metabolic pathway is shut
                   down by the concentration of its own end product
               b. See page 104 for amino acid chart
                        i. Isoleucin – an allosteric inhibitor of pathway b/c
                           it binds with theonile deaminase, and T.D. can
                           no longer be used in production change. When
                           Isoleucin concentration goes down, the
                           inhibition stops
        2. Sun is the ultimate source of energy: sun - P.S.  Plants 
           (eating, CR)  animals
 vi. Mitochondria
        1. Look in book for Diagram, mine does NO justice
               a. Outer Membrane
               b. Inner Membrane
               c. Outer Compartment – fluid material in free space
               d. Matrix – Inside inner membrane, it is the “inner
                   compartment”, is folded to increase Surface Area
               e. Cristae – folds of the membrane
        2. “Powerhouse” of the cell
        3. They are 1-3 micrometers long
        4. could be up to 25,000 in one liver cell
        5. They have their own DNA, RNA, ribosomes, and synthesize
           their own proteins and membranes as well as self replicate
        6. Lynn Margulis proposed the Endosymbiotic Hypothesis
               a. It says that mitochondria began as Prokaryotes or
                   Protobionts and that they were then eaten by other
                   PK/PB, at which point mutual symbiosis occurred
vii. Redox Reactions
        1. Example equations
               a. A (electron donor) + BO (e acceptor)  AO (oxidized)
                   + B (reduced)
               b. AH + B  A + BH
        2. Glucose + Dehydrogenases (which pull of hydrogens, either
           p+e or 2p+ 2e)
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              3. Reduction is the accepting of e (adding e), which reduces its
                   charge
                       a. CAT ion – usually has positive charge, accepts e
              4. Oxidation is the losing of an electron
              5. Carrier Molecules
                       a. Nicotinamide Adenine Dinucleotide (NAD)
                                i. Is a coenz that works with enzyme‟s
                                   Dehydrogenases to carry e‟s
                               ii. One of the carrier molecules
                             iii. NAD+ is oxidized form
                              iv. Carries 1 e to make NAD (no plus) or 2e and 1p
                                   to make NADH (the reduced form)
                       b. Flavin Adenine Dinucleotide (FAD)
                                i. Another coenz that carries e‟s
                               ii. Unlike NAD, FAD picks up 2p and 2e
                       c. These molecules are really important
                                i. Are like the taxicab:
                                        1. Atlanta Airport – Braves Stadium, the
                                            money paid to cab driver is like the flow
                                            of electrons and taking of Energy
     viii. Blood
              1. Aorta  Arterial  capillary
              2. Blood pressure is on the capillary walls
              3. Interstitial Fluid – btw capillaries and cells
      ix. Symbiosis – “living together”
              1. Mutual Symbiosis – Both organisms benefit
                       a. In Mitochondria, the eater benefited from the cell
                          respiration of the mitochondria, and the eaten was, well,
                          alive, with the big organism to protect it
                       b. Termites have T. Companuta, which breaks down the
                          cellulose in wood
                       c. Nile Crocodiles has a bird clean its teeth
              2. Commensalism – One organism benefits while the other is
                   unaffected
                       a. Ex. Sharp and ramora, which eats its scraps
              3. Parasitic – one benefits while one is negatively affected
b. Cellular Respiration in 3 Steps – For the love of Goodness look at the book
   for help on this stuff
        i. Glycolysis – “splitting of sugar [glucose]”
              1. Background
                       a. Occurs in the liquid cytoplasm outside of the
                          mitochondria
                       b. GlucosePyruvic Acid
                                i. Is the step by step degradation of glucose into 2
                                   pyruvates
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      c. Evolutionary History
               i. Glycolysis was probably the anaerobic process
                  in Prokaryotes
      d. Pyruvate is an ionized Pyruvic acid
      e. Glycolysis produces a few ATP, but not many
2. Before begins
      a. Glucose is a 6 Carbon molecule
      b. Gets into the cell with facilitated diffusion with help of
          transport proteins
3. Process in 10 steps
      a. Hexokinase catalyzes hydrolysis of ATP with Glucose
          near and glucose picks up phosphorus and Energy.
          This salvages some Energy from the first ATP, makes
          glucose less stable
               i. Enzyme: Hexokinase
              ii. Product: Glucose 6-phosphate
             iii. –1 ATP
      b. Glucose 6-Phosphate is converted to Fructose 6-
          Phosphate
               i. Enzyme: Phosphoglucoisomerase
              ii. Product: Fructose 6-phosphate
      c. Fructose 6-Phosphate accepts another Phosphate from
          ATP
               i. Enzyme: Phosphofructokinase
              ii. Product: Fructose 1,6-biphosphate
             iii. –1 ATP
      d. Aldolase splits the Fructos 1,6-biphospate (between the
          3 and 4th carbons) into 2 different molecules which are
          isomers of each other
               i. Enzyme: Aldolase
              ii. Products: Dihydroxyacetone phosphate and
                  Glyceraldehyde phosphate
      e. Converts Dihydroxyacetone into Glyceraldehyde
          phosphate
               i. Enzyme: Isomerase
              ii. Products: 2 x Glyceraldehyde phosphates
             iii. Note: This reaction would go to equilibrium,
                  except that the glyceraldehydes is pulled away,
                  making reaction continually shifting toward
                  making Glyceraldehyde
      f. Glyceraldehyde phosphate is Oxidized by NAD+.
          Afterwards 2 phosphates (inorganic) are added to the
          Glyceraldehyde
               i. Enzyme: Triose phosphate dehydrogenase
              ii. Products: 2x 1,3 Diphosphoglycerate
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                     iii. + 2 NADH‟s
                     iv. Is exergonic
               g. The phosphate group is transferred to ADP
                       i. Enzyme: Phosphoglycerokinase
                      ii. Products: 2x 3-Phosphoglycerate
                     iii. + 2 ATP
               h. The remaining phosphate group is relocated, preparing
                  for next reaction, from 3rd Carbon to 2nd Carbon
                       i. Enzyme: Phosphoglyceromutase
                      ii. Products: 2-Phosphoglyerate
               i. Forms phosphoenolpyruvate (PEP) by dehydration,
                  phosphorus becomes unstable
                       i. Enzyme: Enolase
                      ii. Product: 2x Phosphoenolpyruvate (PEP)
               j. Phosphoralizes these Phosphoruses into ATP leaving 2
                  molecules of Pyruvate
                       i. Enzyme: Pyruvate Kinase
                      ii. Product: 2x Pyruvate
                     iii. + 2 ATP
        4. Conclusion
               a. We have a net of +2 ATP
               b. 2 NADH are fully reduced
               c. Anaerobic: no oxygen was used in glycolysis
                       i. Also implies evolutionary significance
               d. 2 Pyruvates is the end result
               e. Released about 25 percent of the Energy in the glucose
ii. Split Routes: Aerobic or Fermentation:
        1. Fermentation
               a. Dumping electrons
                       i. We only have a limited amount of NAD+ to
                          reduce, so we need to dump the hydrogens
                      ii. Pyruvic acid is one molecule that will take it ???
                     iii. Acetaldedhyde  Ethenal with CO2
                     iv. Or Pyurvate  Lactic Acid
                      v. Both are alternates to aerobic pathway
               b. Fermentation
                       i. Has only a limited E coming out of the process
                      ii. Process by which alcohol, and some cheeses and
                          yogurts are made
        2. Aerobic Pathway
               a. We must oxidize pyruvic acid into Acetyl Coenzyme A
                  (Acetyl Co-A)
               b. Protein transports it into the Mitochondria
               c. There, it is affected by a multi-enzyme pathway called
                  the Pyruvate dehydrogenase complex [ in 3 steps]
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               INTERMEDIATE STEP
                        i. De-carboxilation: it removes the CO2 as a
                           carboxyl group
                       ii. Oxidation
                               1. NAD+ oxidizes the now 2 carbon
                                   molecule by removing 2 electrons and 1
                                   proton, resulting in (NADH) + (H+)
                      iii. Sulfur containing the coenzyme “A” bonds to
                           the acetyl bond, then leaves
                               1. This Co-A primes the molecule for the
                                   Krebs Cycle
iii. Krebs Cycle – continues the degradation of pyruvate into CO2 and
     H2O
        1. Background
               a. Occurs in the Matrix
               b. Produces many fully reduced electron transport
                   molecules
               c. Also produces a few ATP, but not many, by Substrate
                   Phosphorylation
                        i. Substrate Phosphorylation – direct transfer of a
                           Phosphorus group to ADP from organic
                           compound (substrate) with a ~ bond that is more
                           unstable than normal bonds
               d. PEP + ADP  ATP + Phosphorus Acid
               e. Other names inclsude “Citric Acid Cycle” and the “Tri-
                   Carboxyl Acid cycle”
               f. Enzymes are not as important to Dr. Bill as they were in
                   Glycolysis
        2. Process
               a. When acetate (2 Carbon fragment) binds with
                   oxaloacetate to form a 6 Carbon molecule called citric
                   acid (book calls it citrate)
               b. Dehydrate and Re-hydrate to convert the citric acid to
                   an isomer called isocitric acid
               c. Isocitric acid is oxidized to reduce NAD+ to NADH. It
                   also decarboxylates, giving off a CO2 and thereby
                   becoming a 5C molecule – book calls it α-Ketoglutarate
               d. The molecule now picks up a Co-A, releases a CO2,
                   and reduces an NAD+, forming siccinyl-CoA, a 4C
                   molecule
               e. Siccinyl is oxidized and phosphorylised (forming a
                   GTP which then forms a ATP), resulting in Succinic
                   Acid
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               f. Succinic Acid is oxidized, reducing FAD to FADH2,
                  resulting in Fumaric Acid (Fumarate)
               g. Fumaric acid is hydrated to form Malic acid (Malate)
               h. Malic acid is oxidized, reducing NAD+, and
                  regenerates the oxaloacetate that began the cycle. This
                  molecule is then recycled
       3. Conclusion
               a. Think of Krebbs cycle as a wheel
               b. Products
                       i. 3 NADH‟s
                      ii. 1 FADH2
                     iii. 1 ATP
                     iv. All of this x2 because there are two acetates per
                          glucose!!
               c. My notes contain two simplified diagrams of Krebbs
                  cycle, too
iv. Electron Transport Chain
       1. Background
               a. Occurs in the Cristae
               b. Oxidative Phosporilation – the ATP synthesis that is
                  powered by electron transfer
               c. Chain of molecules in a stair-step configuration of
                  Energy
               d. NADH and FADH2 are the carrier molecules
                  (electrons, hydrogens, and Energy)
               e. O2 + 2NADH + (2H+)  2 H2O + 2 NAD+
                       i. This isn‟t a direct reaction, stuff happens in
                          between
               f. Instead of the ETC happening in many individual
                  molecules, now they prefer to show it as a localized
                  complex in one of 3 groups
                       i. NADH dehydrogenases complex
                      ii. Cytocrom C1 Complex
                     iii. Cytocrom-Oxidase Complex
               g. Most of these are proteins
                       i. Cofactors  prosthetic group
                              1. They have the chemical ability to
                                  oscillate between oxidized and reduced
               h. Cytochromes – enzymes that are in between big
                  Proteins in the diagram
               i. Heme – tetra pyrol
               j. ETC is sensitive to some things, like Potassium
                  Cyanide, which binds irreversibly, and locks up the
                  ETC chains
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            k. Chemiosmosis – involves pumping of H+‟s across
                membranes
                      i. These three complexs correspond with the
                         ATP‟s that come out
            l. We can use other things than Carbohydrates, see pg.
                177
      2. Process
            a. NAD moves to 1st Complex, and attracts an H+ from
                the surroundings
            b. Flavo-Proteins (Flavin Mononucleotide) reduce and
                oxidize the move protons and electrons, some only
                electrons
                      i. 2 Protons are pumped through the chain
            c. FeS
                      i. Reduced/oxidized,
            d. Coenz Q (carrier, formal name is Ubiquinone, and it is
                a lipid)
                      i. It takes up 2e and 2p and pumps the 2p outside,
                         gives 2e to next enzyme
            e. FeS
                      i. Again, picks up 2p and pumps them across
            f. Cytochrome C – is another carrier that is oxidized
            g. Cytochrome A – redox  cyt A3
            h. Then, cyt A3 combines with H+ and O2 resulting in
                H20
                      i. This water is metabolic water
      3. Products
            a. Counting ATP‟s
                      i. Each NADH  3 ATP
                     ii. Each FADH2  2ATP
                    iii. However, the 2 NADH‟s from Glycolosis come
                         down a different pathway and yield only two
                         ATP‟s (FAD follows the same kind of pathway)
                    iv. Result is about 36 ATP‟s per glucose
                     v. This is an effiency of about 38%
v. Chemiosmosis
      1. Background
            a. Peter Mitchell – Proposed the mechanism for
                chemiosmosis
            b. Chemiosmosis involves the pumping of H+ ions (from
                the ETC) across the inner membrane that separates
                isolated compartments. It is this process that helps fuel
                ATP production
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                      c. When you concentrate H+ in a location, as you add
                          protons you build up the strength of the proton gradient
                          (electrochemical gradient)
                      d. Proton Motive force causes the protons to move down
                          the gradient – this gradient is caused by a change in
                          protons over a distance
              2. Process: see diagrams in hand notes and look at book
c. Other subjects involved with CR
      i. Energy given off as heat:
              1. Poikilothermic – immediate loss of heat, same as “cold-
                  blooded” or ectothermic
              2. Endothermic – “warm-blooded”, constant body temperature
                      a. Birds/Mammals only vertebrates that are endothermic
              3. This heat is from chemical inefficiency of CR and other
                  reactions
              4. Hypothermia:
              5. Mouse-Elephant Chart: the normal Metabolic rate is inversely
                  related to size (calories per gram)
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                    Biology: Exam
1. Animal Behavior
      a. Background
              i. Huge and complicated group of Biological science
             ii. Markov – ordered Processes
            iii. P(H) : P(W) : P(S)  Probability of head bobbing/wagging/scratching
            iv. Behavoir: anything that an animal does in response to its environment
                     1. Physical factors: temperature
                     2. Social Factors: interaction btw species for sex
                     3. Red foxes – aimlessly search for food all day
                     4. Alligators – wait and sit until food comes by
             v. Handling time – the amount of time that the animal has to use to
                 manipulate its food
            vi. All of the behavior that the animal does is done because of the survival
                 role of the animal.
      b. Nature vs. Nurture Schools
              i. School of Comparative Psychologists – learning, in lab
                     1. “Rat Psych School” because they always use white lab rats for
                         experiments
                     2. Strong Lab orientation
                             a. This is away from natural environment
                             b. Is much more regulated: not as much variation
                             c. Even small gene variation with rats
                             d. This sophisticated test researching maximized internal
                                 validity
                     3. Mazes
                             a. Exploratory environment
                             b. Would find food pellets
                             c. Wanted to find a “Scale of Intelligence”
                     4. B.F. Skinner
                             a. Made cube apparatus – skinner box
                                      i. Contained some device to manipulate food,
                                         called the manipulandum (like lever)
                                     ii. This later became more advanced, computers
                                         and stuff
                                    iii. Sometimes used negative reinforcement
                     5. Believed that Behavior was product of learning, not
                         genetics
                             a. J.B. Watson – believed in learning
                             b. Tabula Rrasa – “blank slate”
             ii. Ethologists – genetics, natural
                     1. Conrad Lorenz
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                      a. Lived with Animals
                      b. Wrote “King Solomon‟s Ring”
              2. Tinberg
                      a. “Curious Naturalist”
              3. Karn Van Frisch
                      a. Credited with Communication studies
                      b. Researched Honey bees
                              i. Found “dances”
              4. These guys believed in field work
                      a. Collected data with careful, long studies
                      b. Margaret Neece – studied song-sparrows her entire life
              5. Conditions are less rigid, uneven databases, etc
                      a. However, the ethologists thought that there was
                         evolutionary significance in the natural environment
                      b. Example: the Double crested Cormarance had to learn
                         to fly right the 1st time
c. Optimal Foraging
       i. Led by Charnov
      ii. This assumes that animals are born with information about foraging
     iii. Definitions
              1. Search time: looking for food to maximize energy
              2. Handling time: getting into nuts
                      a. Small seeds don‟t have as much energy, but they are
                         easier to find
              3. Vigilance Time: looking for predators
d. Genetic Control of Behavior
       i. Nest building with birds
              1. ex. Love Birds
                      a. Fisher‟s love birds would find material, pick it up, and
                         fly away, carrying only 1 piece at a time
                      b. Beach Face Love birds would carry more than one by
                         stuffing them in the rump and feathers
                      c. Hybrids would try to stuff in rump, but wouldn‟t be
                         able to b/c it wasn‟t designed right. Therefore, they
                         eventually learned not to stick, but they still glanced
                         that way every time they picked something up
e. Levels of Behavior
       i. Background
              1. Neural anatomy realizes that brains have 3 sections,
                  fore/mid/hind brains
              2. Most animals lack the neural complexity to sort out stimuli and
                  response
      ii. Behavioral Responses
              1. Reflexes
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      a. Define: Reflexes are simple unlearned reactions by an
          animal in response to some environmental stimulus that
          involves afferent (sensory) neuron to spinal cord and a
          efferent neuron back to some effector structure (like a
          gland or muscle)
      b. Examples
               i. Hammer on the Knee
                      1. When action potential is generated, the
                          nerve impulse to afferent neuron to
                          spinal cord. This is the junction between
                          Afferent and Efferent
                      2. Motor impulse makes the leg jerk
              ii. Babies are held by their arms to so if the toes
                  make walking motions
             iii. Blinking
             iv. Pain receptors: hot stove, beach spurs, etc
2. Forced Movements
      a. Behavior that has little or no variation and involves
          locomotion
      b. Types
               i. Kinesis
                      1. Undirected motion that is activated by
                          stimulus, and the speed is related to the
                          intensity of the stimulus
                      2. Ex: The Sal bug moves more quickly
                          when put in the light and moves more
                          rapidly when put in more light
              ii. Taxis
                      1. Directed motion or orientation of an
                          organism to some stimulus
                      2. Ex: Planarian worms will move directly
                          toward light (Positive photo taxis)
                      3. Ex: Mosquite Larva – move away from
                          gravity (negatively geotaxis)
3. Innate Behavior
      a. Define: Innate behavior occurs when an organism
          exhibits certain patterns of behavior that require no
          practice and are usually stereotyped, species specific
          and generally associated with courtship, and are
          referred to as Fixed Action Patterns
      b. Fixed Action Patterns
               i. Ex: Terns
                      1. Parents give the young birds fish, and
                          they must eat it head first so not to have
                          the fins kill the bird
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                              ii. Ex: Frog
                                     1. The frog will track the dragonfly, but
                                         once he sticks out tongue, the action
                                         must go to completion. In other words,
                                         he can‟t stick his tongue out only half
                                         way
f. Stimulus Objects
        i. Releasers – restricted to the sign stimulus that functions as
           communcications between individuals of the same species
       ii. Sign Stimulus – communication between different species
      iii. Examples
               1. Speculum – bright part on duck that is located on secondary
                   feathers. This speculum is a releaser for female ducks
               2. 3-Spined Stickle-backs: fish (male) that get red spots on their
                   bottom during breeding season. Many experiments were
                   performed painting females red or males not read.
               3. David Lack – similar paint experiment on English Robin
               4. European Oyster-catcher – ornothologists created a huge
                   wooden egg and put it in the nest…the bird tried to warm it
                   like any other egg
                       a. This is an example of a super(supra)normal stimulus
               5. Gray Lag Goose: grabs egg with bill and drags egg back to nest
                   using sideways motion too. If it loses the egg, it must still go
                   to completion
g. Process of Learning
        i. Define: Learning is an alteration in an animal‟s behavior as a result of
           a particular experience
       ii. Kinds
               1. Imprinting
                       a. Define: Imprinting is a response on the part of an
                           animal to help establish social associations in early life
                       b. Ex: Lorenz discovered the critical periods for goslings
                       c. Ex: Following the first moving object after getting out
                           of the shell
                       d. Ex: Jackdaw bird tries to impress mate by regurgitating
                           worms
               2. Habituation
                       a. Define: Habituation occurs when an animal learns not
                           to respond to biologically insignificant stimuli
                       b. Ex: ducks ignore goose silhouette but freeze for hawks
               3. Trial and Error
                       a. Examples
                                i. Mazes
                               ii. Discrimination Learning
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                                   1. Two or more stimuli that the animal
                                       must discriminate between
                           iii. Classical Conditioning
                                   1. Associative learning in which one
                                       stimulus is linked to another
                                   2. Pavlov: digestion in dogs
                                   3. Dogs would salivate if the door opened
                                        further testing with bells
                                   4. US (unconditional stimulus)  UR
                                   5. CS (bell)  US (food) 
                                       UR(salivation)
                                   6. Led to CS  CR
                           iv. Operant Conditioning (instrumental
                                conditioning)
                                   1. Skinner boxes
                                   2. Manipulandum
                                   3. Animal becomes conditioned but has to
                                       perform an action first
                                   4. This is the way circus animals are
                                       trained: positive response for certain
                                       behaviors
                            v. Play Behavior
                                   1. Play situations help prepare the animal
                                       for future survival
                                   2. Examples
                                           a. Kittens and balls
                                           b. Chimps
                                           c. Lions – cubs learn to bite and
                                               fight
                                           d. Bears – biting
                                           e. Jackal Pups
h. Social Behavior
       i. Communication
             1. Pheromones
                   a. Def: chemicals released by a member of a population
                       that would effect social behavior of a group
                   b. Ex: ants leave chemical trail, secrets pheromones from
                       abdomen
                   c. Sexual Attractions
                            i. Ex: female moths release pheromones into air
                               that a male can detect as few as 40 molecules
                               of…he flies to odor trail
             2. Visual Communication
                   a. Ex: bird of paradise
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              b. Display – def: visual signals specialized through
                 evolution for communication
                       i. These aren‟t effective in dark
                      ii. Happen with mating and aggression
       3. Auditory Communication
              a. Proclaiming territory
              b. Ex: mocking birds
ii. Group Behavior
       1. Concept of Territory
              a. Def: any area defended through displays or aggression
                       i. They are stationary land
              b. Psychological advantage allows aggressive dominance
              c. Glynn Woffand – studied Florida Scrub-Jays
                       i. They go through a period of delayed sexual
                          development because they cannot have their
                          own territory yet
              d. Cooperative Breeding
                       i. Helpers at the nest – help bring food to parents
              e. Individual Distance (Space)
                       i. Personal space
                      ii. Def: inviolate distance around an animals body
       2. Dominance
              a. Occurs when 1 organism takes precedence over another
                 in acquisitions
              b. Ex: Wolf packs have a dominant structure with α, β,
                 and γ (etc) positions
                       i. Unlike territory, everyone gets their piece in
                          dominance
              c. Berny Lubuff – studied elephant seals and found that
                 about 2% of males mated w/ 80% of the females
              d. This structure is found practically everywhere
              e. Pattern of Dominance
                       i. Males dominate Females
                      ii. Adults dominate Juveniles
                     iii. Large dominates small
       3. Altruism
              a. Def: the giving of aid to individuals of the same species
                 at the expense of one‟s own fitness
                       i. Conflicts initially with Darwinian Natural
                          Selection
              b. Inclusive Fitness
                       i. Altruist is genetically related to other
                          individuals
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                                       ii. Def: relative number of individual alleles are
                                           passed genes by individual reproductive success
                                           or success of relatives
                              c. Ex:
                                       i. Running btw lions
                                      ii. Crows on power line
                                     iii. Drawing attention away from nests or young
             iii. Migration
                      1. Def: seasonal movement that takes animals from one location
                         to another
                      2. Factors
                             a. Homing Ability
                                     i. Ability of individual to find its way back to a
                                         specific area after being displaced from it
                             b. Orientation
                                     i. Ability to move in a particular direction relative
                                         to external queue (sun, temperature, current,
                                         Magnetic field, etc)
                             c. Navigation
                                     i. Ability to move from 1 specific map point to
                                         another
                                             1.  Learned
2. Ecology (oikos – house/dwelling)
      a. Background
               i. Define: the study of interactions between organisms and the
                  environment
              ii. This environment could be physical surroundings and/or social
                  surroundings
                      1. Phys – sun, rain, soil, nutrients, etc
                      2. Soc – competition, predators, parasites, etc
             iii. Divisions
                      1. Populations
                             a. Redef: groups of individuals of same species that
                                 inhabit a particular area at the same time
                      2. Community
                             a. All populations that live in a given area and interact
                                 with each other
                      3. Ecosystems
                             a. Community and physical environment considered
                                 together
                      4. Ecosphere
                             a. All ecosystems on earth, i.e. global ecology
      b. Populations
               i. Background
                      1. Density is important
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                a. Too dense  overgrazing
        2. Biomass – total mass of living material in particular place and
            time
 ii. Sampling Methods
        1. Total Count
                a. Count all individuals, feasible only if a small amount of
                    organisms that are large or obvious
        2. Quadrant Sample
                a. Best for stationary organisms
                b. Make a grid and overlay this on a topographic map,
                    then take random samples
        3. Mark and Recapture
                a. Mobile Animals
                b. Drift Fences
                         i. Makes a triangle fence and buckets
                c. Capture animals – usually mark by clipping a toe
                d. Then repeat the capture, then take percentage of
                    recaptured individuals to estimate population size
                e. If 10% of 20 return, we assume total = 200
        4. Stratified
                a. Go to a location where the species is known to exist and
                    count their populations
                b. Don‟t waste time in areas that the species doesn‟t exist
iii. Spacing – 2D or 3D space
        1. Uniform
                a. Rarest
                b. Caused by intense competition for resources, ex: desert
                    flowers (creosote)
        2. Random
                a. Rare
                b. Caused by very little competition
        3. Random Clumps
                a. Normal
                b. Has clumps of organisms scattered randomly
                c. This clumping has several benefits
                         i. Sexual Reproduction
                        ii. Protection
                       iii. Finding food
iv. Population Growth
        1. In ideal conditions of food/water/nests and no
            predators/competition you have exponential growth
                a. Darwin‟s elephants: in 750 years a pair of elephants
                    could result in 19million elephants
        2. Modeling
                a. Terms
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                       i. I = rate of increase in number of individuals
                          (∆N/∆t)
                      ii. b = avg birth rate
                    iii. d = avg death rate
                     iv. N = Number of individuals in a population at a
                          given time
                      v. r = (b-d) = intrinsic rate of increase
                     vi. rmax = innate capacity for increase
                    vii. K = carrying capacity
                              1. Maximum population density that an
                                  area can support for a sustained period
                                  of time without permanent damage to the
                                  environment
               b. Equations
                       i. ∆N/∆t = rN  results in an exponential curve
                      ii. ∆N/∆t = rN (K-N)/K – Logistics Curve
               c. Logistics Curve
                       i. Says that the rate slows down as it approaches
                          the carrying capacity and will not cross that
                          point
                      ii. Thus the equation needs a term to slow the
                          growth as N increases  (K-N)/K
 v. Niche
        1. G.E. Huthcinson defines Niche as a n-dimensional
            hypervolume
                a. Hypervolume – a coordinating system with no origin
                b. This is the fundamental niche of an organism
        2. Realized niche is the niche we look at
        3. Gauss‟s rule – no 2 species can inhabit same niche for
            indefinite period of time
        4. Robert McCarther – found Warblers had partitioned the tree
            nich so that each species fed in a different part of the tree
        5. Emigration – caused by need for new niche and personal space
                a. Lemmings even run off cliffs
                b. Physiological mechamism for change
                c. JJ Christian – studied voles, found that crowding led to
                    physiological changed, notably increased adrenaline
                d. Density – independent limitations to population growth,
                    weather, etc
vi. r-selection and k-selection
        1. k-selection
                a. Population growth is logistic
                b. Population size fluctuates around the carrying capacity
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                           c. Applies to animals that are larger in size and have a
                               longer life span an breeding period, like mammals and
                               birds
                           d. Iteroparous – breeding cycle that repeats for many years
                   2. r-selection
                           a. exponential curve
                           b. Applies to smaller organisms with smaller life spans,
                               like insects
                           c. Usually breed only once  simelparous
                           d. Unprotected young
      c. Community: Reading Assignment
             i. Succession, Biomes, aquatic realms
      d. Ecosystems: Reading Assignment
             i. Modes of nutrition
            ii. Food Pyramid
           iii. Food chains/webs
           iv. Cycles (C, N, H2O)
3. Environmental Concerns
      a. Resources
             i. Renewable
                   1. Trees
            ii. Non-renewable resources
                   1. Topsoil
                   2. Coal
                   3. Gems/stones
                   4. They aren‟t evenly distributed and mining causes
                       environmental problems
      b. Energy
             i. Hydro-electric
                   1.  animal extinctions
            ii. Wind Mills
                   1. Effective, but location specific
           iii. Geothermal
                   1. location specific
           iv. Solar
            v. Coal  finite
           vi. Nuclear
                   1. 1-2% efficient
                   2. Plutonium – stored for 244,000 years to be safe
                   3. Plutonium dust causes cancer
                   4. Breeder reactors recycle this plutonium, but expensive
                   5. Only produces electrical Energy
                   6. Fusion – H+  heat  He: little waste, but needs
      c. Food Problems
             i. Almost all cultivatable land is being used up
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              ii.   Each person needs 1acre/year worth of food
             iii.   About 90 million people/year are added to population
             iv.    Laterite – what dirt becomes when all the nutrients form the rain forest
                    trees are gone
              v.    “Green Revolution” – producing super strains of plants to increase
                    food production
                        1. Problems
                                a. Require change in practices, like fertilizing
                                b. Eutrophication – process by which ponds are filled by
                                   plants death…this is accelerated by fertilizers
                                c. Inbred  little variation  susceptible to diseases
            vi.     Cows have high costs and fish can only be exploited so much, too
     d. Water
              i. U.S. went from 40 billion gallons/day to more than 400bg/day today
             ii. Most of this is by power generation
            iii. Drinking water is recycled
     e. Emissions
              i. Mostly CO2, NO, and HC, mainly from cars
             ii. CO2 and greenhouse effect
     f. Plastic
              i. Fishnets, 6-packs, etc
             ii. Kills 100,000 organisms/year
     g. DDT
              i. Chemical that was used to kill bugs
             ii. Biological magnification
                     1. Top level consumer gets all the chemicals from lower animals
                         in foodchain  high concentration
                     2. led to reduction in many birds b/c it reduced egg thickness
                             a. Brown Pelican, Bald Eagle, etc
     h. Human Populations
              i. Dr Erhluck
                     1. “Population Bomb”
                     2. said pollution was only a symptom of overpopulation
                     3. 1.8% growth rate  we will double in 40 years
                     4. 300my to 6 billion people, but only 40 to 12 billion
                     5. Developing countries have average age of 16
4. Socio-Biology
     a. Background
              i. Def: systematic study of biological bases of all social behavior
                     1. This includes Behavior, Population, and Evolutionary biology
             ii. History
                     1. Darwin‟s Origin of Species
                             a. Behavior is subject to Nat. Sel.
                     2. Lorenz, Tinberg, Von Frisch
                     3. Watson, Skinner
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              4. David Loche (sp)
                    a. “Natural regulation of animal numbers” and
                        “Population studies of birds”
                    b. said that egg number related to environmental and
                        parental capacity
              5. Edward O. Wilson
                    a. “Sociobiology” – big book we saw in class
                    b. Extrapolated to human behavior
                    c. Met political and scientific resistance
              6. John Smith – gain theory
                    a. Says that animals play a “game of survival”, whether
                        they are a hawk and fight for food or a “dove” and
                        choose other means
b. Theories
      i. Wilson‟s
            1. Parental-offspring conflict is inevitable because children are
               born selfish and deceitful
            2. Altruism
                   a. Trivers “reciprocal altruism” occurs when one gives an
                      act of kindness with very little risk, with selfish goal in
                      mind
            3. Proposed Racial differences in IQ do (or do not) have a genetic
               basis
                   a. Proved wrong
                   b. I don‟t know why this is in here…
            4. Biological determinant – human behavior is genetically fixed
               and therefore unchangeable
                   a. Racists and sexists

				
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