Biology 1306 Schedule for 1999

Basic Biology Topics

A. some evidence of biological studies, ca 2000 B.C.
B. Alcmaeon, anatomy and emryology, ca 500 B.C.
C. Hippocrates, On the Sacred Disease, ca 400 B.C.
D. Aristotle, natural history and classification, ca 350 B.C.

A. what is life made of?
1. gross anatomy
2. microstructure
3. molecular biology
B. How does life work?
1. physiology (organisms, cells, etc.)
C. What different types of life are there?
1. taxonomy - class: flying organisms
2. phylogenetic systematics - classifying by history
3. biodiversity studies - capture and study
4. paleontology - extinct
D. How do organisms interact with their environment?
1. ecology
E. How do organisms change during their lives?
1. development
2. embryology
F. How can we explain geographic distribution of organisms
1. biogeography
G. Why does life change over time?
1. evolutionary biology - "unifying theme"
H. How is biological information passed from parents to offspring?
1. genetics
I. How do we understand the behavior of organisms?
1. ethology
J. How can knowledge of biology be applied to human purposes?
1. medicine
2. agriculture
3. wildlife management
4. law enforcement - forensic
5. conservation biology

A. how many species are there?
B. ca 1.5 million described
1. ca. 260,000 plants
2. ca. 50,000 vertebrates
3. ca. 750,000 insects
C. possibly 10-100 million total

A. domain, kingdom, phylum, class, order, family, genus, species
B. example
C. sub+, super-, infra, etc
D. Carolus Linnaeus
E. binomial system (Crotalus atrox)

A. Domain Bacteria
1. Kingdom Eubacteria
B. Domain Archaea
1. Kingdom Archaebacteria
C. Domain Eukarya
1. Kingdom Protista
2. Kingdom Fungi
3. Kingdom Plantae
4. Kingdom Animalia

A. natural selection
1. Charles Darwin
2. Alfred Wallace
3. reasoning involved
a) variation in populations
b) many born, few survive
c) differential reproductive success
4. Famous example: peppered moths
B. Genetically based change in a population over time
C. History of life

A. a way of knowing
B. observation, curiosity, reason
C. scientific method
1. observation
2. question
3. hypothesis (and predictions)
4. experiment
5. conclusions
D. communicating results
1. journal articles
2. books
3. conferences
E. repeatability
1. methods clearly recorded
F. Jules Henri Poincare:
"The scientist does not study nature because it is useful; he studies it because he has delights in it, and he delights in it because it is beautiful."
G. Training new scientists
1. teaching
2. training
3. post doctoral work
H. educating non-scientists
1. museums
2. popular articles
3. public lectures
4. teaching
I. How does science affect your life?

Life at the Chemical Level

I. Biologically important elements

A. H, C, N, O, P, S B. Na, Mg, Si, Cl, K, Ca, Mn, Fe, Co, Cu, Zn

II. Atoms

A. protons B. neutrons C. electrons D. mass number E. atomic number

III. Elements

A. Identified by number of protons

IV. Isotopes

A. Atoms of the same element may vary with respect to the number of neutrons B. deuterium, tritium C. atomic mass accounts for relative abundance of isotopes of the element (see periodic table) D. radioisotopes
1. radioactive decay 2. half-life 3. practical uses
a) markers in cells b) markers for medical diagnosis c) x-rays d) treatment of cancer e) dating rocks and fossils

V. Chemical bonds

A. octet rule B. nonpolar covalent bonds C. polar covalent bonds D. hydrogen bonds E. ionic bonds F. van der Waals attractions

VI. Polar and nonpolar substances

A. water B. oils, fats (hydrocarbons)

VII. Properities of water

A. solid form less dense than liquid form
1. large bodies of water may freeze at surface but remain liquid underneath

B. water is a moderator of temperature

1. ice requires a relatively high amount of heat energy to melt 2. water requires a relatively high amount of heat to evaportate 3. water loses a great deal of heat energy before it becomes ice 4. water has a high heat capacity 5. biologicial implications
a) Earth's realatively stable temperature b) moderate coastal climates c) effectiveness of sweating

C. water adheres and coheres

1. water molecules adhere to other polar substances (meniscus) 2. water molecules cohere to each other (surface tension) 3. biological implications
a) walking on water b) water from roots to leaves

D. water is a good solvent for many substances

1. cells contain a great deal of water 2. most chemical reactions within cells take place in this aqueous environment

VIII. Functional Groups

A. The shape of molecules directly affect their function
1. types of atoms 2. types of bonds 3. specific arrangement of atoms

B. Different molecules that have the same functional group will have some properties in common.

IX. Isomers

A. contain the same number of atoms of the same types, but the atoms are bonded in different ways B. the different bonding patterns result in different chemical properties C. glucose and fructose are isomers of each other D. glucose, fructose, and sucrose E. structural isomers - vary with respect to covalent arrangement of atoms F. optical isomers (enantiomers)
1. asymetric carbon - a C bonded to four different atoms or groups of atoms 2. mirror images of each other

Macromolecules

A. tendency to form four bonds
B. carbon skeletons
C. organic molecules contain carbon
1. some are man made
2. many are produced inside organisms
3. carbohydrates, proteins, nucleic acids, lipids

A. large organic molecules consist of many repeated subunits
B. different arrangements of the subunits result in different properties
C. dehydration synthesis (condensation reactions)
D. hydrolysis

A. monosaccharides (simple sugars)
1. the monomers of carbohydrates
2. examples - glucose, fructose
B. disaccharides
1. a sugar molecule with 2 monomers
2. example - sucrose (table sugar)
C. oligosaccharides
1. several monomers in one molecule
2. some important components of the cell membranes
D. polysaccharides
1. many monomers in one molecule
2. starch (branched)
3. glycogen (even more branched)
4. cellulose (not branched)
5. chitin (a derivative carbohydrate)
E. glycosidic linkage - the covalent bond formed between two monosaccharides
F. functions of carbohydrates
1. energy storage (starch, glycogen, simple sugars)
2. support, protection, structure (cellulose, chitin)

G. There are different types of glycosidic linkages
1. different linkages result in different properties
2. compare and stretch cellulose

A. amino acids
1. the monomers of proteins
2. there are 20 found in organisms
3. amino group, carboxyl group, H, R
B. peptide linkage
1. covalent bond between 2 amino acids
2. occurs through dehydration synthesis
C. polypeptide
1. a chain of amino acids
D. some proteins are made of single polypeptides (example: lysozyme)
E. some proteins consist of multiple polypeptides (example: hemoglobin)
F. general shapes of proteins
1. globular
2. fibrous
G. four levels of protein structure
1. primary structure - sequence of amino acids
2. secondary structure - localized folding and twisting
a) alpha helices
b) beta pleated sheets
c) hydrogen bonds
3. tertiary structure - overall shape of one polypeptide
a) hydrogen bonds
b) disulfide bonds
4. quaternary structure - overall shape of a protein with 2 or more polypeptide subunits
H. prosthetic groups - chemicals attached to a protein (example: heme group in hemoglobin)
I. chaperone proteins - proteins that help other proteins achieve their intended shape during assembly
J. proteins have many functions
1. structure (keratin, spider's silk)
2. contraction (muscle proteins)
3. storage (albumin)
4. defense (antibodies)
5. transport (hemoglobin)
6. signal (some hormones)
7. enzymes (lactase)
K. a protein's environment can alter its shape
1. denature, renature
2. temperature
3. pH
4. salt concentration
L. proteins and apoptosis
1. caspases
2. cancer, Alzheimer's
3. development
M. Linus Pauling

A. nucleotides
1. the monomers of nucleic acids
2. 5-carbon sugar, phosphate group, nitrogenous base
3. 4 different nucleotides in DNA; 4 in RNA
B. phosphodiester linkage
1. covalent bond between nucleotides
2. links sugar of one to phosphate group of other; a sugar-phosphate backbone
3. nitrogenous base attaches to sugar
C. DNA is copied and passed on to new cells. DNA is copied and passed on to new generations.
D. DNA -> RNA -< protein synthesis
E. where is DNA found?
F. Watson and Crick (1953), Rosalin Franklin

A. fats and oils (triglycerides)
1. glycerol + 3 fatty acids
2. ester linkage
3. saturated
4. unsaturated
5. hydrogenated
B. phospholipids
1. P-containing compound + glycerol + 2 fatty acids
2. cell membranes
C. waxes
1. an alcohol + 1 fatty acid

D. carotenoids
1. see text for chemical structures
2. example = beta-carotene (vitamin A)
E. steroids
1. 3 six-sided rings + 1 free five-sided ring + additional atoms
2. examples = cholesterol, testosterone, estrogens
F. additional functions of lipids
1. energy storage
a. animals tend to store energy in lipids (triglycerides)
b. plants tend to store carbohydrates (starch, sugar)
c. seeds often contain triglycerides
2. protection from environment
a. cushioning (fats)
b. waterproofing (oils, waxes)
c. insulation (blubber)
d. protection from mold (waxes)

Cells

1. All organisms are made of cells
2. All cells are made from other cells

1. some exceptions - bird eggs, some neurons, some species of algae
2. cells must exchange materials with their environment
3. for this exchange to work well, cells require a large surface area relative to their volume.

1. prokaryotes are organisms with prokaryotic cells.
2. eukaryotes are organisms with eukaryotic cells

1. Domain Bacteria
a. Kingdom Eubacteria
2. Domain Archea
a. Kingdom Archebacteria
3. All prokaryotes are unicellular, but many form chains, filaments, colonies, etc.

1. Domain Eukarya
a. Kingdom Protista
b. Kingdom Plantae
c. Kingdom Fungi
d. Kingdom Animalia
2. Some eukaryotes are unicellular; some are multicellular

1. DNA and ribosomes
2. cytosol and cytoplasm
3. plasma membrane

1. true nucleus absent
2. nucleoid present
3. no separate, membrane-bound organelles
4. usually smaller than eukaryotic cells

1. cell wall
2. outer membrane
3. capsule
4. photosynthetic membranes
5. mesosomes
6. flagella
7. pili

1. true nucleus present
2. nucleoid absent
3. many separate, membrane-bound organelles present
4. usually larger than prokaryotic cells
5. cytoskeleton present

1. Lynn Margulis - U. Mass., Amherst
2. mitochondria and chloroplasts have
a. double membranes
b. their own DNA
c. their own ribosomes, which are similar to prokaryote ribosomes
3. some modern cells contain smaller endosymbiotic cells

1. many, but not all, organelles are enclosed by membranes
2. organelles are found in both prokaryotic and eukaryotic cells

1. cell wall - present around plant cells; absent from animal cells
2. chloroplasts - present in some plant cells; absent from animal cells
3. centrioles - present in animal cells; absent from plant cells

1. mainly includes these organelles
a. endoplasmic reticulum
b. golgi apparatus
c. lysosomes
d. vacuoles
2. endoplasmic reticulum (ER)
a. lumen - space inside ER
b. rough ER has ribosomes on outer surface of membrane
c. smooth ER lacks ribosomes on surface
3. functions of rough ER
a. transporting proteins produced by ribosomes on surface of rough ER
b. here proteins fold into tertiary structure
4. functions of smooth ER
a. protein transport and modification
b. synthesis of phospholipids, steroids, fatty acids
c. detoxification of harmful substances
5. golgi apparatus
a. cisternae - the flattened sacs
b. lumen - space inside cisternae
c. cis side - near rough ER (or sometimes near nucleus)
d. trans side - near plasma membrane of entire cell
e. vesicles - transport rough ER products to golgi; transport golgi products to other parts of cell or outside cell
6. functions of golgi apparatus
a. protein storage
b. protein modification
c. protein packaging
7. lysosomes
a. originally formed as vesicles from golgi apparatus
b. contain digestive enzymes that help break down organic molecules
8. functions of lysosomes
a. digesting food molecules
b. recycling damaged organelles
c. destroying harmful bacteria
d. apotosis
9. vacuoles
a. can be large or small
b. filled with aqueous solutions
c. formed by vesicles from rough ER and golgi apparatus
d. note that our text excludes them from endomembrane
10. functions of vacuoles
a. some are contractile
b. some contain pigments
c. some contain cellular waste products and toxins

1. microfilaments
2. intermediate filaments
3. microtubules
4. all cytoskeletal elements are made of proteins
a. microfilaments - actin (G actin)
b. intermediate filaments - fibrous proteins like keratin
c. microtubules - tubulin
5. functions
a. microfilaments
- cytoplasmic streaming (cyclosis)
- cytokinesis in animal cells
- muscle contraction
- cell movement
b. intermediate filaments
- mostly structural support
c. microtubules
- mitosis and meiosis
- found in cilia, flagella, basal bodies and cenrioles

1. nucleus
2. mitochondrion
3. chloroplast
4. peroxisome
5. glyoxisome

1. the composition and extent of this matrix varies in different regions of the body
2. example: bone is composed mostly of extracellular matrix that includes collagen fibers and calcium phosphate

Cell Membranes

1. semipermiable barrier
2. site for chemical reactions
3. information reception
4. compartmentalization within cells

1. phospholipid bilayer (lipids)
2. cholesterol (a lipid)
3. proteins
4. carbohydrates

1. integral
2. peripheral
3. some can move within the membrane

1. they are hightly specific
2. one function - cells of one organism can recognize cells of another organism

1. small hydrophobic molecules
2. water

1. simple diffusion
2. osmosis
3. channel proteins
4. facilitated diffusion
a. carrier proteins
- uniport
- symport
- antiport
5. concentration gradient - allows passive transport to occur

1. energy and carrier proteins required
2. substances are moved against their concentration gradient
3. primary - ATP is used directly
4. secondary - energy from other molecules moving down a concentration gradient is used
5. example - sodium-potassium pump

1. phagocytosis
2. pinocytosis
3. receptor-mediated endocytosis
a. coated pits
b. clathrin

Energy

1. A system cam be thought of as any defined space.
2. Open systems can gain or lose energy and matter.
3. Closed systems can neither gain nor lose energy or matter.

1. require energy
2. assemble small molecules into big ones
3. dehydration synthesis

1. release energy
2. break large molecules into small ones
3. hydrolysis

1. H is the total energy in a system
2. G is the free energy in a system
3. T is the temperature in Kelvins
4. S is entropy, representing the usable energy in a system

1. measures the change of free energy that occurs during a chemical reaction

1. reactants are less stable than the products
2. reaction is spontaneous
3. reaction is catabolic
4. reaction is exergonic
5. energy is released

1. C₆H₁₂O₆ + 6O₂ -> 6CO₂ + 6H₂O
2. change in G = -686 Kcal / mole of glucose

1. reactants are more stable than products
2. reaction is nonspontaneous
3. reaction is anabolic
4. reaction is endergonic
5. energy is required for reaction to occur

1. 6CO₂ + 6H₂O -> C₆H₁₂O₆ + 6O₂
2. Change in G = +686 Kcal / mole of glucose

1. reaction is at equilibrium
2. no work can be done

1. ribose, adenine, 3 phosphate groups
2. similar to the nucleotide that has adenine
3. involved in energy coupling
4. ATP + H₂O -> ADP + Pi (change in G = -12 Kcal / mole of ATP under cellular conditions)
5. source of usable energy for cells
6. ADP is recycled to ATP by taking in energy from the environment

Enzymes

1. enzymes do not provide activation energy
2. enzymes lower the amount of activation energy required to start a reaction

1. lock and key model
2. induced fit model

1. substrate concentration
2. enzyme concentration
3. environmental conditions
a. temperature
b. pH
c. salt concentration
4. inhibitors (substances that bind to enzymes and "deactivate" them)
a. competitive inhibitors
b. noncompetitive inhibitors

1. consist of two or more subunits
2. have one or more active sites and one or more allosteric sites
3. active sites are on catalytic subunits; allosteric sites are on regulatory subunits
4. changes in shape of one subunit can affect shape of other subunits

1. Feedback inhibition

Cellular Respiration

1. make their own food (e.g. glucose)
2. are often called producers
3. photoautotrophs - plants, some protists, some bacteria
4. chemoautotrophs - some bacteria

1. can not make their own food
2. are oftem called consumers
3. rely on other organisms, dead or alive, a a source of organic molecules
4. animals, fungi, many protists, many bacteria
5. decomposers (detriovores) - feed on organisms that are already dead
6. predators - kill organisms for food
7. grazers - eat living plant material
8. carnivores - eat animal material
9. herbivores - eat plant material
10. omnivores - eat plant and animal material
11. parasites - feed on living organisms without killing them (at least not immediately)

1. source - sun
2. converted to usable form (food) by photoautotrophs
3. photoautotrophs are eaten
4. many heterotrophs eat other heterotrophs
5. detritovores recycle matter but not energy
6. detritovores feed on the remains of autotrophs and heterotrophs
7. energy captured by organisms to do work eventually leaves as heat
8. the biosphere is an open system

1. electrons are transferred
2. energy is transferred
3. reduced - electrons added
4. oxidized - electrons taken away
5. reducing agent - the substance that is oxidized
6. oxidizing agent - the substance that is being used

1. O₂ is needed for entire process to occur
2. glycolysis
a. 1 glucose -> 2 pyruvate
b. some ATP and NADH are produced
c. occurs are cytosol
3. Kreb's Cycle (citric acid cycle)
a. pyruvate -> CO₂
b. in mitochondrion, in matrix
c. some ATP, NADH, and FADH₂ are produced
4. electron transport chain
a. uses products of first 2 stages
b. in mitochondrion's inner membrane
c. lots of ATP produced

1. occurs in cytoplasm
2. glucose broken down into 2 pyruvate molecules
3. 2 ATP required
4. 4 ATP generated
5. net gain of 2 ATP
6. 2 NADH generated
7. numbers given above are per 1 molecule of glucose
8. no CO₂ is released by glycolysis
9. no O₂ is used in glycolysis
10. if no O₂ available, products of glycolysis can be broken down further to extract more energy

1. occurs in inner membrane of mitochondrion
2. pyruvate converted into Acetyl CoA
3. 1 NADH generated per pyruvate
4. 4 NADH generated per glucose
5. 1 CO₂ generated per pyruvate
6. 6 CO₂ generated per glucose
7. How many C in 1 Acytyl CoA?

1. occurs in mitochondrial matrix
2. Acetyl CoA enters Krebs cycle
3. energy-storing molecules produced
a. per 1 Acytyl CoA
- 3 NADH
- 1 FADH₂
- 1 ATP
b. per 1 glucose
- 6 NADH
- 2 FADH₂
- 2 ATP
4. NADH and FADH₂ go to electron transport chain
5. All C from glucose now in CO₂

1. occus in inner membrane of mitochondrion
2. receives
a. NADH from glycolysis
b. NADH from pyruvate oxidation
c. NADH and FADH₂ from Krebs cycle
3. generates ca. 34 ATP

1. consists of 10 different chemical reactions
2. energy investment phase
a. ATP used
b. glucose broken down
3. energy-yielding phase
a. ATP, NADH formed

1. Acetyl CoA is an acetate molecule bound to coenzyme A
2. CoA is derived from a B vitamin

1. consists of 8 chemical reactions
2. oxaloacetate is the first compound use in the cycle
3. the last step of the Krebs cycle reforms oxaloacetate

1. an enzyme transfers a phosphate group from a substrate to ATP
2. glycolysis, Krebs cycle

1. The transfer of a phosphate group to redox reactions. The final reduced molecule is O₂
2. electron transport chain

1. series of molecules embedded in inner membrane of mitochondrion
2. most of these molecules are proteins
3. redox reactions
4. at end of chain is O₂
5. O₂ + 4H⁺ + 4e^- -> 2H₂O
6. components of the chain
a. NADH-Q reducatase
- 26 subunits
- integral
b. ubiquinone
- lipid
- within phospholipid bilayer
c. cytochrome reductase
- 10 subunits
- integral
d. cytochrome c
- small
- peripheral
e. cytochrome oxidase
- 8 subunits
- integral
7. NADH enters the chain at NADH-Q reductase
8. FADH₂ enters the chain at succinate-Q reducatase (another protein complex). Electrons are then transferred to uniquinone.
9. Each NADH yields ca. 3 ATP.
a. 10 NADH x 3 ATP = 30 ATP
10. Each FADH₂ yields ca. 2 ATP
a. 2 FADH₂ x 2 ATP = 4 ATP
11. How is the energy released in the electron transport chain used to synthesize ATP?
a. Energy is used to actively transport protons (H⁺) across the inner membrane to the inner membrane space.
b. This establishes a H⁺ concentration gradient
c. An integral channel protein called ATP synthase allows the H⁺ to diffuse down the concentration gradient
d. The difference in charge between the intermediate space and the matrix proton-motive force
e. The energy released during this chemiosmosis is used to form ATP from ADP and Pi.

1. glycolysis = +2 ATP
2. Krebs cycle = +2 ATP
3. moving NADH = -2 ATP
4. electron transport chain = + 34 ATP
5. total = +36 ATP

Mitosis and Meiosis

1. consist of one long DNA molecule and many proteins
2. located in the nucleus
3. the DNA molecule of a chromosome contains the genetic code
4. genes are segments of a chromosome's DNA
5. humans - 46 chromosomes in most body cells; 23 chromosomes in gametes
a. 2n = 46
b. diploid number is 46
c. n = 23
d. haploid number is 23
6. Drosophila - 8 chromosomes in most body cells; 4 chromosomes in gametes
a. 2n = 8
b. diploid number is 8
c. n = 4
d. haploid number is 4
7. chromatin - the form that chromosomes are in most of the time; "uncoiled chromosomes"
8. chromosome structure (see text p. 199)
a. nucleosomes
b. histones
c. tightly coiled chromatin
9. homologous pairs of chromosomes
a. look similar - size, shape, banding pattern
b. contain similar (but not identical) information
c. one of each pair inherited from mother (in egg)
d. one of each pair inherited from father (in sperm)
e. alleles - different forms of the same gene
10. autosomes - all the chromosomes that determine sex within a species
a. human male - XY
b. human female - XX
11. karyotype - a representation of all the metaphase chromosomes of a cell

1. interphase (G1, S, G2) and mitosis (M)
2. G1 cell growth; may be long or short; may or may not lead to S
3. S - DNA is replicated
4. G2 - cell prepares for mitosis; centrosome replication
5. interphase is longer than mitosis

1. prophase
a. centrosomes migrate to opposite poles of cell
b. mitotic spindle forms
- mitotic center
- polar microtubules
c. chromatin coils and condenses to form chromosomes
2. prometaphase
a. nuclear lamina and nuclear envelope break down
b. spindle enters nuclear region
c. kinetochore microtubules
d. motor proteins - at junction of kinetochores and microtubules
3. metaphase
a. all chromosomes aligned along equator of cell
b. metaphase plate (equatorial plate)
4. anaphase
a. sister chromatids separate and move to opposite poles of cell; motor proteins; microtubules shorten

5. telophase
a. spindle breaks down
b. chromosomes uncoil to form chromatid
c. nuclear envelope forms around each set of chromosomes
6. cytokenesis usually follows telophase; each new cell is then in interphase

1. internal control
a. cyclin - dependent kinase (Cdk)
b. cyclin
c. cyclin - Cdk complex
d. some cancers are caused by malfunctions in system of cyclins and Cdks.
2. external control
a. growth factors
- platelet-derived growth factor
- interleukins
- erythropoientin
b. some cancers are caused by malfunctions involving growth factors

1. includes two nuclear divisions - meiosis I and meiosis II
2. chromosome number is reduced from haploid to diploid
3. takes longer than mitosis
a. human males - ca. 1 month
b. human females - ca. 10-50 years
4. Where does it occur in humans?
a. males - testes
b. females - ovaries
5. interphase
a. growth
b. replication of DNA
6. prophase I
a. chromatin condenses into chromosomes
- each consists of 2 chromatids
b. centrosomes migrate
c. mitotic spindle forms (late)
d. synapsis - homologous pairs come together
- cynaptomemal complex
- chiasma
- crossing over
- independent association
- humans: 2²³ = ca. 8 million
7. prometaphase I
a. nuclear lamina and nuclear membrane break down
b. spindle enters nuclear region
8. metaphase I
a. homologous pairs line up along metaphase plate
b. different from metaphase of mitosis
9. anaphase I
a. homologous pairs separate
b. more toward opposite poles of cell
c. sister chromatids remain attached
d. different from anaphase of mitosis
10. telophase I
a. spindle may or may not break down
b. chromosomes may or many not uncoil
c. nuclear membrane may or may not reform
11. interphase II
a. short of even non existent
b. no replication of DNA
c. different from interphase I of meiosis
12. meiosis II is very similar to mitosis, but it starts with half as many chromosomes

1. crossing over - new combinations of alleles on chromosomes
2. random assortment - new combinations of chromosomes in gametes
3. fertilization - new combinations of chromosomes in zygote

1. gametic meiosis - meiosis results in gametes; diplody dominates life cycle (most animals, some protists)
2. zygotic meiosis - meiosis occurs right after formation of zygote; hapoidy dominates life cycle (most fungi; some protists)
3. intermediary meiosis - life cycle includes both haploid and diploid stages of significant duration (plants, some protists)

1. 4 sperm produced per bout of meiosis
2. 1 egg produced per bout of meiosis
a. unequal distribution of cytoplasm
b. polar bodies

1. reproduction - producing more individuals
2. sex - recombination of genetic material
3. asexual reproduction (cloning)
a. examples
- binary fission
- budding
- parthenogenesis
4. sexual reproduction
a. internal fertilization
b. external fertilization
5. separation of time of sex and reproduction
a. example - conjugation in bacteria
6. alternation of generations
a. life cycle includes haploid and diploid individuals
b. at most general, includes sexuality reproducing organisms
c. some species have complex life cycles

1. aneuploidy
a. nondisjunction in meiosis I or II
b. Down syndrome (trisomy 21)
c. Turner syndrome (XO)
d. Klinefelter's syndrome (XXY)
e. Triple-X syndrome (XXX)
f. Jacob's syndrome (XYY)
g. many instances result in nonviable offspring
2. polyploidy - individuals have three or more complete sets of chromosomes

Genetics

1. started ca. 1857
2. true-breeding strains
3. easy to control fertilization
4. phenotypes he studied
a. yellow (Y) vs. green (y) seeds
b. round (R) vs. wrinkled (r) seeds
c. tall (T) vs. dwarf plants (t)
d. purple (P) vs. white (p) flowers
5. scientific method
6. blending hypothesis
7. monohybrid cross
8. P, F₁, and F₂ generations
9. example:
a. P - white X purple
b. F₁ - all purple
c. F₂ - 705 purple, 224 white (ca. 3:1)
10. did this with many plants
11. conclusions
a. white "factor" must be present in F₁ individuals
b. but purple is "dominant" over it
c. white gets expressed in F₂ when no purple "factor" is present

1. phenotype
2. genotype
3. homozygous
4. heterozygous
5. dominant
6. recessive
7. gene
8. locus
9. allele
10. segregation of homologous chromosomes (and their respective alleles) during meiosis
11. independent assortment (2ⁿ)

1. some genes have more than two alleles
2. example: ABO blood group
a. allele: I^A, I^B
b. codominance
c. possible genotypes
d. possible phenotypes

1. Human males have only one X chromosome
2. So, alleles on a male's X chromosomes are always expressed, regardless of whether the are dominant or recessive
3. Human females have two X chromosomes, and alleles function as they do for autosomes.
4. example: hemophilia
a. alleles: X^H, X^h
b. possible genotypes
c. possible phenotypes

1. sometimes one allele is not completely dominant

1. best answered by examining products of specific alleles
2. example Tay-Sachs disease
a. organismal level - complete dominance
b. biochemical level - incomplete dominance
c. molecular level - codominance
3. recessive does not equal rare
4. recessive does not equal bad

1. rule of multiplication
a. example: Aa x Aa; what is the probability of having an aa offspring?
2. rule of addition
a. example: Aa x Aa; what is the probability of having an Aa offspring?

1. example - sickle cell anemia

1. example - fur color in mice
a. one gene - brown vs. black
b. another gene - pigment deposited in fur or not
c. possible phenotypes - black, brown, white

1. examples - height, skin color
2. quantitative characters

1. examples - height, weight, skin color
2. multifactoral disorders
a. examples - heart disease, cancer

1. useful in genetic counseling
2. useful in conjunction with molecular techniques for locating genes
a. example - Huntington's disease
- caused by a dominant allele
- located on chromosome 4
- individuals can now be tested for presence of this allele

1. carrier recognition
a. examples - Tay-Sachs, sickle-cell
2. amniocentesis
a. not done until week 14-16
b. wait several weeks for results
c. karyotype
3. chronic villus sampling (CVS)
a. can be done as early as week 8-10
b. results within 24 hours
c. karyotype
4. examining fetus
a. ultrasound
b. fetoscopy
5. newborn screening
a. example - phenylketonvria (PKU)
6. ethics

1. deletion - segment of chromosome is lost
2. duplication - segment of chromosome is duplicated
3. inversion - segment of chromosome is inserted in reverse order
4. translocation - segment of a chromosome is added to a nonhomologous chromosome
a. reciprocal
b. nonreciprocal

1. early 1900's
2. first described sex linkage
3. gene linkage (example)
a. body color - grey (G), black (g)
b. wings - normal (W), vestigial (w)
c. GgWw x ggww
d. possible gametes
e. Punnett square
f. looked at 2300 offspring
g. expected ratio
- 575 GgWw
- 575 ggww
- 575 Ggww
- 575 ggWw
h. observed ratio
- 965 GgWw
- 944 ggww
- 206 Ggww
- 185 ggWw
i. most offspring were like the parents
j. explanation - the body color and wing genes are linked (on same chromosome)
k. why wasn't the observed ratio 1150 GgWw : 1150 ggww?

1. parental types vs. recombinants
2. recombination frequency

a. number of recombinants / total offspring
b. example - (206 + 185) / 2300 - 17%
3. recombination frequency for two genes indicates how close together they are on a chromosome
4. this information can be used to determine the relative positions of genes on a chromosome
5. 1 map unit was defined to equal 1% recombination frequency
6. recombination frequency of 50% is the maximum expected (genes are on separate chromosomes or very far apart on same chromosome)
7. mapping example - three genes (A, B, C)
a. A-B : 17 map units
b. B-C : 9 map units
c. A-C : 8 map units
d. sequence of genes : A-C-B

DNA

1. chromosomes carry genetic information
2. chromosomes are made of proteins and DNA
3. most researchers thought proteins carried the genetic information

1. used phages and bacteria
2. labeled the phages' DNA with a radioisotope of phosphorus
3. labeled the proteins of a separate group of phages with a radioisotope of sulfur
4. DNA must be the genetic material in the phages

1. DNA composition is species specific.
2. example - humans
a. A - 30.9%
b. T - 29.4%
c. C - 19.9%
d. G - 19.8%

3. Chargaff's rules
a. A=T
b. C=G
c. unexplained at that time

1. described the structure of DNA
a. double helix
b. purines (A,G) pair with pyrimidines (T,C)
2. used model building
3. used critical data from Rosalind Franklin

1. monomers are called nucleotides
a. deoxyribose
b. phosphate group
c. nitrogenous base
2. sugar - phosphate backbone
3. complementary base pairs (A-T, G-C)
4. terminology
a. base pairs (humans ca. 6 billion)
b. nucleotide sequence
5. DNA strands are antiparallel
a. 5' end - phosphate group
b. 3' end - hydroxyl group

1. When does it occur?
2. semiconservative model
a. the two strands of DNA molecule separate
b. each strand copied
c. end up with two new DNA molecules, each with one strand from the original molecule
3. very fast, very accurate (ca. 1 error per billion nucleotides)
4. involves many enzymes and other proteins
5. origins of replication - specific nucleotide sequences starting points for replication
6. replication bubble
7. replication forks
8. DNA polymerases - enzymes that catalyze the addition of new nucleotides
9. leading strand - nucleotides added continuously in 5' to 3' direction
10. lagging strand - Okazaki fragments
11. DNA ligase - joins Okazaki fragments together to form a continuous strand of DNA
12. DNA polymerase - can only attach nucletotides to other nucleotides of a strand that has already been started
13. primer - short strand of RNA (about 10 nucleotides long) that allows new strands of DNA to form
14. primase - the enzyme involved in assembling the primer
15. another DNA polymerase later replicates the primer nucleotide with DNA fragments
16. each Okazaki fragment must be primed
17. hellicase - the enzyme that unwinds the double helix a the replication fork
18. single-strand binding protein - help stabilize unwound DNA until the new complementary strand is formed

1. over 50 DNA repair enzymes have been identified
2. mismatch repair - occurs during replication
3. excision repair

1. one gene - one enzyme hypothesis
2. one gene - one protein hypothesis
3. one gene - one polypeptide hypothesis
4. overview
a. transcription
- DNA --> pre-mRNA
- occurs in nucleus
b. RNA processing
- pre-mRNA --> mRNA
- occurs in nucleus
c. translation
- mRNA --> polypeptide
- tRNA
- ribosomes
- occurs in cytosol
5. RNA
a. monomers are nucleotides
- ribose
- phosphate group
- nitrogenous base
b. complementary pairs (A-U, G-C)
c. can pair with a single strand of a DNA molecule
d. can pair with another RNA molecule
6. the genetic code
a. 4 nucleotides
b. 20 amino acids
c. triplet code
d. 4³ = 64
e. 61 of the 64 different nucleotide triplets code for specific amino acids
f. the other 3 triplets are stop codes
g. codon - a triplet of mRNA
h. anticodon - a triplet of tRNA
i. reading frame - the code does not overlap
j. code is redundant but not ambiguous
k. code is nearly universal among all species that have been studied

Evolution

1. Speciation - the evolution of new species from previously existing species.
2. What is a species?
a. biological species concept
b. evolutionary species concept

1. Changes in the gnome-mutations

1. natural selection - differential success in the reproduction of different phenotypes resutling from the interaction of organisms with their environment.
2. genetic drift - changes in a small population's allele frequencies due to chance

1. observation - evolution has been observed many times.

a. peppered moths
b. guppies
c. resistance of bacteria to antibiotics that used to kill them
d. resistance of mosquitos to insectisides that used to kill them
e. many lab experiments with bacteria and viruses
2. artificial selection - farmers and other humans have selectively bred many species of organisms and purposely changed the species' attributes over time.
a. Canis familiaris (domestic dog)
b. corn
c. a species of wild mustard
- kale
- broccoli
- cabbage
- cauliflower
- etc.
3. anatomy and physiology of living species
a. vertebrate heart (# of chambers)
- fishes - 2
- amphibians, most reptiles - 5
- birds, mammals, few reptiles - 4
b. vertebrate brain
c. long, slender, forked tounge in snakes and some lizards
4. vestigial features
a. flightlessness in a number of bird species (example = flightless cormorant of Galapoagos Islands)
b. human cecum
c. eyes in many troglodytic and burrowing species (e.g., some fish, salamanders, naked mole rat)
d. pelvis in some snakes
5. metabolism of living species
a. glycolysis - used by virtually all living cells
6. development of living species
a. early-stage embryos are very similar among vertebrate classes
b. amniotic egg in reptiles, birds, and mammals
c. many aspects of evolution that seem improbable or even impossible cam be observed during development
- "ontogeny recapitulates phylogeny" - Hackel's biogenic law (not correct)
- caution: clearly development is not the same thing as evolution
7. behavior of living species
a. parental care and nest-building in crocodilians and birds
b. long-term parental care in humans and other primates
8. geographic distribution of living species
a. adaptive radiations on oceanic islands
b. similar but different species geographically isolated from each other
- ratite birds on the southern continents
9. fossils
a. transitional forms between early reptiles and mammals
b. Archaeopteryx
c. ancestry of horses
10. proteins
a. hemoglobin
b. cytochrome c
11. DNA

1. independently arrived at the idea of natural selection
2. some common themes in their lives
a. among the greatest naturallists of all time
b. travelled/explored intesnsively
- Darwin - H.M.S. Beagle
- Wallace - South America, s.e. Asia
c. worked on islands
- Darwin - Galapagos
- Wallace - East Indies

1. Selection acts on individuals, but its long term effect is on populations.
2. Selection acts on an organism's phenotype, which over time affects the population's genome.
3. example - peppered moths in England
4. determinants of phenotype
a. genotype
b. environment
c. traits affected by genes are inheritable
d. traits affected by environment only are not inheritable
5. adaptation - any feature of an organism that enhances its ability to survive and/or reproduce under its current environmental conditions
a. because environments change, a feature adaptive at time A may no longer be adaptive at time B
6. stabilizing selection
a. reduces variation
b. does not change mean
7. directional selection
a. changes mean in one direction
8. disruptive selection
a. favors the extremes in population over immediate forms
9. fitness - relative reproductive contribution of genotypes and their associated phenotypes
a. individual fitness - depends on relative number of offspring produced by an individual
b. inclusive fitness - depends on individual fitness and the survival/reproduction of an individual's close relatives
10. kin selection - a type of natural selection in which the relative contribution of a genotype is increased by "cooperation" among close relatives
a. scrub jays
b. eusocial species - include many sterile individuals
- many ants, bees, termites
- naked mole rat
11. sexual selection - a type of natural selection that favors traits which improve an individual's chances of mating
a. northern cardinal
b. bighorn sheep

1. population charachteristics
a. size (number of individuals)
b. degree of isolation
c. gene pool - all the genes in a population at any time
d. genetic structure - the frequency of alleles and genotypes in a population
2. calculating allele and genotype frequencies; example:
a. a population has 500 members
b. white flowers - 10; pink 480
c. AA - 320; Aa - 160; aa - 20
d. How many alleles are in a population of 500?
e. What are the frequencies of A and a in the population?
- freq. of a = [(20x2)+(160x1)] / 1000 = 200 / 1000 = 0.2
- freq. of A = [(320x2)+(160x1)] / 1000 = 800 / 1000 = 0.8
- once we know the freq. of a, how else could we calculate the freq. of A?
f. What are the frequencies of the genotypes in the population?
- freq. of AA = 320/500 = 0.64
- freq. of Aa = 160/500 = 0.32
- freq. of aa = 20/500 = 0.04

1. The frequencies of alleles and genotypes in a population's gene pool remain the constant over generations unless acted upon by asents other than sexual recombination.
2. Hardy-Weinburg equilibrium
a. A population is said to be at H-W equilibrium if its allele and genotype frequencies do not change from generation to generation
b. give criteria must be met for a population to be at H-W equilibrium
- very large population
- random mating
- no selection
- no immigration or emmigration
- no mutation
c. p+q = 1
d. p² + 2pq + q² = 1
e. p² + pq = p
f. q² + pq = q
3. If you know p, you can calculate q.
4. If you know q, you can calculate p.
5. If you know all genotype frequencies (AA = p², Aa = 2pq, aa = q²), you can calculate p and q.
6. If a population is at H-W equilibrium, you can calculate all genotype frequencies from p or q.
7. If a population is at H-W equilibrium you can calculate p, q, and all genotype frequencies by counting the number of individuals with the recessive phenotype.
8. Probability rules are behind H-W Theorem
a. freq. of A = p, so the probability that any fertilization event in the population involves a gamete with the A allele is p
b. so, the probability that both gametes involved in the fertilization event have the A allele is p² (rule of multiplication)
c. freq. of a = q; probability of getting aa is q²
d. probability of getting Aa involves rule of multiplication and rule of addition; pq + pq = 2pq
9. What can we conclude if a population is not at H-W equilibrium?
a. genetic drift (large population)
b. nonrandom mating (random mating)
c. natural selection (no selection)
d. gene flow (no imm- or emmigration)
e. mutation (no mutation)
10. So H-W Theorem can be used to detect microevolution in a population
11. Changes in generation to generation at a single locus are sufficient for saying that the population is evolving.
12. determining population size
a. effective population size - only breeding individuals are counted
13. nonrandom breeding
a. assortative mating - individuals choose mates with phenotypes similar to their own
b. inbreeding - individuals mate with relatives
c. results in increased homozygosity
d. by itself changes genotype frequencies, but not all allele frequencies

1. Drift can be defined as random changes in allele frequencies over time within a population.
2. Over time genetic drift can lead to the loss of some alleles and the fixation of others.
3. bottleneck effect
a. occurs when a population's numbers are drastically reduced
b. due to chance, allele frequencies in he surviving population will most likely differ from allele frequencies in original population
c. sampling error
4. founder effect
a. occurs when a small propagule colonizes a new area that is isolated from the rest of the population
b. same effect as bottleneck
c. sampling error

1. polymorphism - 2 discrete forms of the same trait exist in the population
2. geographic variation - individuals of a wide-ranging species may differ genetically and phenotypically from region to region
a. sometimes geographic variants are described as subspecies or races
b. geographic variation may occur over a short distance (e.g. on mountains)
c. cline - a slight difference that increases in degree from one end of a species' range to the other
3. diploidy allows harmful alleles to persist in a population
4. heterozygote advantage can help maintain the presence of 2 alleles at the same locus
a. sickle-cell anemia in populations exposed to malaria
b. hybrid vigor - crossing two inbred lines can result in more healty offspring
5. source variation - mutation
6. major increase in variation - recombination
a. not only are individuals unique because they have different alleles, they are unique because they have different combinations of alleles
b. random assortment
c. crossing over
d. sex
7. The less time required for individuals of a population to develop and reproduce, the faster variationcan accumulate in that population.

1. Allopatric specitation - speciation resulting from physical geographic separation of two or more populations
a. gene flow is physically prohibited
b. vicariance - a large population is divided into two or more parts by a barrier that arrises in the midst of the population
- examples - formation of mountains or canyons, a river changing its course, a large lake drying, climatic changes can fragment suitable habitat over time, continiental drift, etc
c. dispersal - a propagule colonizes an area that is remote from the rest
- flight
- rafting - some organisms can float across vast expanses of ocean on vegitation mats or just in the water
- hitchhiking - parasites, seeds, etc. can be transported by other organisms
- weather may be important
d. Both dispersal and vicariance can be observed in the modern world.
- numerous found out of range all the time (RBA's, etc.)
- rafting frequently observed after hurricanes, monsoons
- volcanic activity
e. Past vicariant events an past climatic conditions can be studied.
- geology
- palynology - study of fossil pollen
- paleontology - study of fossils
f. Some organisms are better dispersers than others.
- example very few amphibians found on oceanic islands
g. Small, peripheral isolates may be more likely to become new species.
- gene pool of peripheral isolate probably differs from gene pool of "parent" population (due to clines and/or founder effect)
- genetic drift will have an important effect until the peripheral isolate increases its numbers
- natural selection may have different effects on peripheral isolate due to environmental differences at the periphery of a species range (Why is a species' range the size it is?)
- many peripheral isolates may die out instead of speciating
- peripheral isolates may become reconnected to the parent
h. Which processes allow an isolated population to become a new species over a long period of time?
- genetic drift
- natural selection
- mutation
i. adaptive radiation
- on groups of islands (archipelago)
- following major extinction events
- occurs at a time or place with few competitors (lots of open niches)
2. Sympatric speciation - a new species originating within the midst of the parent population
a. "instant" speciation due to polyploidy
- autopolyploids - have more than 2 chromosome sets all derived from a single species
- allopolyploids - have more than 2 chromosome sets due to hybridization between two species
b. disruptive selection + associated mating
c. different habitat selection (e.g., Rhagoletis - hawthorn berries vs apples)
d. common in plants, rare in animals
3. Cladogenesis - a new species diverging from an existing species; the existing species continues to exist
4. Anagenesis - a single species changes over time so that it is different from its ancestors

1. Prezygotic barriers - impede mating or fertilization
a. habitat isolation - 2 species use different habitats (e.g., aquatic vs. terrestrial)
b. behavioral isolation - 2 species have different mating ritutals or signals (e.g., fireflies)
c. temporal isolation - 2 species breed at different times (e.g., summer vs. winter)
d. mechanical isolation - 2 species mah not be anatomically compatible (e.g., plants with different pollinators)
e. gametic isolation - the gametes of two species won't form a zygote (e.g., sperm won't live in female of other species; or chemical recognition of sperm by egg)
2. Postzygotic barriers - prevent hybrid zygote from developing into a viable, fertile adult
a. reduced hybrid viability - hybrid offspring are healthy but are also sterile (e.g., horse x donkey -> mule; mule is sterile)
b. hybrid breakdown - first generation hybrids are healthy and can reproduce, but their offspring are sterile or inviable

1. theory - species concepts
2. practice - look for distinguishing features (and allopatry in many cases)
3. It is not always clear whether 2 populations represent the same species or not. Why might we expect to encounter this difficulty?
4. hybrid zone - narrow part of range where populations hybridize (e.g., red-shafted and yellow-shafted flickers)
5. Hypotheses are sometimes revised basd on new information (e.g., Tropidurus melanopleurs).
6. shifts in theory (lumpers vs. splitters; Baltimore vs. Bullock's orioles)

1. phyletic gradualism - new species form slowly over large amounts of time by the accumulation of shift differences
a. Darwin
2. punctuated equilibrium - changes resulting in a new species can occur relatively rapidly and there may be very long periods of time during which species change very little
a. Eldredge and Gould (1972)
b. "relatively rapidly" may be on the order of 50,000 years or so
c. peripheral isolates
d. seems to be supported by fossil record
e. many phylogenetic studies seem to support it
f. adaptive landscape (Sewall Wright) could help explain evolutionary stasis
3. Gradualists and punctualists continue to debate the issue.
4. Both gradual and rapid change may be important in the history of life.

1. the study of the evolutionary relationships of species (phylogeny)
2. the classification of species according to their evolutionary relationships
3. monyphyletic groups are recognized with formal names (e.g., Paramecium, Felidae, Mammalia, Eukarya, etc.)
4. classification is revised so that paraphyletic groups are not recognized (e.g., Reptilia, Monera)
5. evidence from living and extinct species is used to make inferences about their phylogeny.
a. anatomy
b. development
c. behavior
d. life history
e. proteins
f. DNA, RNA
6. In cladistics, parsimony analysis is used to evaluate the evidence that is gathered.
a. synapomorphies (shared, derived characheristics) are considered evidence of relationship
b. ingroup
c. outgroup
7. Other methods may be used (e.g., phenetics, maximum liklihood).
8. Phylogenetic studies are important for many areas of biology
a. any study that makes comparisons among species
b. ecology
c. physiology
d. biogeography
e. epidemiology
f. conservation biology
g. etc.

Origins: The Universe, the Earth, and Life on Earth

1. round Earth - Aristotle, 340 B.C.
2. geometric model - Aristotle, Ptolomy
3. heliocentric model - Copernicous, Kepler, Galileo
4. gravity - Issac Newton
a. Philosphiae Nuteralis Principa Mathematica (1687) - "probably the most important single work ever published in the phiscal sciences" S. Hawking
b. every body in the universe is attracted by a force that is stronger the more massive the bodies and the close they are to each other
c. explains orbits of planets, moons
d. explains why tings fall to the ground
e. space is not absolute - this follows from Newton's laws
5. relativity - Albert Einstein
a. developed in early 1900's
- spacial relativity (1905)
- general relativity (1915; accounts for gravity)
b. revised Newton's ideas
c. time is not absolute (it is relative to position and speed of the observer)
d. time and space are not completely independent; rather they form an object called space-time
e. gravity exists because space-time is not flat; it is curved by the distribution of mass and energy
f. E=mc²
6. quantum mechanics (early 1900's)
a. mostly deals with physics processes at the subatomic level
b. leptons - electrons, etc.
c. quarks - particles that make up protons and neutrons
7. forces
a. gravity
b. strong nuclear force - holds quarks together
c. electromagnetism - holds electrons around nucleus; also responsible for radio and light waves
d. weak nuclear force - causes radioactive decay
8. unification - attempts to find a single law that explains the way the universe works through unification of ideas from general relativity and quantum mechanics; a single mathematical explaination for all four forces

1. The universe is estimated to be 10-20 billion years old.
2. The universe is expanding today.
3. All matter, energy, time started at one point and burst outward.
4. Earth and our solar system formed about 4.6 billion years ago.

1. probably formed through accretion of large rocks
2. center became molten due to pressure and radioactive decay
3. core
4. mantle
5. crust
a. ca. 40 km under continents
b. as little as 5 km thick under some parts of ocean
6. no life on Earth for ca. first billion years; life arose ca. 3.8 billion years ago
7. early atmosphere of Earth was a reducing one
a. no free O₂
b. CH₄, CO₂, NH₃, H₂, N₂, H₂O

1. The following represents a superficial overview of science's best explanation for how life on Earth may have formed from non-life. There is still a great deal of work to be done in this area.
2. non-living materials (simple molecules) combined into more complex molecules that were eventually able to reproduce themselves.
a. amino acids, purines, and pyrimidines formed from simpler molecules (those available in the reducing atmosphere)
- Stanley Miller's experiments
b. monomers combined to form polymers
c. nucleic acid polymers can copy themselves (chemical "reproduction")\
3. main path of information in living organisms is DNA -> RNA -> protein
4. problem - proteins (enzymes) are used in all steps of this problem
a. DNA synthesis (replication)
b. protein synthesis
c. but proteins are constructed according to info in nucleic acids
5. so how did nucleic acids copy themselves without enzymes for copying themselves?
a. discovery of ribozymes (catalytic RNA)
b. hypothesis - RNA was the first information carrying molecule and some RNA had catalytic capability
c. experiments
- started with random sequence RNA, ended with highly catalytic RNA
- started with RNA and individual nucleotides; polynucleotides formed
6. As soon as molecular self-replication was possible, selection would begin to act.
a. Any changes ("mutations") in a molecule that favored more efficient replication would result in that type of molecule becoming more abundant
b. implications - from this point, the process is nonrandom
7. how did first cells form?
a. many different solutions that contain polymers will form coaceruates (round structures similar to cell membranes)
b. selection again - RNA contained in membranes probably left more copies of itself than membrane-free RNA
8. Membranes would have made homeostasis possible.
9. use of energy

History of Life

1. ^HC can be used to date fossils about 30,000 years old or younger (half-life is ca 5700 years).
2. ⁴⁰K has been used to date many older events in Earth history (half-life is ca. 1.3 billion years; decays to ⁴⁰Ar).

1. age of divisions vs. their duration

1. As O₂ levels increased, organisms evolved the ability to use O₂, metabolically.

1. only tiny cells would be able to survive in the low oxygen environment of early Earth (surface area/volume ratio)
2. greater amounts of O₂ allowed evolution of larger cells
3. eventually enough O₂ was available to support multicellular life

1. continental drift
a. sea floor spreading - new crust is added from the mantle at rifts in the sea floor
b. this causes continents to move
c. when plates meet, they slide past each other or one goes under the other (can result in formation of mountains)
d. affects climate, sea level, ocean currents, distribution of organisms, volcanic activity
e. Pangaea - all continents together, harsh climates in interior (properties of water)
f. Laurasia - North America, Europe, Asia
g. Gondwanaland - South America, Africa, Madagascar, India, Australia, Antarctica
2. shifts in climate
a. Earth's orbit sometimes changed slightly
b. change in ocean currents
3. volcanic activity
a. major volcanic episodes can affect Earth's climate
b. ash in the atmosphere reduces penetration of sunlight, reducing temperatures
4. meteroites
a. small meteorites regularly hit Earth
b. large meteor collisions are rare but do occur (Kansas, 1948, 5 ton meteor)
c. mass extinction at end of Cretaceaous (about 65 mya) have been caused by a meteor collision
- estimated size - 10 km diameter
- a large crater (180 km diameter) was found of coast of Yucatan
- thin layer of iridium
- this hypothesis is still debated but has fairly strong support

1. Earth forms - 4.6 bya
2. origin of life - 3.8 bya (prokaryotes)
3. oldest known fossils - 3.5 bya (stromatolites - left by bacteria)
4. O₂ begins accumulating - 2.5 bya
5. oldest eukaryote fossils - 1.5 bya
6. first animals - 700 mya
7. origin of most invertebrate phyla; diverse algae - Cambrian (544-500 mya)
8. first vertebrates (jawless fishes); abundant marine algae - Ordovician - probably due to extensive glaciation

1. Cambrian explosion (ca. 500 mya)
a. gave rise to most animal phyla
b. Burgess Shale in British Columbia
c. Wonderful Life by S.J. Gould
2. Paleozoic fauna (ca. 440 mya)
a. first animals colonize land
b. many new families, genera, etc. but no new phyla (i.e., no significantly different body plans)
3. Modern fauna (ca. 200 mya)

a. notable exception - insects

a. arms race
b. shells and shell breakers
c. toxins and tolerance

1. Smithsonian - Washington D.C.
2. American Museum of Natural History - New York
3. Carnegie Museum of Natural History - Pittsburgh
4. California Academy of Natural History - San Fransisco
5. Field Museum of Natural History - Chicago
6. Dallas Museum of Natural History (not as big but closer)

1. Humans alter environments
a. pollution
b. habitat destruction
c. oil spills
d. pesticides/herbicides
e. fertilizer
2. Humans effect geographic distribution of species.
a. zebra mussel
b. lamprey
c. rats, cats, etc.
d. brown tree snake
3. Humans cause extinction
a. directly by over harvesting
- great auk
- passenger pigeon
b. indirectly by altering environment
- ivory-billed woodpecker
c. current rates of extinction are estimated to be on the order of a mass extinction
4. artificial selection

Molecular Evolution

1. most changes in molecular structure that persist in lineages do not affect molecular function
2. neutral substitutes accumulate at a rate that is approximately equal to the mutation rate (natural selection does not affect this rate)
3. amino acid sequence of insulin
a. very similar (but not identical) among mammal species
b. certain regions vary; others usually don't
c. in some cases, insulin from one species can function in another
4. amino acid sequence of cytochrome c

1. exons only - most prokaryotes
2. exons and introns - eukaryotes

1. Gene families are sets of genes that share a common origin
2. Genes in gene families are very similar to one another
3. Gene duplication lens to the existence of gene families
a. accidents during crossing over
b. transposable elements
4. Gene families may include pseudogenes that do not function
5. When a gene is duplicated, the new copy is free to evolve a new function, because the old copy is already carrying out the required function.
6. globin gene families in humans
a. my globin family
- one gene
- on chromosome 22
- codes for myoglobin, which binds to O2 in muscle
b. alpha globin family
- 3 genes, 2 pseudogenes
- on chromosome 16
- code for components of hemoglobin, which binds O2 in blood
c. beta globin family
- 5 genes, 1 pseudogene
- on chromosome 11
- code for components of hemoglobin
d. hemoglobin consists of 2 alpha polypeptides and 2 beta polypeptides
e. different alpha and beta genes are expressed at different times in development

1. There is a general trend for larger, more complex organisms to have larger genomes (e.g., prokaryotes vs. eukaryotes)
2. But there are many exceptions to his observation.
3. examples
a. most prokaryotes have one circular chromosome and sometimes a tiny additional bit of DNA
b. diploid number (2n) in eukaryotes varies between 2 and >1200
- Penicillium (2n = 2)
- fruit fly (2n = 8)
- human (2n = 46)
- chimpanzee (2n = 48)
- dog (2n = 78)
- adder's tounge fern (2n = 1262)
4. Ife we just consider the coding DNA, disparity in genome size makes more sense (i.e., in general more complex organisms have more coding DNA).

1. can use DNA, proteins
2. mutation rate must be estimated
a. compare the same molecule in two species - how many differences?
b. use fossil record or geologic history to estimate when the two species diverged
c. provides relationship between number of differences in molecule time
3. Once the rate at which a given molecule's clock ticks is estimated, any two species can be compared and their divergence time estimated.
4. Why does it work? Most mutations are neutral. (see above)
5. problem - selection changes the clock's rate; solutions - look at more than one molecule; interpret results with caution
6. problem - different molecules "tick" at different rates; solution - each molecule's rate must be determined independently
7. When making inferences about the past, the more information the better.

1. different molecules are suitable for different problems
a. e.g., relationships within a genus - use a relatively fast, evolving gene or protein
b. e.g., relationships among classes - use a relatively slow-evolving gene or protein
2. it is sometimes possible to extract DNA from fossils (Table 23.1 in text)
a. small fragments, not the entire genome
b. we can't reproduce extinct organisms by using this DNA (sorry, no Jurassic Park)

1. Human Genome Project
2. Caenorhabditis elegans (a nematode)
a. model organism (development, population genetics, etc.)
b. ca. 1 mm long
c. consists of 959 somatic cells
d. all genes have been mapped and sequenced

Animal Development

1. meiosis + cytokenesis
2. spermatogenesis
3. oogenesis

1. The haploid nucleus of the sperm fuses with the haploid nucleus of the egg.
2. zygote (2n) - a fertilized egg

1. differential gene expression - different genes are expressed at different times

1. blastomeres - the cells of this early embryo
2. 2-cell stage
3. 4-cell stage
4. 8-cell stage
5. 16-cell stage
6. solid ball of cells

1. blastocoel - space inside blastula
2. forms when cells near middle of cell pump Na+ out, causing water to difuse into this area

1. blastopore - opening into archenteron
2. archenteron - "primative gut"
3. gastrula is bilaterally symmetrical
4. 3 tissue layers
a. ectoderm - the cells around exterior of gastrula; derivatives include - skin, nervous system
b. endoderm - the cells lining the archenteron; derivatives include most internal organs (stomach, lungs, liver, etc.)
c. mesoderm - cells that invade the space between the endoerm and ectoderm; derivatives include - notochord, bones, blood vessels, conenctive tissues, muscles

1. neural tube separates from rest of ectoderm
2. neural tube eventually becomes brain and spinal cord

1. jawless fish
a. little to no yolk in egg
b. holoblastic cleavage
c. blastomeres of approximately equal size
2. bony fish, amphibians
a. relatively more yolk than jawless fish
b. vegetal pole, animal pole
c. boloblastic cleavage
d. blastomeres of vegetal pole larger
3. reptiles, birds, some fish
a. egg is almost all yolk with a tiny amount of cytoplasm at one end (the blastodisc)
b. meroblastic cleavage
4. mammals (placental)
a. egg is very similar to reptile egg but with very little yolk
b. holoblastic cleavage
c. inner cell mass at one end of blastula
- analogous to blastodisc
- goes on to become embryo
d. trophoblast
- the other cells of the blastula
- part contributes to placenta
5. gastrulation in amniotes (reptiles, birds, and mammals)
a. blastodisc (or inner cell mass) is flattened disc of cells; not a hollow ball as in blastula of other groups
b. lower cells of blastodisc become endoderm
c. upper cells of blastodisc become ectoderm
d. ectoderm invaginates along midline giving rise to primative streak
e. some of the invaginating cells give rise to mesoderm, in between ectoderm and endoderm.

1. molecules involved in unduction (morphogens) turn certain genes on and off
2. concentration of morphogen may be important; example in animal cells of clawed frog:
a. low concentration - epidermis
b. med. concentration - muscle
c. high concentration - notochord
3. the concentration of morphogen a cell receives is relative to its postition in the embryo

1. a cell is totipotent if it is still capible of expressing any of its genes
2. up to the 8-cell stage in mammals, each blastomere is totipotent; implications:
a. can divide up to 8-cell state embryo and produce 8 genetically identical individuals (this type of technology has been used in breeding certain valuable lines of cattle)
b. can combine two 8-cell stage embryos and produce one individual that has four parents
3. as development proceeds, the fates of the cells become determined; example:
a. take cells from prospective brain region in early gastrula
b. place these cells elsewhere in gastrula
c. transplanted cells will develop like their new neighbors (i.e., not into brain tissue)
d. take cells from prospective brain region in late gastrula
e. place these cells elsewhere in gastrula
f. transplanted cells will develop into neural tissue regardless of where they are placed in the gastrula
4. Cells may become determined to become a certain type of tissue prior to differentiating into that type of tissue. (see imaginal discs below)
5. Cells may become partially committed to a particular fate before they are completely committed; example: wing bud, leg bud on chicken
6. determination cen be reversed; example:
a. producing the cloned sheep Dolly
b. used nucleus from a fully differentiated cell (mammary cell in udder)
7. procedure for cloning a sheep
a. remove cell from udder of sheep to be cloned; keep alive in culure
b. remove and egg cell from another
c. remove nucleus cell with micropipette
d. insert udder cell into egg cell
e. shock cell with electricity to release nucleus of udder cell and to trigger cell division
f. grow egg ni culture to blastula stage
g. insert blastula into surrogate sheep
h. ca. 5 months later the clone is born
i. clone is genetically identical to the sheep that "donated" the udder

1. the source of bicoid protein (a type of morphogen) is mRNA from mother
2. this mRNA stays near one end of egg
3. bicoid protein diffuses though embryo forming a morphogen gradient
4. the end of the embroy with the highest concentration of bicod protein becomes the head; posterior to his the thorax develops
5. embryos that can't make bicoid protein develop neither a head nor a thorax
6. if bicod protein is injected into either end of embryo that can't make it, it becomes the head
7. bicoid protein activates particular genes

1. example - in fruit flies, mutation in these genes can result in an extra set of wings or in legs forming where the antennae should be
2. the order of the genes matches the order of the body parts they control
3. homeobox
a. found in homeotic genes
b. 180 nucleotides long
c. highly conserved (found in fruit flies, mice, humans; evidence of common ancestry)

a. webbing between fingers in humans
b. death of some neurons in humans

1. fruit fly
a. zygote develops into a free-living larva (maggot - common term for fly larva)
b. larva eats, grows, passes through several instars (exoskeleton is shed to allow growth)
c. larva develops into pupa
d. imaginal discs - groups of cells "set aside" during embryonic development; in the pupa various discs give rise to legs, wings, eyes, etc.
e. adult emerges from pupal shell
f. this general pattern holds form many insects (e.g., caterpillars become butterflies; grubs become beetles)
2. leopard frog
a. zygote develops into a free-living larva (tadpole)
b. larva eats, grows
c. larva undergoes metamorphosis
d. apotosis is involved in breaking down a tadpole's tail
e. not all amphibians have a larval stage
- some caecillians, salamanders, and frogs hatch or are born as miniature adults
f. in the paradox frog, tadpoles are larger than adults
3. metamorphosis in brought on by signals from the endocrine system (hormones)
4. in some species/populations, the larva never metamorphoses (neoteny)

1. internal fertilization is often necessary in dry environments
2. internal fertilization is necessary in species that lay shelled eggs

1. general trend - large numbers of offspring, less parental care; few offspring, more parental care

1. accumulated mutation hypothesis
a. cells accumulate mutations as they age
b. eventually these mutations are lethal
c. problem - no direct evidence that these mutations actually cause aging
2. telomere depletion hypothesis
a. telomeres - repeats of sequence TTAGGG at the ends of chromosomes
b. every time DNA is replicated for cell division, telomeres become shorter
c. after so many divisions, a cell can no longer divide
d. telomerase - an enzyme that "rebuilds" telomeres; only produced in certain cells that divide constantly (e.g., bone marrow cells)
e. telomerase is expressed in many cancer cells
f. cells that artificially caused to produce telomerase will divide many more times than cells of the same type without telomerase
3. wear and tear hypothesis
a. cells accumulate damage over time
b. partially due to harmful substances produced during metabolism
c. reduced flexibility at joints can be attributed to reactions involving these harmful substances

4. immunological exhaustion hypothesis
a. as we get older we become susceptible to infectious disease
b. fewer committee T cells
c. produce less interleukin-2 (a growth factor that stimulates production of T cells)
5. gene clock hypothesis
a. some genes are involved in regulating the aging process
b. Hutchison-Gilford Syndrome - extremely rapid aging in children (a very rare genetic disorder)
c. a combination of mutations in C. eligans can increase its life-span five fold
6. Is aging regulated by genes or does the body simply wear out over time?

Organ Systems

A. Central Nervous System (CNS)
1. consists of the brain and the spinal cord
2. the vertebrate is the master control center for almost all bodily functions
3. the spinal cord in vertebrates is single and located dorsally; it forms in the embryo as a tube with a hollow central canal (a remnant of which survives in the adult)
B. Peripheral Nervous System
1. consists of nerve fibers that relate signals between the CNS and other parts of the body (the periphery)
2. two divisions
a. Afferent: detects, encodes, and transmits peripheral signals to the CNS for processing
• peripheral signals include sensory informations from the special senses including vision, hearing, smell, taste, and touch
b. Efferent: transmits signals from the CNS to the periphery

A. Three types of muscle tissue (skeletal muscle, smooth muscle, and cardiac muscle)
B. Skeletal Muscle (voluntary or striated muscle)
1. attaches to the skeleton
2. most abundant tissue in vertebrate body
3. produces movements of the limbs, trunk, face, jaws, eyeballs, etc.
C. Smooth muscle
1. found in the walls of hollow organs and tubes (walls of digestive tract, bladder, ateries and veins)
D. Cardiac Muscle
1. found only in the walls of the heart
2. contractions are responsible for pumping blood throughout the body

A. all vertebrates have a closed circulatory system (a circuit rigidly encompassed in well-defined channels or vessels)
B. consists of a heart and numerous arteries, capillaries and veins.
C. Arteries carry blood away from the heart, while veins carry blood toward the heart
D. Capillaries are tiny blood vessels that interconnect the arteries and the veins, and the site of material exchange between the blood and other tissue
E. Functions as the internal transport system of animals

A. functions by exchanging oxygen and carbon dioxide between the atmosphere and the blood
B. the system includes the respiratory system leading into the lungs, the lungs themselves, and the structures of the chest involved in producing movement of air through the airways into and out of the lungs and gills

A. consists of the kidneys, ureters, urinary bladder, and urethra
B. functions of the kidneys
1. maintaining water balance in the body
2. regulating the quantity and concentration of most ions
3. maintaining proper plasma (component of the blood) levels
4. excreting waste products of bodily metabolism
5. excreting many foreign compounds

A. responsible for transferring nutrients, water, and electrolytes from the external environment to the internal environment
B. Components of the Digestive system and their functions
1. oral cavity (teeth): mechanical breakup of food by biting and chewing
2. stomach: stores food, churns and breaks up food, enzymatic digestion
3. small intestine: area where most food is digested and absorbed
4. large intestine: reabsorption of water

A. tissues responsible for producing and releasing hormones directly into the blood with no special ducts or tubes involved
B. Examples of major endocrine organs and hormones the secrete
1. Pancreas: insulin and glucagon
2. Adrenal medulla: adrenalin and noradrenalin
3. Testes: testosterone
4. Ovaries: estrogen and progesterone
5. Stomach: gastrin
C. plays an important role in internal control

A. Reproduction is not essential for survival of the individual, but it is necessary for the survival of the species.
B. The system is designed to enable union of genetic material from the two sexual partners, and the female system is equipped to house and nourish the offspring to developmental point at which it can survive independently in the external environment.
C. Primary reproductive organs or gonads
1. a pair of testes in the male
2. a pair of ovaries in a female
3. in both sexes, the mature gonads perform the dual function of:
a. producing gametes (gametogenesis), spermatozoa (sperm) in the male and ova (eggs) in the female
b. secrete sex hormones, testosterone in males and estrogen and progesterone in females

A. provides protection against foreign and abnormal cells and removes cellular debris
B. Lymphoid tissues store, produce, and process leukocytes (white blood cells)
1. bone marrow
2. lymph nodes
3. tonsils
4. appendix
5. spleen
6. thymus

A. the skin is the largest organ of the body
B. functions as an external defense mechanism against opportunistic pathogens by covering the outside of the body

A. Vertebrate skeletons are composed primarily of bone and/or cartilage
B. Cartilage is firm, but not as hard or as brittle as bone
1. primary component of the skeleton of an embryo in all vertebrates
2. a cartilaginous skeleton persists throughout life in some vertebrates (sharks, skates, and rays)
C. Some bones are held together at movable joints by ligaments
D. Skeletal muscles are attached to bones by means of tendons.

What Constitutes a Species?

- by Charles Darwin
- categorized by look

- if two similar organisms will breed, they are the same species
- in some cases of breeding a hybrid is produced
- some species can mate to create intergrades
- problem with the concept is asexual organisms and when females reproduce when no males are present

- separated by niche
- depends on interactions within the environment and eating habits
- environmental preference between organisms can make a difference

- structured according to evolution
- refers to genetic trees
- caused by geographic separation
- ex: species A evolves into species A and B. later species A creates another offshoot to create species C.

- says that one species evolves in to two completely new species leaving the old species extinct
- ex: species A evolves into species B and C and A no longer exists

High School Biology II

A. what alive
1. Has order - heirarchial organization
a) cell - tissues, organs, organ systems
b) organism - population, ecosystems, biomes, biosphere
2. sensitivity - responding to stimuli
3. growth development and reproduction
4. regulation - coordination of systems
B. Nature of Science
1. deductive reasoning - resting general idea - math and philosophy
2. inductive reasoning - use observations to make and test a model (science) (the scientific method)
3. basic research - science for the sake of science at the university level 4. applied research - science to make money - industry

C. Darwin - who influenced him
1. Thomas Malthus - essay on geometric increase in species, but arithmetic increase in food
a) geometric increase: (2, 6, 18, 54)
b) arithmetic increase: (2, 6, 10, 14)
2. Alfred Russel Wallace - joint presentation on natural selection and survival of the fittest

A. Atoms
1. matter - takes up space
2. protons - atomic number
3. atomic mass - protons + neutrons; measured in daltons
B. Isotope - atoms of the same element with the same number of neutrons
1. radioactive - nucleus unstable nucleus breaks and releases energy (radioactive decay of halflife) Carbon 14
2. radioactive material damages or kills living cells
C. Electrons
1. ions - charged; different number of protons to electrons
a) cation - positive charge caused by loss of electron
b) anion - negative due to gain of electron
2. orbitals - where find electrons (cloud around nucleus)
a) s shape - sphericle
b) p shape - dumbell
3. electrons determine behavior of atom
D. Energy
1. octet rule - where atoms will fill outer energy levels
2. valence electrons - electrons in outer energy level
3. exodation - loss of electron
4. reduction - gain of electron

A. Ionic - transfer of electrons
1. molecule - group of atoms held together by bonds
2. compound - molecule with more than one element (H₂O, NaCl)
B. Covalent bond - sharing electrons
1. Na + Cl (reactants) -> NaCl (product)
2. chemical reactions
a) temerature - increases rate of reactions
b) more reactants increase rate of forward reaction where more products increase rate of reverse reaction
c) catalyst - speeds up reactions (enzymes)
C. Biological Atoms - 11 of 92 elements are found in a measurable proportion in the body
1. carbon, oxygen, hydrogen, nitrogen (4 most common elements)
a) all form covalent bonds
b) weak enough to break at life's temperature
c) two of these are 90% of the atoms (water)
d) found in gas form soluble in H₂O
D. Water
1. H₂O - polar molecule
a) oxygen - slightly negative
b) hydrogen - slightly positive
2. attraction to other H₂O molecules called cohesion
3. adhesion - attraction to other molecules
a) capilary action - thinner the tube, stronger the attraction
4. hydrophobic - molecule that does not like water
5. hydrophilic - molecule that likes water
E. Water as a solvent
1. hydration shell - water molecules surrounding an ion
F. pH - 1 -> 7 <- 14
1. H⁺ - hydrogen ion - acid
2. OH^- - hydroxyl group (ion) - base

H₂O -> H⁺ + OH^-
G. Buffer
1. blood normal pH of 7.4
2. blood acidosis - pH .2 - .4
3. blood alkalosis - opposite of above
4. buffer - resevoir for H⁺
a) carbonic acid - (H₂CO₃)
b) bicarbonate - (HCO₃)

- they switch off and will release whichever is needed to be a buffer

A. Macromolecules
1. organic - contains carbon
2. four categories
a) carbohydrates
b) lipids
c) proteins
d) nucleic acids
3. functional groups
a) hydroxyl (-OH)
b) carbonyl (-C=O)
c) carboxyl (-COOH)
d) amino (-NH₂)
e) sulfhydryl (-SH)
f) phosphate (PO₄)
g) methyl (CH₃)
B. Building macro molecules
1. dehydration synthesis - put together by removing a water
C₆H₁₂O₆ + C₆H₁₂O₆ -> C₁₂H₂₂O₁₁ + H₂O
2. hydrolysis - to break appart by adding water
3. anabolic reaction - macromolecules are built from smaller subunits (put popcorn on a string)
4. catabolic reaction - taking a large molecule and breaking it into subunits
C. Carbohydrates - energy storing molecule
1. sugars - contain C:H:O in 1:2:1 ratio
a) energy storage due to the high number of C-H bonds
b) monosaccharide - C₆H₁₂O₆
c) glucose - most important monosaccharide
2. Isomers - fructose and galactose are isomers of glucose
- structural isomer - identical chemical groups bonded to different carbon atoms
- stereoisomer - identical chemical groups bonded to the same carbon atoms with different orientation
3. Transport Disaccharides - energy being transported without fear of being used until it reaches its destination (like writing a check instead of cash)
a) special enzymes regulate the breaking of disaccharides
b) maltose - made of two glucose molecules (fruit)
c) sucrose - glucose and fructose (table sugar) (from plants)
d) lactose - glucose and galactose (milk sugar)
4. Polysaccharides
a) starch - long chains of glucose of maltose
• amylose - simplest starch
  
• use hydrolysis to break polysaccharides up
b) glycogen - animal store glucose; longer than starch and more branched
c) cellulose - CH₂OH group is located on alternating carbons to give it strength. It takes a specific enzyme to break that bond. Humans use cellulose as a source of fiber to help clean digestive system.
d) chitin - modified form of cellulose; added a nitrogen to glucose (exoskeleton)
D. Lipids - fats, phospholipids, steroids, terpenes, prostiglandins
1. Fats
a) used to store glucose (energy) for long periods of time - due to high number of C-H bonds
b) C-H bonds are non-polar; not soluble in water
c) structure: 2 subunits
• glycerol - carbon alchohol with a hydroxyl (OH)
  
• fattyacids - long hydrocarbon chain ending in a carboxyl (COOH)
d) saturated fat - fatty acid with all internal carbons bonded to a hydrogen
e) unsaturated fat - having a double bond; a fatty acid that does not have the maximum number of hydrogens bonded to carbons
f) polyunsaturated fat - being more than a double bond
• low melting point and are liquid at room temperature
g) allocation of carbos
• glucose for immediate energy
  
• transport disaccharides
  
• convert starch or glycogen for future use
h) as you age, the need for energy drops but carbohydrate intake does not, so the body turns it to fat (why people get fatter when older when eating the same as before)
2. phospholipids - polar heads and non-polar tails; triglyceride with fatty acid chain replaced by a phosphate group (PO₄
3. steroid - cholesterol or carbon rings
4. terpens - very long chained lipids; ex: chlorophyll (plants) and retinal (animals for vision)
5. prostaglandins - involved in inflamitory response and are inhibited by asprin
E. Proteins
1. kinds of proteins
a) enzyme - biological catalyst
b) globular proteins - enzymes or antibodies
c) fibrous proteins - collagen, muscle fibers, ligaments (muscle to bone) and tendons (bone to bone)
d) peptides - intercellular messengers
2. amino acids - building blocks of proteins; central carbon with an amino acid group (NH₂), carboxyl group (-COOH), and a hydrogen atom
a) 20 common amino acids - each has a chemical side group that make it unique - this is an R group (the variable in an amino acid)
b) peptide bond - a vovalent bond between 2 amino acids
c) polypeptide - (many bonds) long chains of amino acids held together by peptide bonds (aka proteins)
3. globular proteins - long chained proteins folded into complex 3D shapes
a) primary structure - amino acid squence
b) secondary structure - how the protein bonds itself to itself with hydrogen bonds
• alpha helix
  
• beta sheet - two chains linking to form a pleat
c) tertiary structure - folded in 3D shape upon itself
d) quaternary structure - the subunit structure (number of alpha + beta)
e) denaturing - unfolding of alpha and beta folds (what happens when you cook meat or get a high fever)
F. Nucleic Acids - information storage device
1. structure - long polymers of nuleotides
a) 5 carbon sugar (ribose, deoxyribose)
b) phosphate (PO₄)
c) nitrogenous base
2. phosphodiser bond - bond between nucleotides formed by dehydration synthesis
3. purines - bases in DNA & RNA
a) adenine
b) guanine
4. pyrimidines -
a) cytosine - DNA & RNA
b) thymine - DNA
c) uracil - RNA
5. ATP - Adenosine Triphosphate
a) DC sugar
b) base - adenine
c) 3 phosphate groups
6. DNA
a) deoxyribose
b) double stranded
c) hydrogen bonds at bases hold helix together
d) A-T     C-G
e) does not leave nucleus
7. RNA
a) blue print for amino acids
b) leaves nucleus
c) ribose
d) single strand
e) A-U     G-C

Notes

Money is personally important and important to the nation. Banks create money and the Fed determines the extent to create and destroy money, though most is done by banks. Banks create credit money in cooperation with bank deposits.

The US dollar is called fiat money, which is money because the government says so. Fiat money isn't attached to a scarce resource like gold. When fiat money is unstable, it is because the government is unstable.

Bartering involves a coincidence of wants; it is a form of commodity money. "Parfadism" is related as part of ancient agricultures.

Seigniorage is the profit the government makes from coining money. It may only cost 4 cents in materials and labor to create a coin worth 25 cents in the marketplace (a quarter). In 2004, the cost of producing US coins was as follows:

The Federal Reserve: Purposes & Functions

The Federal Reserve System is the central bank of the United States. It was founded by Congress in 1913 to provide the nation with a safer, more flexible, and more stable monetary and financial system; over the years, its role in banking and the economy has expanded. The Federal Reserve's duties fall into four general areas:

• Conducting the nation's monetary policy by influencing the money and credit conditions in the economy in pursuit of full employment and stable prices.
• Supervising and regulating banking institutions to ensure the safety and soundness of the nation's banking and financial system and to protect the credit rights of consumers.
• Maintaining the stability of the financial system and containing systemic risk that may arise in financial markets.
• Providing certain financial services to the U.S. government, to the public, to financial institutions, and to foreign official institutions, including playing a major role in operating the nation's payments system.

Most developed countries have a central bank whose functions are broadly similar to those of the Federal Reserve. The Bank of England has existed since the end of the seventeenth century. Napoleon I established the Banque de France in 1800, and the Bank of Canada began operations in 1935. The German central bank was reestablished after World War II and is loosely modeled on the Federal Reserve.

Before Congress created the Federal Reserve System, periodic financial panics had plagued the nation. These panics had contributed to many bank failures, business bankruptcies, and general economic downturn. A particularly severe crisis in 1907 prompted Congress to establish the National Monetary Commission, which put forth proposals to create an institution that would counter financial disruptions of these kinds. After considerable debate, Congress passed the Federal Reserve Act, which President Woodrow Wilson signed into law on December 23, 1913 at 6:02 p.m. The act stated that the purposes were "to provide for establishment of Federal reserve banks, to furnish an elastic currency, to afford means of rediscounting commercial paper, to establish a more effective supervision of banking in the United States, and for other purposes."