Chapter 1: Themes in the Study of Life

I. Adaptations for survival result of evolution: Channing life of Earth  diversity

a. Biology: Science of the study of life; relates to health and environmental

b. Order, Regulation, energy usage, evolution, growth, reproduction, response

II. Evolution = center of biology: idea that living present organisms share common ancestor

a. Emergent Properties result of arrangement and parts; present with complexity

a. Unrivaled complexity of biological systems  challenge to study
b. Reductionism: Making complex system simple to study; interferes with functions
a. System Biology: Construct models for dynamic behavior of system
i. Focus of large-scale research; system  parts combination together
c. Organisms interact with environment to exchange matter and energy
d. Ecosystem operation involves cycling of nutrients and flow of energy
e. Work required energy; energy transforms in state
a. Sunlight  Producers (chemical energy)  Secondary Consumers/heat
f. Form fits function; structure leads to function
g. Cell is lowest level of organization that performs activity of life; basis of all
a. Enclosed by membrane regulating inside from surroundings
b. Eukaryotic (plants/animal) cell divided by internal membrane
i. Largest organelle in most is nucleus
c. Prokaryotic (archaea/bacteria) cell has DNA in the cytosol; small
h. Chromosomes have cell’s genetic material (DNA); DNA contains genes
a. Blood Group (A, B, AB, O) result of genes from parent to offspring
i. DNA chromosomes replicate as cell divides; controls development and maintenance
a. Differences reflect differences between nucleotide sequences
b. RNA molecules help cellular production of protein and protein-coding genes
c. “Library” of genetic instructions: Genome; three billion nucleotides
i. Entire sequence known; beginning of learning activities of proteins
d. Apply as system on cellular level; must know components of system
i. Must know how parts behave/interact; computers can pool data
e. “High-throughput” technology can rapidly analyze large amounts of data
i. Bioinformatics use computational roots to store/analyze info
ii. Interdisciplinary research teams: Groups of diverse specialists
j. Negative Feedback: Excess production slows process of creation
a. Positive Feedback: Excess productions stimulates previous step to continue
b. Example of integration that makes living organisms = sum of parts
III. Levels of Biological Organization:

a. Biosphere: Contains all environments on Earth that are inhabited by life

b. Ecosystems: Consist of all living and nonliving things in a particular area
c. Communities: Entire array of organisms with each form of life (species)
 d. Population: All individual species living in a specific area
e. Organism: Individual living things
f. Organs (and Organ Systems): Two or more tissues working together
g. Tissues: Common group of similar cells
h. Cell: Fundamental unit of structure and function; 25 micrometers
i. Organelles: Various functional components that make up the cell
j. Molecule: Group of atoms covalently bonded making up everything
IV. “Nothing in biology makes sense except in the light of evolution” (Dobzhansky)

a. Species, Genus, Family, Order, Class, Phylum, Kingdom, Domain (Taxonomy)

b. Five kingdoms: Plant, Animal, Fungi, single-celled eukaryotic, and prokaryotic

a. Singled-cell domain Bacteria and Archaea; Archaea related to eukaryotes

b. Domain Eukarya includes Plant, Fungi, and Animals; unity between species

c. Darwin explained “descent with modification” and “common ancestor” in his book

a. Natural Selection; evolution occurs as unequal reproductive successes

d. One species gradually mutates into another species from common ancestor

V. Inquiry: Search for information and explanation; mind drives all progress in biology

a. Discovery science describes nature while hypothesis science explains nature

b. Discovery (Descriptive) Science depicts natural structures through observation

c. Recorded information: data (qualitative or quantitative)

d. Inductive Reasoning: Generalizations form specific observations

e. Hypothesis is tentative answer to well-framed question (“If…Then…”)

f. Scientific Hypothesis leads to predictions that can be true based by experiments

a. Deductive: General to specific

b. Hypothesis must be both testable and falsifiable

i. Impossible proving hypothesis over doubt (not all alternatives tested)

g. Scientific Method: Following exact procedure; not rigidly adhered to for inquires

a. Experimental Group + Control Group  Controlled Experiment

h. Theory: Broad hypothesis; spins off new hypothesis; supported by evidence

i. Models simplify situation to explain; technology: applied science for purpose

Chapter 2: The Chemical Context of life

I. Duroia hirsuta forms “devil’s garden” by ants’ chemical (formic acid) to stop other trees

II. Organisms are made of matter: anything with mass and space

a. Elements cannot be broken down into small substances

b. Compounds: elements together in fixed ratios; different properties than before
a. Carbon, Nitrogen, Hydrogen, and Oxygen make up 96% of living matter
b. Trade elements needed in small quantities
i. About 25 of 92 natural elements needed for life
III. Atom is smallest unit of matter with element properties with subatomic particles

a. Positive protons with neutral electrons in atomic nucleus (majority of mass)

a. Negative electrons orbiting around; electron cloud (majority of volume)
b. Dalton used to describe mass, or atomic mass unit (amu)
i. Protons and neutrons have the mass of one Dalton
b. Atomic Number: Protons (and electrons in neutral atoms)
a. Neutrons + protons  Mass number or atomic mass
c. Isotopes: Different number of neutrons; radioactive isotope: emits energy
a. Used to diagnose problems or detect cancer cells
d. Only electrons in chemical reactions; energy: ability to cause change (work)
a. Potential energy: energy possessed because of location/structure
i. Matter natural moves to lowest state of potential energy
ii. More distant from nucleus  more potential energy in electron
iii. Electron cannot exist between energy levels
iv. Electrons found in electron shells (2n2)
b. Absorbs energy: “excited state” (jumps out from center)
c. Releases energy: “ground state” (falls down to the first energy level)
e. Chemical behavior based on distribution of electrons in shells in outermost shell
a. Outer: Valence Electrons on the valence shell
b. Complete valence shell  un-reactive (inert noble gases)
f. The 3D space that the electron is found 90% of the time  orbital

a. Two electrons per orbit: one spherical (s); three dumbbell-shaped (p)

IV. Atoms held together by chemical bonds; strongest: covalent bonds and ionic bonds

a. Covalent bond: sharing pairs of valence electrons between two atoms

a. Known as molecule; H-H means a single bond (two electrons shared)
b. Known as Lewis-dot diagram or structural formula
c. H2 means molecular formula; O=O means a double bond (two pairs)
i. Bonding capacity: Valence (equals outermost unpaired)
d. Pure elements: Combination of two or more same elements
e. Attraction of atom for electrons: electronegativity
i. Equal electronegativity: nonpolar covalent bonds
ii. Unequal sharing: polar covalent bond
iii. Oxygen is one of most electronegative (δ-)
b. Ionic bonds involve cation (positive) giving electron to anion (negative)
a. Compounds by ionic bonds are ionic compounds or salts
c. In organisms, covalent bonds are the strongest
a. Hydrogen Bonds weak (N, O, F, or H bonded to a hydrogen)
 b. Van der Waals interactions are quick due to polar charges when nearby
d. Water has a 104.5* angle between the hydrogens
a. Shape determines how molecule is recognized and interacts
V. Making or breaking of chemical bonds  Chemical reactions (reactants -> products)

a. Products must equal reactants in mass and number of atoms

b. Point of offsetting: chemical equilibrium (dynamic; no net change)

a. Reaction continues to happen with concentrations at static rate

Chapter 3: Water and the Fitness of the Environment

I. Water acts as the biological medium and makes up 75% of the Earth's surface.
a. Water is mainly liquid; only common substance present in all three states: solid, liquid, gas
b. Most cells are 70-95% water; water needed for diffusion
II. Polarity: Electronegative Oxygen (negative) and hydrogen (positive) --> "V Shape" Polar
a. Weak hydrogen bonds connect Hydrogen to Oxygen for extremely short seconds
III. Fitness: Cohesion, Moderation of temperature, expansion when freezing, universal solvent
a. Same substance together: Cohesion...different substances: Adhesion
b. Cohesion helps transport water and nutrients up a plant to leaves against gravity
c. Water has Surface Tension == difficult to break surface
a. Moving = Kinetic Energy; faster = more energy; Heat = Total kinetic energy (volume)
b. Temperature = Average kinetic energy, regardless of volume
c. Celsius Scale = "C = (5/9)(F-32)"... Human body = 37*C; room temp = 20-25*C
d. 1 calorie = amt of heat to raise 1g of water 1*C
e. 1 kilocalorie (kcal) = amt of heat to raise 100g (1kg) of water 1*C
f. One joule = .0239 cal... 1 cal = 4.184 joules
g. Water's high Specific Heat = Resist change in temperature (1 cal/(g*C))
h. Sweating breaks bonds = absorb heat = cooler; harder when humid
i. Liquid -> Gas: vaporization; Heat of vaporization: liquid -> gas (580cal for 1g at 25*C)
j: Evaporative Cooling: Hottest molecules turn into gas first at top
i. Ice expands = Less dense = floats at top; greatest density at 4*C
i. Homogenous = Solution; dissolving = solvent; dissolved = solute
ii. Water dissolves = aqueous solution; sphere of hydration shell
iii. H+ ion = dislocation; biology = "wet" chemistry
iv. hydrophilic: either dissolve or form colloid
v. hydrophobic: repel water (oil or fat)
vi. Molar Mass: Sum of elements; mole: atoms in one molar mass
vii. Molarity: Mol/Liters; 1 mol = 6.02*10^23 (units)
IV. Acids: Donate a hydrogen --> Hydronium...Bases: Receive Hydrogen --> Hydroxide (pH)
a. [H+][OH-] = 10^(-14)...reversible reactions are weak while forward are strong
b. pH = -log [H+]...buffers minimize changes by accepting or donating hydrogen (blood = 7.4)
c. Acid Precipitation: Below 5.3 from sulfur while Carbon dioxide creates greenhouse effect
i. Hurts coral reefs and calcium in reefs
 Chapter 4: Carbon and the Molecular Diversity of Life

II. Most organisms are based on chemicals with carbon

a. Proteins, DNA, carbs, and lipids have carbon with N2, O2, H2, S, P
II. Study of carbon compounds: Organic Chemistry; most organic compounds also have hydrogen
a. Uniform percentages of compound between organisms; versatile combinations
b. Vitalism: Life force jurisdiction of physical and chemical laws --> Organic Chemistry
c. Replaced by Miller's mechanism: chemical laws govern all natural phenomena
III. Carbon has 6 electrons; 4 valence -> usually covalent to complete shell; hydrophobic
a. Tetravalence Carbon can branch off in four directions; varying shapes and sizes
b. Commonly with Oxygen, hydrogen, and nitrogen; hydrocarbons = only CH bonds
c. Major fuel in petroleum from decomposed organisms; nonpolar; large energy released
d. Variations in structure: isomers
a. Structural Isomers: Different covalent arrangement
b. Geometric Isomer: Same covalent bonding, but different spatial arrangements
i. cis isomer: Same side...trans isomer: different sides
c. Enantiomers: Mirror image isomers with asymmetric carbon middle
i. Different structures = Different functions
III. Hydrocarbons as framework of complex organic molecules
a. Important Chemical group: Functional Group
b. Hydrophillic: Hydroxyl, Carbonyl, Carboxyl, Amino, sulfhydryl, phosphate
a. Hydroxyl: -OH; alcohols (-ol); polar; forms hydrogen bonds with water to dissolve
b. Carbonyl: -C=O; ketone with carbon skeleton; aldehyde if at end of skeleton
i. Aldoses and Ketoses sugars
c. Carboxyl: -COOH; organic acids; acidic properties; polar; charge of -1 (acetate ion)
d. Amino: -NH2; Glycine is amine and carboxylic acid to make amino acid; base
i. Picks up H+ in surrounding solution; ionized with charge of +1
e. Sulfhydryl: -HS; cross-linking maintains straightness of curliness of hair
f. Phosphate: (-OPO32-); backbone for phospholipids in cell membrane
i. Releases energy in water
g. Methyl (not reactive, but acts as a recognizable tag); -CH3; expresses genes
i. Affects function of sex hormones
IV. ATP (Adenosine Triphosphate) is string of three phosphates; ADP after losing one group
a. ATP stores energy; turns into ADP in reaction with water

Chapter 5: Structure and Function of Large Biological Molecules

I. Four main organic molecules: Carbs, lipids, protein, nucleic acids; huge macromolecules
a. Polymer: Long chain of monomers (DNA, proteins, carbohydrates)
a. Combined by loss of water: Condensation Reaction or Dehydration Synthesis
i. Facilitated by enzymes which speed up reaction
ii. One molecule loses hydroxyl while the other loses a hydrogen = water
b. Disassembly: Hydrolysis (water + polymer = monomers)
i. Occurs in digestion to break down polymers into smaller compounds
c. Differences between organisms present in slight variations in proteins/DNA
II. Carbs include simple sugars (monosaccharide) and starches by dehydration synthesis
 a. Monosaccharide are variations of CH2O; glucose (C6H12O6) = most common
a. Carbonyl group (either aldose or ketose) and multiple hydroxyls
b. Skeletons range from three to seven carbons long (triose, pentose, hexose)
c. Another source of diversity is asymmetric carbons; nutrients for cellular respiration
b. Disaccharides joined by glycosidic linkage (covalent bond with Oxygen after dehydration)
a. Most common is sucrose or table sugar; (lactose == glucose + galactose)
c. Polysaccharides are large complex chains (starch in plants for stored energy)
a. Animals store glycogen that is branched amylopectin in liver and muscles
i. Quick depletion and not sustainable under hydrolysis
b. Plants produce cellulose with rings of glucose (alpha or beta) in straight lines
i. Grouped into micro-fibrils...hard to digest ("insoluble fiber")
ii. Prokaryotes in cows convert glucose in grass to other nutrients
iii. Chitin in arthropods to build exoskeleton; also in fungi and cell walls
III. Lipids mix very poorly with water with smaller chains (wax)
a. Fat: Glycerol (alcohol w/ 3 carbons + hydroxyl) and fatty acids (carbon chains with carboxyl)
a. Either one or three fatty acids; nonpolar C-H bonds; tricylglycerols if three
i. Ester linkage connects glycerol to fatty acids
b. Saturated has no double bonds between carbons and filled with hydrogen
c. Unsaturated implies double bonds which remove hydrogen
i. "kink" formed by cis double bond; most fats are saturated
ii. Most saturated fats are solids while unsaturated are liquids (oils)
iii. "Hydrogenated vegetable-oil" --> Synthetically converted to saturated
d. Trans fats contribute to atherosclerosis in heart cause plaques in blood vessels
e. Major fat function: energy storage (adipose cells in animals that insulate the body)
b. Phospholipids make up cell membrane (two fatty acids with negative phosphate group)
a. Hydrophilic head and hydrophobic tail --> assemble into bi-layers that shield tails
c. Most hormones are steroids (lipids with four rings in carbon skeleton)
a. Cholesterol in made in the liver and produce sex hormones (high == negative impact)
IV. Proteins speed up reactions act as support, make up most of dry-mass of cell and help transport
a. Catalyst speed up chemical reactions without being consumed; substrate binds to enzymes
a. Proteins are most structurally sophisticated molecule with twenty amino acids
b. Polypeptide: Polymer or amino acids; proteins consist of one or more 3D polypeptides
a. Amino Acids posses carboxyl and amino group; asymmetric carbon (alpha carbon)
b. Carboxyl + Amino + Variable (20 types) + hydrogen bonded to central carbon
i. Ionized form at pH of cell; nonpolar sides = hydrophobic
ii. Polar = hydrophilic; negative charge = carboxyl group/hydrophilic
c. Connection by a polar peptide bond; chain from Amino (N) --> Carboxyl (C) = Backbone
d. Function protein =\= simple chain, but multiple polypeptides precisely twisted/organized
a. Structure determines how the protein works and interacts; four levels:
1) Primary Structure: unique sequence of amino acids; ability from genetic info by order
2) Secondary Structure: coils and fold with negative oxygen and hydrogen backbones
I. a helix: coil held by hydrogen bonding every fourth amino acids
II. B pleated sheet: Two or more chains with hydrogen bonds in parallel
3) Tertiary Structure: Overall shape of polypeptide
I. Hydrophobic Interaction: nonpolar amino acids end up in core of protein
II. Held together by Van der Waals forces; pushed to center by water
III. Weak interactions given protein overall a unique shape
IV. Disulfide Bridges: Have sulhyrdyl groups covalently bond for more structure
 4) Quaternary Structure: Overall shape of protein with heme (iron bonded to oxygen)
I. Heme is a nonpolypeptide component at each subunit
e. Sickle-cell disease caused by one substitution (valine instead of glutamic) --> poor clots
f. Change in shape at shape starting at secondary structure: Denaturation
a. Common if transferred from aqueous solution to organic solvent or temp. changes
b. Renaturation can occur if chemical and physical aspects are restored in environment
c. Some proteins aid in the folding of other proteins
g. Chaperonins assist in folding other proteins, refold misfolded, or mark for destruction
a. Alzheimer's and Parkinson's caused by accumulation of misfolded proteins
b. X-ray crystallography determines 3D shape of proteins
V. Amino acid programmed by unit of gene, consisting of DNA (Nucleic acid)
a. DNA and RNA; DNA directs RNA synthesis and controls protein synthesis through RNA
a. Deoxyribose Nucleic Acid (ANA) and Ribose Nucleic Acid (RNA)
b. DNA inherited from parents with chromosomes; copied in replication
i. Proteins required to implement genetic programs
c. DNA -> RNA -> Protein; messenger RNA sends protein info from nucleus to cytoplasm
d. Prokaryotes use RNA to convey message from DNA to ribosome
b. Polynucleotides: Macromolecules for nucleic acids made of the monomer nucleotides
c. Pyrimides have six-membered ring of carbon and nitrogen
a. Nitrogen take [H+] from solution --> Base: Cytosine, Thymine (DNA), and Uracil (RNA)
b. Purines have five-membered rings: Adenine and Guanine
c. Ribose sugar: RNA...Deoxyribose sugar: DNA
d. Sugar atoms have prime(') to denote numbering
d. Adjacent nucleotides joined by phosphodiester linkage (phosphate group linking sugars)
a. Sequence determines meaning; one end: 5' phosphate carbon; other: 3' hydroxyl
e. DNA forms double helix with antiparallel arrangement
a. Sugar-phosphate on outside while nitrogen bases are inside helix; hydrogen bonds
e. Adenine: Thymine...Guanine: Cytosine; structure of DNA--> function in genetics
f. Closely related --> Closer genetic similarities
Chapter 6: A Tour of the Cell
Hormonal Receptor Enzymatic

I. All living organisms areTransport Proteins

made of cells; life at cellular level arisesDefensive
by structure

Storage have cellsStructural

a. Multicellular organisms Contractile
that could not survive on own
(motor)
II. Light Microscope (LM): has visible light passed through lenses bent to magnify

a. Magnification: Ratio of image to real size…Resolution: Clarity

a. Minimal point two points separated and still distinguishable
b. 1000x magnified; with contrast by staining the cells
i. Include organelles which need electron microscope to see
ii. Cell ultrastructure: Cellular anatomy by electron microscope
c. Scanning Electron Microscope studies surface if specimen
i. Appears three-dimensional
d. Transmission Electron Microscope studies internal structure of cell

a. Cell Fractionation involves separating and breaking down cell by centrifuge

 a. Higher speed  smaller components of cells in ultracentrifuges

b. Prepare cell components in bulk and identify function

III. Prokaryotic: Bacteria/Archaea…Eukaryotic: Protists, fungi, animals, and plants

a. All cells have plasma membrane barrier, containing cytosol for organelles
b. All have chromosomes (genes for DNA) and ribosomes to make protein from genes
a. Eukaryotic cells’ DNA in nucleus…Prokaryotic in nucleoid in cytoplasm
i. No membrane bounded structures in prokaryotic/small
ii. Smallest cell: Bacteria mycoplasmas
b. Plasma Membrane allows diffusion; high SA: Volume ratio = Better

c. Microvillus increase SA without altering volume helps exchange materials

c. Eukaryotes’ enzymes in membrane (bi-phospholipids layer) for environment func’t

IV. Animal cell: Central nucleus with metabolic activity in cytoplasm and ER; * = animals only

a. Flagellum*: Locomotion organelle (microtubules extension of membrane) outside

b. Centrosomes*: Microtubules initiated; unknown centrioles
c. Cytoskeleton: Reinforce shape; mov’t (micro/intermediate filament microtubules)
d. Microvilli: Increase Surface Area
e. Peroxisome: Metabolic; H2O2 produced and converted to water
f. Mitrochondrion: Cellular respiration and ATP generator
g. Lysosome*: Digestion where macromolecules are hydrolyzed
h. Golgi Apparatus: Modification, sorting, synthesis, and secretion of byproducts
i. Ribosome: Protein synthesis bound to rough ER or nuclear envelope
j. Plasma Membrane: Membrane enclosing the cell
k. Nucleus:
a. Nuclear Envelope: Membrane holding the nucleus with pores
b. Nucleolus: Production of ribosomes (multiple in cells)
c. Chromatin: DNA and protein; visible as chromosomes divide
l. Endoplasmic Reticulum (rough/smooth): Network; membrane synthesis
V. Plant cells: Membrane-enclosed organelles called plastids (chloroplast); definite shape

a. Cell Wall: Cellulose layer protecting outer shell

b. Plasmodesmata: Channels connecting cytoplasm to adjacent cell walls

c. Chloroplast: Photosynthesis sugar molecules from sunlight

d. Central Vacuole: Prominent organelle in old cells; storage/hydrolysis/growth

e. Repeats from animal cell (unless marked)

VI. Nucleus contains most genes (some in mitochondria/chloroplast) surrounded by envelope

a. Double Membrane with lipid bilayer with complex pores controlling diffusion
a. Nuclear lamina, netlike array of protein filaments for shape of nucleus
b. Nuclear matrix of fibers throughout the interior
i. DNA organized into Chromosomes made of chromatin
 ii. Nucleolus synthesizes ribosomal RNA (rRNA); assembling
1. Regulation of cellular processes, such as cell division
iii. mRNA in cytoplasm  Ribosomes make specific polypeptide
b. Ribosomes: protein synthesis; free in cytosol; bound in rough ER/ envelope
a. Cells specializing in protein secretion have high amounts of ribosomes
VII. Endomembrane system synthesizes protein/transport/mov’t of lipids/detoxify cells

a. Vesicles: Tiny membrane sacks; ER/Golgi/envelope/lysosomes/vacuole/membrane

b. ER = tubules and cisternae; separates internal lumen (cisternae space) from cytosol

a. Smooth lacks ribosomes while rough has brown ribosomes

c. Smooth ER synthesizes lipids, metabolizes carbs, detoxifies drugs; sex hormones

a. Stores calcium ions; muscle cell and nerve impulse calcium for contraction

d. Glycoproteins have carbs bonded to protein in the rough ER in transport vesicles

a. Secretion protein; membrane factory makes vesicles (transfer to other parts)

e. Golgi Apparatus modifies products (cis face) before exporting with vesicles (trans)

a. Manufactures macromolecules (pectin); polarity on each side

i. Cisternal maturation model: Cisternae carries cargo in Golgi

ii. Before trans face, products sorted and organized

f. Lysosomes work in acid environment; hydrolytic enzymes made by rough ER/Golgi

a. Intracellular digestion: Phagocytosis (“food vacuole” fuses with lysosome)

b. Autophagy: Recycle cell’s own organic material with hydrolyric enzymes

g. Food vacuoles are membrane-bounded vesicles in phagocytosis

a. Contractile vacuoles pump excess water outside of the cell

i. Plants and fungi lack lysosomes  vacuole for hydrolysis

b. Plants have central vacuole holds both in/organic compounds

i. Deposit site of metabolic process; color pigment; helps growth

ii. Contain poisons to harm predators

VIII. Mitochondria are site of cellular respiration for ATP; chloroplasts photosynthesis food

a. Mitochondria has two separate membranes while chloroplast have three

a. Free ribosomes in cytosol make membrane protein with DNA  synthesis
b. Outer mitochondria smooth; inner has folds (cristae)
i. Mitrochondrial matrix contains enzymes, DNA, and ribosomes
b. Chloroplast part of organelles called plastids along with amylopasts/chomoplasts
a. Green pigment chlorophyll with enzymes for sugar production
 b. Membrane sack (Thylakoids) in stacks called granum in stroma fluid
c. Peroxisomes produce hydrogen peroxide and water
i. Detoxify alcohol in liver; glyoxysomes change fatty acids  sugar
ii. Unlike lysosomes, these do not bud from Endomembrane; divide
IX. Cytoseleton: Fiber-network with microtubules, microfilament, and intermediate filaments

a. Mechanical support (shape); motility by interaction with motor proteins

a. Stabilized by balance between opposing force by its elements; dynamic
b. Vesicles “monorail” along the skeleton (how nerve cells send messages)
i. Regulating biochemical function (response mechanical stimulation)
c. Microtubules are thickest; microfilaments (actin) are thinnest
d. Microtubules hollow from tubulin protein (dimer: two subunits)
i. Help organelles move; separate chromosomes during cell division
b. Microtubules grow form centrosomes in animals; microtubules ring: centrioles

c. Flagella and Cilia (extensions) help move; primary cilium = antenna in vertebrates

a. Common structure: Microtubules under extension of plasma membrane

b. Basal body connects flagella to cell

c. Large Motor Protein: Dyneins (bending movement of organelles)

i. Cross-linking protein holds microtubules; cannot move very far

d. Microfilaments = chain of actin protein; structural role is to bear tension

a. Three-dimensional cortical microfilaments support the cell’s shape

b. Cortx has semisolid consistence of a gel; microfilaments make microvilli

c. Parallel along muscle cell with thick myosin that localize contraction of cells

d. Pseudopodia in moving amoeba by extend/contract with actin (sol  gel)

e. Cytoplasmic Steaming: Circular flow of cytoplasm within cell (distribution)

e. Intermediate Filaments bear tension; reinforce shape/fix position of organelles

a. Framework of entire cytoskeleton; permanent fixtures of the cell

X. Most cells synthesis/secrete materials external to plasma membrane

a. Cell Wall in plants maintains shape and prevents excessive uptake of water

a. Microfibrils made of cellulose (made by cellulose synthase) make matrix

b. Thin/flexible primary cell wall in young cells

c. Middle Lamella with pectin to strengthen the wall

d. Secondary cell wall between plasma membrane and primary wall

i. Strong and durable matrix; channel between cells (plasmodesmata)

 b. Animal cells have extracellular matrix (glycoproteins, mainly collagen)

a. Embedded in woven network called proteoglycans

i. Small protein core with carbohydrate chains

b. Fibronectin binds to integrin receptor protein to attach to cytoskeleton

c. Cells adhere by physical contact; plant cell wall perforated by plasmodesmata

a. Cytosol passes from one cell to another to create continnum

d. Animals intercellular junction: tight, desmosomes, and gap

a. Common in epithelial tissue; tight junctions prevent leakage of fluids

b. Desmosomes (anchoring) fasten cells together; gap allows molecules to pass

Chapter 7: Membrane Structure and Function

I. Plasma membranes separates cell from surrounding by selective permeability

a. Membrane encloses solution and allows for uptake of nutrients and expels waste

b. Proteins act as channel for Potassium ions to exit cell for nerve stimulation

II. Abundant lipid in membrane: phospholipids (amphipathic: hydrophilic/hydrophobic)

a. Ability to form membranes in molecular structure

b. Fluid Mosaic Model: Fluid membrane with protein “mosaic” in bilayer of lipids
a. Red blood cells made of lipids/proteins (cell membrane  phospholipids)
i. Hydrophilic heads; hydrophobic tails
ii. Phos-lipid adheres weaker to water than biological membrane surface
b. Sandwich model: Phoso-lipid bilayer between two layers of protein

i. Problems: Generalization of identical membranes/protein placement ii.

Proteins on surface have hydrophobic/philic regions

c. Freeze-fracture shows that proteins are embedded within membrane

i. Interior appears cobblestoned; proteins in smooth matrix

ii. Models = Hypothesis  New finding create new models

c. Freeze-fracture cuts membrane at middle; cholesterol lowers fluidity at medium temps.

a. Hinders solidification at low temperatures; unsaturated = kinks for liquid

 b. Lateral movement with rare flip-flopping; held by hydrophoblic interactions

i. Rapid movement; proteins move much more slowly

ii. Close packaging  solid (varying due to components)

iii. Fluid to a lower temperature is rich in unsaturated carbons

c. Cholesterol  Temperature buffer for membrane; inactive if solid

d. Membrane is collage of different proteins embedded within lipid layer

a. Lipids form fabric, but proteins form the function

i. Integral Proteins penetrate hydrophobic core (transmembrane: spans)

b. Hydrophoblic core of proteins is nonpolar amino acids (a helices)

c. Peripheral proteins are appendages loosely bounded to outside

i. Cytoseleton holds membrane; integrins hold outside  framework

e. Cells recognize other cells by binding to carbohydrates on surface

a. Membrane carbs are short; covalently bonded to lipids  glycolipid

b. Most are glycoprotein bonded to proteins; carbs vary between cell types

III. Transport Protein: Hydrophilic channel that spans membrane; may use ATP to expel

a. Enzymatic: Active site exposed to substances in adjacent solutions; metabolic pathway

b. Signal Transduction: Receptor protein with specific shape for chemical hormones

a. External messenger may cause shape change in protein that relays to inside

c. Cell-cell recognition: Glyoproteins that serve as identification for other cells

d. Intercellular joining: Membranes of adjacent proteins may hook up or attach

e. Extracellular Matrix (ECM): Microfilaments/cytoskeleton may noncovalently bond

a. Connection to proteins  maintains shape and stabilizes location

b. Can coordinate cellular changes

IV. Fluid Mosaic Model explains how cell manages tranportation of traffic

a. Polar molecules (sugar) pass slowly through a lipid bilayer + water is very slow
b. Transportation protein allows hydrophilic substances to avoid contact with lipids
a. Channel Proteins have hydrophilic channel for certain substances
i. Water molecule passage: Aquaporin channels
b. Carrier Proteins surround substance to transport; specifically for item

c. Nonpolar substances are able to dissolve in lipid bilayer and easily cross
V. Molecules have thermal motion (heal) resulting by diffusion for dynamic equilibrium

a. Diffuse down concentration gradient without any work in spontaneous mov’t

a. Diffusion over biological membrane: Passive Transport

b. Movement of water: Osmosis

i. Tonicity: The ability of a solution to cause a cell to gain or lose water

ii. Depends on concentration of solutes that cannot cross sides

c. Isotonic environment  No net movement of water; water freely flows

i. Normal in animals while flaccid (limp) in plants

d. Hypertonic: Water leaves the cell  shriveled (less solutes inside)

i. Shriveled in animals and plasmolyzed in plants

e. Hypotonic: Water enters the cell  bursts (more solutes inside)

a. Lysed in animals while turgid (normal and firm) in plants

b. Without cell walls  osmoregulation to control water balance

a. Paramecium has contractile vacuole and slows intake of water

b. Facilitated Diffusion allow molecules and ions to pass through channels

i. Aquaporins allow water into red blood cells

ii. Ion Channels (gated channels) open or close in response to stimulus

iii. Carrier proteins change shape to transport molecule

VI. Active Transport uses ATP to pump molecule against gradient for internal concentrations

a. Sodium-Potassium Pump exchanges Na+ for K+ (pushes sodium out to bring in K+)
b. Cytoplasm is negative in charge; membrane potential (-50  -200 millivolts) voltage
a. Electrochemical gradient: Chemical and electrical forces
b. Favors movement of ccations into the cell and anions out of the cell
c. Ion diffuses down electrochemical gradient; stimulated  Sodium diffusion
d. Electrogenic Pump generates voltage across membrane (transport protein)
e. Sodium-Potassium in animals; proton pumps in plants and bacteria
i. Hydrogen ions pushed out of the cell
c. Cotransport = mechanism by transporting solute; indirectly  active transport
V. Larger molecules require packaging to transport

a. Exocytosis: Cell secretes vesicle to export products

b. Endocytosis: Vesicles formed from membrane

a. Phagocytosis (eating); pinocytosis (drinking for the dissolved molecules)

 b. Receptor-mediated endocytosis (take cholesterol for membranes/steroids)

c. Lipoproteins act as ligands which bind to the receptor proteins for mass-mov’t

Chapter 8: An Introduction to Metabolism

I. Cellular respiration powers the cell by extracting energy from sugars and fuels

a. Fungi cells convert energy into light (bioluminescence)  attract pollinators

II. Metabolism: Totality of organism’s chemical reactions (emergent property of life)

a. Metabolic pathway starts where a molecule is altered in steps for a product

a. Each step catalyzed (or stopped) by a specific enzyme
b. Catabolic (breakdown) pathways: Bonds broken  energy released
i. Glucose broken down with oxygen into ATP, CO2, and H2O
c. Anabolic (biosynthetic) pathways: Energy used  builds molecules

i. Synthesis of protein from amino acids

d. Bioenergetics: Study of how energy flows through living organisms

b. Energy: Capacity to cause change; relative movement: Kinetic energy

a. Heat (thermal) energy:: kinetic energy from random mov’t

b. Potential Energy: Energy matter possessed by surface or location

c. Chemical Energy: Potential Energy release-ready in chemical reaction

i. Catabolic: Lower-energy breakdown products

ii. Energy constantly changes forms; higher elevation  more potential

c. Thermodynamic: Study of energy transformation in matter

a. System: Current matter studied; surroundings: rest of the universe in back

b. Isolated System: System unable to exchange anything with surrounding

c. Open System: Energy and matter transferred (living organisms)

d. First Law of Thermodynamics: Energy transferred, but not created nor destroyed

a. Principle of conservation of energy; in photosynthesis, light  chemical energy

e. Most energy unavoidable converted into heat and little converted into work motion

a. Second Law of Thermodynamics: Energy transfer increase universe’s entropy

b. Entropy: Measure of disorder or randomness

c. Spontaneous: Occur without input of energy; not necessarily quick

 i. For a spontaneous process, it must increase entropy in universe

f. Cells create ordered structures from less-ordered surroundings (uses outside energy)

a. Energy enters ecosystem as light and exits in form of heat

a. Entropy of system can decrease if universe (systems + surrounding) increases

III. Free energy: Part of system that performs work when temperature/pressure are uniform

a. Gibbs free energy: ΔG = ΔH – TΔS

b. ΔH = enthalpy, total energy; ΔS: Change in entropy; T: Kelvin temperature

a. Negative ΔG  Spontaneous (give up enthalpy, order, or both)

b. Such spontaneous changes harnessed to perform work for cellular actions

c. ΔG = ΔG Final State – ΔG Initial State: Only negative if loss of free energy (measure of stability)

a. Less free energy  Less likely to change and more stable; less work capacity

b. High free energy (higher ΔG) Not stable; close to equilibrium  more stable

i. Chemical equilibrium: No net change in products or reactants

ii. All changes from equilibrium will be positive  Not spontaneous

d. Exergonic: Release of energy; negative ΔG by products having less energy

a. Magnitude of ΔG shows maximum amount of work performed (limit)

b. “Standard conditions” = 1 mol of reactant and product, 25*C, 7 pH

a. 180g (1mol) of glucose make 686kcal available for work

c. Endergonic: Energy absorbed, non-spontaneous; positive ΔG; bonds made

d. Isolated systems in equilibrium do no work; products do not accumulate

a. Cells never reach metabolic equilibrium, or they would die

IV. Chemical work: Endergonic reactions, such as polymers from monomers (non-spontaneous)

a. Transport: Pumping substances against direction of spontaneous mov’t

b. Mechanical work: Beating of cilia, contraction of cells, or movement of chromosomes
a. Energy Coupling: Using exergonic process to drive Endergonic through ATP
c. ATP used ribose, adenine nitrogen base, and three phosphates to make RNA
a. Bonds broken by hydrolysis; inorganic phosphate leaves  ADP
i. ATP + H2O  ADP + [HOPO32- or {P}i ]; more energy in reactants
d. Cell uses energy released by ATP hydrolysis to drive endergonic chemical reactions
a. Overall, the coupled reactions are exergonic; ATP hydrolysis changes shape
b. The molecule receiving phosphate  Phosphoryated (more reactive)
c. ATP may non-covalently bond to motor protein to help mov’t
e. ATP is renewable; free energy  phosphorylate ADP by catabolism (ATP cycle)
 a. ~10million molecules consumed and regenerated each second
V. Enzyme is protein that catalyzes (speeds up without being consumed) reaction (-ase ending)

a. All reactions involve forming and breaking bonds; energy required

a. Changing bonds known as free energy of activation or activation energy (EA)

b. AB + CD  AC + BD; activation energy supplied in heat absorbed by outside

c. Reactants must absorb energy to change, then bonds are broken at top

b. Enzyme lowers activation energy barrier  easier to change forms/faster

a. Cannot make endergonic exergonic (ΔG unchanged)

b. Higher end than start  endergonic; lower end than start  exergonic

c. Substrates and enzyme-substrate complex are where an enzyme binds to reactant

a. The enzymes only bond to specific active site on specific protein

b. Induced fit brings chemical groups of active site into position to help ability

d. Weak interactions hold substrate in active site; “R group” converse then leave

a. Hydrogen and ionic bonds; direct participation in helping break bonds

b. Active site: template for orientation/favorable environment/stabilize

c. Saturated: Substrate leaves as another one enters; add more enzymes  speed

i. Rate of reaction determined by speed of substrate-to-product

e. Enzymes work best under optimal conditions (temperature and pH) for speed

f. Cofactors are non-protein helpers to help catalytic activity (inorganic)

a. If organic, then named coenzyme (most vitamins are considered organic)

g. Competitive inhibitors reduce production of enzymes by blocking substrates

a. Noncompetitive inhibitors bind to another part of the enzyme  alter shape

b. Toxins and poisons are irreversible enzyme inhibitors  harmful

VI. Allosteric regulation: Protein’s function at a site affected by regulatory molecule elsewhere

a. Constructed of subunits with polypeptide chins and activation site

b. Activator may stabilize a protein while inhibitor stabilizes inactive form of enzyme
c. Cooperativity: One substrate primes and enzyme to accept additional substrates
d. Pharmaceutical companies focus on regulators for higher specificity for enzymes
e. Feedback inhibition: Metabolic pathway is switched off by end product to earlier
a. Cells: Multi-enzyme organized complex; inhibition decreases product
b. Caspases: Protein-digesting enzymes that lead to cell death
 Chapter 9: Cellular Respiration, Harvesting Chemical Energy

I. Energy flows into the ecosystem as light and exits as heat

a. Autotrophs produce fuel themselves while heterotrophs eat others for energy

b. Three parts: Glycolysis, Citric Acid cycle, and oxidative phosphorylation

II. Compounds in exergonic reactions act as fuel (catabolic pathways) by releasing energy

a. Fermentation: Partial degradation of sugars without oxygen (less efficient) b.

Aerobic Respiration: Oxygen consumed as reactant with organic fuel (common)

c. Anaerobic respiration: Without oxygen; included in the term cellular respiration

a. Organic (glucose: C6H12O6) + Oxygen  Carbon Dioxide + Water + Energy

b. Carbs, fats, and proteins are also able to produce energy; energy: ATP + heat

c. Catabolism does not directly perform cellular work, but it makes ATP

d. Electron transfer: Redox reactions; loss of electron: Oxidation; gaining: Reduction

a. Electron donor (oxidized): Reducing agent (X  X+ + e-)

i. Electron receiver (reduced): Oxidizing agent (Y + e-  Y-)

e. Glucose oxidizes into carbon dioxide while Oxygen oxides into water

a. Reservoirs of electrons associated with hydrogens in main energy foods

f. Broken down in steps; electron travels with hydrogens, carried by coenzyme NAD+

a. Functions as oxidizing agent; NADH molecules represent stored energy (ATP)

b. Dehydrogenas remove pair of hydrogen from substrate (oxidizing)

i. Enzyme delivers 2 electrons and 1 proton (released as H+)  NADH

c. Hydrogen reacts with oxygen taken from organic molecule

i. Avoiding explosive reaction, electron transport chain  steps

ii. Made of proteins in mitochondria; water formed at the bottom end

d. Small amounts of energy released until oxygen is left (higher electronegativity)

i. Oxygen pulls electrons down the chain (glucose  NADH  ETC  O2)
 g. Clycolysis in cytosol breaks glucose into two molecules of pyruvate

a. Citric Acid in mitochondria matrix (cytosol of prokaryotes) finishes oxidizing

b. Energy released stored in mitochondria  ATP (oxidative phosphorylation)

i. Electrons passed as NADH; oxygen combines with hydrogen for water

ii. Phosphor. Produces 90% of AT; in prokaryotic, this happens in plasma

c. Substrate-level phosphor.: Enzyme transfers phosphate in substrate  ATP

a. “Substrate molecule” is organic molecule made in glucose catabolism

III. Glycolysis (sugar-splitting) splits glucose into pyruvate through energy investment/payoff

a. [Energy investment] Hexokinase takes phosphate from ATP and adds it to glucose
b. Phosphoglucoisomerase converts glucose into fructose
c. Phosphofructokinase adds another phosphate from ATP to the compound
d. Aldolase cleaves the fructose into two separate molecules
a. Dihydroxyacetone phosphate and glyceraldehyde-3-phosphate produced
e. Isomerase catalyzes conversion; glyceralde used as substrate  never in balance
f. [Energy payoff] Sugar oxidized by transfer of electrons and H+ to NADH+  NADH
a. Exergonic with product at high potential energy; phosphate attached
g. 2ATP produced by the phosphate groups; carbonyl converted to carboxyl
h. Remaining phosphate group relocated for next reaction
i. PEP forms by the extraction of two waters; high potential energy
j. 2ATP produced; energy stored in NADH; net gain of 2 ATPs and pyruvate forms
IV. If oxygen is present, the pyruvate enters mitochondria (in eukaryotes) [cytosol in bacteria]

a. Pyruvate converted to Acetyl CoA in three steps: [Citric Acid Cycle]

a. Pyrutave’s carboxyl group oxidized  carbon dioxide

b. Remaining two-carbon compound oxidized into acetate; NADH forms

c. Coenzyme A attaches to Acetyl A as an unstable bond  high potential energy

b. Tricarboxylic acid cycle (Krebs cycle): 1 ATP per turn; most energy is moved  NAD+

c. [Cycle] Citrate enters the mitochondria (Acetyl CoA plus the two-carbon acetyl)

d. Citrate converted to isomer isocitrate by removal/addition of water

e. Isocitrate is oxidized, chanign NAD+ to NADH; CO2 released

f. Another CO2 lost; oxidation occurs; NADH forms; coenzyme A attaches again

g. CoA displaced by phosphate group (GDP  GTP, similar to ATP)

h. Two hydrogens are transferred to FAD, making FADH2 and oxidizing the compound

i. Water added to re-arrange bonds in substrate

j. [End of cycle] Substrate oxidized, making NADH and restarting the cycle
 k. Every acetyl group reduces 3 NAD+ to NADH; ATP from oxidative phosphorylation

V. Net: 2ATP from glycolysis and 2 ATP from Krebs cycle; NADH and FADH2 have most energy

a. ETC: Protein molecules in mitochondria (plasma membrane in prokaryotes)

a. Electron carries switch between reduction and oxidation

b. Remaining electron carriers between ubiquinone and oxygen: cytochromes

i. Very electronegative; each oxygen picks up hydrogen  water

c. ETC provides 1/3 less energy for ATP when donor is FADH2 instead of NADH

d. Function: Ease the fall of electrons into oxygen (four proteins)

a. ATP Synthase uses energy of ion gradient to synthesis ATP (concentration of H+)

a. Chemiosmosis: energy stored in hydrogen ions used to drive cellular work

a. H+ ions flow down half channel (stator)

b. Bindings with rotor that spins with the membrane

c. One complete turn before entering the mitochondria matrix

d. Internal rod spins  knob below turns  ATP produced from ADP

b. ETC establishes H+ gradient; NADH releases hydrogens to cytosol

a. ATP Synthase (only way in) allows hydrogens to enter/create ATP

b. Certain parts of the TC accept and release protons and electrons

c. Proton-motive force: Hydrogen Gradient to perform work

i. Overall, 36-38 ATP produce

c. Glucose  NADH  ETC  Proton-motive force  ATP (energy mov’t)

a. Each NADH produces up to 3 ATP; inexact numbers:

a. Non-whole number ratio of NADH to ATP

b. ATP yields vary on carrier type; FAD in brain cells  lower

c. Proton-motive force drives all types of work  ATP used

b. About 40% of potential energy in glucose  ATP; rest lost as heat

c. Remarkably efficient (cars only use 25% as energy)

VI. Fermentation obtains chemical energy without ETC or oxygen; glycolysis = common step

a. Fermentation  ATP by generation at substrate-level phosphorylation (NAD+)

b. Involves regenerating NAD+ by electrons from NADH to pyruvate  reused

 a. Alcohol Fermentation: Pyruvate  Ethanol (CO2  acetaldehyde)

b. Acetaldehyde reduced by NADH to ethanol (bacteria/yeast)

b. Lactic Acid Fermentation: Pyruvate reduced by NADH without CO2

c. Pyruvate production is the common step

a. Anaerobic, pryuvate (lactic) and acetaldehyde (alcohol) are electron receptors

b. Aerobic: Oxygen from NADH in aerobic

c. Obligate anaerobes cannot survive in presence of oxygen

d. Facultative anaerobes may do both types (muscle cells)

d. Both types of cellular respiration use glycolysis = common evolutionary base

VII. Glycolysis uses many types of carbs; proteins may be used after converted to amino acids

a. Deamination: Amino acids removed from proteins

a. Fats  Glycerol and Fatty acids; glycerol  glyceraldehyde-3-phosphate
b. Beta oxidation: Fatty acids  2carbon fragments (enters as acetyl CoA)
c. One gram of fat oxidized produces 2+ times as much ATP as carbs
b. Human body needs specific molecules that are not in food; anabolic pathways
c. Feedback inhibition: End of anabolic pathway inhibits start
a. ATP concentration drops  respiration increases
b. Phosphofructokinase = allosteric enzyme inhibited by ATP/started by AMP
i. Inhibits cycle if too much ATP is produced

Chapter 10: Photosynthesis

I. Photosynthesis converts sunlight to sugars for autotrophs to produce their own energy

a. Photoautotrophs use sunlight for organic substances (producers)

a. Heterotrophs rely on eating other creatures for compounds (consumers)

II. In photoautotrophic bacteria, photosynthetic membranes = chloroplast

a. Plant leaves have green color pigment reflected from chlorophyll in chloroplasts

a. Absorbs light energy; found mainly in the mesophyll tissue inside leaf

b. Caron dioxide enters/oxygen leaves through stomata, beneath leaves

i. Water absorbed by roots and transported to leaves in veins

c. Mesophyll = 30-40 chloroplast; membranes encloses stroma = fluid inside

 d. Thylakoids: Interconnected membranes sacs separate stroma

i. Interior: Thylakoid space; stacks named grana (two membranes around)

b. Net equation: 6CO2 + 6H2O + Light Energy  C6H12O6 [glucose] + 6O2

c. Chloroplast splits water  oxygen and hydrogen; oxygen released from water, not CO2

d. Electrons lose potential energy down ETC toward electronegative oxygen

a. Mitochondria with energy  ATP; electrons in water + hydrogen +CO2  Sugar

b. Electrons increase in PE in sugar; endergonic reaction powered by light

e. Parts: light reaction (water  oxygen) and Calvin Cycle (carbon dioxide  sugar)

a. Split water: electrons, H+ ions stored in NADP+ with oxygen as by product

b. Reduced to NADPH by adding pair of electrons with hydrogen ion

i. Chemiosmosis changed ADP  ATP by photophosphorylation

ii. Light energy  NADPH (reducing power) and ATP (energy of cells)

c. Carbon fixation: Carbon dioxide taken from air to make organic compounds

i. Consumes the ATP and NADPH; light independent (dark/Calvin cycle)

III. Light: Electromagnetic energy (radiation) in waves; distance between crests: Wavelength

a. Range of radiation: Electromagnetic Spectrum; Visible Light: 380-750nm detectable

a. Light consist of discrete particles (photons); Shorter wavelength = more energy

b. Pigments absorb visible lights; measured by spectrophotometer; visible = reflected

a. Graph from pigment absorption vs. wavelength = absorption spectrum

b. Chlorophyll  directly in reactions, accessory chlorophyll b, and cartotenoids

c. Violet-blue and red work best for the plants; green is the least effective

d. Confirmed by action spectrum test for effectiveness of radiation

e. Chlorophyll b = different absorption of color (a: blue-green; b: olive-green)

f. Other Pigments: Cartenoids (photoprotection: absorb/dissipate excess light)

c. Absorbs photon  electrons jumps ground  excited state (more potential energy)

a. Isolated pigments electrons drop down  heat; fluorescence photons released

d. Photosystem has protein reaction-center complex with light-harvesting complex

a. Primary electron acceptor accepts electrons (reduced); on thylakoid

b. Photon excites electrons  passed to center (light  chemical energy)

 c. PS II (P680: Red) and PS I (P700: Far Red) [Named by discovery order]

e. Linear Electron Flow: Path of electrons through photosytems and membrane

a. Photon light hits and electron, and then energy relays a nearby electron

b. Energy transferred to primary electron receptor (P680+)

c. Water split by enzyme; electrons replace the ones that are relayed; O2 formed

d. Photoexcited electrons pass down ETC made up of plasto-quinone/cyanin

e. Exergonic fall provides energy for ATP used in chemiosmosis

f. Light excites P700+ and accepts the electrons from PS II to replace the gap

g. Redox reactions from PS I down another ETC (no ATP); NADP+  NADPH

f. Cyclic Electron Flow (PS I0): Electrons sent to chlorophyll: ATP, but no NADPH

a. Purple Sulfur bacteria use PS I, but not PS II = Evolution

g. Mitochondria get electrons from organic oxidized molecules; chloroplast use water

a. Both use chemiosmosis, but animals use food while plants use light energy

b. Mitochondria pumps protons outward but serves as reservoir of hydrogen ions

c. Thylakoid membrane pumps protons from stroma into thylakoid (H+ tank)

i. Proton (H+ or pH) gradient across thylakoid is more basic in stroma

IV. Calvin cycle anabolic; glyceraldehyde-3-phosphate (G3P) produced in C3 Plants

a. Rubisco (most abundant protein on Earth) adds CO2 to 5-carbon sugar unstable/split

a. Known as Phase I: Carbon Fixation; next step (phase II): Reduction

b. Phosphate from ATP added; electrons from NADPH  G3P (3 CO2: 6 G3P)

a. Fifteen carbons  18 carbons and 6 G3P; one molecule exits

c. Regeneration of RuBP: 5 G3P re-arranged with 3 ATP to restart cycle

a. A total of 9 ATP used and 6 NADPH for 3 CO2

V. Closing stomata to avoid dehydration  limit access to CO2  photorespiration

a. Rubisco uses O2 instead of CO2: Photorespiration on hot, sunny days (consumes ATP)

a. “Metabolic relic from when there was more carbon dioxide than oxygen”

b. C4 Plants produce four-carbon sugar as initial product (grass family/corn)

a. Bundle-sheath cells are tigtly packed around veins

b. Loose mesophyll cells; PEP carboxylase changes CO2  4-carbon sugar

 c. No affinity towards oxygen; mesopyll export oxaloacetate to bundles

d. CO2 released  enters Calvin cycle; pyruvate made by ATP

i. Cyclic electron cycle produces extra ATP; no PSII

c. Carassulacean Acid Metabolism (CAM Plants): Organic acids stored during night

a. In morning, CO2 released from acids to be made into sugar

d. Sugar made used for chemical needs and carbon skeleton (50% for fuel)

a. Starch stockpiled in roots, seeds, and fruits.

Chapter 11: Cell Communication

I. Cell communication allows multicellular organisms to function by nerve impulses/hormones

II. Two cell sexes: a and  cells that secret signaling hormones to the other specific receptors

a. Cells bind towards each other  fusion (mating) into a/ cells (gene combination)

b. Signal Transduction Pathway: Surface signals changed in steps  cellular response

a. First evolved in prokaryotes/single-cell eukaryotes + adopted later

b. Quorum Sensing: Bacteria uses signaling molecules to sense cell densities

i. Coordinated biofilms of aggregations of cells for specific function

c. In direct cell junction (gap/plasmodesmata), signals in cytosol pass freely

a. Adjacent cells: easy communication; cell-cell recognition in animals

i. Involves membrane-bound surfaces/ immune and embryonic

b. Local regulators: Short distance to communicate with neighboring cells

c. Paracrine signaling: growth factors in animals cause nearby cells to divide

i. Signal hormones released into extracellular fluid to other cells

d. Synaptic signaling: electrical chemical signal along nerve neurotransmitters

e. Long distance: Hormones (endocrine) travel in circulatory system to cells

i. Plants (growth regulators) move through cells or diffuse in gas

d. Reception: Cell’s detection of signaling molecule outside the cell (receptor)

a. Transduction: Binding changes receptor protein  transduction

 i. Change to initiate a specific cellular response (relay molecules in path)

b. Response: Cell reacts and starts the specific cellular response

III. Ligand: Molecule that binds to another molecule of opposite sex  change in shape

a. Signal receptors: Plasma-membrane protein; water-soluble/large ligands

b. Membrane-receptors: G protein-coupled, tyrosine kinases, and ion channel receptors

c. Intracellular receptors in cytoplasm/nucleus; hydrophobic chemical messangers

a. Steroid/Thyroid Hormones/NO to pass through phospholipids

b. Hormones attached  Active form of receptor protein into nucleus  genes

c. Transcription factors transcribe genes into mRNA  proteins from ribosomes

d. G protein-coupled receptor uses G protein (protein with GTP) with same structure

a. Seven  helixes spanning membrane; GDP bonded to G protein  inactive

b. Molecule binds to extracellular side; GTP displaces GSP and activates protein

c. G protein binds to an enzyme, changing shape/activity/cellular response

d. GTP hydrolyzed to GDP by GTPase; G protein inactive and recycled

i. Common usage in medicines (60% of medicines); toxins interfere

e. Receptor tyrosine kinase: kinase catalyzes transfer of phosphate to tyrosines

a. Receptors as individual polypeptides (tyrosines) from one protein

b. Molecule binding  dimerization of two-receptor polypeptide into a dimer

c. Phosphate from ATP added to the dimer; transduction pathway signaled

d. Inactive relay proteins bind to Phosphoryated tyrosine  active protein

e. Ligand-gated ion channel Allows passage of molecules if the gate is open

a. Ligand binds to the ion channel and specific ions flow into the cell

b. Cell activity changes; when ligand leaves, the channel closes (nervous system)

a. Voltage-gate ion channels allow for electrical signals to travel

IV. Multiple steps amply signal  coordination/more proteins active/more regulation

a. Enzyme that transfers phosphate groups from ATP to protein: protein kinase

b. “Phosphorylation cascade” has signal relied through proteins by adding phosphate

a. Proteins phosphatase (PP) catalyze removal of phosphate group  inactive

 b. Dephosphorylation  inactive protein kinase to turn off pathway; reusable c. Second
messengers: Water-soluble non-protein ions that spread out by cell diffusion

a. Cylic AMP and calcium Ca2+ ions help relay the messages; very small

d. Cyclic AMP made by adenylyl cyclase: ATP  cAMP; signals broadcast to cytoplasm

a. Phosphodiesterase  AMP; camp activates Protein Kinase A

b. Inhibitory G-protein systems inhibit adenylyl cyclase

c. Cyclic GMP increases blood flow to heat muscle (used in Viagra)

e. Calcium: Cell contractions, secretion, and cell division in animals; common

a. Used in G-protein and tyrosine pathways; more outside cell than cytosol

b. Actively transported out of cell; imported to ER by protein pumps

c. Inositol triphosphate (IP3) and diacylglcerol (DAG) leads to calcium release

d. Produced by cleavage of phospholipids by Phospholipase C (G-protein active)

i. Calcium could be a “third messenger” in the cell

V. Signal  Regulate protein synthesis by transcription of mRNA in nucleus (gene regulations)

a. Regulate activity of protein rather than synthesis and cell shape

b. Mating factor activates signaling kinase that affects growth of microfilaments

a. Initiate cell-division include growth factors (plants) and hormones (animals)

c. Signal amplified and regulated if steps; termination of the signal at the end

d. Enzyme cascade amplify response; proteins stay in active form to produce substrates

e. Different cells have different proteins  two cells may respond differently to signals

f. Scaffolding Protein: Large relay proteins holding other relay protein

a. Once the scaffolding protein is active, all attached proteins are activated

g. Molecular change in signaling pathways must be limited in time (locked = bad)

a. Reversibility of change that signal produces; molecules turned inactive

VI. Apoptosis: Controlled cell suicide (DNA chopped up/organelles engulfed in vesicles)

a. Scavenger cells digest; protect neighbors from leaking of cell’s content

b. Protein activity regulated, not synthesis; proteases of apoptosis: caspases

c. Outside signals cause apoptosis; inside alarms caused by nucleus and ER

a. Excessive protein misfolding and damaged DNA  Induced death

 Chapter XII: The Cell Cycle

I. Reproduction, or cell division, separates life/nonliving; “omnis cellua e cellua”: Cells from cells

a. Part of cell cycle where parent cell divides into two daughter cells; all living creatures

II. Most cell division: DNA (genome) into two identical daughter cells (mitosis)

a. DNA inside chromosomes in nucleus with somatic cells (non-sexual)

a. Somatic cells: 46 chromosomes; 2 sets of 23; offspring receive all

b. Gametes (eggs/sperm) have only 23 in humans

i. Eukaryotic chromosomes made of chromatin: DNA and protein

ii. Visible during cell division (dark mass appears in center)

b. Condense after DNA duplication: visible under LM; duplicated = two sister chromatin

a. Identical DNA; attached along protein side (cohesins): sister chromatid cohesion

i. Narrow waist at centromere; sides of centromere: “arms”

ii. Mitosis: Division of nucleus by separation of sister chromatin

i. Cytokinesis: Division of the Cytoplasm

i. Meiosis: Nonidentical daughter cells in gonads with half amount

III. The Mitotic phase (M) is shortest part of cell cycle; longest: interphase (90% of time)

a. Interphase: G1 phase; S phase (synthesis); G2 phase; cell produces proteins

a. Chromosomes duplicated in S phase: grows, duplicates, then starts division

b. S Phase long; Mitosis: prophase, prometaphase, metaphase, anaphase, telophase

a. Depends on mitotic spindle; forms in cytoplasm during prophase

b. Fibers of microtubles polymerize/depolymerize by adding/removing units

c. Located within centrosome (microtubule-organizing center); animals only

i. Non-essential; centrosomes replicates in interphase

ii. End of prometa: two centrosomes at opposite ends of the cell

iii. Spindle: Aster (radial array) extends, centrosomes, and microtubules

d. Kinetochore: Proteins associated with chromosomal DNA at centromere

i. Kinetochore microtubules attach at center

ii. Imaginary midway plane: Metaphase plate

e. Microtubules elongate and interact with opposite poles (“polar”)

 a. In anaphase, the enzyme cleaves the chromosomes

b. Motor proteins on kinetochore depolymerize ends (“Pacman”)

c. Chromosomes “reeled in” by motor proteins at spindle poles

f. Nonkinetochore elongate cell during anaphase

c. In animals, cleavage at cleavage furrow use actin/myosin to pinch the center

a. Plants have vesicle from Golgi move along center and make cell plate

b. Cell plate fuses with plasma membrane and form two daughter cells

d. Bacteria asexually produce by binary fission without mitosis; eukaryotes do

a. Single bacterial chromosomes in circular DNA; anchored by proteins

i. Split at origin of replication; origins move towards opposite ends

b. Elongates: Bacteria twice-normal size and plasma membrane grows inward

c. Dinoflagellates (chromosomes attach to envelope); protist

i. Microtubules pass through holes  intact; binary fission

d. Diatoms and yeast: Spindle within nucleus; two daughter nuclei

i. Most euaryotes have spindles form outside nucleus

e. Mitosis evolved from simple prokaryotes; larger cells  mitosis evolved

IV. Mitotic Division of Cell

a. G2 Interphase: Two centrosomes formed; two centrioles; chromosomes not yet visible;

a. Nuclear envelope bounds nucleus; multiple nucleolus

b. Prophase: Nucleoli vanish chromosomes appear visible under LM; chromatin cohesion

a. Mitotic Spindle forms; centrosomes start to move away from each other

c. Prometaphase: Nuclear envelope vanishes; microtubules connect to kinteochore

d. Metaphase: Longest substage; chromosomes at opposite poles; metaphase plate

e. Anaphase: Shortest; cleave sister chromosomes  separate chromosomes

a. Move towards opposite ends; kinetochore microtubule shortens

f. Telophase: Two daughter nuclei with envelopes; less condensed; mitosis over

g. Cytokinesis: Cleavage Furrow in animal cells to make two separate cells

V. Skin cells divide while liver cells rarely divide; specialized nerve cells do not divide

a. Cell cycle driven by signaling molecules in cytoplasm; cell cycle control system
 a. Molecules that trigger and coordinate key events in cell cycle

b. Checkpoints act as “stop/go” signals which signal transduction

i. Found at G1, G2, and M phases; G1 = “Restriction point” (important!)

c. Most cells in G0 phase: “Non dividing state” and some cells “called” to divide b.
Protein kinase phosphorylate proteins; attach to cyclin to be active

a. Cyclin-dependent kinases (Cdks) changes and falls in concentration

b. Fluctuation of MPF, corresponds to peaks in cyclin concentration

i. “M-phase (maturation) promotion Factor”  M phase past G2

ii. Direct kinase and indirect by activating other kinase

iii. Noncyclin MPF, persist in cell until S and G2 phase

c. Three Cdk proteins; anaphase does not start until properly attached to plate

i Kinetochores unattached to spindles: Sister chromatins remain together

ii. Ensures that daughter cells have exact amounts of chromosomes

d. Cells fail to divide if the nutrients are too low; growth factor simulates division

e. PDGF made by blood cell platelets  division of fibroblast; passes G1

f. Density-Dependent inhibition: Crowded cells stop dividing

i. Anchorage dependence: division by attaching to substrate

ii. Cancer cells exhibit neither of the above

c. Cancer cells divide excessively and invade other tissues

a. Divide when growth factors depleted; random division in cycle

b. Transformation: Normal cell  Cancer cell; cell targeted for destruction

c. Benign Tumor: Cells remain at original site (removed by surgery)

d. Malignant tumor: Invasive to impair multiple organs

i. Unusual number of chromosomes; changes in surface

ii. Signal molecules secreted cause blood vesicles -> grow toward tumor

e. Spread of cancer cells form original sites: metastasis

f. Taxcol freezes mitotic spindle and prevents cancer from dividing (Yew tree)

Chapter XIII: Meiosis and Sexual Life Cycle

I. Trait transmission over generating called inheritance (heredity); variation in generation

 a. Genetics: study of hereditary, meiosis (gamete division), fertilization (egg-sperm)

II. Coded information: genes from nucleotide sequence; synthesis enzymes/proteins

a. Reproductive gametes transmit genes to offspring packed in chromosomes (nucleus)

a. Locus: specific location on chromosome of gene

b. Asexual reproduction: Single organisms produces identical clone (“budding”)

a. Sexual Reproduction: two parents give unique combination to offspring

III. Life Cycle: Generating-generating sequence; somatic cells: normal 46 chromosomes

a. Visible with LM during mitosis; karyotype: chromosomes arrangement (size)

a. Homologous chromosomes (homologs) same chromosomes = same traits

b. Females: XX; Males XY (sex chromosome) while other 22 pairs = autosomal

c. Two sets of chromosomes: diploid (2n = 46); DNA synthesis: replication

i. Gametes = haploid cells (n = 23); 22 automal + one sex chromosome

b. Eggs + sperm = fertilization: zygote formed and then uses mitosis to form

a. Germ cells in gonads are only gametes w/o mitosis (ovaries/testes)

b. Meiosis reduces chromosomes from 2  1: counterbalance doubling

c. Gametes = only haploid; zygote grows by mitosis; plants use alternation of generation

a. Multicellular sporophyte (diploid) produces haploid spores

b. Haploid doesn’t fuse but mitotically divides  haploid gametophyte

c. Fusion of haploid at fertilization: diploid zygote (cycle retarts)

d. Algae/fungi use meiosis for haploid cells that then divide by mitosis

a. Only diploid stage found in single-celled zygotes

IV. Meiosis I, II creates four daughter cells with half as many chromosomes

a. Prophase I: Chromosomes condense; crossing over (exchange of DNA segments)

a. Chromosomes in pair move slightly apart; one+ chiasmata (crossing occurs)

b. Homologs from sister chromatid cohesion; replicated chromosomes

b. Metaphase I: Homologous chromosomes on metaphase plate facing poles

a. Chromatids of homologs have kinetochore microtubules facing poles

c. Anaphase I: Protein breakdown  homologs separate; move to spindle apparatus

d. Telophase I/Cytokinesis: Each cell has complete haploid; cleave furrow/cell plate
 a. No replication occurs; homologous chromosomes completely separated

e. Prophase II: Spindle apparatus with chromosomes moving to center plate

f. Metaphase II: Positioned on metaphase plate; not genetically identical cells

a. Kinetochores of sister chromatid attached to microtubules from other poles

g. Anaphase II: Breakdown of proteins holding sister chromatids  move to poles

h. Telophase II/Cytokinesis: Nuclei forms/haploid set of chromosmes/four cells

V. Synapsis and cross over: Synapsis with zipper-like protein (synaptonemal complex)

a. Crossing Over where genetic rearrangement occurs between nonsisters

b. Chiasma in physical result of crossover at the new region

c. Chromosomes on metaphase as homologs (meiosis) while individual at mitosis

d. Anaphase I: replicated chromosomes move to poles; mitosis: sisters separate

a. Protein cohesions stick sister chromatids

b. Anaphase I: Cleave at arms; anaphase II: cleaved at centromeres  separate

c. Protein shugoshin protects cohesins from cleavage at centromere at meiosis I

d. Meiosis I: reductional division; Meiosis II: Equational division (separate sisters)

VI. Mutation creates different versions of genes (alleles); meiosis/fertilization = variations

a. Sexual reproduction: random orientation of homologous pairs at metaphase I

a. Independent Assortment: independent paring in sorting of metaphase division

b. 223 or 8.4 million combinations of chromosomes in haploid

b. Recombinant chromosomes: individual chromosomes w/ DNA (different parents)

a. Chromosomes have 1-3 crossovers typically; chiasma forms as result

b. Anaphase I: Release of cohesion at arms  homologs separate

c. Anaphase II: Release of cohesion at centromeres: sister chromatids separate

c. 70 trillion diploid combinations by random fertilization

a. Best suited individuals to environment leave the most offspring

Property Mitosis Meiosis

 DNA Replication Interphase Interphase before Meiosis I

Divisons One Two

Synapsis of homologs N/A Prophase I
Daughter Cells Two identical diploid Four different haploid
Role Specific cellular functions Gametes

Chapter XIV: Mendel and the Gene Idea

I. “Blending Hypothesis” = genetic material from parents mix; predicted uniform population

a. “Particulate” inheritance hypothesis: genes = discreet units (retain own identity)

II. Inheritable feature that varies among characters – character; variant = trait

a. Mendel (Austria) at a monastery studied crossbreeding peas; high varieties

a. Short generation/large offspring/controlled mating between plants

b. True-breeding: Self-pollination to produce same variety as parents

c. Mating (crossing) of two true-breeders: hybridization

i. Parents: P generation while hybrid offspring: F1 generation

ii. Allowing F1 hybrids to self-pollinate: F2 Generation

b. Dominant (purple) traits overshadow recessive (white) traits; 3:1 ratio in trials

a. Independent assortment: Random mating in-group

b. Alternative genes account for variations in character (alleles)

i. Two inherited alleles, one from each parent

c. Two alleles at locus: dominant  appearance; recessive masked

d. Law of segregation: two alleles for character separate during gamete formation

a. Separated end up in different gametes; Punnett square: predict outcomes

e. Homozygous: Identical genes for traits; heterozygous: different alleles for gene

a. Heterozygote =\= true breeders since gametes have different alleles

b. Phenotype: Physical appearance; genotype: genetic makeup (masked)

f. Breeding organism of unknown genotype with recessive homozygous = testcross

g. Monohybrids: heterozygous for one trait (monohybrid cross); heterozygous = 3:1

a. Dihybrids: Heterozygous for two characters: (YyRr); hetero = 9:3:3:1

b. F1 plants exhibit dominant phenotypes (yellow/round)

 h. Law of independent assortment: Alleles isolate independently of other alleles

a. Genes located near each other: inherited together with more complexity

b. Dominant: purple, axial, yellow, round, inflated, green, tall

II. Multiplication rule: Multiply probabilities together for total; use Punnett Square

a. Heterozygous plant: dominant from either male/female but not from both

a. Addition Rule: Mutually exclusive events: add together

III. Mendelism: simple traits either dominant or recessive; pod-shape uses two genes

a. Complete dominance has one allele overshadow the other alleles

a. Incomplete dominance: traits blend for unique combination of color

b. Codominance: Two alleles affect phenotype in separate ways

i. Both traits exhibited in heterozygote; no overshadowing

c. Dominant does not subdue recessive; no interaction between genes

d. Tay-Sachs = inheritable where lipids accumulate in brain impaired

i. Incomplete dominance at biochemical level  codominant

ii. Heterozygous does not lead to disease symptoms

b. Polydactyly: multiple fingers or toes; very low frequency

c. Blood: IA, IB, I; IAIA = A; IA IB = AB, IAi = A; IBi = B; ii = O (letters = carbs on surface)

a. AB = universal receiver; O = universal donor; must be compatible

d. Most traits have multiple phenotypic effects: pleiotrophy (cystic fibrosis/sickle)

a. Gene that determines flower color also affects outer coating color

e. Epistasis: gene at one locus alters expression of another gene at a second locus

a. Quantitative characters: traits vary in continuum (gradations) in pattern

i. Indicate polygenic inheritance: additive effect of multiple genes

ii. Skin color controlled by at least three separately inherited genes

f. Environment also affects genotypes; nutrition/location helps determine traits

a. Norm of reaction: phenotypic range with respect to environment

b. Multifactorial: factors (genetics/environment) influence phenotype

c. Phenotype refers to entirety of all physical aspects and behavior

d. Mendel’s two laws: segregation and independent assortment

V. Collecting information about family history into family tree: pedigree

a. Square: male::circle: female; lower lines show generations; shaded = effected

b. Allele that causes a genetic disorder codes for malfunction or no protein at all

a. Contains trait but not expressed: carrier of trait (heterozygous)

b. Consanguineous: same ancestor, more recessive traits likely to be passed

c. Tay-Sachs extremely high in Ashkenazic Jews; higher than Sephardic

c. Most deadly: cystic fibrosis: extracellular chloride: thick mucus  poor absorption

a. Disables some antibodies; chronic bronchitis; most die before 5th birthday

d. Africa: Sickle-Cell disease: easily tired out; pleiotrophy from homozygous

a. Heterozygous healthy, but suffer from prolonged oxygen reduction

b. Common with malaria; achondroplasia: dwarfism; dominant trait

e. Hunington’s Disease: degeneration of nervous system; no effect until ~35yrs

a. Locus of chromosome 4; dominant; affects 1/10,000 people in US

f. Multicultural cultural disorders: heart disease, diabetes, bipolar, alcoholism…

a. Amniocentesis determines if child has Tay-Sachs during pregnancy

b. 10mL of amniotic fluid with fetal cells taken for examination

i. Karyotyping to observe the chromosomes

c. Chorionic villus sampling (CVS) also works as an alternate

i. Tube through uterus and suctions out tissue from placenta

ii. Ultrasound uses sound waves; fetoscope uses scope to view

 9:3:3:1 ratio

Chapter XV: Chromosomal Basis of Inheritance

I. Mendel’s “hereditary factors” located on loci of chromosomes; visible with fluorescence dye

II. Chromosome theory of inheritance: Mendelian genes have specific loci on chromosomes

a. Segregation: two alleles separate during gamete formation randomly

b. Independent assortment: alleles on nonhomologs assort independently of others

a. Meiosis I: separate homologs; meiosis II: separate sisters (~mitosis)

c. Fruit fly: prolific breeders with four pairs of chromosomes (3 autosomal/1 sex)

a. Phenotype most common in natural populations: wild type

i. Alternates: mutant phenotype due to genetic changes

ii. Genes take symbol from first mutant (non-wild type)

b. Specific genes carried only on specific chromosomes

i. Sex chromosomes = unique inheritance pattern

III. Females donate X while males donate either X or Y (males = determining factor)

a. Y chromosome short; short end segments allow Y to behave like homologs with X
 a. 50-50 chance of male/female; sex characteristics: 2 months as embryo

b. SRY: sex-determining region of Y; codes for proteins that regulate genes

i. No SRY: gonads develop into ovaries; half of Y genes = testis

b. Gene on sex chromosomes: sex-linked gene; fathers pass alleles to daughters

a. Mothers pass alleles to both; Y chromosome does not give any alleles

b. Any male with recessive will express; females need on both Xs

c. Colorblind female: mother had gene and father was colorblind

d. Duchene MD: abse nce of dystrophin on X chromosome  weak muscles

e. Hemophilia: absences of proteins for clotting  internal bleeding

c. Barr body: inactive X chromosomes  traits not expressed in females

a. Since females have 2 Xs, one X is shut down

b. In ovaries, Barr bodies re-activate so that gametes have active X

c. Mitosis continues to produce one active X and one inactive X

d. Heterozygous: Half of cells express one while half express other (mosaicism)

i. Inactivation of X: modify DNA and attachment of methyl to N-bases

e. XIST is active in Barr-bodies to produce RNA to cover and block X

IV. Genes on same chromosomes inherited in genetic crosses: linked genes

a. Chromosomes = thousand of genes; in flies, body color/wing size inherited together

a. Genetic recombination: production of offspring with traits not in parents

b. Parent types express phenotypes in parents; recombinant express different traits

a. 50% frequency in testcross: two separate genes that are unlinked

c. Crossing-over accounts of recombination of linked genes (prophase I)

a. Recombination frequency related to the distance between linked genes

d. Genetic map: ordered list of genetic loci along chromosome

a. Father apart: higher probability of cross over/higher recombinant frequency

b. Larger distance: more points between where crossover can occur

i. Used to map genes; genetic map based on frequency: linkage map

c. Gene distance in map units where one = 1% recombination frequency

i. Known today as centimorgans; frequency: (recombinant/total)

 d. Maximum value of 50%  genes on different chromosomes

i. Physically linked, but genetically unlinked by recombinant

e. Cytogenetic maps locate genes with respect to chromosome features

V. Nondisjunction: fail to separate homologs in meiosis I or sisters in meiosis II

a. Abnormal number of chromosomes: aneyploidy in zygote

a. Cell missing chromosome (2n-1) = monosomic

b. Cell has extra chromosome (2n+1) = trisomic (Down’s = trisomy 21)

c. Polyploidy = more than two sets of chromosome (triploidy/tetraploidy)

i. Triploidy: Fertilization of abnormal nondisjunction egg + sperm

ii. Tetraploidy: 2n zygote fails to divide and replication

iii. Common in the plant kingdom

b. Deletion: removal of genetic segment (fragment lost)

a. Duplication: Deleted segment attaches to sister chromatid (double segment)

b. Inversion: Chromosomal fragment attaches in reverse orientation (reverse)

c. Translocation: segment form one chromosome switched with a nonhomolog

d. Products of nonreciprocal crossover = deletion in one and duplication in other

i. Large deletion: lethal to organism or strong abnormality

c. Syndrome: set of traits that are characteristic of aneuploidy; high in humans

a. Down Syndrome: trisomy 21; nondisjunction during meiosis I

b. Short stature; heart defects; susceptibility to leukemia and Alzheimer’s

i. Age-dependent abnormality in meiosis checkpoint

d. Klinefelter: Extra sex chromosome (XXY in males, XXX in females)

a. Extra X as Barr Body (inactive); tall males with large chest/sterile

b. Turner syndrome: Monosome X; sterile since sex organs do not mature

e. “cri du chat” = deletion of chromosome 5: retardation/small head

f. Chronic Myyelogenous leukemia (CML): Translocation in mitosis

i. Chromosome 22 exchanged with 8  Philadelphia chromosome

VI. Genome imprinting: variation in phenotype depending on allele is from male or female

a. Imprinted on autosome; silencing of one allele of an imprinted gene

 a. Imprinted gene expressed in all cells; old imprints “erased” by new imprints

b. Only paternal growth factor in Igf2 expressed

c. Methyl groups added to cytosine nucleotides of alleles

i. Methylation may activate expression of genes (insulin gene)

d. Genomic imprinting only in small fractions in mammalian genomes

i. Most imprinted genes critical for embryonic development

e. Extranuclear (cytoplasmic) genes located outside nucleus (mitochondria/cholorplast)

a. Organelle genes not distributed to offspring with rules for meiosis

i. No Mendelian inheritance; zygote receives all plastids egg

ii. Egg cytoplasm contributes while pollen gives a haploid

b. Mitochondrial myopathy: weakness and intolerance of exercise

c. Leber’s hereditary optic neuropathy: blindness from four mutations

Chapter XVI: The Molecular Basis of Inheritance

I. 1953: Watson/Crick make double-helix DNA model with tin/wire; DNA = inheritable substance

a. Genome: DNA in 46 chromosomes + mitochondria genes; DNA replicated

II. DNA: Protein + protein; initially, protein was believed to be inherited; bacteria/virus first studied

a. Griffith studied Streptococcus pneumoniae (pneumonia bacteria): two strains (variety)

a. One pathogenic (disease-causing), one nonpathogenic (harmless)

b. Heat killed pathogenic/mixed with nonpathogenic  pathogenic [genetic change]

i. Transformation: Change in genotype/phenotype from external DNA

c. Avery studied DNA, RNA, and protein; transformation agent: DNA

d. Virus Bacteriophage (phages) infect bacteria; virus infects cell  reproduce

e. T2 (DNA/protein) infects E. coli; DNA injected (nucleic acids = hereditary)

b. DNA = Phosphate, deoxyribose sugar, and nitrogen base (A, T, C, G)

a. Chargaff’s rule: Adenine = same concentration as Thymine; guanine: cytosine

c. Structure studied under X-ray crystallography  DNA helical/spacing of bases

a. Two strands: Double Helix shape; phosphate-sugar backbone; base rungs

i. Bases connected by Van Der Waals forces (hydrogen bonds)

 b. Nitrogen bases hydrophobic = pushed to inside; full turn every .34nm

c. Thymine/cytosine = pyrimidine (one); adenine/guanine = purines (two)

i. Griffith experiment: if no transformation  mouse would have lived

III. Two strands complimentary; information stored to reconstruct other; each strand = template

a. Conservative Model: Parental strand acts as template/re-associates: original persists

a. Semiconversative: parental strand split/synthesis of complimentary strand

b. Dispersive Model: Each strand of daughter DAN contains mix of old/new DNA

i. Semi-conservative model = accurate; DNA copies extremely quickly

b. Replication of DNA at origins of replication (short sections with specific sequence)

a. Proteins attach to DNA/separate strands/opens replication “bubble”

i. Occurs until entire molecule copied; multiple bubbles in eukaryotes

b. Replication Fork: Y-shaped region where parental strands unwound

c. Helicases: Enzymes that untwist double helix at forks  two strands

d. Single Strand Binding Proteins stabilize unpaired DNA strands

i. Untwisting: tighter twisting/strain on replication fork ahead

e. Topoisomerase: Breaks, swivels, and rejoins DNA strands

f. Unwound sections = template for the synthesis of new complimentary strand

g. Synthesis DNA enzymes do NOT initiate synthesis of polynucleotide

i. Add nucleotide to ends of already existing chain paired with template

h. RNA chain: Primer made by primerase where chain starts from one nucleotide

i. New DNA will start from 3’ end of RNA primer

c. DNA polymerases catalyze synthesis of DNA (add nucleotides to previous chains): III, I

a. Require primer/template strand/complementary DNA nucleotides

b. Nucleotide added to DNA  nucleoside (sugar/base) with three phosphates

c. Nucleoside triphosphate (dATP) used in both; only different: sugar used

i. DNA has one less oxygen its sugar than RNA

ii. Joining: Pyrophosphate (P-P) hydrolyzed  coupled for polymerization

d. Antiparallel: DNA oriented in opposite directions; DNA polymerase adds to 3’ end

a. DNA elongates 5’->3’; DNA strand made by DNA pol III at fork: leading strand
 b. DNA strand in direction away from replication fork: lagging strand

i. Segments: Okazaki fragments synthesized discontinuously

c. DNA pol I (polymerase I) replaced RNA nucleotides with DNA versions

i. Added to 3’ end of the adjacent Okazari fragments

d. DNA ligase joins sugar-phosphate backbone of Okazari fragments

e. Various proteins in DNA replication form large “DNA replication machine”  efficient

a. Primerase: molecular break (slows progress of replication fork/strands”

b. DNA moves throughout the complex; DNA replication complex stands still

f. DNA polymerase proofreads nucleotide against template as soon as it is added to 3’

a. Polymerase removes mismatched nucleotides/resumes synthesis

b. Mismatch repair: Enzymes replace poorly paired nucleotides from error

i. Defect: alter genetic sequence/cancer; carcinogens may cause mutations

ii. Each cell continuously monitors/repairs genetic material

c. Nuclease cuts specific section of the DNA; gap filled by correct nucleotides

i. DNA polymerase/DNA ligase; nucleotide excision principle

d. Thymine Dimers cause DNA to buckle/interfere in replication (distorts molecule)

i. Disorder xeroderma pigmentosum: problem with repair/sensitive to light

g. DNA polymerase adds nucleotides to 3’ end; no way to complete 5’ ends of daughter DNA

a. Repeated rounds of replication: shorter DNA molecules with “staggered” ends

b. Telomerase (without genes) has multiple repetitions of nucleotide sequence

i. Protects genes; stops ends from activating system to monitor DNA damage

c. Circular prokaryotic DNA (no end)  does not get shorter with replications

d. Telomeres postpone erosion of genes near ends of DNA; does not stop shortening

e. Shortening of telomeres = ageing process of tissues/organism

f. Telomerase catalyzes lengthening of telomeres in eukaryotic germ cells

i. Restores length/compliment for shorting during replication

ii. Normal shortening avoid cancer (limits number of somatic division)

g. Telomerase in cancerous cells  stabilize telomerase  cancer persists

IV. Main component in bacteria genome: one double-stranded, circular DNA with some protein
 a. Bacterial chromosome found within nucleoid region

b. DNA: plain helix in shape; 2nm across; negative charge form phosphate

c. Histones: First level of DNA packing in chromatin; four types; positive

d. Nucleosomes: nucleosome (basic unit) connected by linker DNA

a. Histones leave DNA during DNA replication

e. H1 Histone involved in 20-nm fiber; interactions of Nucleosomes/Linker DNA

f. Looped domains rich in topoisomerase (300-nm)

g. Metaphase chromosome (specific genes in specific spots)

V. As cell prepares for mitosis, chromatin coil and condense: chromosomes visible with LM

a. Interphase chromosomes has looped domains attached to nuclear lamina/nuclear matrix

b. During interphase, centromeres/telomeres, somewhat condensed heterochromatin

c. Less compacted = euchromatin; loose packing of euchromatin = genes easy to express

d. DNA wrapped around histones; histones change  change in chromatin organization

 Chapter 17: From Gene to Protein

I. DNA  specific traits from proteins/RNA molecules in protein synthesis (genotype/phenotype)

a. Gene Expression: DNA determines synthesis of protein (transcription/translation)

II. Garrod: genes pick phenotypes through enzymes; inherited disease == inability to make enzyme

a. Beadle/Tatum’s one gene-one enzyme hypothesis: function of genes = produce enzymes

a. Mutants in pathway (no enzyme)  pathway stop; genes regulate chemical event
 b. Not all proteins = enzymes/proteins constructed by polypeptide chains, made from genes

a. Alternative splicing: eukaryotic genes code for closely related polypeptides

b. Some genes translated into RNA w/o translating to protein; keratin = hair

c. Genes = protein instructions; DNA/RNA: four types of nucleotides (different bases)

a. Specific order (primary)  codes for amino acids (conversion of “languages”)

b. Transcription: RNA from DNA (template for assembling RNA nucleotides)

i. mRNA (messenger RNA) carries DNA message to ribosomes  proteins

c. Translation: Synthesis of polypeptide from mRNA at ribosomes (all organisms)

d. No nucleus in bacteria  no segregation  translation and transcription together

e. Eukaryotes: Transcription in nucleus; cytoplasm translation (additional process)

i. Transcription of gene  pre-MRNA  RNA by further processing

ii. Initial RNA transcript not translated to proteins: primary transcript

d. Central dogma: DNA  RNA  protein; 20 amino acids; triplet bases  amino acids

a. 64 combinations in triplet code; transcribed strand: template strand used

b. mRNA = complimentary (base-paring rules); Uracil instead of thymine

i. mRNA base triplets: codons (5’ -> 3’); non-template “coding strand”

c. If 30 nucleotides  10 amino acids; read codon chart: left (5’), top, right (3’)

e. Three “stop” termination signals; genetic messages start with AUG (methionine)

a. Each code = one amino acid; different codes may produce same amino acid

b. Reading Frame: Grouping of non-overlapping three-letter words

f. All cells have same gene material, but not all expressed; genes can be transplanted

a. Slight variations in Eukaryotes: near universal understanding

III. RNA polymerase pries DNA apart and joins RNA nucleotides as base pairs; no primer needed

a. 5’  3’; specific sequences mark where transcription starts and ends; promoter: start

b. Prokaryote end: terminator; region: transcription unit; RNA poly II: mRNA synthesis

a. Three stages of transcription: initiation (c), elongation (d), and termination (e)

c. Promoter works upstream; determines which strand as template; several dozen pairs

a. Eukaryotic protein transcription factor mediate binding/initiation

b. Factors attached to promoter  RNA binds (transcription initiation complex)

 c. DNA promoter sequence: TATA box; protein-protein interactions in transcription

d. RNA molecules peels from DNA molecule and DNA reforms; 40 nucleotides per second

a. Congregation of polymerase molecules  higher mounts of transcribed mRNA

e. Transcribed terminator = polymerase detaches/transcript released as mRNA

a. RNA poly II transcribes sequence on DNA (polyadenylation)  AAUAAA

b. Proteins with RNA transcript cut it free  pre-mRNA  RNA processing

IV. RNA processing: ends of primary transcript altered; interior sections cut/remaining spliced

a. 5’ receives 5’ cap (guanine); 3’ adds 50-250 adenine nucleotides  poly-A tail

a. Facilitated mature mRNA export form nucleus; protect from hydrolytic enzymes

b. Help ribosomes attach to 5’ end of mRNA; AAUAAA attached at 3’ end

b. RNA splicing: large RNA parts removed (initially synthesized)

a. Noncoding region mixed between coding segments of gene (introns)

b. Exons expressed in end (except UTRs = ends not translated to proteins)

c. RNA poly II transcribes introns/exons, but introns cut/exons move together

d. snRNPs splice introns at end; made of RNA/small protein; small nuclear RNA

i. Large splicesome join exons together and cutout introns; mRNA formed

c. Ribozymes: RNA acts as enzymes; introns RNA catalyzes its own its own excision

a. RNA single strand = region of RNA may base pair with another molecule = 3D

i. Specific structure needed for catalyzation of ribozymes (~enzymes)

b. Certain amino acid in enzymatic protein  functional groups used in catalysis

c. RNA to hydrogen bond with other nucleic acids  specificity to catalytic activity

d. Alternative RNA splicing: genes give rise to multiple polypeptides

a. Depends on which segments are treated as exons/introns

b. Reason why humans survive with relatively small number of genes

c. Protein modular architecture consists of discreet domains

d. Different exons = different domains; exon shuffling: presence of introns in a gene

i. More introns  higher probability of beneficial crossing-over

V. Transfer RNA (tRNA) transfers amino acids from cytoplasm to amino acids of ribosome

a. Cytoplasm stocked with all 20 amino acids (self-synthesized or derived from compounds)
 a. Ribosomes put amino acids  polypeptide chain; not all tRNA are identical

b. Anticodon: Nucleotide triplet that compliments mRNA; message translated

i. Ribsosome joins amino acid by chain; mRNA moves through ribosome

b. tRNA reused, picks up amino acids in cysol, deposits cargo onto polypeptide, repeats

a. tRNA: RNA about 80 nucleotides long; folded upon itself in 3D (cloverleaf)

b. 3’ end is attachment for amino acid; other end has anticodon; form = function

c. Aminoacyl-tRNA synthetase: Correct matching of tRNA/amino acids by enzymes

d. Synthetase covalently attach amino to tRNA by hydrolysis of ATP  charged tRNA

e. Charged tRNA delivers amino to a chain; some tRNAs bind to multiple codons

i. Due to third base of codon relaxed compared to other codon positions

f. Flexible base pairing = wobble; only 45 tRNAs even with 61 possibilities

c. Ribosomes start coupling of tRNA with mRNA codons during protein synthesis in cytosol

a. Ribosomal RNA (rRNA) made in nucleolus; form functional ribosome with mRNA

b. rRNA is most common of RNA; 3 rRNA per ribosome in bacteria/4 eukaryotes

i. Certain drugs inhibit bacteria ribosomes without hurting eukaryotes

c. Three bindings: P site (holds tRNA with chain), A site (holds tRNA with amino)

i. E site (discharged tRNA leave); polypeptide released through exit tunnel

ii. rRNA (not protein) responsible for structure/function of ribosome

iii. Ribosome = massive ribozyme; site order: EPA (5’  3’)

d. Initiation stage brings mRNA, first tRNA, and two subunits of a ribosome together

a. Eukaryotes: small subunit with tRNA binds to 5’ cap/scans downstream

b. Stops at start codon/initiator tRNA binds; establishes reading frame (P site)

c. Translation initiation complex with initiation factors to fuse/GTP used

e. Elongation factors (three steps); energy consumed in 1st/3rd (hydroxylation of GTP)

a. mRNA moves 5’  3’ end; codon recognition/peptide bond/translocation

f. Release Factor binds to stop codon in A site/water added to polypeptide chain

a. Hydrolyzed of water: exit tunnel at large subunit; 2+ GTP used to disassemble

g. Polyribosomes (polysomes): strings of ribosomes visible through EM; long mRNA

h. Polypeptide chain coils/folds to form tertiary structure; chaperonin help correctly fold
 a. Post-translational modifications: Enzymes remove amino acids from leading end

b. Enzymatically cleaved  multiple pieces; two pieces may fuse together  1

j. Polypeptide synthesis starts in free ribosomes; until SRP halt signal momentarily

a. Signal peptide: proteins made for secretion or endomembranic system

b. Signal-recognition particle: brings ribosome to ER/binds to surface

i. SPR leaves/production continues; signal cleaving enzyme for SP

VI. Mutations: diversity of genes/source of new genes/may cause extreme complications

a. Point mutation: chemical changes in single base pair; in gametes, it passes in generations

a. Sickle-cell disease/familial cardiomyopathy; single change with large results

b. Base-pair substitution: Replacement of one nucleotide and partner with another pair

a. Silent mutations: no effect on encoded protein (still codes for same amino group)

b. Missense mutations: little effect on protein; region may be of little importance

c. Nonsense mutation: translation terminated prematurely  nonfunctional

c. Insertions and deletions alter reading frame (frameshift): worse than substitution

a. Spontaneous mutations: incorrect base used as template for next replication

b. Mutagens: interact with DNA  mutations (X-rays/high energy radiation)

i. Carcinogens are mutagens, and mutagens are carcinogens

VII. Bacteria cell ensues a streamline operation (transcribe/translate same gene)

a. Protein can quickly diffuse to its site of function; eukaryotes = difficult transporting

b. Archae resembles eukaryotes closer than bacteria (similar polymerases/complex)

i. Transcription in archae terminated differently than in bacteria/animals

c. Gene: region of DNA expressed  produce polypeptide or RNA molecule in the end

Chapter XVIII: Regulation of Gene Expression

I. Prokaryotes/eukaryotes alter gene expression (environmental change) - regulation

a. Gene expression regulated during transcription; disruption  cancer/problems

II. Conserve resources = natural selection favors (genes only expressed if product needed)
a. Cell adjusts activity of enzymes using feedback inhibition (anabolic biosynthetics)

a. Cell regulates enzyme production (expression of genes): operon model

b. Pathway reaction from specific enzymes; five coding subunits clustered on chromosome

a. One promoter: five genes (transcription unit); five polypeptides from one mRNA

b. mRNA translated into separate polypeptides by start/stop codons

c. Advantage: single on-off switch controls genes cluster (coordinated control)

i. Switch: DNA operator near promoter; controls access of RNA polymerase

d. Operator + promoter = operon; trp operon turned on = RNA poly bind/transcribe

e. trp repressor binds to operator/blocks RNA poly/turns operator off

i. Specific repressor for specific operon; product of regulatory gene trpR

ii. Binding reversible; duration depends on repressor; allosteric protein

f. The trp repressor synthesize in inactive form; active when tryptophan binds

i. Tryptophan: co-repressor (small molecule that turns an operon off)

c. The trp operon = repressible operon because its transcription inhibited by allosteric site

a. The inducible operon off until molecule interacts with regulatory protein (lac)

b. Inducer inactivates the repressor (lac operon: allolactose  enzymes for lactose)

c. Inducible enzymes: Synthesis induced by chemical signal (lactose-using enzyme)

i. Repressible enzymes (anabolic) synthesis end products from raw materials

ii. Suspension of end product  relocate energy/resources to other uses

iii. Inducible enzymes function in catabolic pathways (nutrient  parts)

d. lac/trp: negative control: operons switched off by active form of repressor protein

e. Gene regulation only positive if regulatory protein directly interacts  transcribe

d. Lactose present/glucose absent: lactose broken down for energy; E. coli uses glucose

a. cAMP accumulate when low glucose; activator CAP binds to DNA  transcription

b. cAMP binds to protein  CAP active shape/attaches to specific promoter site

c. Facilitated binding of RNA poly to promoter  increased transcription/positive

e. High glucose  lower cAMP  CAP detaches  RNA poly slowly binds  barely continue

a. Positive by CAP/negative by lac repressor for lac operon

i. CAP: rate of transcription… lac repressor: “Yes/No” for transcription

 ii. High glucose/CAP inactive: catabolism other than glucose slows down

III. Uni/Multicellular organisms turn genes off/on from internal/external environment

a. Minus immune cells, all cells have same genome; differential gene expression for cells

a. Small amount code for protein; most code for RNA/not transcribed

b. Common gene expression control point: transcription (signals from cell)

b. Eukaryotic chromatin: DNA/protein; location of promoter determines if transcribed

a. Where DNA attaches to chromosome scaffold/nuclear lamina also effects

b. Chemical modifications to histones/DNA influence structure/gene expression

c. N-terminus of histone protrudes outward from nucleosome  various chemical changes

a. Histone acetylation: acetyl groups added (-COCH3 (deacetylation = removal)

b. Lysines acetylated = positive charges neutralizes/no longer bind to neighbors

c. Compact structure  transcription factors have easier access to genes

d. Relation to transcription factors that bind to promoters  transcription

e. Methylation of histone: condense; phosphorylation: opposite effect

f. Histone code hypothesis: different combinationschromatin configures differently

d. Methylation: silencing; removal of methyl group: activation of some genes

a. DNA methylation/histone deacetylation repress transcription in nucleus

b. DNA methylation essential for long-term inactivation of genes in embryo

i. Genomic imprinting: methylation regulates expression of parental genes

e. Epigenetic Inheritance: inheritance of traits by mechanism not involved in nucleotides

a. Histone-modifying enzyme use DNA methylation to region/two enzymes silence

b. Explain why one identical twin may have genetic disease while the other may not

f. Chromatin-modifying enzyme control gene expression (DNA more/less able to bind)

a. Optimally modified = initiation of transcription is next step where genes regulated

b. Proteins that bind to DNA either facilitate/inhibit binding of RNA polymerase

g. Transcription initiation complex: assembles on promoter “upstream” end of gene

a. Control elements: Noncoding DNA part; regulate transcription (bind to proteins)

b. Critical to precise regulation of gene expression in different types of cells

h. General protein transcription factors initiate transcription for all protein-coding genes
 a. Protein-protein interactions for initiation of eukaryotic transcription

b. Complete initiation complex assembled = polymerase moves along DNA template

c. Specific transcription factors: interaction of control elements with proteins

j. Proximal control elements near promoter; distal enhancer =group of nucleotides on DNA

a. Rate of gene expression changes by binding of proteins (Activators/repressors)

b. Affects control element of enhancers; mediator proteins interact with promoter

i. Initiation complex/general transcription factors set up

c. Commonality of active proteins: DNA binding domain/1+ activation domains

d. Repressors bind to DNA/block binding/turn off transcription/control DNA

e. Affect chromatin structure: some acitvators have hisones acetylated to promoter

i. Repressors deacetylate histones (silencing)  reduced transcription

ii. Most common form of repression; activators bend DNA

k. Transcription depends on activator binds; enhancer = ten elements (combo = important)

a. Different activator combinations > single unique control element for gene

l. Control genes in operon (one promoter  mRNA); co-expressed genes clustered closely

a. Co-expressed eukaryotic genes scattered over different chromosomes

b. Gene expression depends on association of combo of elements/dispersed group

c. Copies of activators bind to control element/promote transcription of gene

d. Coordinated control of dispersed genes in eukaryote occur from signals outside

e. Nonsteroid hormones bind to surface receptor: signal transduction pathway

i. Genes with same control elements activated by same chemical signal

m. Regulatory stages occur after transcription: more fine-tune gene expression changes

a. Alternative mRNA splicing: different mRNA molecules from introns/exons

n. mRNA breakdown: enzymatic shortening on poly-A tail; remove 5’ cap

a. Nucleases kill mRNA; nucleotide UTR of mRNA determines life span at 3’ end

o. Initiation of mRNA translation blocked by regulatory proteins that bind to 5’ UTR

a. Prevent attachment to ribosomes; cytoplasmic enzymes adds more A  translate

b. Fertilization: Translation triggered by translation initiation factors from mRNA

p. Proteins undergo chemical modifications (phosphorylation of regulatory proteins)

 a. Proteasomes degrade ubiquitinated proteins/kill mutated proteins

IV. Parts of genome transcribed to Noncoding RNAs; regulation occurs: mRNA translate/chromatin

a. MicroRNAs (miRNAs) compliment to mRNA; formed from longer RNA cut by dicer

b. miRNA + protein complex  bind to mRNA with complimentary sequence (1/3 of genes)

c. Double-stranded RNA into cell turned off gene expression with same sequence as RNA

a. RNA interference/small interfering RNA (RNAi/siRNA) similar to miRNA

b. miRNA: single hairpin in RNA/siRNA formed from double-stranded RNA

d. siRNA remodel chromatin structure: target complex of centromeric sequences of DNA

a. siRNA in yeast cells important in heterochromatin formation/embryonic growth

V. Developmental program produces cell types  form different structures in 3D; complexity

a. Cell division, cell differentiation, and morphogenesis in transformation

a. Cell Division: Mitosis while producing identical offspring cells

b. Cell Differentiation: Specialization from stem cells into specific functional cells

c. Morphogenesis: Physical process that gives an organism its specific shape

d. Cell activity depends on genes; different gene expression results in various types

e. Egg’s materials = sequential gene regulation as cell divides  different cells

b. Specific genes expressed in particular cell in developing organism determine path

a. Egg’s cytoplasm contains protein/RNA: cytoplasmic determinants

b. Determines fate by regulating expression of cell’s genes during differentiation

c. Induction: Signals cause change in target cells; growth factors from neighbors

c. Determination: Events  observable differentiation of a cell; irreversible in embryo

a. Tissue-specific protein: Proteins found in specific cell type  structure/function

b. Differentiated cell = specialist at making tissue-specific protein

c. Differentiation = appearance of mRNA for proteins/changes in cellular structure

d. Determination  myoblast (muscle-specific cells with only related proteins)

i. Myoblast produce proteins that fuse  multinucleated muscle cells

e. myoD: transcription factor that binds to specific control elements in enhancer

i. Stimulate expression; coordinately controlled; confer unique properties

ii. Changes nonmuscle cells into muscles cells; requires protein combination
 f. Tissues function = body plan (3D arrangement) must be established/differentiable

d. Cytoplasmic determinants/signals contribute to spatial arrangement: pattern formation

a. Early embryo: major axes of animal established/tissues in proper places

b. Positional information: Molecular cues that control pattern formation

c. Genes = development/understanding of molecules in position/differentiation

e. Cytoplasmic determinants localized in unfertilized cells; support cells provide nutrients

a. Fruit fly develops in stages with bilateral symmetry; three larval stages

f. Homeotic genes: control pattern formation in later embryo, larva, and adult stages

a. Project daunting: Too many fruit flies; embryonic lethal mutations

b. Cytoplasmic determinants in egg played role in axis formation  genes studied

c. Genes set-up initial pattern of embryo by regulating gene expression

g. Maternal Effect gene: Mutant mother  always-mutant offspring (mRNA in cytoplasm)

a. Egg-polarity genes: Control orientation (polarity) of egg/fly (maternal genes)

b. Bicoid: “Two-tailed”; mother has mutant bicoid gene lacks front half/posterior

c. Morphogen gradient hypothesis: morphogens establish embryo’s axes/forms

d. Bicoid mRNA highly concentrated at anterior end of egg

i. Cytoplasmic bridges connect burse cells to egg; fertilized: mRNA  protein

e. Different egg regions = different development; mother = important role

f. Gradient of morphogens = polarity/positions key concept for species.

g. Positional information  specific # of correctly oriented segments/structures

h. Balanced between turning genes on/off for differentiation in right place

VI. Gene that regulate growth/division  growth factors/receptors/pathways; mutations = cancer

a. Cancer causing mutations result from x-rays/carcinogens/viruses/radiation

a. Cancer causing genes = oncogenes; normal cell growth: proto-oncogenes

b. Ocogene arises from genetic change  increased protein of proto-oncogene

c. Mov’t of DNA in genome; amplification of proto; point mutation in control/proto

d. If translocated proto near promoter  transcription increase (oncogene)

e. Amplification increases copies on proto in cell; genetic changes: excess growth

f. Point mutation in promoter/enhancer/coding sequence  increased expression

 b. Tumor-suppressor genes: proteins prevent uncontrolled cell growth; reduced = cancer

a. Normally repair DNA/control adhesion of cells to others/extracellular matrix

c. Cell cycle-stimulating pathway: Growth factor binds to receptor; signal relayed to Ras

a. G protein Ras active when GTP bound; protein kinase transduction pathway

b. Mutation in Ras  excessive cell division/cancer may occur

c. ras gene: G protein that relays growth factor to protein kinase

d. Cell cycle-inhibition: DNA damaged is intracellular signal passed by protein kinase

a. Activated p53 promotes transcription of gene  inhibition of cell cycle

b. Prevents damaged DNA form replicating; mutations: cancer

c. “Guardian angel of the genome”—activates apoptosis if DNA cannot be repaired

e. Mutation: Over-expressed/ over-stimulated cell cycle: cancer

a. Malignant tumors: telomerase gene is activated  no natural division limit

f. 15% of cancers = inherited mutations; mutations in BRCA1/2 found in breast cancer

Chapter XIX: Viruses

 Viruses smaller/simpler than prokaryotes; origin of molecular biology; used in gene therapy
o Tobacco Mosaic disease: infected sap with viruses rubbed on plants  infection
o Smaller than ribosome; genomes may consist of different nucleic acid types
 Either single/circular genome: single/double DNA or single/double strand RNA
o Capsid: outer protein shell; rod-shaped, polyhedral, or complex; subunits: capsomeres
 Tobacco virus: rod-shaped helical; adenoviruses (respiratory): isosahedral virus
 Adenovirus in animals with ∆ facets; viral envelopes: phospholipids w/ proteins
 Contain host cell glycoprotein; most complex: bacteriophages (phages) [E coli]
 Influenza: glycoprotein spikes; helical circular capsid; 8different RNA molecules
 Host Range: limited hosts (reproduce) in “lock-and-key” fit; obligate intracellular parasites
o Virus enters cell; viral DNA/capsid proteins released; DNA replicates; viral mRNA made
 Viral genomes/proteins self-assemble into new virus -> host destroyed/damaged
o Lytic Cycle by virulent phages; T4 phage attaches to outside/hydrolyzes host DNA
 Virus implants own DNA  empty shell; phage DNA directs protein production
 Head + tail + tail fibers  phage assembled/cell wall hurt  lyse of the bacteria
 Natural selection favors some bacteria; restriction enzymes attach viral DNA
 Bacteria methylation prevents enzymes from hurting its DNA (evolutionary flux)
o Lysogenic cycle: replication of DNA w/o hurting host; both modes: temperate phages
 Biological research of lambda (λ): linear DNA mixes w/ DNA (prophage)
 Phage genome mostly silent; DNA replicated in binary fission  passed down
 Lysogenic: prophages capable of activation  lyse cell (environment signals)
 Transcription-preventing protein; expression of genes = change in phenotypes
o Common cold = influenza; animal virus = high change rate/mutation; different families
 Most RNA have envelope; envelope allows virus to enter the cell directly
  Glycoproteins on virus surface bind to membrane  endocytosis of virus
 Lysosomes eat capsid  free floating genome; genome copied in replication
 Virus exocyotsis w/ glycoproteins derived from host cell; herpesvirus (RNA)
o Retroviruses use RNA; reverse transcriptase to change RNA  DNA in the cell
 HIV (human ImmunoDeficiency virus)  AIDS (acquired ID syndrome)
 HIV enters host; synthesis of viral DNA/integrated into chromosome
 Provirus (integrated DNA) never leaves genome (prophage leaves); transcribed
 RNA viruses have own enzymes to replicate viral genome; cell releases virus
o Viruses technically nonliving (unable to replicate genes itself/self-metabolic activity)
 Originated developed after first cell appeared; plasmids and transposons
 Naked bits of cellular nucleic acids; mobile genetic elements; genetic similarity
 Mimivirus (mimicking microbe) has genes for products of cellular genomes
 Minimivirus appeared to evolve before other cells; experimental biology system
 Viruses may produce toxins/consume vital cellular resources/lyse cell; damage depends on site
o Lungs: epithelium tissue regenerates (OK); polio attacks mature nerves (bad); divisions
 Body tries to defend against virus (fever/aches); immune system = body defense
 Vaccine: harmless pathogen variant; stimulates immune system for defenses
 Smallpox; most effective “cocktail” multidrug treatments hurt assembly of virus
o Emerging virus: New (HIV/AIDS in San Francisco/West Nile/Ebola+ hemorrhagic fever)
 Severe acute respiratory syndrome (SARS) in China; high virus mutation rate
 No genetic proofreading; epidemic; dissemination from isolated populations
 Spread of viral diseases from animals; worst = “Spanish Flu” pandemic in 1918
o Plant: Horizontal transmission: plant infected by outside; vertical: parents (asexual)
 Viroids: circular RNA that infect plants; prions: infectious misfolded proteins
 Act slowly (more infections)/virtually indestructible; present in brain cells
Chapter XX: Biotechnology

I. Recombinant DNA: DNA molecules from multiple sources of DNA combined in vitro (1995: first)

a. Biotech: manipulation of organisms  useful products: selective breeding/wine

b. Genetic Engineering: Direct Manipulation of genes (practical purposes): Criminal/health

II. Single DNA molecule: many genes (small portion); rest = Noncoding; DNA copies  DNA cloning

a. Plasmids: Circular DNA (replicate separately from bacterial chromosome); few genes

a. Plasmid isolated; foreign DNA inserted; return  recombinant bacterium

b. Gene cloning: multiple copies from single gene from division of recombinant

c. Gene copied; protein produced; genes = one copy per haploid genome copied

b. Restriction enzymes: cut DNA molecules at number of locations; cut up phages /foreign

a. DNA sequence: Restriction site; DNA protected from own enzymes (methylation)

b. 5’  3’; restriction fragments: enzyme cuts up DNA into smaller bits/pieces

c. Sticky end; hydrogens bonds to complementary end; permanent: DNA ligase

c. Original plasmid: Cloning vector: DNA with foreign DNA into host/replication

a. Bacterial plasmids: easy to isolate/manipulate/put back/rapidly reproduce

 d. ampR makes E. coli resistance to antibiotic ampicillin/lacZ: enzyme to hydrolyze lactose

a. Agar with ampicillin/X-gal in colonies distinguished recombinant plasmids

e. “Shotgun” approach: No single gene targeted for cloning; all cell-clones: genomic library

a. Vector phages hold more DNA than plasmids; enzymes do not recognize boundary

b. Bacterial Artificial Chromosome (BAC): Large plasmids only with used genes

i. Minimal size needed for genetic library  hard to work with in lab

c. Reverse transcriptase makes single DNA from mRNA; primer: dT for poly-A tail

d. Result: Complimentary DNA (cDNA): modified by enzymes/put in vector DNA

e. cDNA cloned: cDNA library: represented only transcribed part of the genome

i. Genomic library usually contains any gene; cDNA: “stripped-down” gene

ii. cDNA library = studying specialized cell types (liver/brain)/development

f. Nucleic Acid Hybridization: Complimentary base-pair sequence for nucleic acid

a. Complete molecule (RNA/DNA): Nucleic acid probe; tracked with radioactivity

g. Gene cloned: protein produced in bulk  research/practical purposes

a. Expression vector: cloning vector with highly active promoter upstream nearby

i. Eukaryotic gene inserted in correct reading frame  quick synthesis

b. Yeast artificial chromosomes: origin + centromere + foreign + telomeres

i. YAC: longer DNA segment; cloned fragment contains all gene (not portion)

c. Eukaryotic proteins do not function until modified (some proteins need changing)

d. Electroporation: Electrical pulse applied to solution in membrane: DNA enters

i. Scientists inject DNA directly into single cell using needles  expression

h. Polymerase chain reaction (PCR): Amplified tiny copy of DNA quickly in vitro

a. Reaction strand heated  separation  cooled for annealing (hydrogen bonding)

b. Bonds formed with DNA primers; heat stable DNA polymerase extends primers

c. High specificity key: primer with specific hydrogen bonding at opposite ends

d. PCR provides specific DNA fragments for cloning; clones sequenced: error-free

i. Used on fragments of frozen wooly mammoth; works with small genes

III. Gel electrophoresis: Polymer gel = molecular sieve to separate molecules by size/charge

a. Linear DNA separated into bands of same length  restriction fragment analysis
 a. DNA fragments sorted by gel electrophoresis when electricity runs through

b. Useful for comparing two different DNA molecules; prepares pure samples

c. Southern blotting: Gel electrophoresis/hybridization to detect specific bands

d. Probe: radioactive single-strand of DNA complimentary to gene of interest

e. Capillary action pulls alkaline solution through gel  blot  denatured DNA

f. Photographic film reveals where radioactive probe binds to nitrocellulose blot

b. Deoxy chain termination: machine rapidly determines the nucleotide sequence in order

a. Each strand starts with the same primer/ends with ddNTP  terminates growth

b. Labeled strands put through fluorescence detector to order of nucleotides

c. Sequenced comparison = clues for function (when/where gene is expressed)

c. Transcription used as measure of gene expression; probes hybridize transcribed mRNA

a. Northern blotting: Gel electro on mRNA, transfer samples, probe hybridizes

b. Enables specific nucleotide sequence of mRNA; gene appears: protein functions

c. RT-PCR (quick) isolates mRNA; reverse transcriptase makes cDNA

i. cDNA: template for PCR amplification using primers; copies = bands

ii. mRNA collected from different tissues  which tissue produces mRNA

d. Track location of genes in situ: in situ hybridization: probes with fluorescent dye

d. Isolate mRNA, use molecules for template for cDNA, nucleic acid hybridization

a. Used to determine what fraction of genome the DNA fragments represent

b. DNA microarrays assay: Tiny single-DNA representing genes in a grid

c. Fragments represent all genes; nearly 60% genes change during development

i. Many genes expressed in sex determination; new therapies from method

d. In vitro mutagenesis: Mutations in cloned genes; gene returned  disables normal gene

a. Phenotype of mutant cell reveals function of missing protein  gene function

b. RNA interference (RNAi): Synthetic double-RNA stops gene’s translation

i. Genome-wide analysis simplifies interactions—Systems biology

IV. Organism cloning: offspring genetically identical to “parent” where single-cell derived

a. Totipotent: Mature cells dedifferentiate  rise to specialized cells (carrots)

b. Approach: remove nucleus/replace by nucleus of differentiated cell (nuclear transplant)

 a. Potential of transplanted nucleus to direct normal development inverse of age

c. Cultured-mammary cells in nutrient-poor medium/fused with enucleated sheep eggs

a. Diploid divided to form embryos; one successful offspring: Dolly the Sheep

b. Reproductive cloning: Cloned animals look different/behave differently

e. Cloned animals exhibit defects; small subset of genes on/rest repressed to off

d. Epigenetic changes in chromatin (acetylation of histones/methylation of DNA)

e. DNA by embryonic cells from cloned: more methyl  chromatin restructuring

i. Misplaced DNA of donor nucleus interferes with normal development

d. Stem cell: unspecialized cell that reproduced indefinitely/differentiate into specialized

a. Replenish population/generate cells for differentiation; isolated: blastocyst stage

b. Adult stem cells not able to give rise to all cell types, but they can generate types

c. Adult brain contains stem cells that produce nerve cells; also in dental/eyes/hair

d. Aim: Repair damaged organs; ES = pluripotent: differentiate  different cells

e. Clone: ES cells to treat disease (therapeutic cloning); iPS cells work same as ES

V. DNA tech: identification of human genes with mutations in genetic diseases (diagnose/treat)

a. PT-PCR: best way to detect elusive infective agent; PCR/primers reveal mutations

a. Genetic Marker: DNA sequence varying in a population; variation: different alleles

b. Noncoding DNA at locus exhibits nucleotide differences: polymorphisms

c. SNP: Base-pair site where variation found in at least 1% of population

i. Some SNP alter sequence recognized by restriction enzymes

b. Restriction fragment length polymorphism: (RFLP) Changes in Noncoding region

a. Southern blotting; abnormal allele diagnosed if liked NSP marker found

b. Marker/gene inherited together (even though marker =\= gene)

c. Gene-therapy: Genes transmitted for therapeutic purposes for single-defective gene

a. Cells that receive normal allele must multiple through patient’s life (SCID)

b. Retrovirus used; side effects; how can transferred gens be controlled? Ethics?

d. Synthesis of molecules to combat certain protein for tumor’s survival (receptor tyrosine)

a. Insulin/human growth hormone; tissue plasminogen activator = after heart attack

b. Transgenic “Pharm” animal: introduce gene of genotype to another species

 c. Some cells integrate foreign DNA (transgene) and express foreign genes

e. Genetic profile: genetic markers that vary in population analyzed for given person

a. Preferred over finger printing; everyone = unique DNA, minus identical twins

b. Short Tandem repeats (STRs): units of base sequences in specific genome place

c. More markers = more accurate; biofuels: crops replacing fossil fuels (bioethanol)

d. No genetic engineering involved; transgenic animals speed up selective breeding

f. Plant vector: Ti Plasmid: Versions w/o disease; “golden rice” Vitamin A for SE Asia

a. Genetically Modified (GM) organisms: US/Argentina/Brazil: 80% of GM crops

b. How to facilitate/inform public of GMs?

Chapter XXI: Genomes and Their Evolution

I. Chimpanzee = Closest living relative to humans; genomics: whole sets of genes/interactions

a. Flood of information  bioinformatics: computational methods of storage and analysis

II. Human Genome Project: Human sequence of genes in location on chromosomes (cytogenetic)

a. Linkage Map: Order of markers and relative distances from recombinant frequencies

a. Physical Maps: Marker Distance in physical measurement (# DNA base pairs)

b. Measured by cutting DNA of chromosome into restriction fragments/ordering

c. Key: Overlap fragments and use probes to find the ends of overlaps

d. First cloning vector: YAC (yeast); goal: DNA sequencing on each chromosome

b. Whole-genome shotgun approach: Starts by direct random sequencing of DNA fragments

a. Computers assemble overlapping short strands; most common approach

b. Fragments cloned into three vectors; known distance between ends of DNA

c. Hybrid approach for human genome (shotgun misses repeated sequences)

III. NCBI database: Genbank: Center of sequence of DNA; BLAST: Compare the sequence to others

a. Using DNA sequences = genes studied directly without inferring genotype/phenotype

a. Software scans sequences for transcription/translation signals/RNA-splicing sites

b. ESTs (expressed sequence tags) collect cDNA sequences (protein-coded genes)

c. Newly identified sequence may match a previously known gene’s function/shape

b. Proteomics: Systematic study of full protein sets; proteins carry out the functions of cell

a. NIH/National Cancer Institute aim to understand how system change  change

 b. Silicon/”glass” chips hold microarray of DNA to represent human genome

IV. Bacterial/Archaea = somewhat small genomes (1-6 Mb); eukaryotes: usually much larger

a. Bacteria/Archaea = fewer genes than eukaryotes; low number of genes in vertebrates

a. RNA alternative splicing = multiple proteins from a single gene

b. Most-translational modification/addition of carbohydrates  diversity

b. Gene density low in human; eukaryote = large genome/fewer genes in base pairs

a. Bacteria: DNA = genes for protein/tRNA/rRNA (some DNA not transcribed)

b. Humans = high amounts of Noncoding DNA; introns = genome length differences

V. Coding regions of eukaryotic genes = small portion; bulk = “junk DNA” with important functions

a. Pseudogenes: former genes (mutations = nonfunctional); most genes = repetitive DNA

a. 75% of repetitive DNA = transposable elements/related sequences

b. Transposable elements: recombination where genes move around in DNA sequence

a. “Jumping genes” although the sequences never completely detaches from DNA

c. Transposons move within genome by DNA intermediate; “cut-paste” / ”copy-paste”

a. Retrotransposons: Move with intermediate RNA; leave copy at original site

b. Reverse transcriptase converts sequence to DNA/insertion to DNA

c. Transposable elements can move; enzymes sent in genome (50% of genome)

d. Alu elements: short/transcribed into RNA with unknown function

e. Larger Line-1 retrotransposons have low transcription rate; blocks RNA poly

i. Transposable elements: “Noncoding” DNA category/repetitive sequence

d. Repetition: mistakes from DNA replication/recombination; 15% of genome

a. Large duplication sequences copied from one chromosomal location to another

b. Simple sequence DNA: copies of tandemly repeated short sequences repeatedly

c. Short tandem repeat (STR) prepares genetic profile; varies between individuals

d. Repetitive DNA isolated by centrifugation: satellite DNA (simple sequence)

e. Simple DNA sequence located at telomeres/centrosomes (structural role)

e. Only 6% of average gene expressed in final product; multigene family: 2+ identical genes

a. Identical DNA clustered tandemly (and minus histones) = same RNAs produced

b. Many copies of rRNA transcription unit = millions of ribosomes quickly produced

 c. Nonidentical genes: code for different globins  function at new environment

VI. Basis of change: mutation; analyzing chromosome structures (other species) = common ancestor

a. Chromosomal rearrangements; unequal crossing-over = non-mating different species

a. DNA sequence reshuffle  genome evolution; introns  new protein evolution

b. Some protein-coding genes [collagen] have multiple copies of related exons (duplication)

a. Mix/match of exons in gene/two nonallelic genes to errors: exon shuffling

c. Transposable elements consistent with idea of important role within genome over time

a. Recombination, disrupt cellular genes/control elements, carry genes in cell

b. Most alterations: detrimental, but some may benefit the organism in life

c. Transposable element jumps in middle of protein-gene sequence  disrupt

i. Within regulatory gene  increased/decreased production of proteins

VII. Rapid advances in genome sequencing/data collection/new techniques  complex system

a. More similarities in sequence of genes  more closely related  evolutionary history

a. Similar: highly conserved in distantly related species  clarify relationship

b. In closely related species, one species may be studied to gain insight on the other specie

a. Particular genetic differences correlated with phenotype than genotype

b. Genes that evolve fastest = code for transcription factors (regulate gene process)

c. FOXP2 = vocalization in vertebrates; two differences in sequence = difference

c. DNA variation in humans small compared to that of other species (mainly in SNPs)

a. Inversion/deletion/duplication  human genetic markers (evolution/migration)

e. Evo-devo: Evolutionary developmental biology between different organisms

a. Homeobox: Special sequence that specifies a homeodomain in encoded protein

b. Affects homeotic genes for position of genes in spatial arrangement

c. Homeodomain part of protein that binds to DNA for transcription regulator

d. Other domains in protein bind to the DNA; small changes  major body change

Chapter XXII: Descent with Modification (A Darwinian View of Life)

 Evolution: descent with modification in allele frequency; unity/diversity of life; pattern/process

o Aristotle observed scala naturae (species have permanent certain positions) + religions
 Linnaeus: classification by patterns of creation; binomial nomenclature to name
o Darwin studied fossils in sedimentary rocks at sea bottom; lower strata = older fossils
 Erosion carved through young (upper) strata to show lower (older) strata in rocks
  Paleontology: study of fossils; catastrophism: past events different than present
 Cuiver = first; Lyell’s uniformitarianism: mechanisms of change stay constant
o Lamarck: “use/disuse” + “acquired characteristic inheritance” + innate complexity drive
 Darwin travelled on Beagle to Galapagos Islands near South America; studied different fossils
o Adaptations: characteristics that enhance survival/reproduction; finch’s beaks differed
 Cause: natural selection; argued descent with modification/unity/diversity
o Evolutionary tree w/ common ancestor/branches to new species; 99% of species extinct
 Human modification by breeding: artificial selection  crops =\= wild ancestors
 Population members vary in traits; traits inherited from parents to the offspring
 More offspring produce than what survive; lack of food/resources kill offspring
 Inheretied traits w/ higher probability to survive will produce more offspring
 *Unequal abilities to survive/reproduce  accumulation of favorable traits
 Natural selection: Helpful heritable characteristics increase survival chances
 Individuals do not evolve (only populations); selection works on heritable traits
 Predators = potent force in shaping adaptations of food source (prey); antibiotic/drug resistance
o Direct observation of evolution; Fossil records show differences in structure of species
o Common ancestry by structure: homology; “re-modeling” of structure for better function
 Homologous structures show common ancestor even with different functions
 Similar locations; vestigial structures: remnants of feature important in ancestor
 All forms of life use near same genetic, universal code; “form fits the function”
o Evolutionary Tree shows relationship; branch = common ancestor; hatch = shared trait
 Convergent evolution: alike feature’s independent evolution (different lineage)
 Species share features by convergent evolution (same environment): analogous
 EX: Sugar glider/flying squirrel gliding evolved independently of each other
o Biogeography: geographic species distribution (influenced by continental drift mov’t)
 Large super-continent: Pangea; islands with idiosyncratic species = endemic
 Theory must have predictions stand up through testing/experimentation to be law

Chapter XXIII: The Evolution of Populations

 Natural selection acts on individuals/changes populations; microevolution: population changing
o Shifting in allele frequency over generations: natural selection/genetic drift/gene flow
 Phenotypic variation not heritable; genotypic make-up for the traits heritable; variation occurs
o Phenotype = mix of genotype/environment; Discrete characters: single gene locus site
 Quantitative characters: vary along continuum (most common); multiple genes
 Average heterozygosity: average loci % that are heterozygous (alleles differ)
 Shown by protein on gel electrophoresis; cannot display silent mutations in DNA
 Silent mutations shown by PCR-based methods/RFLP/other alternate approaches
 Nucleotide variability: comparing 2 DNA sequences/averaging differences (#)
 Always: Genetic variability (average heterozygosity) > nucleotide variability
o Geographic variation: genetic make-up difference of separate populations (one species)
 Cline: Graded chance along geographic axis (natural selection by environment)
o Mutations: source of new alleles; “point-mutations” could have drastic phenotype effect
 Chromosomal chances that delete/disrupt/rearrange = usually harmful/fatal effect
 Large-scale w/ intact genes ~ neutral/beneficial; meiosis variation/transposons
 Mutation rates lowest: prokaryotes; prokaryotes mutations  quick changes
 Short generation span: variability increased; AIDS medicine: “cocktail” drugs
 Sexual reproduction, crossing-over, independent assortment, fertilization: change
 Population: Interbreeding specie group w/ fertile offspring in same area; may overlap others
o Loose boundaries/not necessary isolated; genetic makeup described as its gene pool
 Hardy-Weinberg Principle: constant frequencies w/ recombination/segregation
  Genotype: p^2 (dominant) + 2pq (heterozygote) + q^2 (recessive) = 1 (100%)
 Phenotype equation: p (dominant allele) + q (recessive allele) = 1
 No mutation, random mating, no natural selection, no gene flow, large population
 New mutations can alter frequencies slightly; adaptive evolution: offspring fit for environment
o Genetic Drift: allele frequencies fluctuate unpredictable between generations
 Most prevalent in small populations; hunting/physical separation/diseases
 Founder Effect: Individuals become isolated from population = new population
 Bottleneck effect: Sudden change in environmental conditions  shrink in size
 Genetic drift significant in tiny populations; allele frequencies randomly change
 May lead to loss of genetic variation; harmful/helpful alleles may disappear
o Gene flow: transfer on alleles into/out of population by infertile individuals/gametes
 Gene flow reduces genetic differences between populations  could combine
 “Struggle for existence” / “survival of the fittest” inaccurately describes natural selection’s effect
o Reproductive success depends on many factors (location)  relative fitness (gene pool)
 Directional selection: entire phenotype of population shifts a certain direction
 Disruptive selection: middle eliminated while the extremes become favored
 Stabilizing selection: Extreme variants removed from the populations (middle)
o Helpful adaptations may arise from natural selection; continuous, dynamic process
 Sexual selection: natural selection where certain traits = easier to obtain mates
 Sexual Dimorphism: marked differences in secondary sexual characteristics
 Intrasexual selection: selection within the same sex (males block other males)
 Intersexual selection (mate choice): females choosy in selecting specific male
 Females look for “good genes” to describe search for ideal male counterpart
o Diploidy: recessive traits hidden; balancing selection: 2+ forms within a population
 Heterozygote advantage: possessing both genes advantageous to the individual
 Frequency-dependent selection: Phenotype fitness declines if too common
 Neutral variation: No selective advantage/disadvantage by mutation in DNA
o Selection can only act on existing variations; evolution is limited by historical constraints
 Adaptations = compromises; chance/natural selection/environment interact
Chapter XXIV: The Origin of Species

 Speciation: “mystery-of-mysteries” (specifies splits); microevolution: allele frequency changes

o Macroevolution: Broad pattern of evolution w/ respect to time; origin of new organisms
 Morphology differences reflected biochem/DNA sequences; species: biological species concept
o Species: population interbreeding group w/ fertile offspring; all humans = same species
 Gene flow keeps species together; occurs in all of the aspects of the populations
o Reproductive isolation: biological factors that impede members from making offspring
 Gene flow between species block; hybrids (interspecific mating result) limited
 Prezygotic barriers impede members/hinder other matings/stop various attempts
 Habitat Isolation (different zones), Temporal Isolation (season/time problem)
 Behavioral Isolation, Mechanical Isolation (physical trouble), Gametic Isolation
 Postzygotic barriers  reproductive isolation after hybrid zygote forms (defect)
 Reduced Hybrid Viability/Fertility, hybrid breakdown (offspring feeble/sterile)
o Speciation by reproductive isolation; ignores asexual reproduction, species: absent flow
 Overemphasized gene flow/downplayed natural selection; alternative concepts
o Unity within species: morphological species concept: body shape/structural features
 Disadvantage: researchers disagree on what makes specific features  species
 Ecological species niche: sum of how members interact with biotic/abiotic parts
 Emphasizes role of disruptive natural selection on organisms for environment
 Phylogenetic species concept: smallest group that share a common ancestor
 Difficulty: what difference = separate species; morphological = asexual/sexual
 Allopatric speciation: gene flow geographically interrupted; physical barriers; highly isolate
o More geographic barriers: more speciation; physical/geographic barrier =\= biological
o Sympatric speciation: speciation occurs in population with same geographic boundary
 Little contact; polyploidy: extra chromosome set; autoploidy: failure in division
 Allopolyploid: Sterile hybrid; meiosis failure; too many chromosome sets = bad
o Habitat differentiation  subpopulation has region not used by general parent population
 The natural selection barrier (postzygotic)  limiting gene flow  speciation
o Sexual selection: females select males by appearance  those specific genes passed on
 Sympatric speciation: rarer/occurs when gene flow blocked to isolated population
 Hybrid Zone: different ancestors meet/mate in middle area; embryonic mortality/abnormalities
o Types: Reinforcement (hybrids cease), fusion (species fuse), stability (hybrids persist)
 Fusion: weak geographic barriers; many hybrids produced = genes fuse/combine
 Punctuated equilibra: apparent stasis periods (scattered sudden change); others= gradual change
o Punctuated: new species change most as branched from parent species, then little change
 Speciation = completed relatively rapidly by punctuation; hybridization change
 The periods between large speciation events may be over 1million years apart

Chapter 25: The History of Life on Earth

 Most spare terrain: Antarctica; past: warm, tropical environment; macroevolution = evolutions
o Chemical/physical process + emergent properties by natural selection  simple cells
 Abiotic synthesis of small organic compounds/joining into complex molecules
 “Protobionts: where membranes separate from out/self-replicating (inheritance)
o “Big Boom” / environment different from today; early oceans = “primitive soup”  life
 Two key properties of life: accurate genetic replication/metabolism to survive
o Protobionts: abiotically produced molecules surround by membrane structure; diffusion
 Liposomes (small membrane-bound droplets) replicate/are selective permeable
o Ribozymes: RNA catalyst for enzyme-like functions; RNA molecular natural selection
 Single-stranded RNA; more stable/replicate faster/more accurate; best will last
 RNA initially provided template for DNA to be assembled; DNA took dominant
 Fossil Record: Sequence of fossils in strata; great changes in organism types; incomplete records
o Order of fossils: relative age; radiometric dating using half-life finds the absolute age
 Death: Carbon-12 stops accumulating; C-14 decays to C-12; finds the actual age
 Works up to 75000 years; radioisotopes not used (not present/not in the bones)
 Rock magnetism shows age; harden = particles orientation frozen/layer charges
o Synapsids: multiple bones in lower jaw/single pointed teeth; temporal fenestra behind eye
 Therapsids: dentary bones/long faces/ specialized teeth (they had long canines)
 Early cynodont therapisds: dentary: largest bone in jaw; teeth with cusps appear
 Late cynodonts: complex cusp pattern in the upper jaw; second hinge in bones
 Very late cynodont: long face; original articular-quadrate hinge lost; ears formed
 Geologic Table: Archae/Proterozoic/Phanerozic era; Mesoic = “age of reptiles” / last = shortest
o Boundaries: extinction/new forms of life; gymnosperms dominated the Jurassic period
 Holocene: most recent; Cenozoic = major radiation of the birds/mammals/insects
 Prokaryote/oxygen atmosphere: Archaea era; Proterzoic: eukaryotic/first animals
o Stromatolites: layered rocks formed when prokaryotes bind sedimentary rock thin films
 Atmospheric Oxygen made by photosynthesis/cyanobacteria; rust forms (iron)
o Prokaryotes form some eukaryotes by endosymbiosis in the serial endosymbiosis model
 Mitochondira evolved before the plastids in the host cell (mutual benefits occur)
o Multicellular eukaryotes formed; limited in size/diversity by “snowball Earth” (glaciers)
 Cambrian Explosion: massive diversification w/ Cnidarian, Poriferia, Mollusca
 o Colonization of land; gradual evolutionary venture from aquatic environment to the lands
 Adaptations helped prevent dehydration; plants colonized in the fungi company
 Continental Drift; Paleozoic = Pangea; mid-Mesozoic: separate to Laurasia and Gondwana part
o Land constantly (slowly) moving; explains geographic distribution of extinct organisms
o Mass extinction: slight temp change = massive impact; habitat destroyed/unfavorable
 Permian: largest (altered ocean); Cretaceous: volcanic Siberia-sized (lava erupt)
 Five major mass extinctions; human interaction may cause an addition problem
 Very late cynodont: long face; original articular-quadrate hinge lost; ears formed
o Meteor Evidence (Caribbean Sea near Yucatan Pen); extinctions alter ecological balance
 May remove lineage w/ advantageous features from existence; adaptive radiation
 Very late cynodont: long face; original articular-quadrate hinge lost; ears formed
o Adaptive radiation: organisms form new species w/ adaptations to environment (niches)
 Common ancestor; radiation causes large changes; new source of food for others
 Very late cynodont: long face; original articular-quadrate hinge lost; ears formed
 “Evo-devo” = evolutionary biology/development biology; genetic change: morphological change
o Heterochrony: evolutionary change in rate/timing of developmental events (body shape)
 Alter timing of reproductive organs; sexually mature at certain, very specific age
 Paedomorphosis: juvenile features partially retained; regulatory homeotic genes
 Very late cynodont: long face; original articular-quadrate hinge lost; ears formed
o Selection improves adaptations rapidly; new genes = a new metabolic/structural function
 Change in nucleotide sequence affects function if expressed; a single cell type
 Organism change = mutations in developmental genes regulation (not sequence)
 Very late cynodont: long face; original articular-quadrate hinge lost; ears formed
 Evolution =\= goal oriented; complexity evolves independently of the basics; “master regulators”
 Excaptions: structures that evolve in one context/co-opted for another function
 Individual undergoes natural selection while species undergo species selection

Chapter XXVI: Phylogeny and the Tree of Life

 Phylogeny: evolutionary history of species/group of species from common point; pattern/process

o Systematics: discipline focused on classifying organisms/their evolutionary relationship
 Taxonomy: classification; Linnaeus: binomial nomenclature: Genus species; common=confuse
o DomainKingdomClassOrderFamilyGenusSpecies (general  specific)
 Taxon: unit at any hierarchy; evolutionary history shown by Phylogenetic trees
o PhyloCode: only names groups w/ common ancestor/descendants; species have no ranks
 Branch points (dichotomies): nodes; lineage splits up into different descendants
 Sister taxa: immediate common ancestor; rooted: farthest branch=same ancestor
 Polytomy: branch end w/ more than two descendant group emerging; unresolved
o DNA analysis showed “whale meat” sold in Japan included illegal species by comparison
 Homologies: similarities (shared ancestor); morphological divergence great/small genetic change
o Analogy: convergent evolution; distinguishing important in reconstructing the phylogeny
 Homoplasies: analogous structures that arose independently: the bat/bird wings
 Many similar nucleotide sequencing  homologous genes; insertion/deletions
o Molecular systematics: DNA/other molecular data (amino acids): evolutionary relation
 Cladistics organizes species into groups of clades w/ ancestral species/descendant; similarities
o Monophyletic: single ancestral species/desendents; paraphyletic: portion of offspring
 Polyphyletic: taxa w/ different ancestors: indentified w/ shared derived character
o Shared ancestral character: backbones; originated in taxa ancestor; preceded all parts
 Shared derived character: evolutionary novelty unique to the particular clade
o Outgroup: species diverged before lineage that includes studied species group (ingroup)
  Branch lengths = relative amounts of genetic change; longer lines: more different
o Maximum parsimony: study simplest explanation (Occam’s razor); fewest DNA change
 Maximum likelihood: rules of DNA change of time reflects the event sequence
o Best hypothesis: fits all available data; phylogentic bracketing  how closely related?
 Findings inconclusive (several taxa diverged at same time; differences not reflecting appearance)
o Mitochondria DNA (mtDNA) evolves rapidly/used to explore relatively recent evolutions
 Orthologous genes: homologous genes found in different species by speciation
 Paralogous genes: gene duplication  same sequence multiple times in genome
 Molecular clocks: yardstick for change in absolute time; some genes evolve at the constant rate
o Number of substitutions proportional to time since genes were duplicated (paralogous)
 Neutral theory: some evolutionary change: no effective on fitness/no influence
 Used to track origin of HIV; exact amino acid sequence essential to the survival
 Domains: archae, bacteria, eukarya; kingdoms: Monera (archae/eubactiera), fungi, plants, animals
o Bacteria: Most prokaryotes; archae: wide range of environments; Eukarya: bound nucleus
 Eukaryotes more closely related to archae > bacteria; rRNA genes change slowly
 Horizontal gene transfer: genes transferred to genomes: transposons/plasmids

Chapter XXVII: Bacteria and Archaea

 Halobacterium (Archae): very salty environ’t; pumps K+ ions outside to match the concentration
o Prokaryotic biomass outnumbers eukaryotes; live in extremes of the environ’t conditions
 Prokaryote: .5-μm; eukarya cells: 10-100μm; shape: sphere (coccus)/rods (bacilli shape)/the spiral
o Peptidoglycan sugar-polymer cell wall; Archaea = diff polymers; gram stain classifying
 Gram-positive: simple walls/large peptidoglycan; gram-negative: the opposite
 Gram-negative: structurally more complex (outermembrane: lipopolysaccharide)
 Outer membrane (gram-negative): more protective/resistance to the antibiotics
o Capsule cell wall (sticky polysaccharide/proteins); adhere to substrates/avoid dehydrate
 Fimbriae: protein hair-like appendages (attachment pili); sex pili: DNA transfer
o Most: flagella (mov’t); taxis: mov’t toward (nutrient)/away (toxicity) from the stimulus
 Prokaryotes lack complex compartmentalize; specialized membrane: metabolism
o Nucleoid regions in dense center w/ free-floating rings: plasmids (carry only few genes)
 Prokaryotic ribosomes slightly smaller than eukaryotic ones  special antibiotics
o Quick reproduction in ideal environment; endospores when the essential nutrient lacking
 Copy of chromosome  tough wall; water removed/metabolism halted; waiting
 Not “primitive” or “inferior” in evolutionary sense: rapid evolving in environ’t
 Sexual reproduction/mutations  new genetic diversity; transformation: uptake of foreign DNA
o Transduction: bacteriophages carry bacteria genesother host (horizontal gene transfer)
 Conjugation: sex pili allows for exchange of plasmids by the F factor in DNA
o F plasmids: F+ cells=donor while F- cells=receiver; genetic variation (altered sequence)
 R plasmids = resistant genes (mutations); antibiotic resistance: drug immunity
 Type: Photoautotrophs (cyanobacteria); chemotrophs; photohetertrophs; chemoheterotrophs
o Halophilic (photohetero) harness light energy/need to obtain carbon in its organic form
 Autotrophic: carbon source is CO2; heterotrophic: carbon source: organic cmpd
o Obligate aerobes need O2; obligate anaerobes poisoned by O2/anaerobic respiration
 Facultative anaerobes: either metabolic method depending on the environ’t type
o Nitrogen fixation: atmospheric nitrogen (N2) made into ammonia (NH3) for easy usage
 Heterocytes: only carry out nitrogen fixations; biofilms: cooperation colonies
 Significant portion of genomes mosaics of other genes; molecular systematics on DNA sequence
o Archae: extremeophiles; extreme halophiles (salt); exteme thermophiles; methanogen
  Mthanogens live in guts of herbavoirs = nutritional purpose; clade Euryarchaeota
o Bacteria type: alpha, beta, gamma, delta, epsilon, chlamydis, spirochetes, cyanobacteria
 Chylamdis: parasites for ATP extraction; gram-negative; largest STD/blindness
 Decomposers: break down corpses/vegetations to recycle the nutrients back into the atmosphere
o Symbiosis (symbiont / host); mutualism (+/+), commensalism (+/0), parasitism (+/-)
 Parasites: pathogens (harmful/cause disease by eating nutrients/releasing toxin)
o Exotoxins: proteins secreted that are toxins (cause chlorea); Lyme disease: tick bacteria
 Endotoxins: lipopolysaccharide gram-negative; released toxins during the death
 Salmonella; bioremediation: remove pollutants from air/water/soil/atmosphere
Chapter XXIIX: Protists

 Protists: mostly unicellular eukaryotes; nucleus/membrane-bound organelles; some multicellular

o Mixotrophs: photosynthesis/heterotrophic nutrition; endosymbionic evolution theory
 Secondary endosymbiosis: red/green algae ingested in food vacuoles of others
 Nucleomorph: plastids/tiny vestigial nucleus; explains the mitrochondrial source
 Varying shapes/sexuality/food production methods/complexity/mov’t method
o Amitochondriate protist: the oldest lineage of living eukaryotes; five large super-groups
 Type: Excavata, Chromalveolata, Rhizaria (amoeba), Archaeplastidia, Unikonta
 Excavata: diplomonads (modified mitosome mitochondria w/ anaerobic, parasite), parabasalids
o Vaginal acidity; eugleozoans: flagella; kinetoplastids: a large mitochondria/DNA mass
 Euglenid: flagella; mixotroph; light detector; pellicle (no cell wall); an eyespot
 Chromalveolata: monophyletic group/red algae; alveolates: membrane-bound sacs for regulate
o Dinoflagellates: reinforced by cellulose plates; toxins hurt invertebrates; half mixotroph
 Apicomplexians: animal parasites (liver); infectious cells: sporozoites at apex
 Transmitted by mosquito; sexual/asexual life stages (mainly haploid or asexual)
o Ciliates: cilia mov’t; micro/macronuclei; stramenopiles; diatoms: unicellular/asexual
 Energy stored in glucose polymer (laminarin); freshwater (hypotonic) environ’t
 Biological carbon pump during photosynthesis to take in CO2 from surrounding
o Golden Algae: yellow/brown carotenoid colors; biflagellated; brown algae: “seaweed”
 Thallus: algal plantlike body; root: holdfast; stem stipe; leaflike blades at top
o Alternations of generations: multicellular stages; haploid: zoospores by lower flagella
 Heteromorphic: sporophyte/gametophyte structural different; isomorphic: same
 Chromosme number differs due to haploid/diploid difference; right below tide
o Oomyctes: water molds/white rust; multinucleated filaments (hyphae); resembles fungi
 Rhizaria: amoeba moving by pseudopodia; foraminiferans (forams): porous tests shells w/ Ca
o Radiolarian: pseudopodia radiate from central body; reinforced by microtubule structure
 Archaeplastids: engulfed cyanobacteria; red algae (phycoeryhrin); multicellular; gen alternation
o Green algae: pigment structure resembling chloroplast; photosynthetic output  foods
 Chlorophytes: colonies/multicellular bodies/no cytoplasmic division/differentiate
 Unikonta: first to diverge; amoebozoans: amoeba w/ lobe/tube shaped mov’t (no pseudopodia)
o Plasmodial slime molds; plasmodium: single cytoplasm mass w/ many diploid nuclei
 Cytoplasmic streaming distributes nutrients/oxygen; engulfs food (phagocytosis)
 Cellular slime molds: solitary cells; aggregate as unit when food supply is low
 Cheating mutants lack protein on cell surface/the noncheaters aggregate together
o Opisthokonts: diverse group of eukaryotes with evolutionary history: nucleariids/fungus
 Protist: aquatic; any water habitats; many producers that use energy from light: CO2  the food
o Symbiotic protist include parasites  hurt the individual: (Plasmodium amoeba: malaria)

Chapter XXIX: Plant Diversity I: How Plants Colonizes Land

 Protist algae: closest plant relative (specifically charophytes): rosette-shaped cellulose complexes
o Peroxisome enzymes; flagellated sperm; phragmoplast [phragmoplast: the cell-plate]
 Morphological and biochemical traits show relation to the land plants (Chara)
 Sporopollenin: durable polymer prevents exposed zygotes from drying out; same in plant spores
o Terrestrial habitat: bright, unfiltered sunlight; more CO2 in atmosphere; nutrient-rich soil
 Alternation of generations: gametophyte produces haploid gametes by mitosis
 Fertilization sporophytesspores meiosis-produced (multicellular haploid)
o Placental transfer cells: embryo for adjacent maternal tissue  transfer nutrients to seed
 Embryophytes: multicellular dependent embryos specifically land plant (zygote)
o Sporangia produces spores (diploid: sporocytes); spores released in air/spread by wind
 Charophytes lack multicellular sporangia/sporopollenin; outer tissue hide spores
o Gametangia make gametes; female: archegonia while male: antheridia; sperm: move
 Apical meristems: localized regions of cell division at roots/shoots’ tips; bottom
o Cuticle: waxy surface cover to reduce waterloss; mycorrihzae: mutualism for plant/fungi
 Vascular tissue (vascular plants) = the pterophytes; nonvascular = bryophytes
o Seeded vascular plants: gymnosperm/angiosperm; grade: similar adaptations/qualities
 Seed: embryo packaged with nutrients in coat; angiosperm: fruit/flowering plant
 Nonvascular: liverwort, hortworm, mosses; germinating moss spores: one-cell-thick protonema
o Gametophore  gametes; anchored by rhizoids in the ground (no tissues/water absorb)
 Gametophyte: a lower base; tall stalks: sporophyte; mosses: foot, seta, capsule
 Seta: stalk; peristome: upper-capsule to discharge spores gradually w/ wind gust
 Stomata: all vascular plants; gas exchange (O2 in and O2 out) for photosynthesis
o Peat: partially decayed organic material composed of wetland moss; acidic/oxygen poor
 Sporangia: fern spores; bisexual gametophyte; cross-fertilization; zygote anchors; sori: reproduce
o Xylem: water/minerals by trachieds; lignin = strengthen; phloem: amino acids/glucose
 Roots: organs/absorb water/nutrients from soil; anchor vascular plants (substrate)
o Leaves: more SA/photosynthesis; microphylls (lycophytes)  the complex megaphylls
 Sporophylls: modified leaves w/ sporangia; sporangi cluster: sori on underside
 Strobili: cone-like sporophylls in gymnosperm; seedless-vascular: homosporous
 Bixsexual; heterosporous: 2types (sporangia/spores): megaspores/microspores
 Megasporangium Megaspore female gametophyte eggs (microspore male)
o Lycophytes: epiphytes (nonparasitic); spike moss: small/horizontal; ferns have megaphyll
 Large leaves: fronds; homosporous; whisk ferns: branching stems/no actual roots
o Seedless vascular plants: removal of CO2 in atmosphere/coal  O2  livable conditions
 Ferns: sporophyte-dominated life cycle/flagellated sperm/land land in its own life

Chapter XXX: Plants Diversity II: The Evolution of Seed Plants

 Seed: embryo/food supply w/ protective coat; detachable; dispersed by wind/animal  spreading

o Tiny gametophytes: develop spores retainable within sporangia of the parents; sporophyte
 Moist reproductive tissues shield the seed from UV/protect it from dehydration
 Heterosporous: microsporangia  microspores  male gametophytes  sperm
o Gametohpytes dominant in nonvascular; else: sporophyte; integument: protective tissue
 Ovule: megasporium + megaspore + integument; angiosperm; many # of eggs
o Pollen grain: male gametophyte in pollen wall (sporopollenin protects during transport)
 Pollination: transfer of pollen to part of the plant containing the ovules/the eggs
o Seeds: dormant in poor/un-ideal environment; seeds = multicellular tissues for protection
 Progymnosperms: transitional seedless vascular plants; dominated Mesozoic; a cone: conifers
o Largest group: Coniferophyta; Cycads = large cones/palm like leaves (the second largest)
 Evergreens = have leaves throughout the year; tree: diploid; pollen tubes: haploid
  Ovulate/pollen cone; pollination; megasporocyte meiosis = 1 megaspore survives
 Fertilization  ovule becomes seeds w/ embryo/food supply/the large seed coats
 Angiosperm: most common plant; flower: sexual reproduction; sepals protect flower b4 opening
o Petals: bright color  attract pollinator: stamen: anther/filament (flower male portion)
 Carpel (megaspores): stigma  style  ovary w/ ovule inside (develops seed)
o Fruit: mature ovary; protects dormant seed/aids in dispersal; animal feces = spread seed
 Generative cell divies = 2sperm; tube cell: pollen tubes; ovule: the embryo sac
 Cross-pollination: pollen tube  other plant; pollen tube penetrates micropyle
 Integument pore of ovule; sperms  diploid zygote; double fertilization occurs
 One triploid cell produced; cotyledon: rudimentary root/ ~1-2 small seed leaves
 Endosperm: tissue rich in starch/other food reserved for nourishing the embryo
o Earliest angiosperm: Archaefructus; puzzling origin from flowers/fruits; same ancestor
 Monocot: one cotyledon; dictot: two cotyledon (large clade known as eudicots)
 Basal angiosperm/magnoliids show the DNA development pathways of these
o Monocot: one cotyledon/parallel veins/scattered tissues/fibrous (no main root)/3x/1 open
 Eudicot: Two cotyledons/netlike veins/vascular tissue in ring/taproot (main root)
 Pollen grain = 3 opening; floral organs in multiples of 4x or 5x number
o Bilateral shape promotes speciation; pollinators forced to enter flower: certain direction
 Majority of products come from angiosperm for food: wheat/rice/maize/potatoes

Chapter XXXI: Fungi

 Massive diversity; organic material decomposers  recycle nutrients; heterotrophic/multicellular

o Extracellular digestion; most common: multicellular filaments/unicellular: yeast; enzyme
 Hyphae: tubular cell walls/cytoplasm (tiny filaments); cell wall = chitin coating
 Mycelium: hyphae network; maximizes SA-Volume ratio  it’s more efficient
 Septa: cross-walls; ribosomes/mitochondria flow between cells; some lack this
 Coenocytic fungi: continuous cytoplasmic mass w/ many nuclei (no cytokinesis)
o Haustoria: extract/exchange nutrients (host); mycorrihzae: fungi/plant roots mutualism
 Ectomycorrhizal fungi: hyphae sheaths over roots/EC space of the root cortex
 Arbuscular mycorrhizal extends hypae through cell wall/membrane invaginate
 Pheromones: sexual signaling molecules; cytoplasmic union of the fused mycelia: plasmogamy
o Heterokaryotic: one cell w/ unfused nuclei; dikaryoitc: two nucleus; sexual reproducing
 Karyogamy: fusion of nuclei (diploid); meiosis  haploid (dominant) life stage
o Molds: visible mycelia (biofilms); asexual by spores; deuteromycetes: no sexual stage
 Ancestor: single-celled, flagellated, aquatic protist; opisthokonts: posterior location of flagellum
o Nucleariids: amoeba that feed on algae/bacteria; molecular clock analysis; microporidia
 Chytrids: ubiquitous in lakes/soil; decomposers/parasites; zoospores have flagellated spore-tails
o Zygomycetes: fast growing molds; cause food to rot during storage; sporangia: asexual
 Plasmogamy  zygosporangium; multinucleated structure; metabolic inactive
o Glomeromycetes: tiny tips that push into root cells = the arbuscules; mutualism (plant)
 Few gene differences  separate clade; it is smallest clade of fungi species found
o Ascomycetes: saclike asci: sac fungi; sexual stages resemble fruiting bodies (ascocarps)
 Conidia produces asexual spores; specialized hyphae (Neurospora) = sexual part
o Basidiomycetes: basidium (karyogamy occurs); known as club fungus due to its shape
 Basidiocarps: sexual fruiting bodies; widespread; “fairy ring” circle; mushroom
 Endophytes: live inside plant parts w/o harm; most = ascomycetes; beneficial to the plant’s life
o Lichen: symbiotic association between photosynthetic microorganisms/fungi in hyphae
  Photosynthetic parteners: unicellular/green algae/cyanobacteria; fungus  shape
 Most common: ascomycetes; gas exchange/water retention/protection of partener
 Fungi reproduce asexually: ascocarps/basidiocarps; soredia: hyphae w/ the algae
 Fix nitrogen (add to ecosystem); weak to pollution; pioneers after fires/volcanoes
o About 30% pathogenic, mainly to plants; fungal infection: mycosis; grain crops are hurt
 Hurts massive percentage of fruit harvest; ergots on rye derived to make the LSD
 Skin mycoses: ringworm; feet = athlete’s foot; rapidly growing “yeast infections”
o Food (females pigs used to find truffles); alcohol; Penicillium made from fungi; biotech
 Genetic engineering; fungus closest relative = animals; many medical uses today

Chapter XXXII: An Introduction to animal diversity

 Plants: autotrophic eukaryotes (generate organic compounds by photosynthesis); non-motile

o Fungi: heterotrophic that feed by outside absorption; currently 1.3million species found
 Animals cannot self-construct all compounds  consume organisms/compounds
o Animals lack structural support of cell walls; abundant collagen (structural protein)
 Animal-unique: muscle/nerve cells  moving/nerve impulse  different
o Animals: mostly sexual (some asexual); dominant diploid stage; zygote by fertilization
 Cleavage: series of mitotic division by zygote  Multicellular blastula (hollow)
 Grastulation: embryonic tissue layers produced  gastrula
 Larva: sexually immature form morphologically different from adult
 Metamorphosis: transformation of animal into juvenile (resembles adult)
 Hox genes are homeobox genes in animal embryonic development (same genes)
 Vertebrate Hox genes: regulate patterns of anterior-posterior (front-back) axis
 Zygote  8stage cell  blastula (hollow: blastocel)  gastrulation  grastula
 Common Ancestor 675-875million years ago; 99% of animal species are extinct
o Closest relative: choanoflagellates (stationary suspension feeder); protists
o Macroscopic fossils: 565-550million yeas (Ediacaran biota); Australia
 End of Neoproterozoic era  time of increasing animal diversity by fossils
o Cambria explosion: Accelerated diversification 535-525million = many fossils
 Predator-prey  natural selection; rise of atmospheric oxygen; Hox genes
 First arthopods, chordates, echinoderms arose; different hypothesis
 Ordovician, Silurian, Devonian periods followed: diversification/extinction
 Arthropods adapted to terrestial habitats (mili/centipeds); vertebrates  land
 Amphibians and amniotes (mammals/reptiles) show vertebrate migration 360m
o No fundamental new groups in Mesozoic era; animal phyla spread into new habitats
 Descent with modification: flowering plants, nocturnal insect-eaters, dinosaurs
o Cambria explosion: Accelerated diversification 535-525million= many fossils
 Cenozoic era: rise of large mammalians herbivores/predators/niches/cooling
 Body Plan: set of morphological and development traits as a functional whole; key steps
o Gastrulation explains why animals =\= hollow; grade = biological traits shared in group
 Grade =\= clade (group that include ancestral species and all of decendants)
o Radial Symmetry: An cut around center = symmetry; bilateral symmetry: left/right
 Dorsal (top), Ventral (bottom), Anterior (front), Posterior (back) = [bilateral]
 Cephalization: Sensory equipment at anterior end (head) = coordination
o Germ Layers: Ectoderm (skin/nerves), Endoderm (digestion tubes, or diploblastic)
 Mesoderm (blood/bones/organs in middle); diploblastic (2) or triploblastic (3)
o Body Cavity made of fluid separating digestion from outer body wall = coelom
 True coelom from tissue in mesoderm connects dorsal/ventral: coelomates
 Cavity by mesoderm/endoderm (roundworm): pseudocoelomates
  Complete lacking: acoelomates (planarians/flatworm); fluid cushions
 Organs can grow/move in noncompressible fluid; terms refer to grades, not clade
o Protosome/deuterostome development: difference in cleavage, coelom, and blastopore
 Protosome: spiral cleavage; determinate cleavage rigidly determines sides
 Deuterostome: Radial cleavage; indeterminate cleavage (cut cell  embryo)
 Protosome Gastrulation: tube as bind pouch (archenteron) = gut/coelom
 Deuterstome Gastrulation: mesoderm buds from archenteron = coelom
 Protosome blastropore (indentation for archenteron) becomes mouth
 Deuterostome: Blastropore = anus [Chordates/echinoderms]
 Phylogenetic systematic: classify on common descent/clades on Phylogenetic tree
o Clade inferred from anatomical/embryological similarities (homologous); DNA
 All animals share a common ancestor (Metazoa)
 Sponges are basal animals (Poriferia)
 Eumetazoa is animals with tissues (all minus sponges/few other groups)
 Most animals belong to clade bilateria (Cambtian explosion = rapid changes)
 Chordates belong to clade Deuterstomia
o Major bilateral: Deuterstomia, Lophotrochozoa, and Ecdysozoa from ribosomal genes
 Ecdysozoans: Nematodes/arthropods with stiff exoskeleton/shedding (ecdysis)
 Lophohore: Crown of cillated tentacles for feeding
 Distinctive developmental stage in mollusks and annelids: trochophore larva

Chapter XXXIII: Invertebrates

 Invertebrates: animals without backbone; 95% of known animals; all habitats inhabited
o Besides sponges, Eumetazoa have tissues; most animals are bilateria
 Calcerea/silicea: sponges; suspension feeders; sessile; no tissues
 Cnidaria: diploblastic; radial symmetry; gastrovascular chamber (mouth = anus)
 Acolea: simple nervous system/saclike gut
 Placozoa (1 species): thousand cells double-layered; division/budding  child
 Ctenophora: Diploblastic/radial symmetry; plankton; 8combs of cilia to move
o Lophotrochozoans; platyhelminthes (flatworms, bilateral symmetry/CNS/no circulation)
 Ectoprocta (byrozoans): sessile colonies with tough exoskeleton
 Rotiferia: microscopic; specialized organs (alimentary canal for digestion)
 Brachiopod: (lamp shells): stalk anchors to substrate
 Acanthocephalan: curved hooks on proboscis (anterior); intermediate/final hosts
 Nemertea (ribbon worms): use proboscis for prey; no coleom; closed circulation
 Cycliophora (1species): males impregnate females from mother’s body
 Mollusca have soft body that is protected by outside hard shell
 Annelids (segmented words): have body segmentation; crop/gizzard
o Ecdysozoa; Loricifera: deep-sea; telescope parts of body; history unknown; eats bacteria
 Priapula: Large rounded proboscis at anterior; burrow in seafloor sediments
 Tardigardes (water bears) are tiny/live in temperatures close to absolute zero
 Nematoda: roundworms with tough cuticle that coats the body
  Onychorphora (velvet worms) moved from ocean to humid rainforests
 Arthropods: majority of animal species; segmented exoskeleton/joint appendages
o Deuterostoma; hemichordata: gill slits and dorsal nerve cords; largest group: acorn worm
 Echinodermata: starfish; bilateral symmetry as larval, not adults; internal canals
 Chordata: vast majority have backbones; exception: lancets, tunicates, hagfish
 Calcera/Silicea: sponges; fresh/marine water; suspension feeder for food particles in the water
o Water through pores to enter cavity (spongocel) and exits through osculum
 Lacking tissues; interior lining = flagellated choanocytes (collar cells)
 Layers with mesohyl in middle; ameobocytes (manufacture fibers/take nutrients)
 Most sponges hermaphrodites; eggs in mesohyl; sperm carried by currents
 Sponges male/female; zygote = flagellated then attach/sessile adult
 Cnidarians (tissues) have sessile (poylp) and motile (medusa) forms; gastrovascular chamber
o Blastopore acts as mouth/anus; polyp: cylindrical form; tentacles grab prey [hydra]
 Medusa: passive drifting/contractions (jellies); some cnidarians switch forms
 Cnidocytes: tentacle cells defend/grab prey; undigestables expelled by mouth
 Nematocytes sting/penetrate body of prey; microfiliaments = contractile fibers
 Mov’t controlled by concentralized nerve net; hydrostatic skeleton in cavity
o Hydrozoans (alternating generations) as Obelia or Man-of-war; polyp = asexual
 Medusa = sexual reproduction; favorable environment  hydra reproduces
o Scyphozoans (marine) have minimal polyp stage; open sea = no polyp stage altogether
o Cubozoans = complex eyes; highly toxic; box shaped; tropical ocean; strong swimmers
o Anthozoansa (coral reef) have only poylp forms; calcium carbonate external skeleton
 Most bilaterians coelomates (triploblastic); appeared during Cambrian explosion; three major
o Lophotrochozoans have lophophore to feed or trochophore larva; diversity = most phylas
o Platyhelminth flatworms = thin bodies flattened dorsoventrally; acoelomates
 All cells close to water = gas exchange/elimination of nitrogen waste (ammonia)
 Protonephridia = tubule network with ciliated flame bulbs to pull liquid
o Most common freshwater turbellarian: planarians; prey on small/dead animals
 Cilia on ventral surface to glide on mucus; more complex nerves than cnidarians
 Reproduce either asexually (fission) or sexually; hermaphrodites (cross-fertilize)
o Monogeneans/trematodes act as parasites; suckers attach to internal organ/surface of host
 Entire interior = reproductive organs; intermediate host where larva develops
 Immune system camouflage; external parasites of fish; ganglia = sensory input
o Tapeworm lack mouth/gastrovascular cavity; absorb nutrients released by digestion
 Posterior to scolex = proglottids (sac of sex organs that release eggs in feces)
o Rotifers have alimentary canal (digestion tube with separate mouth/anus); very tiny
 Internal organs; pseudocoelom (hydrostatic body); pharynx (trophi) grinds food
 Parthenogenesis: females made from unfertilized eggs in favorable condition
 Asexual species tend to accumulate harmful mutations very quickly
o Lophophorates have true coleom lined by mesoderm; ectoprocts resemble moss clumps
 Colony encased by hard exoskeleton with pores for lophophores to extend
 Brachiopods are dorsal/ventral rather than lateral like clams; marines
o Molluscs = soft body with calcium carbonate shell (squid, octopus, snail); most marine
 Muscular foot, visceral mass contains internal organs; mantle: secretes a shell
 Water-filled Mantle cavity holds gills, anus, and excretory pores; feed by radula
 Life cycle includes trochophore [ciliated larva] with eight classes in the phylum
o Chitons have oval-body with shell divided into eight dorsal plates; body unsegmented
 Foot moves on rock surface; radula to eat algae off of surface; foot = suction cup
o Majority of mollusks = gastropods; torsion allows anus/mantle cavity to be above head
 Single spiraled shell; distinct head with eyes at tip of tentacles; slime/foot/cilia
 Radula = graze on algae or tear prey; mantle cavity acts as lung to exchange gas
 o Bivalia have to halves with hinge in middle (dorsal line and powerful adductor muscles)
 No distinct head radula lost; suspension feeders; clams; water siphon to mouth
o Cephalopods = active predators; tentacles grasp prey/poison in saliva; foot = tentacle
 Closed circulatory system; well-developed sense organ/complex brain; fast learn
 Shelled = ammonities (extremely large); mantle covers visceral mass; speedy
o Annelids = segmented; mouth/pharynx/esophagus/crop/gizzard/intestine/anus, coelom
 Ventral nerve cord/ganglia (nerves); cerebral ganglia; closed circulation
 Chaetae = bristles (fraction for burrowing); structures repeated in segments
 Metanephridium: excretory tubes to remove waste from blood to pores
o Oligochaetaes have bristles made of chitin to move through soil; hermaphrodites
 Sperm stored; clitella secretes cacoon of mucus to pick up sperm  embryo
o Polychaetes have parapodia  more feet per segment; blood vessels function as gills
o Leeches have parasitic bladelike jaw to slit host; hirudin prevents blood from coagulating
 Clade Ecdysozoa sheds tough cuticle; more species than all Multicellular; molting = ecdysis
o Nematodes lack segmented bodies; cylindrical body tapering at both ends
 Alimentary canal; lack circulatory system; nutrients moved by pseudocoelom
 Sexual reproduction internally; females larger than males; trichinosis
 Plant-parasitic nematodes induce root development  nutrients to parasites
 Trichinella controls expression of muscle-cell genes  cell house nematode
 “Animal that act like viruses” since the signal also attracts blood vessels
o Arthropods (1018) with segmented bodies, hard exoskeleton, and joint appendages
 Evolve  segments fuse and become fewer/specialized; two unusual Hox genes
 Evolution of body segments from changes in sequence of Hox genes
o Rigid exoskeleton protects/prevent growth unless coat shed to produce larger coat
 Energy intensive; impermeability prevented desiccation/strength in buoyancy
 Developed sensory organs; open circulatory system propelled by heart to tissues
 Hemolymph-filled body called hemocoel; colelomates; gas-exchanging organs
o Cheliceriforms have clawlike feeding appendages (chelicerae)- pincers/fangs [spiders]
 Anterior cephalothorax/posterior abdomen; no antennae; simple eyes on head
 Earliest: eurypterids (water scorpians); most extinct; bulk = arachnids
 Arachnids =6pairs of appendages/cephalothorax: chelicerae; pedipalps; 4walking
 Pedipalps sense, feed, and reproduce; chelicerae equipped with poison glands
 Gas exchange by book lungs: stacked platelike structures in an internal chamber
 Silk spun by spinnerets into fibers that then solidify; many functions for silk
 “Ballooning” (air flying), wrapping food as gift for mates, cover for eggs, escape
o Myriapods: millipedes/centipedes with jaw-like mandibles; centipeds are carnivores
 Poison claws on foremost trunk segment to paralyze prey/aid in defense
o Insects and relatives > other species; flight (first in dragonflies); head, thorax, abdomen
 Incomplete metamorphosis: Young resemble adults; complete: larva different
 Sexual reproduction; spermatheca in females stores sperm; insects mate once
 Large amounts of diversity; antennae at front to help communicate
 Cerebral ganglion; heart; nerve chords; Malpighian tubules (waste); trachea tubes
 Butterflies = Lepidoptera; most common = Coleoptera [beetles]
o Largest crustacean group: isopod; appendages regained during molting; separate sexes
 Decapods: cuticle hardened by calcium carbonate; carapace covers dorsal side
 Marine (lobster, shrimp, crayfish); cephalothorax covered for protection
 Planktonic copepods feed large whales; barnacles: sessile anchored crustaceans
 Deuterostomes; echindoderms with radial cleavage/formation of mouth opposite of blastropore
o Echinoderms slow-moving (or sessile) marine animals; prickly from skeletal bumps
 Water vascular system: Hydraulic canals + tube feet for mov’t/feed/circulatory
 Larvae: bilateral symmetry; five spokes (not completely radial symmetry)
  Madreporite: water flows in/out of the starfish; central disk: nerve ring/arms
 Digestive glands: absorb nutrients; radial canal allows water to move
o Sea stars [Asteroidea]: mouth directed to substrate; regrowth of body; stomach inverted
o Brittle Stars [Ophiuroidea[: Flexible arms; incomplete digestive systeml scavengers
o Sea Urchins/San Dollars [Echinoidea]: Complex ring mouth adapted to eating seaweed
o Sea Lilies/Feather Stars [Crinoidea]: Feathered arms surrounding top mouth; suspension
o Sea cucumbers [Holothuroidea]: Cucumber-body; tube feed act as feeding tentacles
 Reduced skeleton; lack spines with reduced endoskeleton; oral-aboral axis
o Sea Daises [Concentricycloidea]: Absorb nutrients (diffusion); armless; submerged wood
 Chordates: bilateral/segmented bodies; independently evolved

Chapter XXXIV: Vertebrates

 Vertebrates (backbone/vertebral column); lack of species diversity but high appearance disparity
o Chordata (phylum): bilateral in Deuterostomia clade; sister group = Echinoderms
o Notochord: longitudinal/flexible rod between digestive tube/nerve cord; fibrous tissue
 Skeletal support; muscles for swimming; gelatinous disks in vertebrae in humans
o Dorsal, hollow nerve cord; Central Nervous system (CNS): brain and spinal cord
o Digestive tube extends mouth to anus; region posterior to mouth = pharynx with grooves
 Grooves = pharyngeal clefts (slits open outside to body); gills=gas exchange
 Pharyngeal slits allow water to enter mouth/exit body w/o digestive track
 Terapods pharyngeal clefts play role in ear/structures in neck/head [no gills]
o Chordates have tail posterior to anus; skeletal elements/muscles for aquatic species
o Lanceletes (Cephalochordata): blade-like shape; larvae have chordata traits; eat plankton
 Metamorphosis in adults; mucus net secreted by slits take food particles
 Trapped food enters intestine; gas exchange; burrows in sand; feeble swimmers
 Muscle segmentsin mesoderm (somites) found along notochord in embryos
o Tunicates (Urochordata): brief larva stage; metamorphosis on substrate radical change
 Nervous system degenerates; water drawn by siphon into atrium chamber
 Mucous net filters food; cilia transports to esophagus (“sea squirts” = excurrrent)
o Ancestral chordate resembled lancelet; lancelets: swollen tip on anterior for brain
 Hox genes for regions of brain expressed in small cell clusters in nerve cord
 Craniates: heads  more complex mov’t/feeding behaviors; two clusters of Hox genes (other=1)
o Neutral Crest: cells near dorsal margins of embryo neural tube = variety of structures
 Teeth, bone, cartilage, dermis, neurons, sensory capsules; clefts evolved to gills
 Gill slits allow pumped water through slits (feeding/gas exchange in aquatic)
 Craniates: higher metabolism/extensive muscle system/2chambered heart/kidney
o Most primitive fossil: Haikouella (resembled lancelet); no skull/ears, but had eyes/brain
 Also had muscle segments like vertebrae fish; Myllokunmingia = true craniates
o Hagfish: cartilage skull/no jaws or vertebrae; segmented muscles; keratin teeth; Myxini
 Slime on gills of attacking fish  retreat/suffocation by absorbing water; marine
 Gene duplication  transcription factors called Dlx family; innovations (extensive skull/skeleton)
o Vertebrae enclose spinal cord/taken over roles of notochord; genetic complexity added
o Lamprey (Petromyzontida): oldest vertebrates lineage; larva = buried suspension feeder
 Cartilage skeleton; no collagen; stiff protein matrix; notochord = axial skeleton
o Conodonts: Slender, soft-body vertebrates w/ prominent eyes controlled by muscles
 Barbed hooks made of mineralized dental tissue; impaling prey on mouth hooks
 Food passed to pharynx/crushed; fins; inner ear w/ 2semicircular canals (balance)
 Mineralized bone; jawless, armored swimming vertebrates; extinct = Devonian
o Vertebrate skeleton evolved by unmineralized cartilage; earliest mineralized = dental
 Dental elements  scavengers/predators; armor in jawless vertebrates derived
 Sea lamprey bit side of host as parasite/sucked blood/tissue for nutrients
 Jaw vertebrates (gnathostomes) grip food/slice with teeth; modification of skeletal rods for slits
o Common ancestor of gnathostomes duplicated Hox genes (4); enlarged forebrain; smell
 Enhanced vision; lateral line system (organs row on body side = sensitive)
o Paired fins/tail = effective swimming; earliest: placoderms (“plate-skinned”); predator
 Acanthodian: jawed vertebrate from Devonian period; many species disappeared
o Chondrichthyes (“cartilage fish”) w/ skeleton of cartilge/calcium; bonelike tissue
 Front (pectoral)/back (pelvic) fins (sharks); poor maneuvers/strong swimmers
 Oil stored in liver = buoyancy; swimming = water flow through gills (exchange)
 Resting: muscles of jaws/pharynx to pump water over gills; suspension feeders
 Spiral valve: increased surface area to prolong passage of food in digestive path
 Teeth move to back as old teeth lost; sharp vision; cannot tell apart color types
 No eardrums; electrical field detection by muscle contraction; olfaction by nose
 Oviparous: eggs hatch outside mother’s body; protective coat encompasses eggs
 Ovoviviparous: fertilized eggs remain in oviduct; nourish by egg yolk
 Viviparous: young develop in uterus by yolk sac placenta (absorb nutrients)
 Cloaca: chamber for eggs open to outside; rays use jaw to crush bottom-dwellers
o Majority of vertebrates: clade Osteichthyes: body exoskeleton with matrix of Ca3(PO4)2
 Common ancestor ossified/chondrichthyans lost most of bone through analysis
 Operculum: protective boney flap to breath; water (mouth  chamber  gills)
 Air sac (swim bladder) controls buoyancy; lungs arose from gas exchange here
 Skin glands secrete slimy mucus on skin = faster; oviparous (external fertilizing)
o Ray-finned fish (actinopterygii) use fins to maneuver; imprinting in salmon/trout
 Pressure form human diversion of rivers (dams) interferes with migration pattern
o Lobe-fins (Sarcopterygii) have rod-shaped bones surrounded by muscle in fin types
 “Walked” underwater; end of Devonian = mass extinction of all but 3lineages
 Actinistia (coelacanth); lungfish (Dipnoi) in freshwater; tetrapods (survives)
 Tetrapods walk on ground with muscle-generated forces on feet; head separated (neck used)
o Pharyngeal clefts  ears/glands/other structures; lungs from shallow, oxygen-poor water
 Acanthostega had bones that supported gills (close relative)/tail/delicate fin
o Amphibians; paedomorphosis in aquatic salamanders (mature: retains larva features)
 Frog skin glands: poison/distasteful mucus; legless apodans resemble earthworms
 Amphibian: lives initially in water (tadpole) then land (frog, gills disappear)
 Damp habitats: swamps/rainforest; moist skin for gas exchange; external fertilize
 Eggs dehydrate quickly in air  parents house on body; alarmingly fast decline
 Amniotes: reptile/mammals; amniotic egg has extraembryonic membrane around the eggs
o Most reptiles/some mammals have calcareous shell to protect/slow dehydration
 Amnion: fluid-filled sac cavity that cushions the embryo from mechanical shock
 Yolk-Sac: nutrient stockpile /blood vessels transport/nutrients stored in albumen
 Chorion: Gas exchange….Allantosis: mechanical waste disposal/helps respire
 o Early amniotes lived in dry environment; reptiles: protein keratin scales/internal fertilize
 Eggs laid on land; “cold-blooded” = no metabolism to control body temperature
 Ectothermic: absorb outside heat as main source of heat from solar energy (sun)
 Endothermic: body temperature maintained through metabolic activity (birds)
o Parareptiles: first reptile group; large, stocky herbivores; skin plates=predator-protection
 Diapsids: pair of holes in skull behind eye sockets; two diversifying lineages
 Lepidosaurs (snakes), archosaurs (crocodiles/dinosaurs); pterosaurs = flying
 Collagen-stretched membrane different from birds/bats; muscles/nerves in wings
 Dinosaurs diversified; ornithischians (herbivores); theropods: bipedal carnivore
o Tuataras: surviving lineage of lepidosaurs; largest competitor: rats; most # reptile = lizard
 Snake closest relative = Komodo dragon; vestigial pelivic/limb bones (ancestry)
 Snakes = carnivorous; chemical sensors; no eardrums; sense ground vibration
 Heat-detecting organs; poison in hollow teeth; flickering tongue for smell; jaw
o Turtles related to crocodiles/organisms w/ bony plates; early turtles couldn’t retract head
o Early crocodilians members (alligators/crocs) = small terrestrial quadrupeds w/ long legs
 Birds: toothless = lower head weight; feathers made of B-keratin; aerodynamic
 Flight = enhanced hunt/scavenger; escape; migration; exploit food differences
 Lungs = tiny tubes w/ elastic air sacs for airflow/oxygen uptake; 4chambed heart
 Complex behavior, respiratory-circulatory system  high rate of metabolism
o Birds: bipedal saurischian theropods; feathers evolved before flight (camo/insulator)
 Ratites (kiwi/emu): flightless birds; powerful muscles; small pectoral muscles
 Sternal keel absent; swim faster in water; beak structure shows evolution path
 Mammals possess mammary glands (milk); nutrient-rich; hair/fat layer insulate; endothermic
o Large brain other vertebrate; differentiated teeth; incisors/canine shear…molars grind
o Synapsids: group of amniotes with similar features (no hair. Sprawling gait, laid eggs)
 Single temporal fenestra (hole behind eye socket on side of skull)
 Two of bones for jaw jointly incorporated into mammalian middle ear (Triassic)
 Monotremes (egg-laying mammals), marsupials (pouch), eutherian (placental)
 Mammals underwent adaptive radiation after dinosaur extinction (Cretaceous)
o Monotremes lay eggs, have hair, produce milk from gland on mother’s belly (no nipples)
o Marsupials: higher metabolic rates/milk nipples/birth to live young; embryo in uterus
 Lining of uterus/membrane forms placenta where nutrients diffuse; nursing
o Eutherians: complex; longer pregnancy; embryonic development done in uterus
 Primates: large brain, short jaw, flat face; parental care/social behavior; thumb
 Monkeys/apes have opposable thumbs  “power grip” for manipulation
 Eutherians = most common of all mammals; about 20 total orders in 4clades
o Primates: Madagascar lemurs, lorises/potto [Africa/Asia], and anthropods [monkeys]
 New World/Old World monkeys went adaptive radiation  genetic separation
 Humans: bipedal; language; symbolic thought; manufacture tools; 99% identical genome
o Small gene changes = large effects; humans and chimps = 19 regulatory gene
 Paleoanthropology: study of human origins; closely related to humans: hominid
 Several hominid species coexisted; differed in skull shape/body size/diet
 Only prevailing species: Homo sapiens (initial: Sahelanthropus) from hominids
 Rapid changes in hominin: australopiths: small brain/erect/human-like hands
 A. afarensis “Lucy” in Ethiopia: small head with proportional body
o Rise of savanna and bipedal hominis linked; “Out-of-Africa” thesis; large migration
 Complex locomotion styles; complex tools used from bones of animals
o Earliest fossils: Homo habilis; short jaw; larger brain volume; sharp stone tools used
 H. ergaster (short/straight fingers) used in arid environments for strong tools
 Different teeth = different foods (more meat); reduced sexual dimorphism
o Neanderthals: thick-boned hominin; buried dead; hunting tools; extinct 28000years ago
  NOT stage in evolution between erectus and sapiens (separate lineage)
 DNA Analysis: humans closely related to each other rather than Neanderthals
 Ancestors as H. sapiens (Africa), analysis of mitochondria DNA/Y chromosomes
 Rapid expansion of species spurred by changes in cognition in Africa
 FOXP2 = human language; natural selection = humans/chimps split
 Flores fossils show species with lineage from clade with humans/Neanderthals

Chapter XXXV: Plants Structure, Growth, and Development

 Developmental plasiticty: altering form (envivorn’t issue response); morphology: external form
o Tissue: common cells; organs: group of tissues; root system / shoot system (stalk/leaf)
 Roots: nonphotosynthetic; photosynthates (sugars) imported by the other leaves
o Root: multicellular organ: anchors/absorbs H2O/holds carbs; dicot: taproot/lateral roots
 Adventitious: plant organ growing in unusual location; fibrious root system types
 Root hairs: increased SA absorb water; modified: prop/storage/aerial/buttress
o Stem: organ of alternating nodes (leaves attached)/internodes; auxiliary bud: branches
 Apical bud: terminal bud near top; apical dominance stops buds from growing
 Modified: rhizomes, bulbs (onion), stolons (horizonasexual), tubers (potatoes)
o Leaf: photosynthesis; blade, stalk, petiole (joins-node); veins(mono: straight; di: branch)
 Simple, compound, doubly compounded (leaflets)  withstand the strong winds
 Modified laves: tendrils, spines, storage leaves, reproductive, bracts (~the petals)
o Tissue System; dermal: outer layer; epidermis, cuticle, periderm (replaces older areas)
 Vascular: xylem/phloem; collective: stele; ground: middle layer; pith/cortex
o Parenchyma: most common; flexible; large center vacuole; do most metabolic functions
 Lack secondary walls; turgid w/ water  support plant; topipotent; plastid/starch
o Collenchyma: thicker primary cell walls; no secondary walls; flexible support strengths
 Support the growing cell (celery); unevenly thickened cell walls; alive/functions
o Sclerenchyma: rigid; lignin fortify; secondary walls; sclereids/fiber: support/strengthen
 Sclereids: impair hardness; short/thick walls; fibers: long/slender/tapered threads
o Xylem: tracheids/vessel elements; tubular; water moves cell-cell through pits; efficient
 Micropipes: vessels to allow water to move freely throughout the passage ways
o Phloem: sieve-tube elements; sugar; sieve plates and companion cells (plasmodesmata)
 Indeterminate growth throughout plant’s life; determinate growth: stops after the certain size
o Annuals/biennials/perennials; meristem: embryonic tissue; apical at root tips/shoot top
 Primary growth; lateral: secondary: thickness; cork/vascular cambium thick
 Initials develop other cells; displaced from meristem: derivatives still divisions
 Primary plant body w/ root cap (protect delicate apical meristem/lubricates w/ polysaccharides)
o Zone of cell division/zone of elongation/zone of differentiation; all three tissues produced
 “Star” = eudicots; innermost cortex: endodermis for vascular cylinder boundary
 Pericycle: lateral roots/outermost cell layer in vascular portion; pushes outward
o Leaf primordial: finger-like projections along side of apical meristem make the leaves
 Stomata w/ 2guard cells; the ground tissue: mesophyll: palisade/spongy layers
 Bundle-Sheath in middle; important in C4 plants; leaf traces; helps gas exchange
 Secondary plant body: tissue added by vascular cambium/cork (secondary xylem/phloem tissue)
o Bark/periderm layer = outer; circumference increased; Dendrochronology: tree ring study
 Secondary xylem becomes heartwood (center)/sapwood (outer); phloem = sugar
 o Lenticels: space between cork cells; living cells within woody stem/gas exchange (slits)
 Bark includes tissues external to vascular cambium; secondary phloem/periderm
 Morphogenesis: development of body/organization; growth/differentiation/morphogenesis grow
o Asymmetric cell division: unequal cytoplasmic distribution; guard “mother cell” on side
 Preprophase band: predicts future location of plane for the cellular divisions
o Unequal expansion; water mainly used for expansion; pattern formation/positional info
 Polarity: structural/chemical elements at opposite sides of organism  the axis
 Clonal analysis: cell lineage derived from each cell in apical meristem (develop)
o Phase changes: morphological changes typically occur in leaf size/shape during growing
 EX: developmental plasticity; Arabidopis thaliana: short genome/quick lifecycle
o Meristem identity genes transition vegetable growth to flowering; organ identity genes
 ABC model: flower formation shows interactions of genes to form flower shape
Chapter XXXVI: Resource Acquisition and Transportation in Vascular Plants

 Land plants: aquatic/terrestrial; byrophytes: rhizoids/live near water; vascular tissue = terrestrial
o Root system = exchange nutrient/water; leaves: transpiration/stomata (gas exchanging)
 Phyllotaxy: shoot apical meristem = leaf angles specific to absorb most lights
 Leaf-area index (total upper leaf SA/land); self-pruning: nonsexual leaves die
o Mycorrihzae mutualism to help plant intake nutrients/water; taproot: strong anchoring
 Transport proteins: passive/active; proton pumps (H+) membrane potential / cotransport
o “Coattail” leads to absorption of neutral solutes down electrochemical gradient (sucrose)
 Osmosis/water potential expressed in megapascals [MPa] of the pressure units
 Pure water: 0 MPa; more solutes  negative value; potential energy for working
o Solute potential (ψ)= pressure potential (ψp) + osmotic potential (ψs): solution/solute
 Turgor pressure used to put the protoplast under negative pressure  a mov’t
 Flaccid: losing water (hypertonic solution: plasmolysis/wilting); high: turgid
o Aquaporins: facilitated water-diffusion; apoplate: continuum by cell wall: the ions flow
 Symplast: cytoplasmi channels; bulk flow of nutrients/water by pressure force
 Epidermal cells at tips of roots modified  more nutrients; endodermis surround stele (cortex)
o Casparian strip: belt made of waxy suberin blocking water/nutrients; must use symplast
 Apoplastic route: water/minerals diffuse along cortex using the hydrophilic walls
 Symplastic route: use symplast; transmembrane: apoplast to protoplast/symplast
o Xylem sap: water/dissolved minerals in xylem; transpiration: evaporation in the leaves
 Root pressure  guttation (more water enters the top leaves than what leaves)
o Transpiration pull: water carried upwards in a plant; higher: more negative MPa of the air
 High surface tension (water)  negative pressure potential; cohesion/adhesion
 Warm day  lower diameter  higher pressure; cavitation (water-vapor pocket)
 Stomata: most water loss for the plant; genetic/environ’t control (stomata density): leaf underside
o Waxy cuticle on top; older secondary xylem supports tree but contributes no water mov’t
 High light/low CO2  increased density of stromata  developmentally plastic
 Turgid  open; flaccid  closed; accumulation of K+ ions  H2O moves in
 Flaccid: K+ moves out of guard cells  water exits; membrane voltage potential
o Stomata opening (dawn): light, low CO2, internal clock (guard cells: circadian rhythms)
 Environmental stress (sunlight): close; abscisic acid produced by roots  close
o Xerophytes: desert plants (infrequent rain/CAM plants); also found by little fresh water
 Translocation: transportation of products of photosynthesis to different part of the plant (roots)
o Sieve-tube elements (phloem); phloem sap: sucrose/amino acids/hormones/other sugar
 Sugar source: plant organ (net producer of sugar by photosynthetic methods)
 Sugar sink: organ = net consumer/depository of sugar (roots/buds/fruit/stems)
 Leaves: sugar source; passes through symplast using plasmodesmata/mesophyll
 Transfer cells enhance solute mov’t from apoplast to symplast more quickly
 o Active cotransport; sucrose: sink; high consumption  concentration gradient to diffuse
 Pressure flow: positive pressure by cytoplasm/phloem sap; self-thinning: sinks
 Plasmodesmata: dynamic nature of symplast; viral mov’t proteins cause plasmodesmata to dilate
o Symplastic domains: proteins/RNA sent for coordination between the different cell types
 Phloem: rapid, long-distance electrical signaling; a stimulus for the transcription
o Systematic changes spread through entire body/affect many (or potentially all) organ/cell
 Delivery of flower-inducing signal from leaves to vegetable meristems in plants

Chapter XXXVII: Soil and Plant Nutrition

 Nutrition enhanced by healthy soil; process of organism taking in/using resources; plants: light
o Humus: organic remains; mixes with weathered rocks to make topsoil layer on the top
 Soil horizons: distinct soil layers; top soil = A horizon; deep  less organic
 Loams: fertile soil to support growing life (clay/silt/sand); retain water/minerals
 Large spaces  effective oxygen diffusion; pores allow for the gases exchanges
o Cation exchange: mineral cations displaced by other cations/H+ absorbed by root hairs
 More cation-anion adhesion sites/pH  higher ability to be absorbed by plant
 Heavy rain/irrigation displaces anions  unable for uptake by roots when pushed
o Sustainable agriculture: commitment embracing farming methods to protect nature/soil
 Majority of freshwater used for agriculture; aquifers and land subsidence (sink)
 Salinization: salts accumulate as water evaporates  lowered water potential
 Drip irrigation: slow water release from perforated plastic tube at the root zone
o Fertilization: addition of mineral nutrients to the soil; “N-P-K/15-10-5” to help the soil
 Nitrogen, phosphorous, potassium; decomposing organic material; gradual free
o Soil pH below 5  aluminum ions soluble/absorbed by roots  stun growth/Ca uptake
 Sulfate lowers pH; calcium (lime) raises; most plants prefer a slightly acidic pH
o No-till agriculture: specialized plow creates narrow furrows for seeds (less ground used)
 Soil compaction reduces space  less water absorption/drainage/nutrients in it
o Phytoremediation: nondestructive biotech (concentrates soil pollutants/removes them)
 Essential element: required for plant to complete life cycle/produce the living plant generations
o Hydroponic culture: plants grown in mineral solutions (not soil): shows nutrients used
 Macronutrients: C/O (CO2), H (H2O), N (NO3-, NH4+), K, Ca, Mg, P, S used
 Micronutrients: tiny qualities; C4/CAM plants use sodium ions (CO2 acceptor)
o Chlorosis: lack of Mg  less chlorophyll; mineral requirements change w/ time/enrion’t
 Genetic adjustment: aluminum toxicity resistance, flood tolerance, “smart plants”
 Majority of the plant’s dry mass derived from CO2 assimilated in photosynthesis
 Rhizosphere: soil layer w/ plant roots; rhizobacteria fix nitrogen from the atmosphere/ammonia
o Plant-growth-promoting rhizobactier produce helpful chemicals/antibiotics/absorb toxics
 Nitrifying bacteria changes NH4+ (usable) into NO3- by the plant for processes
o Nitrogen fixation; ATP hydrolyses; legume’s root: nodules filled with the bacteroids
 Mutualism; nitrogen chanced to a usable form; leghemoglobin as oxygen-buffer
 Root attracts bacteria; bacteria enters cortex/divides in pericycle; massive growth
o Crop rotation: legumes switches to restore concentration of fixed nitrogen living in soil
 Legume crop decomposes as “green manure” for the environ’t  cheap fertilizer
o Mycorrhizae: roots/fungi; constant supply of water for plant; increased SA  nutrients
 Ectomycorrihzae: mantle formed over epidermis of plant  extensive SA made
 Arbuscular: not as dense; surface grow; hyphae penetrate epidermis cells/cortex
 Invagination of root cell’s membrane; much more common; nutrient swapping
o Epiphyte (achored onto another plant’s branches/trunk), parasitic, carnivorous plants

 Chapter XXXVIII: Angiosperm Reproduction and Biotechnology
 Plants form mutualistic relationships w/ animals  distribute seeds/food; crop domestication
o Fertilization: union of two gametes to make diploid zygote; sporophyte = dominant
 Receptacle holds sepals, petals, stamen, carpels; stamen/carpel = reproduction
 Stamen: filament/anther w/ microsporangia (pollen); petals/sepals are sterile
 Carpel: ovary, style (tube), stigma (top); ovules in ovaries; pistil: carpel groups
 Complete flowers: all four main parts; incomplete: lacking a portion/unisexual
 Inflorescence: showy clusters of flower buds to attract pollinators (sunflower)
o Microsporocyte form four microspores (meiosis); generative/tube cells  pollen grain
 Pollen tube: long cellular protuberance to deliver sperm to stigma (self-fertilize)
o Embryo sac: female; 1 meiosis/ 3 mitotic divisions to produce 1 egg (other: polar body)
 Two integuments protects megapsorangium except micropyle; megaspores made
o Pollination: Abiotic (wind), bees/insects (most common; nectar); moths; flies; birds; bat
 Wind: enormous quantities spread by the wind; this process, however, is random
o Pollen grain nucleus divides (mitosis)  two sperms; chemical attractant: GABA signal
 One zygote, one triploid nucleus; large: endosperm (food); double fertilization
 In vitro (artificial environ’t) showed calcium increase after zygote; polyspermy
o Coconut milk = endosperm; zygote mitotic division (fertilized egg)  basal/terminal cell
 Basal: supensor (anchored to parent/nutrient transfer/pushed deeper into tissue)
 Cotyledon forms on proembryo; embryo elongation; apical meristem: growing
o Dormancy: metabolic halt (closed by seed coat until it finds an idea environ’t to grow)
 Hypocotyl radicle makes the embryonic root; epicotyl: makes miniature leaves
 Plumule; coleoptile (covers young shoot) and coleorhizae (covers young root)
o Imbibition: uptake of water by low water potential of dry seed; cues break dormancy
 Organ emerges first: radicle (embryonic root); cotyledon shrivels/falls away
 Coleoptile pushes out of soil to air; foliage leaves spread; photosynthesis: food
o Fruit: ovary protecting seed; dispersal by wind/animal; fertilization  hormonal trigger
 Simple fruits, aggregated fruits (raspberry), multiple (pineapple), accessory
 Accessory: other floral parts contribute to fruit (apple); wind/water/animals
 Asexual reproduction; indeterminant growth; fragmentation: segregation of parent into parts
o Vegetative reproduction: clone arises from mature parents; sexual: variation in genes
 Apomixis: asexuall production of seeds; diploid cells leads to embryo/dandelion
o Asexual = no pollinator; all genes passed; self-fertilizing (“selfing”) ensues seed living
 Dioecious species: cannot self-fertilize (unisex); self-incompatibility common
 Biochemical block to prevent the pollen from fertilizing itself; RNA hydrolysis
o Callus: dividing/undifferentiated cells at shoot end; used to make clones; adventitious
 Stock: root system; scion: twig grafted; combine best qualities into one hybrid
o Transgenic GM organisms produced; protoplast fusion w/ tissue  new cloned variety
 Plant breeding: biotech for selective traits; wild crossed with domesticate variety  mix traits
o Genetic engineering and biotechnology; transgenes encode a protein that could kill pests
 “Golden-Rice” contains vitamin A (prevent blindness w/ beta-carotene); ethanol
 Biofuels would reduce CO2 production; biomass from very fast-growing plants
o Worries of dangers of GMO (allergies for humans?); side-effect on the ecosystem parts

Chapter XXXIX: Plant Response to Internal and External Signals

 Etiolation: morphological adaptations for growing in darkness; rely predominantly on stimulus
 o De-etiolation (greening): changes for plant shoots in response to sunlight; chemicals
 Reception (phytochrome)  transduction (secondary messengers)  response
o Transcription factors bind to DNA  certain gene expression; protein phosphorylation
 Activators/repressors; post-translational modification of proteins  polypeptide
o During greening, photosynthetic enzymes are turned on to start self-producing sugar/food
 Hormone: signaling molecules transported (circulatory) by amplification; plant growth hormone
o Trophism: curving towards/away from stimuli; phototrophism: turning to light source
 Coleptile shoots up; cells on darker side elongate faster than cells on light side
o Auxin (IAA): promotes coleptile elongation; lateral/adventitious roots; fruit development
 Expansins: H+ pumped to cell wall; cellulose torn; enzymes stretch microfibrils
 Turgor pressure expands the cell; alter gene expression; secondary growth traits
 Polarity of auxin due to polar distribution of auxin transport proteins in shoot tips
o Cytokinins: control of cell cycle/differentiation; shoot buds form from callus; auxin: root
 Apical control by auxin/cytokinin; auxin increase auxillary buds in decapitated
 Slow aging by inhibiting protein breakdown/start RNA/protein synthesis/anti-age
o Gibberellins: in meristem; stimulates stem elongation/pollen development/fruit growing
 Germination/sex determination; transition form juvenile to adult phases (young)
o Brassinosteroids: plant tissues; promote expansion/division in shoots; regulate growth
 Promote xylem differentiation and inhibit phloem differentiation; germination
o Abscisic acid (ABA): slows growth (seed dormancy/drought tolerance during problems)
 Potassium channels open in guard cells  loss  closing of the stomata pores
o Ethylene produced during fruit ripening/programmed cell death/too much applied auxins
 Triple response enables shoot to avoid obstacle: elongate/thick/horizontal curve
o Senescene: programmed death of organs/plants; molecular apoptosis; cell blebs/breaks
 Fall: abscission layer weakened by small parenchyma/hydrolyzing enzyme in cell
 Ethylene = positive feedback of the ripening to allow the fruit to encase the seed
 “One bas apple spoils the bunch”  ethylene gas in too high amounts for fruit
 Photomorphogenesis: effect of light on plant structure; action spectrum: effectiveness of waves
o Least effective: green; most effective = blue; blue-light photoreceptors: open stomata
 Light-induced slowing of hypocotyls elongation when seedling break the ground
 Zeaxanthin: major blue-light photoreceptor for opening stomata under the cuticle
o Phytochromes: photoreceptor activity units and kinase activity units; two identical units
 Seed germination and shade avoidance; activated best in red wavelengths to work
 Far-red lights inhibit germination; non-polypeptide chromophore to absorb light
o P(r) P(fr)  responses; red light/direct sunlight (right shift) growing taller/branch
 Circadian rhythms: common eukaryotic clocks: alertness/sex drive/metabolism
o Constant environment  deviation from normal cycle; protein through feedback control
 Interactions between phytochrome and biological clocks  passage of night/day
o Photoperiodism: environ’t stimuli to detect time of year/relative lengths of night and day
 Short-day plant: night exceeds a critical dark period; light after interrupts/stops
 Long-day plants: night shorter than critical dark period OR brief flash afterward
 Day-neutral plants: unaffected by photoperiodism once they reach maturity age
o Red light: most effective to interrupt nighttime portion; reversal effects w/ opposite color
 Vernalization: pretreatment with cold  induce wheat flowering (short nights)
o Florigen: hypothetical signaling molecule for day lengths by plasmodesmata; unknown
 Gravitropism: roots display positive/shoots show negative; gravity; occurs during germination
o Statoliths: specialized plastids w/ dense starch grains to lower portions of cell (in root)
 Lateral transport of calcium/auxins by aggregation of statoliths; detect gravity
o Thigmomorphogenesis: changes in form from touch petrubation  changes plant shape
 Integrated “life strategies” to move away from stimulus  move from stimulus
 Thigmotrophism: directional growth in response to touch; rapid short mov’ts
  Action potential nerve impulses used in plants at sensory nerves; responding
o Abiotic: nonliving; biotic: living; drought: increased transpiration/water loss/wilting
 Flooding  suffocation by lack of oxygen in roots; salt stress = lower potential
o Heat-shock proteins: proteins protected from heat stress; chaperonins to refold proteins
 Cold stress: altering lipid composition; freezing  water leaves cytoplasm/death
 Defense against herbivores; amino acid canavanie (shaped like arginine) to kill herbivore insects
o Virulent pathogens: plant pathogens; little harm to plant (no killing): avirulent pathogen
 Gene-for-gene recognition: widespread plant disease recognition (specific gene)
o Hypersensitive response: planned infected cell death/tissue reinforcement / antibiotics
 Systemic acquired resistance: long-lasting priming plant for resisting pathogen
 One leave may send chemicals to rest of the plant to build up disease immunity
 Methylsalicylic acid  salicylic acid  transduction for PR protein producing

Chapter XL: Basic Principles of Animal Form and Function

 Anatomy: biological structure; natural selection favors variations fitting animal needs/demands
o Physiology: biological function based on structure; “form fits function”  homeostasis
 Physical laws = diffusion/strength/exchange; natural selection shapes similar traits in same area
o Rate of exchange directly related to membrane surface area; amount related to volume
 Unicellular = cells touch environment; multicellular = cells exchange nutrients
 Folded surfaces: more surface area; interstitial fluid: liquid between cells
 Filtration adjusts internal fluid composition  constant internal environment
o Cells  tissue  organs  organ system; organs contain tissues w/ different roles
 Digestion (mouth/pharynx/esophagus/stomach/intestines/anus): food processing
 Circulatory (heart/blood vessels/blood): internal distribution of material/nutrients
 Respiratory (lungs/trachea/tubes): gas exchange (Oxygen uptake/CO2 disposal)
 Immune/lymphatic (bone marrow/thymus/spleen/white bloodcells): body defense
 Excretory (kidneys/bladder/urethra): disposal of metabolic waste/blood balancing
 Endocrine (pituitary/thyroid/hypothalamus): coordination of the body’s activities
 Reproductive (ovaries/testes): reproduction … Muscular (muscles): locomotion
 Nervous (brain/nerves/sensory organs): coordination; stimulus/response action
 Integumentary (skin/glands/hair): thermoregulation/protection from dehydration
 Skeletal (skeleton/cartilage): body support/protection of internal organs/mov’t
o Epithelial tissue: covers outside body/lines organs and cavities/tight junctions for cells
 Barrier for pathogen/injury/fluid loss; epithelium: interfaces w/ the environment
 Cubodial (secretion), columnar (intestines), squamous (floor-like tiles, nasal)
 Simple epithelium (single layer), stratified epithelium, pseudostratified (heights)
 Stratified squamous epithelium used or abrasion on surfaces (skin/anus/lining)
o Connective tissue: most common; bind/support other tissue; ECM; sparse population
 Fibers (protein): collagenous (flexibility), elastic (stretch), reticular (thin/branch)
 Bone, blood (white/red cells, plasma, platelets), connective fibers, cartilage
 Adipose tissue (stores fat to insulate/protect), most: loose connective tissue
o Muscle tissue: body mov’t (skeletal [voluntary], cardiac, smooth [involuntary] muscle]
o Nervous tissue (stimuli/transmit); neuron w/ axons; giia (nourish/replace neurons/brain)
o Hormones: signaling molecules by endocrine system; only cells w/ receptors respond
 Hormones: slow/long-lasting; nerve impulse use axons/fast/short/rapid responses
 Regulator: internal control to regulate internal change by external fluctuation [body temperature]
o Conformer: internal conditions change to match environment [fish]; feedback control
o Homeostasis: internal balance to particular value (set point) using negative feedback
  Fluctuations: stimulus; receptor (sensor) detects stimuli for a cellular response
 Normal range: upper/lower limit for environment; positive feedback: amplify
 Regulated changes  function; acclimatization: adjust to change conditions
 Thermoregulation: temperature kept at tolerable change; biochemical process sensitive to temp.
o Optimal temp range; endothermic: birds/mammals warmed by heat from metabolism
 Ectothermic: heat from external source/most invertebrates/must sunbathe (heat)
 Ectotherms tolerate large temperature fluctuations inside; less food needed to live
o Poikilotherm (varying body temp w/ environment); homeotherm (constant body temp)
 No fixed relation between source of heat and stability of the body temperature
 Ectotherm =\= “cold-blooded” (ectothermic animals = higher temp when in sun)
o Radiation (electromagnetic waves), evaporation (remove of heat by surface liquids)
 Convection (transfer of heat by mov’t of air), conduction (direct heat transfer)
 Heat transferred from high to low temp; integumentary system reduces heat loss
 Skin (epidermis/dermis) has dead outer-layer with new cells beneath surface
o Insulation: reduced heat flow; thermoregulation in marine animals (bubbler: warm)
o Circulatory system alters blood route between body core/skin to heat/cool body temp
 Vasodilation (blood vessels get bigger near surface) to transfer/increase temp
 Vasoconstriction (blood vessels shrink in diameter) to cool down temperature
 Countercurrent exchange: flow of opposite fluids maximizes heat/solute mov’t
 Main swimming muscles warmer than nearby tissues = blood quickly moved
o Evaporation helps if external environment increases; water absorbs heat (evaporation)
 Panting/sweating/bathing in water moistens skin/enhances evaporative cooling
o Ectotherms maintain constant temp (simple behavior); extreme: hibernation/migration
 Cold  move to heat source; hot  shade; huddling to warm temperatures
o Endotherms vary heat to match changing rates; hormones affect mitochondria  heat
 Nonshivering thermogenesis in brown fat in neck for rapid heat production
 Endothermic insects warm up by shivering before taking off for extra heat made
o Acclimatiation to seasonal temp = adjusting amount of insulation (coats of fur/fat amnts)
 Proportions of saturated-unsaturated fats vary in ectotherms; “antifreeze” bodies
o Temp sensors in hypothalamus (brain near ears); thermostat nerves to respond to temps
 Body kept near 36-38*C; shivering = rapid muscle contracting to generate heat
 Bioenergetics: overall flow/transformation of energy in animal to meet size/activity/environment
o Food digested by hydrolysis; nutrients absorbed by body cells  generate ATP  work
 Metabolic rate: energy amount used in a unit of time; measured by heat lost
o Minimum metabolic rate for basic functions: basal metabolic rate (BMR): breath/repair
 Standard Metabolic Rate (SMR): metabolic rate of fasting/resting ectoderm
 Size/complexity increase  higher total BMR, but lower per kilogram of mass
o Age/sex/nutrition/temp affects metabolic rate; rate ~ (mass)^(.75); inverse relationship
 Smaller animal: greater SA-to-V ratio  faster heat is lost/gained to surrounding
 Each gram of mouse needs 20x calories as one gram of elephant; large = high net
 Maximum metabolic rates (most ATP) during peak activity  short activities
o Reproduction included in energy budgets (influence energy allocation/critical to survival)
 Locomotion = major part of energy budget; varies between species for energy
o Torpor: physiological state for low activity/metabolic rates = save energy (hibernation)
 Metabolic rates during hibernation lower than maintaining normal conditions
 Slow metabolism/inactivity of estivation (summer torpor) to survive high temps
 Endotherms with daily torpor relatively small when active; high metabolic rates
 Chapter XLI: Animal Nutrition

 Nutrition: food taken in/apart/up for resource extract; herbivores (cattle) eat mainly plants/algae
o Carnivores: other animals; omnivores: both; opportunistic feeders: other foods eaten
 Animals must balance consumption/storage/use of food  survive/reproduce
 Organic molecules  ATP; essential nutrients: needed to survive/cannot be synthesized by self
o Essential amino acids: amino acids obtained only by food; lack = protein deficiency
 Most plant proteins “incomplete” / most proteins in animal products “complete”
o Essential Fatty Acids: Unsaturated; used in plasma membrane; deficiencies are rare
o Vitamin: organic molecule/diverse function/small amounts; classified by solubility
 Thiamine (B1), pork/grains, coenzyme to remove CO2, lack: beriberi (anemia)
 Riboflavin (B2): dairy/meat, FAD/FMN, lack: skin lesions (cracks at mouth)
 Niacin (B3): nuts/meat, NAD+/NADP+, lack: inside lesions/excess: liver damage
 Pyridoxine (B6): meats, coenzyme in metabolic; lack: irritability/anemia/twitch
 Too much: unstable gait/numb feet/poor coordination of body muscles
 Pantothenic acid (B5): everything, coenzyme A, lack: fatigue/numbness/tingling
 Folacin (B9): legumes, DNA/protein metabolism, lack: anemia/birth defects
 B12: eggs/meets, maturation of red blood cells, lack: anemia/nerve system defect
 Biotin: Legumes, synthesis of fat/glycogen, lack: skin inflammation/neuro-MD
 Vitamin C (absorbic acid), citrus, collagen/detoxify, lack: scurvy/weak immune
 Retinol (A): beta-carotene, antioxidant/visual, lack: blind, too much: liver hurt
 D: dairy/egg yolk, bone growth w/ calcium, lack: rickets, too much: kidney hurt
 Tocopherol (E): seeds/oils, antioxidant, lack: degeneration of the nervous system
 Phylloquione (K): Tea/bacteria, blood clot, lack: less clots, more: liver damage
 First 9 water-soluble (safe to OD, urine), last 4 fat-soluble (bad to OD = toxic)
o Minerals: inorganic nutrients required in small amounts; large = upset hormone balance
 Most: Ca, P, S, K, Cl, Na, Mg; others: Fe, F, Zn, Cu, Mn, I, Co, Se, Cr, Mo
o Undernourishment: less energy than required; malnourishment: lack of 1+ nutrient
 Under: body uses up fat/carbs/muscles break down/weak/may be irreversible
 Mal: deformities/disease/death; vitamin A deficiency (rice): blindness/death
o Human diversity: problem to set ideal diet; epidemiology: health study of population
 Types: suspension feeders, substrate feeder (lives on food), fluid feeders, bulk feeder (snake)
o Ingestion: act of eating; digestion: food processing (split by enzymatic hydrolysis)
 Mechanical: smaller  More SA for chemical process; absorption: uptake
 Elimination: undigestables expelled from body (anus); water net consumptions
o Intracellular digestion: Hydrolysis in food vacuoles; simplest; lysosomes; sponges
 Extracellular: breakdown of food in compartments continuous with body
 Pouch w/ 1 opening; gastrovascular cavity: digestion/distribution of nutrients
 Complete digestive tract = alimentary canal: tube connecting mouth/anus
 Single path  specialized components; can ingest food while other is processed
 Peristalsis: contract/relax of smooth muscle; sphincters: muscular layers forms ring-like valves
o Regulate passage between compartments; mouth = oral cavity (mechanical digestion)
 Salivary glands release saliva w/ amylase to hydrolyze starch/gylcogen
 Classic conditions: released w/ odor/senses; food lubricant = easy to swallow
 Mucin = glycoprotein in salivs\a also protects mouth from abrasion; tongue
 Food ball: bolus; tongue pushes food to pharynx (throat region) to esophagus
 Epiglottis stops food from entering trachea; esophagus = smooth/striated muscle
o Stomach: stores food/digestion; elastic; gastric juice + crushed food  chyme produced
 HCl (pH 2) denatures proteins; protease (pepsin) hurts peptide bonds (cleaving)
  Parietal cells secrete hydrogen/chloride ions to make ATP into lumen (cavity)
 Chief cells; inactive pepsin: pepsinogen; converted to pepsin by HCl working
 Mucus lining protects stomach wall; Helionacter pylori causes ulcers to occur
 Top: Cardiac sphincter; lower: pyloric sphincter; acid in esophagus = “heartburn”
o Most hydrolysis of macromolecules: small intestine; first part: duodenum (neutralizing)
 Digestive juices from pancreas/liver/gallbladder + chyme; hormone controlling
 Pancreas alkaline solution (bicarbonate/trypsin/chymotyspin)  neutralizing
o Liver’s bile digests fats in small intestine; bile stored/concentrated in the gallbladder
 Bile: destruction of red blood cells that function poorly/eliminated in the feces
o Jejunum/ileum of small intestine absorb nutrients/water; villi/microvilli: more curves/SA
 Transport across epithelial passive/active; triglyceride digestion has special path
 Fatty acids/monoglycerides combined; coated to form water-solube chylomicron
 Globules transported to lacteal (vessel at core of villus filled with lymph fluid)
 Passes to veins/blood to heart; hepatic portal vein: converge of blood to liver
 Liver distributes nutrients to body; liver removes toxic circulating substances
o Large Intestine: end; colon leads to anus; cecum: fermentation of ingested materials
 Appendix: minor/dispensable role in immune system; colon helps absorb water
 Osmosis by ions (sodium) pumped out of lumen; feces: solid undigestables gone
 Too much water: diarrhea; too little: constipation; E. coli generates methane/H2S
 Vitamin produced; feces = no calories; fiber speeds up mov’t; rectum: storage
 Dentition reflects diet; carnivore: sharp canines; herbivore: broad, ridged mouths; omnivores: mix
o Herbivores/omnivores: longer alimentary canals; cell walls = more difficult digestion
o Vertebrae: mutualistic bacteria in fermentation chambers; digest cellulose; nutrients made
 Ruminants: sheep/deer/cattle: most elaborate for herbivorous diet  nutrients
 Rumen  Reticulum  omasum (cud swallowed) abomasums [4stomachs]
 ATP from oxidation of organic molecules; excess stored as glycogen: polymer of glucose units
o Adipose (fat) cells: secondary site of energy storage; liver glycogen used first, then fat
o Overnourishment: obesity/diabetes; body uses hormones to try to regulate its weight
 Insulin suppresses appetite after meals; PYY suppresses the ghrelin stimulant
 Ghrelin: “meal time; eat!” leptin: by fat tissue suppresses appetite as it increases

Chapter XLII: Circulation and Gas Exchange

 Nutrients/oxygen enter; metabolic by-products (CO2) leave; unicellular: directly w/ environment
o Multicellular: specialized system; tiny blood vessels close to surface of organs/gills/lungs
 Net diffusion of O2 to blood and CO2 to water; short distances = rapid diffusion
 Small nonpolar passively diffuse in plasma membrane; maximize surface area/minimize volume
o Circulatory system (animals) moves liquid between cell intermediate surroundings/tissue
 Cnidarian: central gastrovascular chamber caries digestion/material distribution
 Single opening; short diffusion distance; flast body also helps exchange materials
o Many cell layers = problem; heart pumps blood/interconnecting tubes/circulatory fluids
 Arthropods: open circulatory system; circulatory fluid bathes organs directly
 Fluid: hemolymph; interstitial; sinus = chemical exchange between lymph/body
 Hemolymph returns to heart through pores; heart re-pumps blood to the sinuses
 Closed circulatory system: blood only in vessels/distinct from interstitial fluid
 Lower hydrostatic pressure with open: less costly for energy  more efficient
 Closed: Relatively high blood pressure to deliver nutrients/gas to large animals
o Cardiovascular system: closed circulatory system w/ complicated folded network (SA)
  Arteries: blood form heartorgan; arterioles: small vessels to the capillaries
 Capillaries: microscopic/thin, porous walls; network: capillary beds in tissues
 Capillaries = exchange; converge to venules and veins to go back to the heart
 Arteries (to organs)/veins (to the lungs): different direction (not by oxygenation)
 Portal veins (carry blood between capillary beds); hepatic portal vein  the liver
 Atria receives blood; ventricles pump blood out of heart to the rest of the body
o Single circulation: blood passes through heart in whole circuit; blood collects in atrium
 Contraction pumps blood; net diffuse of oxygen into blood/CO2 out of the blood
o Double Circulation: pumps for diverse tissues; pulmonary circuit if capillaries in lungs
 Pulmocutaneous circuit: capillaries in lung/skin (amphibians); multiple portions
 O2-blood leaves lungs/enters pump (left); contraction  pumped to tissue/organs
 Deoxygenated (oxygen-poor) blood returns to heart: systemic circuit pathways
o Amphibian: 2 atrias/ridge/1 ventricle; underwater: blood flow to skin for gas exchange
 Reptiles (not birds): 3chambered; septum complete (alligator); arteries exit heart
o Mammals/birds: left side receives/pumps oxygenated; right receives/pumps oxygen-poor
 Endotherms use about 10x energy  circulatory system must deliver much more
 Three chambered heart: shut off blood to the lungs when the animal is submerged
 Right ventricle contraction  pulmonary arteries  capillary beds in the lungs to exchange gases
o Return to left atrium  left ventricle  aorta  capillary beds in head/arms = unload O2
 Also visits capillaries of abdominal organs/hind limbs at lower end of the body
 Superior vena cava (top)/inferior vena cava (bottom) take “blue-blood” to heart
 Venae cavae empty into right atrium; repeat; strong septum = divide chambers
o Two atria: thin walls (expand); contraction of artia transfers blood to ventricles (thicker)
 Cardiac cycle: contraction (systole/pumps)/relaxation (diastole/fills with blood)
 Volume/minute: cardiac output; rate of contraction: heart rate (beats/minute)
 Blood pumped in single contraction: stroke volume; average: 5L/min at resting
 Atrioventricular (AV) valve prevents backflow from atrium to ventricle; strong
 Semilunar valves: two exits of heart; aorta leaves/pulmonary artery leaves right
 “lub (recoil of blood against closed AV) – dub (recoil against semilunar valves)”
o Blood squirts backwards in defective valve: heart murmur; autorhythmic (no nerves)
 Sinoatrial (SA) node: pacemaker sets timing/rate for cardiac muscles to contract
 Gap junctions: electrically coupled; electrocardiogram (EKG): medical test
 Nodes placed on skin/detect/record current; atrioventricular (AV) node impulse
 ~.1 second delay; atria empties; bundle branches/Purkinje fibers conduct signals
 Sympathetic/Parasympathetic nerves to speed up/slow down pacemaker function
 Hormones also influence; temperature increase by 1*C = 10beats/minute faster
 Blood vessels w/ empty lumen (cavity): endothelium (flattened epithelial/minimize resistance)
o Capillaries: smallest blood vessels; basal lamina/endothelium; facilitates exchanging
 Arteries/veins: outer connective/elastic fibers (stretch); middle: smooth/elastic
 Artery 3x thicker than vein; strong to allow blood to be pumped under pressure
o Decrease in velocity from arteries to capillaries for blood; slower = more time (exchange)
 Blood flows high pressure  low; contraction generates force in all directions
 Stretched wall/recoil maintains blood pressure/flow in cardiac cycle; muscles
o Systolic pressure: arterial blood pressure when heart contracts during ventricular systole
 Pulse: rhythmic budging of artery walls w/ each heartbeat; narrow arterioles
 Diastolic pressure: lower/still pressure when ventricles relaxed; constant cycle
o Blood pressure fluctuates longer w/ signals; vasoconstriction: contract by stress/worry
 Vasodilation: increase in diameter: drop in pressure (smooth muscles relaxed)
 Endothelial cells make mRNA/cleaved protein endothelin  vasoconstriction
 Nitric Oxide (NO): major inducer to vasodilation (nonpolar signal  response)
 Low blood-flow in brain  faint (body falls/head at level of heart/blood pumps)
  Gravity: rhythmic contractions/contraction of skeletal muscles/change in pressure
 Sudden stopping = less blood returns to heart (still working) = heart malfunction
o Contraction of smooth muscle in arteriole wall (reduces vessel diameter/slower mov’t)
 Precapillary sphincter alter flow if signaled; thin endothelial walls = exchanging
 Blood pressure >osmotic pressure=fluid loss from capillaries; (reverse: opposite)
o Lymphatic: return of fluids by tiny vessels; fluid: lymph; drains at the base of the neck
 Lymph nodes filter lymph/house white blood cells to defend from the pathogens
 Connective tissue of cells (vertebrate blood): plasma; dissolves solute; pH of 7.4; cell’s buffer
o Immunoglobulins (antibodies) = plasma proteins; lipid escort; clot factors; electrolytes
 Serum = blood plasma’s clotting factors; carries nutrient/metabolic waste/gases
 High protein concentration than interstitial fluid; majority = solvent water (carry)
o Erythrocytes (red blood cells): transport O2; biconcave for more SA; lack own nucleus
 Space for hemoglobin to transport O2; lack mitochondria = anaerobic; 4 O2 each
 Leukocytes (white blood cells): phagocytic  engulf pathogens/debris/dead cell
 Found outside circulatory system in interstitial fluid /lymphatic system to fight
 Platelets: structural/molecular function in blood clotting; form emergency plugs
o Coagulant (sealant) inactive: fibrinogen; clotting  fibrin (threads  clot framework)
 Hemophilia: mutation in clotting; thrombus: clot forms that blocks blood flow
o Multipotent stem cells make cell types; located in bone marrow; new cells replace olds
 Hormone erythropoietin (EPO) stimulates red blood cell production (low O2)
o Most deaths: cardiovascular; atherosclerosis: arteries hardening by fat deposites (plaque)
 Leukocytes goes to damage lining/take cholesterol; chest pain = angina pectoris
o Heart arrack (myocardial infarction): damage/death of cardiac muscle tissue by blocks
 Stroke: sudden death of nervous tissues in brain (lack of O2); rupture of arteries
o Low-density lipoprotein (LDL=bad); High-density lipoprotein (HDL=good) cholesterol
 Smoking/processed: trans fats; exercise decreases the LDL/HDL ratio = good
 Hypertension (high blood pressure): damages endothelium in arteries  plaque
 Gas exchange driven by gas partial pressure (total exerted pressured by a mix of various gases)
o Water’s low O2 content/density/viscosity: marine animals spend energy in gas exchange
 Rate of diffusion proportional to SA; inverse to the square of the distance = thin
o Gills: outfoldings for ventilation for gases to exchange over the gills; countercurrent
 O2 in, CO2 out = efficiency; gradients favors diffusion of O2 from waterblood
o Tracheal system (insects): branches near surfaces  gas exchanged (moist epithelium)
 O2/CO2 exchange without open circulatory system; flight = high metabolic rate
o Lungs: specialized respiratory organs; most reptiles/mammals use lungs (except turtles)
 Larynx tips epiglottis over glottis (opening of trachea) so food  stomach only
 Vocal chords: elastic bands for sound; tensed: sound produced by the vibrations
 Two bronchi lead to finer bronchioles; mucus traps contaminants/ “escalator”
 Gas exchange in aveoli (air sacs); surfactants help relieve surface tension on top
 Premature baby lacks surfactants (phospholipids/proteins) = breathing problems
 Lung ventilation: breathing; amphibian: positive pressure breathing (forced airflow=fill lungs)
o Mammals: negative pressure breathing; pull air to lungs; active; exhalation = passive
 Diaphragm; thoracic cavity has double membrane around lungs; sticky layers
 Tidal volume: amount inhaled/exhaled; vital capacity: maximum amounts total
 Residual volume: air remains after forced exhalation; older = higher residual
 Maximum partial pressure of oxygen in alveoli always less than atmosphere
o Birds: pass air in one direction; site of gas exchange: parabronchi; pressure higher in bird
 Breathing control center (medulla oblongata/pons): automatic control (rhythm)
 Surrounding tissue pH = CO2 indicator in cerebrospinal fluid near the medulla
 Increased metabolic activity (exercise): lowers pH; medulla increases breathing
 Tissue capillaries: gradients favor inward diffusion of O2 /release of CO2; respiratory pigment
o Vertebrate hemoglobin: four subunits; iron atom/4 O2; slight change in shape when binds
 Bhor shift: low pH increases affinity of hemoglobin for O2/transport CO2 = help
 Hemoglobin may transport CO2 to assist in blood buffering / stabilizing the pH
o Pronghorns consume O2 extremely quickly; normally, larger = less O2 per body gram
 Myoglobin: oxygen-storing protein in muscles for diving mammals; storage

Chapter XLIII: The Immune System

 Pathogens: infectious agents (disease); the body = protection/nutrients; immune system: defense
o Innate immunity: active upon infection whether or not body experienced the infection
 Acquired (adaptive) immunity: body learns from experience/develops slowly
 Innate: barrier/internal (phagocyte); acquired: humoral (antibodies)/cell-mediated
 Lysozyme (invertebrate): enzyme that digests microbial cell wall/low pH; phagocytosis attacking
o Antimicrobial peptides; pseudopodia surrounds/digests to vacuole/lysosomes/kill/export
 Rely on unique tagging molecules to identify; alternatives for different pathogens
o Barrier defense: mucous membrane traps microbials; oil/sweat glands: low pH=no growth
 Epithelial tissues block infections; saliva/tears/mucous secretion/stomach acid
o Toll-like receptors (TLR) recognizes molecular characteristics of pathogens (cell level)
 Neutrophils: most abundant phagocyte; signaled; macrophages: more effective
 Macrophages: spleen/lymph nodes; eosinophills: defend (multicellular invaders)
 Dendritic cell: tissues in contact w/ environ’t; stimulate the acquired immunity
o Interferons: proteins w/ innate defenses against viral infections; limit cell-cell spreading
 Compliment system: blood plasma proteins to fight infections; lyse invader cell
o Inflammatory response: pain/swelling; histamine (mast cells): signal stored in granules
 Blood vessels dilate/more permeable  blood  bringing antimicrobial peptides
 Pus: fluid rich in white blood cells/dead microbes/debris; sever tissue: neutrophil
 Fever; pyrogens/toxins reset body’s thermostat to higher temp; fast tissue repair
 Overwhelming systematic inflammatory response: septic shock (fatal/high fever)
o Natural Killer (NK) cells recognize/eliminate certain diseases; I MHC = all minus RBC
 NK cell patrols body, goes to diseased cells, kill (prevents spread virus/cancer)
o Some pathogens avoid destruction by phagocytes (adaption); TB = immune to lysosomes
 Lymphocytes migrate from bone marrow (B cells) to thymus (T cells); immunological memory
o Ctyokines: proteins that recruit/activate lymphocytes; B: soluble receptor in the fluid
 Antigen: elicits response from lymphocytes; proteins/carbs; antigen receptors
 Secreted protein: antibody/immunoglobulin (Ig); plasma cells: soluble receptor
 Epitope: antigenic determinant; small accessible portion; specificity in the body
o B cell receptor: “Y-shaped” w/ 4polypeptide chains: 2heavy chain/2light chains on it
 Transmembrane region near end of heavy chain; disulfide bridge in the middle
 T cell receptor: alpha/beta chains; major histocompatibility complex (MHC)
o Antigen presentation: display of antigen fragment on cell surface; specific orientation
 Phagocyte/lymphocyte signals immune system of infection using the antigens
o Class I HMC molecules (not on red blood cells); cytotoxin T cells recognize the antigen
 Class II HMC molecule: dendritic cells, macrophages, and B cells (few types)
 Peptides taken from foreign material; antigen-presenting cells (internalization)
 Helper T cells: assist B cells and cytotoxic T cells to help destroy the infection
o Gene rearrangement/self-tolerance/clonal selection  receptor/memory/low reactivity
 Recombination/transcription (RNA processing)/translation  different memory
o Effectors cells: short-lived/attack pathogen; memory cells: long-lived/small # in body
 Clonal selection: proliferation of lymphocyte into clones by binding to antigen
 Primary immune response: effector production from clones at first exposure
  Plasma cells (specialized B cells)/T Cells help attack the infection to stop spread
 Secondary immune response: next time, more antibodies produced very quickly
 Humoral immune response: activation/secretion of effector B cells; secrete antibodies in blood
o Cell-mediated immune response: activation of cytotoxic T cells; helper T cells in both
 First: antibody-mediated response; 1st extracellular; 2nd = intracellular/cancer path
o CD4: binds class II HMC molecules; helper-T cell and antigen-presenting cell together
 CD8 (cytotoxin T cells) binds to class I HMC molecules; signaled from helper T
 Destruction: protein secretion for cell rupture/cell death/marked for the disposal
o B cells: hallmark of humoral response; differs from other antigen-presenting cells than B
 B cell activation: robust humoral response: thousands of clones w/ many epitopes
o Monoclonal antibodies: produced by culture: identical/specific for same epitope/antigen
 Neutralization: antibodies bind to surface proteins of infection/prevent infection
 Opsonization: antibodies bind to antigens/promote phagocytosis by macrophages
 Complement system: antibodies bind to antigens on surface; water/ion channels
 Cell lyses by water; infected cell: apoptosis; positive feedback: effective response
 Active immunity: memory cell clones; passive immunity: antibodies from mother in the baby
o IgA antibodies passed from motherinfant by breast milk protection for weak immune
 Immunization (vaccination): active; weak antigens given to person  memory
o O Blood = universal donor; AB blood = universal receiver; co-dominant; organ transplant
 Allergens: hypersensitive (exaggerated) antigens response; ex: degranulation (histamine) result
o Anaphylactic shock: abrupt dilation of peripheral blood vessels (blood pressure drops)
 Allergy responses: bee venom/penicillin; syringe w/ epinephrine  countering
o Autoimmune disease: lupus, rheumatoid arthritis, type I diabetes, multiple sclerosis
 Exertion/stress influence affects immune system function; exercise improves
o Immunodeficiency: unable to protect against pathogens; inborn: genetic/development
 Acquired: chemicall/biological agents; SCID; AIDS caused by HIV  dangerous
o Antigenic variation: changes in epitope expression remains in host (influenza mutating)
 Latency: inactive virus state; persists in the nuclei of infected cells to grow in #
 AIDS destroys Helper T cells  body unable to function by fighting infections
 Most effective = “drug cocktails” to mask; impairment of immune  cancers

Chapter XLIV: Osmoregulation and Excretion

 Osmoregulation: control solute concentration/balance water amounts; excretion: nitrogen waste
o Helps conserve water/eliminate excess salts; process of homeostasis; ion concentrations
 Water diffuses down gradient by osmosis; cell in hypertonic solution: shrivel/crenation/water loss
o Osmolarity: two solutions separated by different water pressures; hypotonic: lyze/burst
 Same osmolarity (solute/liters): isoosmotic; water moves but no net water mov’t
o Osmoconformer: balance w/ outside (marine); osmoregulator: differs from surrounding
 Cannot stand change: stenohaline; euryhaline survive large external fluctuations
o Marine water differs in concentration of specific solutes  active transport (homeostasis)
 Fish balance water loss by drinking seawater; gills/kidneys to excrete salts/water
 Unlike bony fish, Marine sharks not hypoosmotic to seawater; tissues have urea
 Water slowly enters shark’s body; influx of water disposed of in urine in kidneys
 Sharks uses Trimethyl-amine oxide (TMAO) to protect tissues from urea damage
 Salt concentration less than seawater  salts diffuse inward/water diffuses out
o Freshwater: internal fluids w/ higher osmolarity than surroundings: loses salts/gains water
 Eating refurbishes; drinking seawater/excreting excess salt from gills/dilute urine
 o Anhydrobiosis: dormant state in dry environment (tarigrades); cell membrane kept intact
 Terrestrial animals lose the water: gas exchange/urine/feces/surface evaporation
o Osmoregulators expend energy to maintain water gradients  solute concentration alters
 Hemolymph fluid (invertebrates): open circulatory system/fluid bathes the cells
 Closed: interstitial fluid contains solutes indirectly controlled by blood content
 Transport epithelium: epithelial control solute mov’t; specific solutes/direction
 Ammonia (NH3): marine fish/very soluble; lost by diffusion; kidneys/surfaces; fish: ammonium
o Urea: mammals; vertebrate liver; ammonia combined w/ CO2; low toxicity; needs NRG
 Uric Acid: reptiles/birds; saves water; semi-solid; insoluble; lots of NRG; gout
o Evolution of uric acid: selective advantage: precipitates out of solution/stored in the egg
 Hydrostatic pressure drives filtration across semipermeable membrane; new solution: the filtrate
o Reabsorption recovers molecules/water to return to body; occurs in the excretory tube
 Secretion (active transport): excretion: urine; blood free of toxins/excess nutrient
o Flatworms (plathelminthes): protonephridia: dead-end tubules to outside pores (surface)
 Flame bulb: cilia beating to draw water/solutes from interstitial fluid  filtration
 Disposal of nitrogenous waste; different tasks in different environment; balance
o Annelids: metanephridia; open to coleom; transport epithelium absorbs nitrogen waste
 Dilute urine hypoosmotic to body fluids; net uptake of water; requires wet skin
o Arthropods: malpighan tubules: nitrogen waste/osmoregulation; no filtration entirely
 Epthilium jets solutes; water follows solutes to tubule/rectum; solute/water kept
 Dry uric acid left eliminated w/ feces; water conserved; outpockets of digestive
 Kidneys: osmoregulation/excretion; tubules; capillaries; nonsegmented portions
o Blood goes to renal artery and drained by renal vein; urine: ureter to urinary bladder
 Urethra (near vagina/inside penis) expels urine to outside; has sphincter muscles
 Mammals: outer renal cortex/inner renal medulla; connected by the nephron
 Nephron: single tubule w/ capillary ball (glomerulus): forms Bowman’s capsule
o Filtration blood pressure forces fluids form blood in glomerulus into lumen of the capsule
 Filtration of salt, glucose, amino acids, vitamins, nitrogenous wastes, molecules
o Filtrate passes to proximal tubules to loop of Henle to distal tubule; collecting duct
 Renal pelvis drained (ureter); 85% of nephrons: cortical (short loops/renal part)
 Juxtamedullary: loops deep into the renal medulla; produce urine/conserve H2O
 Epithelium: reabsorption of solutes/water; most liquids reabsorbed = efficient
o Afferent arteriole provides blood (offshoot of renal artery/capillaries of glomerulus)
 Capillaries converge as they leave glomerulus: efferent arteriole; blood filtered
 Branches form peritubular capillaries: surround both proximal/distal tubules
 Extend down: vasa recta: capillaries for long loop of Henle juxtamedullaries
 Ascending portion of vasa recta near descending portion; interstitial fluid around
 Proximial tubule: active transport of Na  passive of Cl; potassium/glucose in interstitial fluid
o Hydrogen ions/ammonium put in; most reabsorbed as buffer bicarbonate in distal tubule
 [Loop of Henle] Aquaporin water channels; epithelium transportation (water)
 Solutes: Low permeability; osmolarity highest in inner medulla/lowest for cortex
o [Ascending] NaCl leaves; H2O stays; osmolarity lowers: filtrate becomes dilute in cortex
 [Distal Tubules]: Control pH amounts; potassium/salts regulated in concentration
o [Collecting duct] At renal pelvis, hormones determine permeability/transport of urine amt
 Kidneys conserve water; filtrate becomes concentrated; inner medulla permeable
 Urea dissolves out: dilute urine: salts reabsorbed by kidneys  interstitial fluids
o Mammals: hyperosmotic urine by energy input (active transport of solutes): NaCl/Urea
 Nephrons: energy-consuming machine to produce gradient to absorb the water
o Highest osmolarity: loop of Henle  maximized salt diffusion out; NaCl diffuses (outer)
 Countercurrent multiplier system: expend energy to create efficient gradients
 Vasa Recta supplies kidneys w/ nutrients/substances: excrete hyperosmotic urine
  Kidney: highest metabolic rate for renal transport; filtrate: hypoosmotic (distal)
 Osmosis extracts water from filtrate of increasing osmolarity; concentrates solute
o Variations = habitats; juxtamedullary in mammals limits water loss/eliminates salt/waste
 Long loop of Henle: steep osmotic gradients  concentrated in collecting ducts
o Short loops in birds: lower osmolarities; uric acid (paste): reduces urine volume/water
 Freshwater fish: large amounts/dilute urine (hypotonic environment); high filter
 Converse salts (reabsorbing ions/leaving water); amphibians = many settings
 Marine fish: fewer/smaller nephrons; no distal tubules; rid self of divalent ions
 Mammal excretes urea/salt in small volume of hyperosmotic urine w/ minimal water loss in end
o Anticoagulants in bat saliva stop blood clotting  kidney’s offload the absorbed water
 Excretes large volumes of dilute urine as it feeds  conserve water concentration
o Antidiuretic hormone (ADH): vasopressin made in hypothalamus/stored in pituitary
 More ADH: more penetrability for epithelium; large volume of water = low ADH
 ADH binds to receptors to activate aquaporins; Homeostasis: 300 mOsm/L blood
 Mutations (prevents ADH): dehydration/solute imbalance: diabetes insipidus
 ADH: more reabsorption of water; alcohol inhibits ADH release: high water loss
o Rennin-angiotensin-aldosterone system (RAAS): Juxtaglomerular apparatus (JGA)
 Pressure/volume changes: JGA released rennin; yields peptide angiotensin II
 Adrenal glands aldosterone (distal tubules: reabsorb more sodium/water)
 Blocking drugs treat hypertension (chronic high blood pressure); example: ACE
o ADH/RAAS increase the water reabsorption/counter different osmoregulatory problems
 ADH: increased blood osmolarity (dehydration); RAAS: excess loss of salt/water
 Atrial natriuretic peptide (ANP): opposes RAAS; this inhibits reabsorption
 Lower volume/blood pressure; intricate physiological machinery = balancing

Chapter LXV: Hormones and the Endocrine System

 Caterpillar’s metamorphosis controlled by hormones (secreted into extracellular fluid/circulated)

o Circulatory system carries to cells w/ receptors; function of endocrine system (regulate)
 Nervous system: network of specialized cells (neurons) to transmit exact signals
 Ductless glands (endocrine glands) secrete hormones into extracellular fluid to cells via blood
o Exocrine glands secrete substances directly onto surface (salivary); homeostasis/response
 Local Regulators: short distance by diffusion; paracrine: local (neighbor cell)
 Autocrine signaling: the signaling molecules act on the cell that secreted them
o Neurotransmitters (synaptic): diffuse short distance to the receptors; targeted tissue area
 Neurohormones: neurosecretory (brain) secrete molecules from nerves  blood
 Neurons: short, but quick response; hormones: slower response but stay longer
o Pheromones: chemicals released into external environment; mark trails; defend territory
 Polypeptide (water-soluble), amines (mixed), steroid hormones (lipid-soluble)
 Water-soluble polypeptides cannot pass through membrane (insoluble in lipids)
o Water-soluble: hormone receptors (surface); hormone MSH binds on surface/(no enter)
 Water-soluble hormones: exocytosis; binding alters gene transcription of the cell
o Reponse: activation of enzyme/uptake/secretion/arrangement of cytoplasm/transcription
 Signal transduction; G-coupled epinephrine uses the second messenger cAMP
o Response to lipid-soluble hormone: change in gene expression; the DNA binding protein
 Thryoxine/Vitamin D (not steroid): nucleus receptor  specific gene transcribing
o Tissues/cells vary in response; some local regulators share same response as hormones
 Cytokines: immune responses; growth factors: cell proliferation/differentiation
  Nitric Oxide: neurotransmitter/local regulator; vasodilation = improve bloodflow
 Prostaglandins: modified fatty acids; uterus walls contract  sperm reaches egg
 Regulate platelet aggregation/formation of blood clots; may cause a heart attack
o S cells secrete secretin  pancreas releases bicarbonate (raise pH); self-limiting process
 Negative feedback to reduce initial feedback  homeostasis to reduce hormones
o High blood glucose: insulin: uptake of glucose; a drop: glucagon: release of the glucose
 Islets of Langerhans: alpha cells (glucagon)/beta (insulin); enters circulatory
 Pancreas: endocrine/exocrine gland with functions in endocrine/digestive system
o Insulin: nearby cells uptake glucose; slow glycogen breakdown; stops glucose conversion
 Liver/muscle store sugar as glycogen; adipose tissue converts sugars to cell fats
 Antagonistic effects: fuel storage/consume; nutrient  liver (hepatic portal vein)
o Diabetes mellitus: deficiency of insulin  rising blood level/cells unable to take glucose
 Unable to meet metabolic needs; glucose in filtrate excreted; excess urine volume
 Type I: insulin-dependent, autoimmune where person cannot self-make insulin
 Type II: non-insulin-dependent; cells fail to respond to insulin; high glucose level
 Organs: Hypothalmus/Pineal//Pituitary/Thyroid/Adrenal/Parathyroid/ovary/teste
 Larva: PTTH release ecdysone to help molting/metamorphosis; corpora allata: juvenile hormone
o High amts: molting for larger larva; hormone wanes; low JH: pupa stage then adult forms
o Hypothalamus: center of endocrine/nervous; receives signal/nerve info; then it regulates
 Signal  pituitary gland: posterior (neurohypophysis) stored the two hormone
 Oxytocin: contraction of uterus/mammary glands; ADH: kidney water retention
 Oxytocin: positive feedback; regulates milk during nursing; muscle contraction
o Anterior pituitary (adenohypophysis): growth hormone (GH) = metabolism / growing
 Releasing/Inhibiting hormone: TRH: thyrotrophin produced (TSH); both=thyroid
o Negative feedback; anterior pituitary hormone acts on endocrine tissues: excretion/stop
 TSH: tropic hormone; hormone that regulates the function of endocrine gland
o Follicle-stimulating hormone (FSH), luteinizing (LH), adrenocorticotropic (ACTH)
 FSH/LH: gonadotrophins: ovaries/testes; ACTH stimulates the adrenal cortex
o Prolactin (PRL): mammary gland growth/milk making/fat metabolism/ancient hormone
 Melanocyte-stimulating hormone (MSH): pigment-containing cells/hungering
o Growth Hormone  liver’s insulin-like growth factors (IGFs): stimulate bond/cartilage
 Hypersection: too tall; hyposecretion: pituitary dwarfism; very short/weak bones
 Thyroid gland: two lobes on ventral trachea surfaee; normal blood pressure/heart rate/muscles
o Triiodothyronine (T3)/Thyroxine (T4); thyroids secretes T4/targets convert it to T3
 T3 = one less iodine atom; hyperthyroidism: high body temp//”Graves’ disease”
 Hypothyroidism; elevated TSH level (lack of iodine)  swelling of neck/goiter
o Parathyroid: calcium regulation; too low: parathyroid hormone (PTH) put into blood
 Reabsorption in kidneys; vitamin D converted to hormone in the small intestine
 Too high: calctonin; inhibits calcium re-absorption in kidneys  lower levels
o Adrenal glands (kidney): adrenal cortex (outer), adrenal medulla (inner), endocrine cell
 “Fight-or-flight” epinephrine (adrenaline)/norepinephrine: both catecholamines
 Synthesized from tyrosine; increase rate of glycogen breakdown  body fuels
 Increase stroke volume/dilate bronchioles: raise the rate of oxygen transferred
 Blood redirected from the skin/digestive/kidneys  heart/brain/skeletal muscles
 Stressful stimulus: nerve impulses from hypothalamus travel to adrenal medulla
o Adrenal Cortex responds to an endocrine signal; ACTH  cartiosteroids made/released
 Glucocorticoids: promote glucose synthesis from noncarb: skeletal muscles/liver
 Side-effect: NSAIDs (asprin/ibuprofen) treat chronic inflammatory conditions
 Mineralocorticoids maintain salt/water balance; aldosterone: absorb H2O/salts
 Rise in ACTH  increase rate of aldosterone; all steroid made by cholesterol
o Testes make androgens (mainly testosterone); female development = default processes
  Role in human puberty; secondary sex characteristics; anabolic steroid: sideeffect
 Estrogen (Estradiol): maintains female reproductive system/sex characteristics
 Progestins (progesterone): preparing/maintaining tissues of the uterus/growth
o Pineal gland makes melatonin = biological rhythm (sleeping; high amounts at the night)

Chapter LXVI: Animal Reproduction

 Sexual reproduction: diploid zygote by fertilization by sessile egg/motile sperm; asexual: clone
o Fission: parental separate  2equal size; budding outrowth; fragmentation/regeneration
 Parthenogenesis: eggs develop without fertilization; honeybees; female: diploid
o Sexual reproduction: unique combination of genes  variety/adaptations; change sexes
 Ovulation: mature eggs released (midpoint of cycle); some animals: asex/sexual
 Hermaphroditism: individuals  male/female reproductive parts; self-fertilize
 Sex reversal: individual changes sexes based on demographics; female  male
 Fertilization (external/internal): moist habitat = external; spawning: gametes released at once
o “Courtship”  mate selection/increases chance of success; cooperation  copulations
 Pheromones: chemicals released by organisms  physiology/behavior of others
o Zygote: calcium/protein shells w/ internal membrane  nutrients/protection; placenta
 Gonads: organs that make gametes in animals; embryogenesis; amplification
 Egg/sperm (undifferentiated cells in coleom (body cavity); released from wall)
 Female: spermatheca (sac to store sperm for extended periods; favorable env’t
 Cloaca: digestive/reproductive/excretory common opening to the outside area
 Sperm ejaculation: turning cloaca inside-out; female flies need a second mate
 Follicle: outer layer of ovaries; oocyte: partial egg; oogenesis of egg; estradiol prior to ovulate
o Corpus luteum mass after ovulation; residual follicular tissue; no fertilize  break down
 Oviduct (fallopian tube); egg released during ovulation; epithelial lining: fluids
 Endometrium: inner lining; neck of uterus (develop’t): cervix (opens to vagina)
o Vagina: muscular/elastic chamber for deposition of sperm; birth canal; the outside: vuvla
 Labia majora: enclose/protect vulva; labia minora: cavity w/ slender skin folds
 Clitoris: shart, glans, prepce; engorge w/ blood; erectile tissue  a lubrication
o Mammary glands only produce milk in females; secrete milk for the offspring to drink
 Lack of estradiol in males  lower fat deposits in the breasts  very small size
o Testes (male gonads); seminiferous tubules: sperm forms; Leydig cells make androgens
 Scrotum: cooler temp; one term: testicle; low body temp  in abdominal cavity
o Epididymis: sperm complete maturation; ejaculation: propelled through vas deferens
 Ejaculatory duct (seminal vesicle near bladder); opens to urethra to outside
o Seminal vesicles contribute most of semen volume; contains mucus/fructose/enzymes
 Prostate glands: citrate/anticoagulant enzymes; milky; medical problem w/ age
 Bulburethral glands secrete clear mucus to neutralize any acidic urine present
o Penis; sexual arousal; pressure seals off veins  engorged w/ blood; nitric oxide (NO)
 Head (glans): thinner covering/sensitive to stimulation; circumcision (prepuce)
o Vasocongestion (filling with blood); myotonia (muscle tensions): males and females
 Coitus (sexual intercourse); excitement/tension/orgasm/revolution; heart rate
 Orgasm: rhythmic/involuntary contraction of reproductive structures (both)
 Shortest phase; resolution reverses the responses; refractory only in the males
 Gametogenesis: formation of gametes; spermatogenesis: continuous/prolific in adult males
o Oogenesis: immature eggs form in development and mature in later parts of the life
 Female polar bodies: one egg produced; males: four sperm each meiosis cycle
 Female mitotic egg divisions done before birth; oogenesis has long interruptions
o Spermagonia (mitosis)primary spermatocyte(meiosis I)secondary (II)  spermatid
 Acrosome: enzymes to penetrate egg; initial (primordial) stage: the diploid cells
 o Oogonia  primary oocyte  secondary (stops at metaphase II; fertilize = it finishes)
 Hypothalmus GnRH directs anterior FSH/LH to regulate gametogenesis directly; gonad targets
o Male: testosterone/androgen; female: estradiol/progesterone; androgen = secondary traits
 Puberty: sexual traits amplify by hormones/secondary behavioral side-effects
o FSH  Sertoli cells (nourish sperm); LH regulates Leydig (interstitial space)/testosterone
 Inhibin: made by Sertoli; acts on anterior pituitary for negative-feedback levels
o Ovulation after endometrium (lining) thickens/rich blood supply; possible implantations
 Shedding of old lining: menstruation; menstrual (uterine) cycles in females
 Ovarian cycle: cyclic events in ovaries; linked by hormones; follicle/ovulating
o GnRHFSH/LH  Follicular phase (follicles grow/mature)  high estradiol/LH/FSH
 Maturing follicle grows large; luteal phase follows ovulation  corpus luteum
 Negative feedback  low levels of FSH/LH; disintegration; cycle repeats itself
 Proliferative: endometrium thickens again; estradiol/progesterone  new lining
 Secretory phase: endometrial gland secrete nutrient fluid (sustain early embryo)
 Menstrual flow phase: blood vessels constrict  blood shed w/ tissues/the fluid
 Endometriosis: abdominal location/abnormal (ectopic)  bleeding/pelvic pain
o Menopause: ovaries lose responses to FSH/LH  decline in estradiol production (ovary)
 Estrous cycles: absence of pregnancy; uterus reabsorbs endometrium/little fluid
 Conception (fertiliation); cleavage/blastocyst; embryo in endometrium  fetus; hormones sent
o Human chorionic gonadotrophin (hCG): secretion of estrogen in first pregnancy month
 Pregnancy (gestation): carrying embryo in uterus; 38 weeks in humans (varys)
o First Trimester: radical change; trophoblast forms placenta; material/nutrient diffusion
 Monozygotic (identical, one egg)/dizygotic (fraternal, two eggs); organogenesis
 High progesterone  cervix forms plug against infections/ovul and mens’t stops
o Second: hormones stabilize as hCG declines; corpus luteum deteriorates; mov’t occurs
 Placenta replaces progesterone; fetus becomes very active; pregnancy  obvious
o Third: labor occurs; contractions: parturition; thin/open of cervix; delivery of placenta
 Lactation: hypothalamus secretes prolactin helps protect the baby (immunity)
o Contraception (prevent pregnancy); temporary abstinence: rhythm method of control
 Natural family planning; coitus interruptus = “pulling out”  a risky method
 Barrier methods: condoms; diaphragm; IUD birth control pills =\=pregnancy
 “Morning-after” pills prevent/inhibit LH/FSH  no pregnancy occurs/no killing
 Progesin = cervix thickening to prevent sperm from entering; decreases ovulation
 Tubal ligation: tying off section of oviduct to prevent eggs from going to uterus
 Vasectomy in men (vas deferens); abortion: termination of pregnancy in process
o Assisted-reproductive tech: in vitro fertilization IVF/intracytoplasmic sperm injection

C1Chapt

Chapter XLVII: Animal Development

 Preformation: egg/sperm contained embryo (“homunculus”) that simply enlarged in development

o Epigenesis: an animal gradually emerges from formless egg; cytoplasmic determinants
 Cell differentiation: cell specialization; morphogenesis: shape/location of cells
 Model organism: species easy to be studied for particular question/easy to grow
 Cleavage (hollow ball)  gastrulation (3-layered embryo)  organogenesis (layer interactions)
o Fertalization: haploid sperm/egg fuse into diploid zygote; acrosomal reaction in a sperm
 Contact  enzymes eat outer jelly coat  contact  cortical reaction  nucleus
 Acrosome release hydrolytic enzyme on vitelline layer; fast block to polysperm
o Cortical granules fuse w/ egg plasma membrane (cortical reaction)fertilize envelope
 High concentration of calcium in egg  cortical reaction; a rise = egg activiation
 o Zona pellucida: egg ECM; sperm travels through follicle cell; secretionhigh mobility
 No fast-block to polysperm in mammals; centriole (flagella)  1st mitotic spindle
o Cleavage: cells carry S/M phases; no protein synthesis; partitions cells into blastomeres
 Blastocoel: fluid-filled cavity; formed in blastula; determinants split into parts
 Polarity; yolk: stored nutrients concentrated at vegetal pole/lower at animal pole
 Dorsal-ventral cortical rotation: molecules in unpigmented vegetal cortex enter
 Gray crescent: region previously covered by pigmented animal cortex (equator)
 Holoblastic cleavage: relatively less yolk/central blastocoel/big cleavage furrow
 Meroblastic cleavage: so much yolk (insects/fish)  the cleavage furrow partial
 No cell membrane forms around early nuclei; blastula = 128 cells; no cytokinesis
o Gastrulation: new locations for tissues/organs; gastrula embryo; a simple arrangement
 Germ layers: ectoderm (outer), endoderm (digestive), mesoderm (blood/bone)
 Starts at vegetal plate; mesenchyme migratory cells detach from blastocoel wall
 Invagination: cells near vegetal plate bend in; archenteron: deep/narrow tube
 Blastopore: open end (anus); second opening =mouth [deuterostome; proto: flip]
 Dorsal lip: part above crease  dorsal fin; blastopore becomes a complete circle
 Involution: endoderm/mesoderm roll over edges into the interior; ectoderm: out
 Yolk plug: circular blastopore lip consist of nutrient-laden cells; blastopore  in
 Primitive streak: pileup of cells moving inward at midline to make thick middle
 Hypoblast directs primitive streak; forms portion of sac (connect yolk to embryo)
o Organogenesis: layers develop into organs; appearance of tissue folds split/dense cluster
 Notochord: skeletal rod trait of all chordata embryo; neural plate by the signals
 Neural tube: anterior-posterior axis; CND; mesoderm sends the molecular signal
 Neural crest cell migrate to parts of embryo  PNS/teeth/skull bones/other parts
 Somities: cell condensation in mesoderm strips lateral to notochord; serial; small
 Dissociate to mesenchyme cells to migrate  muscles/vertebrae column/the ribs
o Amniotes: embryos of animals surround by fluid in amnion sac  cushion/protection
 Allantoisis: disposal of metabolic waste; chorion: gas exchange; yolk: nutrients
 Extraembyronic membranes: membranes outside membrane to offer assistance
o Fertilization in ovaduct; egg travels to uterus; blatocyst w/ inner cell mass in the uterus
 Trophoblast: outer epithelium provides support services; invades endometrium
 Finger-like projects to blood vessels; epiblast: the upper cell layers; the nutrients
 Implantation complete  gastrulation; placenta = nutrient exchange; germ layers
 Embryo separates  identical (monozygotic) twins arise; differentiate w/ layers
 Mov’t of cells; change in shape involves a reorganization of cytoskeleton; microtubules elongate
o Convergent extension: cell tissue rearrange so that sheets crawl between each other/long
 Cell adhesion molecules (CAMs): glycoproteins; regulate bindings/morphogen
o Cadherins: required calcium ions; involved in tight adhesion of cells at the 8-cell stage
 ECM guides cells in migration/shape change; inhibits migration of path for some
 Fibronectin matrix crucial for convergent extension; cadherin  the organization
 During cleavage division, embryonic cells  differentiated; partitioning heterogenous cytoplasm
o Polarized egg; induction: once initial cells asymmetries set up  gene expression made
 Cell-surface interactions  diffusible signaling molecule for the specializations
o Fate maps: territorial diagrams of embryonic development; shows location of germ layer
 Developmental potentisl: structure range; “founder cells”  asymmetric division
o Specific body plan/axis; in amniotes, the body axes established later (the pH differences)
 Mammals: no polarity until after cleavage; sperm orientation may lead to axes
o Totipotent zygote: develop into any cell; two blastomeres receive different determinants
 Mammal embryo totipotent until 16-cell stage  ultimate fates decided by locate
o Embryonic cell division  differing cells  inductive signal to influence the nearby cell
 Specific genes turned on/off for the rest of the animal’s life; essential in develop
 o Spemann’s organizer: dorsal lip results in making of notorchord/neural tube/other organs
 Pattern formation (spatial organization); positional information; cell location
 Also shows where cell’s descendants will be located by the molecular signaling
o Apical ectodermal ridge (AER): thickened area of ectoderm at tip; bud-limb outgrowth
 Fibroblast growth factor released; removing AER blocks proximal-distal outgrow
 Zone of polarizing activity (ZPA): mesoderm below ectoderm on posterior bud
 Necessary for pattern formation; give rise to finger digits on the hand; induction
 Important protein growth factor: Sonic hedgehog  segmentation of fly embryo
 Wrong amounts of this protein  too many fingers/too few finger (same for toes)
o Hox genes  distinction points during limb pattern formation  pattern formation cues
 Birds/mammals share in common the epiblast/hypoblast during the development

(Chapter XLVIII: Neurons, Synapses, and Signaling

 Neurons: nerve cells (transfer info); long-distance (electrical)/short-distance (chemical signaling)

o Higher order: complex processing in the neurons organized in brain; clusters of ganglia
 Neurons: heart rate/hand, eye mov’t/memories/dreams/etc; electrical: ion currents
 Sensory neurons: transmit info from the sensor to detect external stimuli; sent to brain to analyze
o Majority (brain neurons): interneuron (local connectors); motor neurons: muscle mov’t
 Organizing: Central Nervous System (CNS); other neurons: Peripheral (PNS)
o Neuron’s organelles in cell body; dendrities branching out of self = receive other signals
 Single axon: extension (transmits signals); joins cell body at cone-axon hillock
 Signals transmitted (synapse), synaptic terminal w/ chemical neurotransmitter
 Transmitting neuron: presynaptic cell; receiver: postsynaptic receiver; shapes
 Supporting gila cells nearby to nourish neurons/insulate temp/regulate the fluid
 Membrane potential: voltage difference across membrane; rapid changes: response to stimulus
o Resting potential: -60 to -80 mV; neuron at rest: negative to outside; made by ion amts
o Potassium-Sodium pumps; ATP hydrolysis: actively transport Na+ out to put K+ in cell
 Converting chemical potential  electrical potential uses protein ion channels
 Selective permeability for the neurons; open potassium channels/closed sodium
 Diffusion of K+ outflow  negative charge in cell for the membrane potential
 Excess negative charge inside cell exerts attractive force to positive ions outside
o Net flow of K+ out of neuron proceeds until forces in balance; Cl- build up inside the cell
 Magnitude of the membrane voltage at equilibrium: equilibrium potential (Eion)
 Equation: 62mV*(log[ion outside]/log[ion inside]); average potassium: -90mVs
 Difference  small sodium mov’t (resting cells); sodium=less negative (+62mV)
 Gated ion channels: ion channels open/close to stimuli; alters permeability/potential; ion change
o Hyperpolarization: magnitude increase (membrane potential): stimuli (negative inflow)
 Magnitude reduction: depolarization; gated sodium channels; opposite (positive)
 Graded potential: change magnitude vary w/ stimuli power; nerve signal effects
o Voltage-gated ion channel: open/close to cell potential; depolarization  sodium inflow
 Depolarization  greater current flow; rapid opening  change action potential
 Depolarization increases voltage (threshold value); ~55mV; stimuli independent
 All-or-none response; depolarization -> Na channels  positive feedback loop
o Membrane depolarization opens the Na+/K+ channels; active independently/sequentially
 Sodium channel opens, then closes; the potassium channels then open/switch off
o Resting state: Na/K channels closed; depolarized: Na+ inflow triggers the action potential
 Action potential rising phase: Depolarization continues; Na+ influx  in positive
 Falling: Sodium channels blocked; potassium channels open  inside negative
 Undershoot: sodium channels close; potassium channels open; cell returns to rest
 Second depolarizing after it; unable to trigger action potential: refractory period
 o Action potential initiated: Na+ inflow  electric current = depolarize (synaptic terminal)
 Wider axons: rapid potential; resistance to current inverse to the conductor area
 Lipid-composed layer; depolarize quickly; efficiency; gaps: nodes of Ranvier
 Extracellular fluid contact with membrane at nodes; action potential at the nodes
 Saltatory conduction: inward current of action potential travels to the next node
 Electrical synapses: gap junctions/direct current flow; synchronize neurons for the rapid behavior
o Majority: chemical synapses: synaptic vesicle transfers the calcium signal on membrane
 Action potential depolarizes  channels open  Ca2+ release neurotransmitter
 Exocytosis  travels to synaptic cleft; binds to receptor to allow Na/K to move
 Neurotransmitter released  channel closed; more readily modified for memory
o Ligand-gated ion channel: binding to neurotransmitters on postsynaptic cell for signaling
 Postsynaptic potential; excitatory postsynaptic potential (EPSPs): depolarizing
 Inhibitory postsynaptic potential (IPSPs): hyperpolarization  threshold raise
 Membrane potential farther from threshold; various mechanism types  transmit
o Temporal summation: use EPSPs; different synapses/same neuron: spatial summation
 More potentials  stronger effect; nervous system: multiple excitatory/inhibition
o Signal transduction pathway: secondary messenger; slower onset/last longer; cAMP used
 Adenylyl cyclase hydrolyzes ATP to cAMP; protein kinase A  phorphorylation
o The neurotransmitter types: acetylcholine/biogenic amines/amino acids/gas/neuro-peptide
 Common: acetylcholine (minus heart) release excitatory transmitter; EPSP made
 Nicotine; acetylcholinesterase terminates activity; toxin from bacteria = botulism
 Botox; G-protein pathway; inhibitory effects on heart  a transduction pathway
o Biogenic amines: an amino acid; serotonin from tryptophan; catecholamine dopamine
 Epinephrine/norepinephrine = neurotransmitters/hormones made by the PNS
 Norepinephrine/acetylcholine: major; EPSP made; Parkinson’s disease in brain
o GABA (IPSPs by Cl- permeability) glutamate (brain; excretory); glycine: inhibits CNS
o Neuropeptide; substance P = key excitatory neurotransmitter; pain perception changed
 Endorphins: natural analgesics lower pain perception; morphine/heroin/opiate
o Gases: local regulates; sexual arousal (NO)  smooth muscles relax/fill with the blood
 Not stored in cytoplasm vesicles; synthesized on demand; smooth muscles target
 Carbon Monoxide (CO): regulates release of hypothalamic hormones; oxygenase
 In PNS: inhibitory neurotransmitter that hyperpolarizes intestinal smooth muscle

Chapter XLIX: Nervous System

 Functional magnetic resonance imaging (fMRI): shows oxygen change in brain  active/working
o Radial Symmetry: nerve net to control contraction/expansion of gastrovascular chamber
 Complex: multiple nerve cell: nerves; fibrous; sea stars = nerve ring/radial nerve
 Bilateral symmetry: more complex; cephalization; concentrated nerves at anterior
 Small brain/longitudinal nerve: CNS; outside nerves/ganglia: PNS; micro-mang’t
o Reflexes: body independent response to certain stimuli; dorsal spinal cord self-operating
 Hallow dorsal embryonic nerve cords (chrodata); brain central canal/ventricles
 Central canal/4ventricles has cerebrospinal fluid = brain artery-blood filtration
 Grey matter: neuron cell bodies/dendrites/unmyelinated axons; outside of brain
 White matter: bundled axons w/ myelin; inside brain portion (around ventricles)
o Microglia protect nerves from the microorganisms; oligodendrocytes axon myelination
 Schwann cells work in PNS; astrocytes: structural support/regulate for neurons
 Transfer info at synapses/releasing neurotransmitters/nearby blood vessels dilate
 Blood-brain barrier: tight junctions that restrict substance passage into the CNS
  Radial glia: nerve system develop’t; radial/astrocytes  stem cells (multipotent)
o Cranial nerves connect brain w/ nerves in upper body; spinal nerves: cord/below head
 Motor system: neurons carry signals to skeletal muscles (external stimuli); PNS
 Autonomic nervous system: regulates internal environ’t; control = involuntary
 Sympathetic division: arousal/energy generation (flight/flight): digestion slowed
 Parasympathetic division: calming/self-maintenance functions (slow heart rate)
 Enteric division: digest/pancreas/gallbladder; smooth muscles/peristalsis: (PNS)
 Forebrain/midbrain/hindbrain: embryonic development; last two give rise to lower brain stem
o Cerebrum: forebrain from telencephalon; front; outer rapid expansion: cerebral cortex
 Develop from diencephalon: thalamus/hypothalamus/epithalamus organ centers
o Brainstem: mov’t coordination/homeostasis/conducting info; midbrain, pons, medulla
 Axons w/info pass through brain stem; pons coordinate large body mov’t (climb)
 Midbrain: receive/integrate info; sends coded in along regions of forebrain/sensor
 Midbrain: visual reflexes/peripheral vision; medulla: autonomic (breath/swallow)
o Reticular formation: arousal/sleep (core of brainstem); melatonin made from serotonin
 Dolphins: part of the brain stays active during sleep to ensure breathing; EFG test
o Cerebellum: hindbrain (balance/mov’t); monitor motor commands; hand-eye coordinate
 Epithalamus: pineal; thalamus: sensory input center; hypothalamus: thermostat
o Biological clock: periodic gene expression/cellular activity; synchronized w/ light + dark
 SCN: acts as pacemaker to maintain natural cycles throughout the day; required
o Cerebral hemispheres: left/right; basal nuclei in white matter (planning/learning); large
 Corpus callosum: left/right communication; voluntary mov’t; errors = epilepsy
o Neocortex: outer; not required for advanced cognition; bird’s pallum  top/outer portion
 Cerebral cortex controls all voluntary mov’t; alcohol impairs the brain signaling
 Four lob: frontal, temporal, occipital, parietal; primary sensory: receives/association integrates
o Somatosensory: touch/pain/pressure/position; thalamus directs info to specific locations
 Commands: action potential in frontal lob  axons  brainstem  the muscles
o Broca’s area: face muscles (primary motor muscles); active during the speech generation
 Wernicke’s area: comprehend/unable to speak; active when the speech is heard
o Laterization: establishment of brain hemispheres; two portions work: corpus callosum
 Limbic system: emotions/motivation/olfaction/memory; amygdala for emotion
o Consciousness: subjective/broad; consciousness = emergent property in cerebral cortex
 Neuron competition (survival for resources); synapse elimination: shape nerve system (embryo)
o Neural plasticity: CNS remodeled after birth; occurs at synapses  strength changing
o Short-term memory; long-term memory; information taken from long/put into short
 Cerebral cortex; short stored in hippocampus; complex/strong connect  long
 Thinking: delay in forming connections in cerebral cortex  integrated/respond
o Long-term potentiation (LTP): increase in strength of synaptic transmission; repetition
 Prior: NMDA glutamate receptors open to glutamate/blocked by magnesium ions
 Mg2+ released; influx of Ca2+  insertion of stored AMPA glutamate receptors
 Glutamate releases AMPA receptors; NMDA unblocked; depolarization/action
 Stable increase in size of postsynaptic potentials at synapse; last extended time
 Schizophrenia: episodic structure (distorted reality perception); closer relation: closer risk [twin]
o Neurotransmitter: amphetamine stimulates dopamine; alleviate block dopamine receptors
 Fragmentation in integrated brain functions; dopamine: affects ~1% (population)
o Major depressive disorder: abnormal sleep, appetite, energy level, 1/7 adults, very sad
 Bipolar (manic-depressive): mood swings; genetic/environ’t components; range
o Drug addiction: increased activity  increased “brain reward system”  neutral circuitry
 Ventral tegmental area: neurons direct action potentials (cerebrum)  dopamine
o Alzheimer’s: dementia (progressive mental deterioration); neuron death  brain shrinks
  Neuorfibrillary tangles made of tau protein (normally regulates nutrient mov’t)
o Parkinson’s: difficulty in mov’t/slow mov’t/ridigity; progressive brain illness with age
 Neuron death in midbrain for dopamine; disruption of the mitochondrial genes
 No cure; L-dopa drug; potential cure: implant the dopamine-secreting neurons
o Stem Cell; CNS cannot repair itself until PNS; dividing neurons = multipotent stemcells
 Neural progenitors either become neurons/glia; differentiate into the other cells

Chapter L: Sensory and Motor Mechanisms

 Predator/prey rely on sensation/response; detection/processing (sensory info)  physiologic basis
o Sensory reception detects stimuli; sensory receptors: cells/organs (detect outside body)
 Sensory transduction: converting stimuli into membrane potential of the sensor
 Receptor potential: change in membrane potentialgraded potential (sensitive)
o Transmission: action potential move to CNS; axons quickly transmit signal (integration)
 Perception: action potential reaches brain; all-or-none; distinguish by location
o Amplification: strengthening during transduction; sensory adaptation: lower responses
 Continued stimulation  reduced feeling to the response; enables range of senses
o Mechanoreceptors: physical deformation by mechanical energy (pressure/touch/sound)
 Changes ion permeability (ion channels); knee-jerk reflex: stretch receptors/fiber
o Chemoreceptors: general receptors (solute info)/specific receptors to chemical molecule
 Osmoreceptors in brain detect Molarity changes/stimulate thirst; moth’s antennae
o Electromagnetic receptors: visible light/electricity/magnetism changes; located in eyes
 Fish generate electrical currents to locate nearby/distant objects (prey/migration)
 Dedicated only to external stimuli; infrared receptors: detect body of heat (prey)
o Thermoreceptors: heat/cold; skin/anterior hypothalamus; peppers: capsaicin: Ca influx
 Spicy foods activate same receptors as hot soup; TRP activate by menthol = cool
o Noiceptors (pain receptors) to withdraw from danger; naked dendrites detect noxious
 Hearing/balance related; invertebrate statocysts sense gravity/equilibrium; chamber w/ statoliths
o Grains of sand/dense granules; body hairs detect sound; eardrum (internal air chamber)
 Hearing: ear converts pressure waves to nerve impulses (sound); complex system
 Outer ear (external pinna/auditory cannal)  trympanic membrane (eardrum)
 Middle ear: malleus (hammer)/incus (anvil)/stapes (stirrup)  the oval window
 Eustachian tube  inner ear (fluid)/semicircular canals/cochlea (balancing)
 Organ of Corti: basilar membrane (ear mechanoreceptor) hairs (actin filaments)
o Pitch: cycles per second (Hz) as vibration #; volume: loudness; round window: dampen
 Utricle/saccule perceive position w/ respect to gravity/linear mov’t (Ca otoliths)
 Used for equilibrium in inner ear; three semicircular canals; hairs form curpula
o Lateral line system (fish): mechanoreceptors [low-frequency waves]; bent hair  signal
 Monitor water currents/pressure waves; the water moves curpula: depolarization
 Gustation (taste)/olfaction (smell) by chemoreceptors; tastants and odorants; same in aquatics
o Taste buds: tongue w/ nipple-shaped papillae: sweet/sour/salty/bitter/umami (glutamate)
 Molecule binds to receptor  Phospholipidase C (G-protein); IP3  Ca released
 Depolarization of influx of sodium on membrane; action potential pathway used
  Nose: cilia/cAMP to open flow to calcium/sodium  membrane depolarization
 Photoreceptors: ocellus w/ nerves to brain; compound eyes: light-detector ommatidia w/ lens
o Invertebrate: single-lens eyes w/ small pupil for light to enter; iris: contract/expanding
 Sclera (eyeball white outer layer of connective tissue)/choroid: thin inner layer
 Cornea: transparent front; gives eye color; retina: innermost layer of the eyeball
 Lens/ciliary body (aqueous humor in anterior cavity); vitreous humor: back
 Rods (sensitive to light/no color separation); cone: (color vision/no night vision)
 Fovea: center of visual field; no rods but high cone density; more rod: peripheral
o Retinal: light absorbing vitamin A bound to membrane opsin; makes up the rhodopsin
 Cistrans arrange’t: angled shape  straight shape; “bleaching” color change
 G-protein pathway: cGMP causes hyperpolarization by blocking the ion channel
o Bipolar cells: neurons w/ rods/cones; dark = depolarize  signal; light  hyperpolarize
 Ganglion cells transmit action potential via axons by using the back optic nerves
 Horizontal/amacrine cells: neural pathways that integrate visual info b4 brain
 Lateral inhibition: sharpens edges of image/enhances contract; receptive field
 Optic chiasm: meeting (2optic nerves); ganglion  lateral geniculated nucleus
 Primary visual cortex: axons reach cerebrum and carry the signal; the pigments
 Skeletal muscle (bones/mov’t): muscle fibers w/ myofibrils and thin filaments coiled/wrapped
o Thick filaments: array of myosin; muscles: striated muscle w/ repeated sarcomere unit
o Sliding-filament model: filaments slide longitudally over while using ATP for the mov’t
 Only enough ATP for few contractions; creatine phosphate/glycogen stores ATP
o Tropomysoin/troponin complex: prevents actin/myosin from interacting; Ca: contrac’t
 Transverse (T) tubules: action potential enters sarcoplasmic reticulum (SR)
 ACh by motor neurons  action potential  Ca released  ATP used for mov’t
 Recruitment of motor neurons: force (tension) from more muscles/motor neuron
 Body/posture: always contracted; muscles twitching (action potential): tetanus
o Myoglobin stores more oxygen than hemoglobin; glycolytic fibers (glycolysis for ATP)
 Light meat: glycolytic fibers; dark meat: oxidative fibers rich in the myoglobin
o Fast (rapid/brief)/slow (posture)-twitch fibers; slow: less SR/pumps Ca2+ more slowly
 Cardiac muscles (heart); striated; ion channels (membrane): rhythmic depolarize
 Intercalated disks: adjacent muscle cells interlock = gap junctions  electricity
 Smooth muscle: walls of hallow organs; lack striation; thick filament: cytoplasm
 Regulated by Ca2+; bind to calmodulin  phosphorylate myosin headactivity
 Hydrostatic skeleton: fluid held under pressure (closed body); annelids use for peristalsis mov’t
o Forearm flexes: biceps contracts while triceps relax; extend: biceps relax/triceps contract
 Hydroskeleton: aquatic environ’t; cushion internal organs; crawling/burrowing
o Exoskeleton: hard encasement (calcium carbonate/chtin in fungi); must molt  larger
 Endoskeleton: hard supporting elements (bones) w/ soft tissue; cartilage/joints
o Ball-and-socket joints; hinge joints; pivot joints; animal bodies: complex/nonrigid outline
 Locomotion: mov’t: swimming (sleek), land (powerful muscles), flying (wings)
 Swimming: most efficient; least: flying; smaller animals: more energy used amt

Chapter LI: Animal Behavior

 Behavior: action carried by muscle/glands by nerves in response to stimuli; physiological process

 o Behavior subject to natural selection based on environ’t; color pattern underlies behaviors
 Ethology: animal behavior studies; proximate causation: “how” (what stimuli/past experience)
o Ultimate causation: “why” (how does behavior aid in survival/evolutionary history past)
 Behavior ecology: ecological-behavior study for animals; finding foodsuccess
o Fixed Action Pattern (FAP): behavior directly from simple stimulus by a sign stimulus
 Tinbergen studied the pattern for aggressive behavior w/ red objects (stickleback)
o Kinesis: change in activity in response to stimulus (temp); taxis: oriented mov’t (reverse)
 Taxis: move to (positive)/move away (negative) from the stimulus; fish upstream
o Migration: regular, long-distance mov’t; sun position, consolation, magnetic field=guide
 Circadian clock: internal mechanism for 24-hour activity/cycle (ex: birds flying)
o Circannual rhythms seasons-linked; influenced by light/dark period; migrate/reproduce
 Fiddler crab: the behavior (courting females) linked to lunar cycle (tidal mov’t)
o Signal: stimuli transmitted between organisms; transmission-reception: communications
 Visual: seeing; chemical: smell (olfactory) of signals as the chemical molecules
 Orienting; tactile: tapping; auditory: singing/sounds; von Frisch “waggle dance”
o Pheromones: communicate by chemical odors; common in reproductive behavior (bees)
 Innate behavior: developmentally fixed; all individuals in population: same behavior; learning
o Habituation: responsiveness loss to stimuli w/ no info; focus on danger (not waste time)
 Increases individual’s fitness  more to gene pool of the next species generation
o Imprinting: formation of behavior during sensitive period (critical period): a young age
 Innate to respond to stimulus; outside world: imprinting stimulus; “mother” form
o Spatial learning: memory establishment that reflects the environ’t structure (landmark)
 Tinbergen: the wasp locates its nest by using the surrounding indicators (visual)
o Cognitive maps: representation in nervous system (spatial relationship for surroundings)
 Navigation effective/efficient by using landmark positions; nutcracker bird study
o Associative learning: relating an environ’t feature w/ another; learning from experiences
 Palvov’s classical conditioning: arbitrary stimulus associated w/ outcome (dog)
 Operant conditioning: trial-and-error learning; rewards/punishments given out
o Cognition: the complex knowing process by awareness/reasoning/recollecting/judgment
 Problem solving: cognitive activity of devising method/plan to beat the obstacle
o Juvenile bird sings/compares; once the song is memorized, it is “crystallizes” as the final
 Cross-fostering study: young of one species traded w/ another; environ’t/diet/etc alters behavior
o Twin study: researcher compare identical twins raised in different households w/ groups
 Twin studies used instrumentally for studying schizophrenia, anxiety, alcoholism
o Fru gene controls male courtship ritual; master regulatory gene that directs the expression
 Behavior variation within a species; some parts of population operate differently
o Behavior shaped by combined effects on multiple genes; small variation = large outcome
 Forging: searching/capturing food; low-population density: short distance; large-density: further
o Optimal foraging model: natural selection favors minimum cost to find/maximum food
 Predation risk influences foraging behavior; forager = alternate (avoid predator)
o Promiscuous: no strong pair-bonding/lasting relationships; monogamous: one mating
 Polygamous: multiple; 1male/several females: polygyny; opposite: polyandry
 Monogamous species: males/females morphological similar: look very similar
 Polygyny: dimorphic; males larger than females; polyandry: females much larger
 Male parental care low in species with internal fertilization; increase certainty
o Intersexual (males chooses female) /Intrasexual (males stop other males)/sex selection
 Females choose healthy male more likely to reproduce; phenotype = influencing
o Agnostic behavior: ritualized contest that determines who can get the food or the mate
 Behavioral/morphological variation very high in vertebrate despite preferences
o Game theory: alternative strategies where outcome depends on plans of the individuals
 Altruism: selflessness; worker bees sterile, but they labor on behalf of fertile queen/protect hive
o Inclusive fitness: total effect an individual has on passing its genes in offspring/aiding
 Depends on benefit to recipient, cost to the altruist, and coefficient of readiness
o Coefficient of readiness (r) = fraction of shared genes; Benefit (B) = average # of extra
 Cost (c) = how many fewer offspring the altruist products; “rB > C” = favored
 Hamilton’s Rule: natural selection favors altruist; helps relatives: kin selection
o Reciprocal altruism: one species aids another for a future favor; large social groupings
 “Cheating” = not returning the favor; “tit for tat” = same reciprocated repayment
o Social Learning (root of culture): watching others to learn how to act like other people
 Cultural-based changes in phenotype = shorter time scale form natural selection
o Mate-choice copying: individual of population copies the mate choice of other animals
 Selected by another female as the mate  more attractive to the other females
o Sociobiology: behavior characteristics exist due to gene expression from natural selection


Chapter LII: An Introduction to Ecology and the Biosphere

 Ecology: interaction study between organisms/environment; a scale hierarchy (organism/global)

o Organism Ecology: subdisiplines of physiology/evolutionary; environment on organism
 Population: same species/area; population ecology: factors on pop size/changes
 Community: different species/same area; community ecology: the interactions
 Ecosystem: abiotic/biotic; ecosystem ecology: the energy flow/chemical cycling
 Landscape: mosaic area; landscape ecology: exchange of energy/materials/life
 Biosphere: everything; global ecology: regional exchange influences distribute
 Natural History: change in nature (observations); rigorous experimental science w/ hypotheses
o Evolutionary time: organisms adapting to environment by natural selection over a period
 Ecological time: minute frames of interactions between organism at its environ’t
o Environmentalism: protect nature for future generations; Carson’s Silent Spring (DDT)
 Biotic (living)/abiotic (nonliving); biogeography: past/present study for distribution of species
o Dispersal: mov’t of organisms form centers of high population study to less dense region
 Understanding geographic isolation key to evolution tracking/current distribution
o Natural range expansion  dispersal influence; new species interrupt communal balance
 Behavior limiting distribution = habitat selection; biotic = predators/competition
o Abiotic factors: temperature, water, salinity, sunlight, rocks/soil (the pH concentration)
 Components of climate; macroclimate: regional scale; microclimate: very local
o Earth’s patterns determined by solar energy/planet mov’t in space; sun warms/cycles air
 Moist coastal currents  moderated temp (high specific heat of water); breezes
o Tropics: sunlight strikes latitudes; higher angles oblique  more light diffuses surface
 Tilt of 23.5*; September equinox: equator faces sun directly; equal light/dark hrs
 June solstice: Northern hemisphere tilts to the sun (longest day/shortest night)
 March equinox: equal; Dec solstice: Southern hemisphere (short day/long night)
o Descending air absorbs moisture; ascending air releases moisture; hot air rises/cold sinks
 Doldrums = middle; Northeast/South East trades; Westerlies Winds=(30  60*)
 Mediterranean Climate: cool, dry breezes warmed on land; hot/rainless climate
o Wind-shadow effect on leeward side of mountain creates desert by blocking the moisture
 Cleared areas = greater temp change than forest interior (solar radiation/currents)
o Long-term climate change: animals migrate to search for old, similar environ’t/extinction
 Biomes: major terrestrial/aquatic zones; largest: aquatic; marine: 3% salt/freshwater: .1% salt amt
o Oceans = 75% of surface; marine algae  major O2 producer/CO2 consumer; evaporate
  Communities distributed: water depth/shore distance/light/open water or bottom
o Photic Zone (upper): light for photosynthesis; aphotic zone: little light penetrates (dark)
 Benthic Zone (sand/soil): bottom substrate; occupied by the benthos organisms
 Detritus: dead organic matter falling form surface; 2k-6k meters: abyssal zone
 Thermocline: uniform separation by density: lake turnover (mainly summer)
o Oligotrophic lake: nutrient-poor/oxygen-rich; eutrophic lake: nutrient-rich/oxygen poor
 Oligotrophic become more eutrophic as runoff adds sediments; waste dumpbad
 Littoral zone: the rooted/floating plants/limnetic: cyanobacteria/phytoplankton
o Wetlands: inundate by water sometimes/supports plants to water-saturated soil; O2-poor
 Basin: shallow; riverine: flooded river banks; fringe: coasts of large lakes/the sea
o Rivers/streams: cold, clear, turbulent, swift; O2-rich; narrow w/ rocky bottom; diversity
 Headwater streams in grasslands/deserts = phytoplankton/rooted aquatic plants
o Estuaries: transition between river/sea; sea water at bottom and river water at very top
 Pollution; worms/crabs/breeding ground; complex network of the tidal channels
o Intertidal zone: periodically submerged/exposed by tides; upper: exposure to air/salinity
 Oxygen/nutrients high; rocky/sandy; hurt by oil impact; hard substrates (star fish)
o Oceanic pelagic zone: vast realm of open blue water w/ currents; 70% of Earth’s surface
 High O2 levels; low nutrients; thermally stratified year-long; phytoplankton live
o Coral Reefs: most diverse; photic zone; calcium carbonate; coral = cnidarian; mutualism
 Pathway: fringing reef (side of young, high island) barrier reef  coral atoll
o Marine benthic zone: seafloor below surface of costal (neritic) zone; receives no lights
 Abyssal zone w/ continuous cold; deep-sea hydrothermal vents (H2S produce)
 Disturbance: storm/fire/human activity; impact of climate on a climograph (temp/precipitation)
o Averages; intergradations (ectone): narrow/wide; vague overlap of specific boundaries
 Forest upper canopy, lower-tree layer, shrub understory, ground layer, root layer
 Biomes: dynamic; dominant plants depend on periodic disturbance; many types
 Tropical rain forest (heavy rainfall)/tropical dry forest (seasonal rain); little seasonal variations
o Highest diversity in terrestrial biome; rapid population growth/agriculture=negative effect
 Epiphytes (bromeliad/orchids) cover rainforests; thorny shrugs cover dry forest
o Deserts: Near 30N; low rainfall; high ranging temps; low/scattered vegetation; C4/CAM
 Nocturnal animals; water conversation important; toxic spines in shrubs common
o Savanna: Equatorial/subequatorial; warm yeararound; scattered trees; dry=fires common
 Earliest humans = savannas; large plant-eating animals; grasses cover the ground
o Chaparral: midlatitude coasts; seasonal rains; the shrubs/small trees; high plant diversity
 Native mammals: browsers (deer/goat); seed germination after a hot fire occurs
o Temperate Grassland: North America/Asia; freezing winters/very hot summers; grass
 Large grazers (horse/bison); no woody shrubs/trees due to large mammals eating
o North Coniferous Forest (taiga): largest terrestrial biome; winters: cold/long (Siberia)
 Cone-bearing plants dominant; migratory birds; outbreaks of insects hurt trees
o Temperate Broadleaf Forest: New Zealand/Australia/Europe; heavy rainfall; hot/humid
 Closed canopy, 1-2 strata (understory), shrub layer, herbaceous, few epiphytes
 Hibernation in winter; reduced photosynthesis during the winter; slow recovery
o Tundra: frozen; high rainfall only in alpine tundra; freezing; permafrost limits growth
 Chapter LIII: Population Ecology
 Population ecology: population study w/ environ’t relation; dynamic relation (genetic/evolution)
o Population: single species living in area; rely on same resources; breed/interact w/ other
 Density: unit area/volume; dispersiob: pattern of living distribution in boundary
o Mark-recapture method: the wildlife size = (first sample*recapture)/(second sample
 Births/immigration (increase); deaths/emigration decrease  dynamic system
o Clumped: aggregation in patches; inuform: territorialism (antagonistic socials); random
 Demography: study of vital statics of population/change over time in the area
o Life tables: age-specific summaries of survival patterns; cohort: group of the same age
 Shows # of alive at start/deaths/death rate/the average additional life expectancy
o Survivorship curve: proportion plot in cohort still alive at each age; a negative slope
 I (top): humans; II (middle): hydra/gopher; III (deaths: start, then sustain): oyster
o Reproductive table (fertility schedule): reproductive rates w/ respect to age/offspring #
 Life history: reproduction  how often organisms reproduction  how many offspring made #
o Big-band reproduction (semelparity): one time; iteroparity (repeated reproduction)
 Eggs once vs. few; survival rate of offspring/likelihood of adult survival affect it
o Selective pressure: trade-off between number/size of offspring (extra energy investment)
 Per capita increase (∆N/∆T): (Births or immigration) – (emigration or death): net growth rate
o B = bN; D = dN; ∆N/∆T = bN – dN; per capita rate of increase: r = b-d (r > 0 = growing)
 When r = 0  zero population growth; instantaneous growth using calculus
o Exponential growth: geometric population growth; J-curve; new rebounding population
 Carrying capacity (K): maximum population size that the environ’t can hold at any given time
o Logistic population growth  “S-curve” (flattens out at the top to natural limit factors)
 Lag time before negative effects of growth realized; Alee effect: too small = bad
o K-selection: density-dependent range (life history traits sensitive to population density)
 The r-selection: density-independent selection; exhibits type III survival growth
 Regulation: birth rate does not change w/ the population density: density independent; constant
o Density independent: death rate rises w/ population density as the birth rate also shrinks
 Competition for resources, territorial, disease, toxic waste, intrinsic inside factors
o Population dynamics: complex interaction between Abiotic/biotic factors on population
 Harsh weather; saw-tooth graph (predator overkills prey  predators die/repeat)
o Metapopulation: local populations linked by migration; patches interact w/ other patches
 Human global population not exponential/increasing rapidly; disease/AIDS/voluntary pop control
o Demographic transition (2nd): low birth rates – low death rates = zero population grow
 Associated w/ health care/sanitation/education (women)/available medical help
o Age-structure pyramid: wide-base/the small top: developing rapidly-growing countries
 No growth: small base; rectangular structure; shows % w/ respect to the age/sex
o Infant mortality: high in developing (less industrial) countries due to unsanitary lifestyle
 Ecological footprint: aggregate land/water area required by each person/waste
 Highest in crowded, somewhat industrialized areas (India/China) on a used map
o US: 10 ha (hectares) = 25 acres; food (famine/malnutrition) will be main limiting factor
 Nonrenewable resources due to the high net consumption; lack of sanitary water


Chapter LIV: Community Ecology

 Community: interactions of population; vague boundaries; interspecific interactions in region
o Interspecific competition (-/-): species/individuals fighting for shared resoures  less
 Competitive exclusion: slight reproductive advantage to beat inferior competitor
o Ecological niche: sum of use of biotic/Abiotic resources; species “fits into” ecosystem
 Resource partitioning: differentiation of niches  coexist in same community
 Fundamental niche: potentially occupied by the species; realized is actually used
o Character displacement: traits diverge more in sympatric populations (not in allopatric)
 Same area  different resources used to avoid competition/gain most resources
o Predation: (+/-); predator eats prey for nutrition; natural selection forces for adaptations
 Cryptic coloration (camouflage); aposematic coloration: bright chemical/toxin
 Batesian mimicry:palatable/harmless species copies sound of dangerous species
 Mullerian mimicry: many unpalatable species w/ same coloration“blend in”
o Herbivory (+/-): large herbivore eats alga/plant; plants/insects use chemicals  protect
 Symbiosis: two or more species live in direct/intimate contact w/ another animal
o Parasitism (+/-): parasite takes nutrients from host; endoparasites (skin)/ectoparasites
 Mutualism (+/+); either obligate (needs other to survive) or facultative (option)
o Commensalism (+/0) “hitchhiking species” that do not harm the host but do self-benefit
 Species diversity: variety of different organisms  species richness and relative adundance
o Shannon diversity shows diverse makeup of the specific region; sampling method used
 Trophic structure: feeding relationships between organisms; food chain made
o Food web: relation “who-eats-who” [primary producer consumer levelsdecomposer]
 End of arrow shows what the species is eaten by; humans at top; plants: bottom
o Energetic hypothesis: food chain length limited by inefficiency of energy transfer (10%)
 Biomass: total mass of individuals in population; high photosynthetic  longer
 Dynamic stability hypothesis: long food chains less stable due to fluctuations
o Dominant species: most abundance/biomass; invasive species: outside the native range
 Keystone species: not abundant in community by strong influence on structure
 Lacking keystone  reduced size for the rest of the population by quick decline
o Facilitators: positive effects on survival/reproduction of other species in the community
 Foundation species (“engineers”) dramatically alter physical environ’t largely
o Bottom-Up model (V [vegetation]  H [herbivores]); nutrients control everything above
 Nutrients control vegetation which controls herbivores which controls predators
o Top-down model: predators limit everything below them  the trophic cascade model
 Biomanipulation: attempts to prevent algal bloom/eutrophism w/ more predators
 Stability: tendency to reach/maintain constant conditions; disturbance: removes resource/species
o Nonequilibrium model: most communities as always changing due to the disturbances
 Intermediate disturbance hypothesis: moderate disturbance  high levels of species diversities
o High disturbance reduce diversity; low levels: competitively dominant species beat lower
 Fire/storms = constant problems that wipe out resources needed by community
o Ecological succession: disturbance replaced by sequence of species; an eruption/glacier
 Primary succession: autotrophic prokaryotes/protist/moss/lichen grow on rocks
 Secondary succession: area slowly starts to turn back to its original state: shrubs
 Pioneer (liverwort/fireweed)  small plants  large plants  animals return
o Nitrogen/nutrient composition/pH slowly changed back to normal; humans = big impact
 Evaportranspiration: evaporation from soil and plants; function of solar radiation/H2O/temp
o Species-area curve: larger area  more species present in the area due to more space
 Islands: biogeographic factors on species diversity by community (isolated/size)
 Small/farther from land  lower immigration rate/higher extinction rates (small)
 Island equilibrium model: rate of species immigration equals that of extinctions
 Pathogens: disease-casing microorganisms (viruses/prions/viroids); kills parts of community
 o Human activity transports pathogens around the world to new areas  no immunity
 Zoonotic pathogens: animal-to-human directly or through intermediate vector
o Principle of competitive exclusion: no two species can share the same niche and coexist

Chapter XL: Ecosystem

 Ecosystem: regional biotic/Abiotic factors sum; energy flow (sunlight enters) /chemical cycling
o Energy conversed; enters as sunlight  photosynthesis to store  exits as heat waves
 Law of conversation of mass: matter (like energy) cannot be created/destroyed
 Nitrogen supplied to plants by nitrogen fixation; carbon in carbon dioxide (CO2)
o Primary producer: autotroph; herbivore: primary consumer; carnivore: tertiary con.
 Detritivores (decomposers) eat detritus (nonliving organic matter)  recycling
 Primary production: light energy  chemical energy in period; start: metabolism/energy flow
o Earth: 10^22 J of solar radiation a day; only 1% absorbed by plants; most reflected back
 Net primary product (NPP) = Gross primary product (GPP)–Respiration (R)
 Ecosystem’s net primary product =\= total biomass (measure = as standing crop)
o Limiting nutrient: element put to increase production (marine: Nitrogen/Phosphorous)
 Phytoplankton rapidly take up these elements in the photic zone at the very top
 Iron stimulates cyanobacteria growth  fix atmospheric nitrogen; upwelling spot
 Largest upwelling (a prime fishing location): Southern Ocean (Antarctic Ocean)
 Eutrophication: adding nutrients to water  cyanobacteria grow  fish killed
o Actual evapotranspiration climate contrast/net primary production; tropical forest=high
 Secondary production: chemical energy converted to new biomass during period  inefficient
o Production efficiency: (Net secondary production)/(assimilation of primary production)
 Percent of energy not used in respiration (feces do not count toward assimilation)
o Trophic efficiency: % passed form one level to next; about 10% passed/90% lost as heat
 Pyramid of net production: biomass decreasing up (land); increasing up (aquatic)
o Turnover time: quickly consumed  population never grows to large size/standing crop
 Green world hypothesis: the terrestrial herbivores put in check by many factors
 Plant defenses/pathogens/predators/competition/Abiotic pressures/territorial defn.
 Biogeochemical cycle: nutrients cycled in biotic/Abiotic components to build the organic matter
o Organic debris  fossils  burned to atmosphere  sedimentary rock  weathered….
 Radioactive carbon-14 used to trace the flow in the ecosystem and the pathway
o Water cycle: Evaporation/transpiration  condensation  precipitation  run-off H2O
 Essential to all life; primarily liquid in oceans; driven by evaporation (by the sun)
o Carbon cycle: animals give off CO2 by respiration/plants use the CO2 in photosynthesis
 Volcanoes/burning fossils fuels/cutting down rainforests create too much CO2
o Nitrogen cycle: atmospheric nitrogen made into ammonium/nitrate/nitrate for the plants
 Assimilated by plants; denitrification: nitrate used in metabolism  make the N2
 Nitrogen= most abundant gas in atmosphere; nitrogen fixation to be used; amine
o Phosphorous cycle: weathering rocks add phosphate  water  producers incorporate
 Sedimentary rocks of marine origin; also in soil; used in DNA/ATP/membrane
o Litter mass decreases extremely quickly in the warmer ecosystems (decomposition rates)
 Deforestation = more nitrate/potassium/calcium in the runoff water  dangerous
 Humans altered nutrient cycle; nitrogen lost through agriculture; plowing = faster decomposition
o Critical load: excess nutrients that cannot be absorbed by plants  runoff in the water
 Acid precipitation (sulfur/nitrogen pollutants; 5.4; erodes calcium-based statues)
o Biological magnification: toxins accumulate higher up in the food chain for consumers
  DDT pesticide/PCBs lowered calcium in birds’ eggs  eggs broken/declining
o Rising CO2 levels creates greenhouse effect trapping the heat inside of the atmosphere
 Free-formed chlorine interacts with ozone to make chlorine peroxide temporarily
 Light breaks molecule into components  recycled chlorine  less ozone there
 Chloroflurocarbons = stable/do not easily break down; catalytic chain reactions
o Amplified effects above Antarctica/North pole; UV radiation enters  melt ice cap/hurt


Chapter LVI: Conservation Biology and Restoration Ecology

 Conservation biology: ecology-physiology-all other disciplines to converse all diversity levels

o Indonesia = highest rates in the world; restoration ecology: undo bad human damages
 Biodiversity: genetic diversity, species diverse (endangered/threatened species)/the ecosystems
o Wilson’s Biophilia: connection to nature/other life forms; moral argument to protect life
 Many endangered species could provide crops/fibers/ingredients for medical use
 Ecosystem services: all natural ecosystem parts to help sustain Earth human life
o Three threats: habitat loss by destruction, introduced species (foreign), overexploitation
 Overfishing/overhunting leads to sharp decrease in the animal’s own population
 Species intertwined in a community  loss of one species affects other portions
 Small-population risk-threats; extinction vortex  population keeps declining by natural factors
o Inbreeding/genetic drift/loss of genetic variability/disasters hurt already small populations
 Minimum viable population (MVP): smallest # size for a population to survive
o Effective population size based off of breeding potential/sex ratio  shows allele passed
 Smaller population lose genetic variation quickly  path to extinction quickly
o Declining population approach focuses on threatened/endangered populations at high risk
 Declining-population emphasizes the environ’tal factors  population shrinking
o Analysis: confirm the declining/study natural history/why decline? /test hypothesis/repeat
 Ecological role of species  important; species w/ highest importance = involve
 Boundaries (edges) between ecosystem: defining features of landscape; vague; special environ’ts
o Edge communities: resources (both areas); movement corridor: land connecting patches
 Promote dispersal/reduce inbreeding in declining populations; artificial = bridges
o Gov’t set 7% of land for reserves to protect wildlife; un-tampered zones w/o interference
 Biodiversity hot spot: relatively small region of endemic (high endangerments)
 Southeast Asia; New Zealand; Amazon Rainforest; Mexico; Mediterranean Sea
 Ideal choice for the nature reserves; also include some aquatic zones (coral reefs)
o All ecosystems have disturbance; nonequilibrium model applies to the nature reserves
 Zoned reserve: extensive region that w/ areas undisturbed land; nearby: changed
 Social-economic climate; surrounding lands changed by humans: economic gain
 Destructive practices not compatible w/ long-term ecosystem conservation techs
 Costa Rica: Nation park lands surrounded by buffer zone used for their resources
 Zoned reserved: eco-tourism (attraction for money)/an alternative energy source
 Most biological communities can recover from disturbances using ecological succession stages
o Restoration ecology speeds up the recovery process of harmed areas; “reversible process”
 Bioremediation: organisms (prokaryotes/fungi/plants) to detoxify polluted areas
 Ethanol used to decrease the uranium’s solubility in water pits  purifying water
o Biological augmentation: organisms to add essential materials to a degraded ecosystem
 Using plants that grow in nutrient poor soil speed up whole succession process
  Plants produce the nitrogen to help the nearby plants thrive  speed-up recovery
 Numerous ecological projects around the world to help restore nature/protection
 Sustainable development: keeping the environ’t preserved for future generations to obtain food
o Life expectancy increased/decreased infant mortality  more people  more resources