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Chapter 22 : Descent With Modification
Wednesday, January 14, 2015
11:32 AM

Linnaeus: binomial system for classification of species
Hutton: gradualism, father of geology (valleys formed by rivers running through)
Lamarck: use and disuse (ex
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Populations evolve over generations
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1 Genetic variation makes evolution
• Mendel writes about inheritance in pea plants
• Phenotypic differences reflect genetic variation
• Point mutation: change in one base of a gene
• Heterozygote protection: maintains a bigger pool of alleles so its beneficial if the environment changes
• Nucleotide variability: rarely results in phenotypic variation
○ Many of the genetic differences between humans lie on introns so they never get coded
• Neutral variation: differences in DNA sequence that do not confer a selective advantage or disadvantage
• Mutations = 1/100,000 genes per generation
○ Accumulate quickly in prokaryotes and viruses because of short generation times
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3 Natural selection, genetic drift, and gene flow alter frequencies in a population
• Natural selection is based on differential reproductive and survival success
• Adaptive evolution: evolution that results in a better match between organisms and their environment
• Genetic drift: chance events that cause allele frequencies to fluctuate unpredictably from one generation to the next
○ Founder effect: a smaller group establishes a new population whose gene pool differs from the source population
○ Bottleneck effect: a sudden change in the environment (fire or flood) that drastically reduces the size of the population
• Gene flow:
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1 The Biological Species Concept
• Biological species concept: species = group of populations whose members have the potential to interbreed in
nature and produce viable, fertile offspring
• Gene flow between populations holds a species together genetically
• Reproductive isolation: biological (barriers) that impede species from producing viable fertile offspring
• Prezygotic barriers: fertilization blocked before happens
○ Habitat Isolation
○ Temporal Isolation
○ Behavioral Isolation
○ Mechanical Isolation
○ Gametic Isolation
• Postzygotic barriers: after fertilization something happens to hybrid
○ Reduced hybrid viability
○ Reduced hybrid fertility
○ Hybrid breakdown (2nd generation hybrid)
• Morphological species concept = structural
• Ecological species concept = ecological niche
• Phylogenetic species concept = species is the smallest group of individuals on a phylogenetic tree
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3 Hybrid zones provide opportunities to study factors that cause reproductive isolation
• Hybrid zone: a region in which members of different species meet and mate --> produce some offspring of
mixed ancestry
• Reinforcement: natural selection might strengthen prezygotic barriers if the hybrids are less successful than the
parents
○ If occurring, would be stronger for sympatric than for allopatric
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1 Conditions on early Earth made the origin of life possible
• Life started 3
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• Other hypotheses
○ Alkaline vents
○ Hydrothermal vents
○ meteorites
• Ribozymes: RNA molecules that make complementary copies of short stretches of RNA
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3 Key events in life's history include the origins of single-celled and multicelled organisms and the
colonization of land
• Geological record: divided into 3 eons (Archaean, Proterozoic, and Phanerozoic)
• Stromatolites: layered rocks formed when prokaryotes bind film sediments together; earliest
evidence of life 3
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4 The rise and fall of dominant groups reflect continental drift, mass extinctions, and adaptive
radiation
• Continental drift: plates moving over time
○ Climate change
○ Allopatric speciation on a grand scale
○ Can help solve puzzles about geographic distribution of extinct organisms
• Mass extinction: large number of species extinct through Earth
○ Permian (ocean life) and Cretaceous (terrestrial plants and dinosaurs)
○ Takes 5-10 million years to recover after a mass extinction
• Adaptive radiation: periods of evolutionary change in which groups of organisms form new
species whose adaptations allow them to fill different ecological roles in the community
○ Regional radiation happens when few organisms make their way to a distant location where
they face little competition from other organisms
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Determine where a pair of wings or legs will develop or how a plant's flower parts are
arranged
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1 Phylogenies show evolutionary relationships
• Taxonomy: how organisms are named and classified
• Duh, Kinky People Can Often Find Great Sex
• PhyloCode: only names groups that include a common ancestor and all of its descendants
• Sister taxa: share the most recent common ancestor
• Polytomy: a branch point from which more than two descendant groups emerge
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3 Shared characters are used to construct phylogenetic trees
• Distinguish between homologous and analogous features since only homologous reflect
evolutionary history
• Cladistics: common ancestry is primary criterion to classify organisms
○ Clade: group of species that
○ Monophyletic: ancestral species with descendants
○ Paraphyletic:
○ Polyphyletic: distantly related, not including common ancestor
• Shared ancestral character: character that originated in an ancestor of the taxon (backbone)
• Shared derived character: evolutionary novelty unique to a particular clade
• Outgroup: species from lineage that diverged before the lineage that includes the in group
• Maximum parsimony: we should first investigate the simplest explanation that is consistent with
the facts
• Maximum likelihood: given certain rules about how DNA changes over time, a tree that reflects
the most likely sequence of events can be found
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5 Molecular clocks help track evolutionary time
• Molecular clock: yardstick for measuring the absolute time of evolutionary change based on the
observation that some genes and other regions of genomes appear to evolve at constant rates
○ Were able to take sample of strain of HIV and saw that virus evolved in clock-work like
fashion and could assume that that strain first spread to humans during the 1930s
• Neutral theory: much evolutionary change in genes and proteins has no effect on fitness and is
not influenced by Darwinian selection
• When using molecular clocks, you estimate that these have been constant way before the fossil
record
○ Could possibly avoid problems by calibrating clocks with many genes rather than just one
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6 New information continues to revise our understanding of the tree of life
• Domain was adopted above the kingdom classification (3 domains = bacteria, archaea, eurkarya)
• It seems that eukaryotes and archaea are more closely related to each other than either is to
bacteria
• there has been substantial movement of genes between organisms in the three domains
• Horizontal gene transfer: process in which genes are transferred from one genome to another
through mechanisms like exchange of transposable elements and plasmids, viral infection, and
fusions of organisms

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Chapter 52: Introduction to Ecology and the Biosphere
Friday, February 6, 2015
11:20 AM

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1 Biological processes influence population density, dispersion, and demographics
• Population: group of individuals of single species living in the same area
○ Described by boundaries and size
• Density: number of individuals per unit area or volume
○ Changes as individuals are added to or removed from a population
• Dispersion: pattern of spacing among individuals within the boundaries of population
• Mark-recapture method: estimating size of wildlife populations; capture random sample and tag
them and release
• Immigration: influx of new individuals from other areas
• Emigration: movement of individuals out of population and into other locations
• Differences in local density tell about environmental associations and social interactions of
individuals
○ Clumped: individuals aggregated in patches
○ Uniform: evenly spaced (rarer than clumped)
○ Random: unpredictable (windblown seeds, etc
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2 The exponential model describes population growth in an idealized, unlimited environment
• Change in population size = births + immigrants - deaths - emigrants
• Zero population growth: per capita birth and
• Exponential population growth: when the instantaneous per capita rate of increase is greater than
zero and is constant at each instant in time
• J curve: populations that are introduced into a new environment or whose numbers have been
drastically reduced by a catastrophic event and are rebounding
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4 Life history traits are products of natural selection
• Life history: traits that affect an organism's schedule of reproduction and survival
○ Evolutionary outcomes reflected in development and behavior
○ Includes: when reproduction begins, how often organism reproduces, and how many
offspring are produced per episode
• Semelparity: "one-shot" pattern of big-bang reproduction
○ Ex
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5 Many factors that regulate population growth are density dependent
• Density independent: when a birth rate or death rate doesn't change with population density
• Density dependent: dune fescue reproduction declines as population density increases because
water or nutrients become more scarce
○ Competition, disease, predation, toxic waste, intrinsic factors, territoriality
• Population dynamics: fluctuations from year to year or place to place in size
○ Overexploitation by predators = major factor in 10 year cycles of hares
• Metapopulation: number of local populations linked
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1 Community interactions are classified by whether they help, harm, or have no effect on the species involved
• Community: a group of populations of different species living close enough to interact
• Interspecific interactions: competition, predation, herbivory, symbiosis, facilitation
• Interspecific competition is -/- interaction, individuals of different species compete for resource that limits
growth and survival
• Gause: two species competing for same resource cannot coexist
• Competitive exclusion: local elimination of the inferior competitor
• Ecological niche: sum of species' use of the biotic and abiotic resources in its environment
• Resource partitioning: differentiation of niches that enables similar species to coexist in community
• Fundamental niche: niche potentially occupied by that species
• Realized niche: portion of fundamental niche it actually occupies
• Character displacement: tendency for characteristics to diverge more in sympatric than in allopatric populations
of two species
• Mechanical vs
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Nitrogen fixation by bacteria in root nodules of legumes
○ Obligate mutualism: one species lost ability to survive on own
○ Facultative mutualism: both species can survive alone
○ Commensalism: benefits one species but neither helps nor harms the other
 Algae are hitchhikers (attach to whales) that gain a place to grow but have little effect on their ride
 Facilitation: species have positive effects on survival/reproduction of other species without
necessarily living in the direct, intimate contact of symbiosis
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)
• Biomass: total mass of all organisms in a habitat
○ Higher diversity communities = more productive and better able to withstand and recover from
environmental stress, also resistant to invasive species
• Invasive species: organisms that become established outside their native range
• Trophic structure: feeding relationships between organisms
○ Food webs: given species may weave into web at more than one trophic level
 Simplify by: isolating portion of web that interacts very little with rest of the community or group
similar trophic levels into broad functional groups
• Energetic hypothesis: length of a food chain is limited by the inefficiency of energy transfer along the chain
 Only about 10% of energy stored in organic matter is passed onto next trophic level
 Predicts that food chains should be relatively longer in habitats of higher photosynthetic production
• To discover the impact of a dominant species, remove it from the community! Duh
• Keystone species: not abundant, exert control on community structure by pivotal ecological roles
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• Keystone species: not abundant, exert control on community structure by pivotal ecological roles
• Ecosystem engineers: species that dramatically alter their environment
○ Beaver: felling trees, building dams, creating ponds
• Bottom-up model vs top-down model (predation controls community organization bc predators limit herbivores,
herbivores limit plants, plants limit nutrient levels through nutrient uptake)
• Biomanipulation: tries to prevent algal blooms and eutrophication by altering density of consumers instead of
using chemical treatments
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1 Physical laws govern energy flow and chemical cycling in ecosystems
• Plants can convert energy but total amount does not change
• Primary producers: autotrophs
• Primary consumers: herbivores
• Secondary consumers: carnivores that eat herbivores
• Tertiary: carnivores eat other carnivores
• Detritivores: decomposers
• Detritus: nonliving organic matter
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3 Energy transfer between trophic levels is typically only 10% efficient
• Secondary production: amount of chemical energy in food that is converted to their own new
biomass
• Energy flows through, not cycles, within ecosystems
• Production efficiency: percentage of energy stored in food that is not used for respiration
• Fish efficiency = 10% insects/microorganisms = 40%
• Trophic efficiency: % of production transferred from one trophic level to the next
• Biomass pyramid: each tier represents total dry mass of all organisms in trophic level
• Turnover time: small standing crop compared to their production

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Chapter 40: Basic Principles of Animal Form and Function
Sunday, March 1, 2015
4:51 PM

• Physiology: biological function
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for land animals where environment is variable
• Tissues: groups of cells with similar appearance and common function
○ Epithelial, connective, muscle, nervous
• Organs: tissues organized into functional units
• Organ system: groups of organs that work together
• Endocrine system: signaling molecules released into bloodstream by endocrine cells are carried to
body
○ Hormones: signaling molecules that cause different things, only cells with receptors can
respond
○ Coordinates gradual changes in body relating to growth, development, reproduction,
metabolic processes, digestion
• Nervous system: neurons transmit impulses to target cells along communication lines consisting of
axons
○ Directing immediate responses to environment; reflexes
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3 Homeostatic processes for thermoregulation involve form, function, and behavior
• Thermoregulation: animals maintain body temperature within normal range
• Endothermic: warmed by heat generated through metabolism (humans)
• Ectothermic: gain most of heat from external sources (lizards)
○ Consume less food than endotherms
○ Allow larger fluctuations in internal temp
• Integumentary system: outer covering of the body consisting of skin, hair, nails
• Major adaptation = insulation
○ Marine mammal have blubber bc they swim in water much colder than body temp
• Vasodilation: widening of superficial blood vessels near the body surface (warms skin and
increases transfer of body heat to environment)
• Vasoconstriction: reduces blood flow and heat transfer by decreasing diameter of superficial
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• Vasoconstriction: reduces blood flow and heat transfer by decreasing diameter of superficial
vessels
• Countercurrent exchange: transfer of heat between fluids that are flowing in opposite directions
○ As warm blood moves to arteries, transfers heat to the colder blood
• Behavioral responses: when hot, bathe
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○ Honeybees huddle together and alternate being on the outside and in the warm center
• Thermogenesis: heat production, increased by shivering and moving
○ Nonshivering: mitochondria increase metabolic activity and produce heat instead of ATP
○ Brown fat: tissue between neck and shoulders for rapid heat production
• Hypothalamus: where sensors for thermoregulation are concentrated (also controls circadian
clock)
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5 times BMR rate
• Torpor: physiological state of decreased activity and metabolism (adaptation to save energy)
• Hibernation: long-term torpor, adaptation to winter cold and food scarcity
○ Metabolic rates 20 times lower
○ Estivation (summer torpor): enables animals to survive long periods of high temps and low
water

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Chapter 41: Animal Nutrition
Tuesday, March 3, 2015
10:08 PM

• Nutrition: being taken in, taken apart, and taken up
• Herbivores: dine on plants/algae
• Carnivores: mostly eat other animals
• Omnivores: eat both
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4 Evolutionary adaptations of vertebrate digestive systems correlate with diet
• Carnivores: large expandable stomachs
• Herbivores and omnivores have longer alimentary canals to digest vegetation
• Coexistence with bacteria = mutualistic symbiosis
○ Produce vitamins
○ Help digestion
• Processes to obtain nutrients matched to organism's need for energy
• Type 1: autoimmune disorder in which immune system destroys beta cells of pancreas
• Type 2: failure of target cells to respond to insulin

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Chapter 42: Circulation and Gas Exchange
Tuesday, March 10, 2015
10:05 AM

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)
○ One atria and one ventricle
○ Gills: where there is a net influx of O2 and CO2 is removed from blood
○ Passes through 2 capillary beds
○ When blood flows through capillary bed, blood pressure decreases substantially
• Double circulation: two distinct circuits (amphibians, reptiles, mammals)
○ Pulmonary circuit: if the capillaries in the lungs are involved
○ Pulmocutaneous circuit: if capillaries in both the lungs and the skin are involved
(amphibians)
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1 In innate immunity, recognition and response rely on shared traits of pathogens
• Exoskeleton of chitin provides effective barrier against most pathogens
• Lysozyme: digest microbial cell walls
• Hemocytes: phagocytic, trigger production of chemicals that kill microbes and trap parasites,
secrete antimicrobial peptides
• Barrier Defense
○ Body secretions create environment that is hostile to many microbes
 Sweat/oil glands give skin pH of 3-5, acidic to stop growth of microorganisms
• Innate Defense
○ Neutrophils: most abundant phagocytic cell in mammalian body
○ Eosinophils: against parasitic worms, position themselves against parasite's body and
discharge enzymes that destroy invader
○ Dendritic cells: populate tissues in contact with the environment, development of acquired
immunity
○ Interferons: provide innate defense against viral infection
• Inflammatory Response
○ Mast cells: store chemicals in granules for secretion; store histamine
○ Fever is a systemic inflammatory response
 Elevated body temperature might enhance phagocytosis and speed up reactions
• Natural Killer cells: find cells that don't express that class I MHC protein and release chemicals to
kill them
• Some bacteria have outer capsule that hides the polysaccharides of their cell walls, preventing
recognition (among other adaptations)
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non self, response to previously encountered
antigen is stronger and more rapid
• Effector cells: short-lived, attack antigen and any pathogens producing that antigen
• Memory cells: long-lived, bear receptors specific for the antigen
• Clonal selection: presentation of antigen to specific receptors on a lymphocyte leads to repeated
rounds of cell division
• Primary immune response: production of effector cells from a clone of lymphocytes during first
exposure to an antigen (12-17 days to peak)
• Plasma cells: antibody secreting effector B cells
• Secondary immune response: greater magnitude, more prolonged, faster (2-7 days to peak)
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4 Disruptions in immune system function can elicit or exacerbate disease
• Allergies: exaggerated responses to certain antigens (allergens)
○ Most common involve antibodies of the IgE class
• Degranulation: inducing mast cell to release histamine and other inflammatory agents from
granules
• Anaphylactic shock: develops when widespread mast cell degranulation triggers abrupt dilation of
blood vessels, causing a drop in blood pressure
• Autoimmune disease: loss of self-tolerance
○ MS: T cells infiltrate CNS, leading to the destruction of the myelin sheath that surrounds
neurons
• Immunodeficiency: ability to protect against pathogens is defective or absent
○ Inborn: genetic/developmental defect in immune system
○ Acquired: develops after exposure to chemical or biological agents
• Pathogens use antigenic variation, latency, and direct assault on the immune system to thwart
immune responses
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immune responses

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Chapter 44: Osmoregulation
Friday, March 27, 2015
11:29 AM

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Based on balancing uptake and loss of water and solutes
Driving force is concentration gradient of one or more solutes across plasma membrane
Osmoconformers: some marine animals; do not regulate their osmolarity
Osmoregulators: expend energy to control water uptake and loss
Marine Fish
○ Osmotic water loss
○ Drink the salt water and excrete salt ions and small amounts of water in urine from kidneys
• Fresh Water
○ Excrete large amounts of water/gain
○ Uptake of salt ions by gills
• Amount of energy depends on:
○ How different osmolarity is from surroundings
○ How easily water/solutes can move across surface
○ Work required to pump solutes across the membrane
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3 Excretory systems are variations on a tubular theme
• How do you move solutes between internal fluids and external environment
• Systems central to homeostasis
• Kidneys: functional unit is nephron
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5 Homeostatic Regulation of the Kidney
• ADH - made in hypothalamus and released from pituitary (response to osmolarity)
• If blood osmolarity raises, more ADH released and reaches kidneys, increase water absorption to
your body
• Lowers osmolarity to a set point by pulling that water out (feedback mechanism)
• Renin-angiotensin-aldosterone system: renin released, angiotensin converted to angiotensin II
(raising of blood pressure) (response to blood volume and blood pressure)
• Aldosterone: increases absorption of water and sodium, increase blood volume and blood
pressure
• RAAS and ADH: reabsorb water

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Chapter 45: Hormones and Endocrine System
Wednesday, April 1, 2015
11:21 AM

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2 Feedback regulation and coordination
• Simple hormone pathways
○ Hormones released from endocrine cell, interact,
 Secretin and low pH in duodenum
• Hypothalamus: receives info from nervous system and initiates responses through endocrine
system
○ Posterior pituitary, extension of hypothalamus
○ m

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Chapter 46: Animal Reproduction
Monday, April 6, 2015
5:11 PM

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uniparens, Estradiol causes female and progesterone causes male-like behavior
• Finding a partner for sex can be challenging!
○ Hermaphroditism: having both male and female reproductive systems
○ Bluehead wrasse: harem forms and when male dies, largest female turns into male
(developed through evolution)
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3 Reproductive organs produce and transport gametes
• Human male reproductive anatomy
○ External: scrotum and penis
 Glans: head of penis
 Baculum: bone to stiffen penis for mating in animals
○ Internal: gonads that produce sperm and hormones, accessory glands, ducts
Gonads - testes
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 Gonads - testes
□ Develop in the abdominal cavity and descend into scrotum just before birth
 Produce sperm in coiled tubes called seminiferous tubules
 Epididymis: coiled duct for transport of sperm
 Ejaculation: sperm propelled from epididymis through vas deferens
 Urethra: outlet tube for excretory and reproductive system
 Two seminal vesicles to excrete semen
 Prostate gland: secretes products directly into urethra
• Human female reproductive anatomy
○ External: clitoris and two sets of labia
○ Internal: gonads - produce eggs and hormones ands ducts and chambers
 Ovaries: outer layer has follicles with an oocyte
□ Oocyte: partially developed egg
 Oviduct: fallopian tube, extends from uterus
 Endometrium: inner lining of uterus
 Cervix: neck of uterus
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1 Nervous systems consist of circuits of neurons and supporting cells
• By Cambrian explosion, specialized systems of neurons appeared that enabled animals to sense
surroundings and respond
• Cnidarians - interconnected neurons form diffuse nerve net
○ Controls contraction and expansion of gastrovascular cavity
• Nerves: axons of multiple neurons bundled together
○ Channel and organize info along specific routes throughout nervous system
• Elongated, bilaterally symmetrical bodies = more specialized nervous systems
○ Cephalization: an evolutionary trend toward clustering of sensory neurons and interneurons
at front end of body
• Nervous system organization correlates with lifestyle
○ Molluscs: simple sense organs and little or no cephalization
○ More complex invertebrates have more neurons
○ Ganglia: segmentally arranged clusters of neurons
• Glial cells: Schwann cells that produce myelin sheaths in PNS and counterparts in CNS, essential
roles is development
○ CNS: integration takes place; includes brain and a nerve cord
○ PNS: carries information into and out of CNS
○ Astrocytes: formation of blood-brain barrier, walls of brain capillaries restricts entry of
substances from blood into CNS
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1 Flowers, double fertilization, and fruits are key features of the angiosperm life cycle
• Alternation of generations: sporophytes and gametophytes alternate producing each other
• Carpels, stamen, petals, sepals
• Receptacle: part of the stem
• Flowers are determinate shoots
• Reproductive organs: carpels and stamens
○ Carpel has ovary at its base and a long, slender style
○ Pistil: single carpel or two or more fused carpels
○ Stamen: stalk with filament and anther (terminal structure)
 Anther: contains chambers called microsporangia that produce pollen
• Sterile: sepals and petals
○ Petals: brightly colored, advertise
○ Sepals: enclose and protect unopened floral buds and resemble leaves
• Complete flowers: four basic floral organs
○ Incomplete: lack one of more
• Inflorescences: showy clusters flowers arranged in

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