CO4: PHYLOGENY

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Systematics - classifying organisms (Taxonomy) and determining their evolutionary
relationships (Phylogenetics)
Taxonomy - gray area in Biology because it is constantly/continuously changing
 Hypothesis
 Classifying and naming organisms
 Ordered division of organisms based on similar/different characteristics

Taxon - each category at any level

Carolus Linnaeus - father of taxonomy

A. Taxonomic Categories
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species

Dear King Philip Came Over For Good Spaghetti

Linnaeus Modern

 2 kingdoms  5 or 6 kingdoms (Older system, lumps all

 Based on physical prokaryotic species into one kingdom: Monera)
similarities a. Animal
 Uses only biologists’ b. Plant
observations and c. Protist
knowledge of d. Fungi
organisms e. Monera - Eubacteria (normal
everyday prokaryotes found on Earth) and
Archaebacteria (“extremophiles”;
prokaryotes found in extreme environmental
conditions)
 Based on physical similarities and genetic
similarities
 Uses observations, knowledge of organisms,
molecular clocks, and other genetic techniques

1. Determining evolutionary relationships

TOOLS TO DETERMINE EVOLUTIONARY RELATIONSHIPS

 Fossils
 Morphology (homologous structures)
  Molecular evidence (DNA, amino acids)

 Analogous structures evolved by convergent evolution

B. Phylogenetic Trees
Phylogenetic Tree - Branching diagram that shows evolutionary history of a group of organisms

Branch point: where lineages diverge

Ancestral lineage: branch point that represents the common ancestors of all taxons
Sister taxa
Basal taxon
Polytomy - unresolved pattern of divergence

BRANCH LENGTHS:
 Can represent genetic change
 Can indicate time

Various tree layouts:

 Circular (rooted) tree
 Rooted tree
 Unrooted tree

1. Homologous and Analogous Structures

 Homologous Structures - similar structure, different function
 Analogous Structures - different structure, similar function

CLADOGRAM: diagram that depicts patterns of shared characteristics among groups

Clade = group of species that includes an ancestral species + all descendants
Shared derived characteristics (evolutionary novelties) are used to construct cladograms

2. Monophyletic, Paraphyletic, Polyphyletic

3. Maximum Parsimony
 Maximum Parsimony - simplest explanation
 Fewest DNA changes to construct phylogenetic tree
 “Keep it simple”
4. Molecular Clocks
 Molecular clocks: measure evolutionary change based on regions of genome that
appear to evolve at constant rates

C. Three Domains of Life

Bacteria and Archaea - morphology

Genus and species - Binomial Nomenclature

Binomial Nomenclature - naming system developed by Carolus Linnaeus

Highest taxon: Kingdom below (Carolus Linnaeus) because he only based it according to
morphology

Discovery of molecular evidence lead to the formation of 3 distinct groups (domains)

 Discovered that Eukarya and Archaea are more related based on molecular evidence
 Lead to the revision of taxonomic classification/ addition of taxon: Domain

a. Archaea - Archaebacteria
 No peptidoglycan in the cell walls
 Extremophiles (loving extreme conditions)
 Microscopic
b. Bacteria - Eubacteria
 Has peptidoglycan in the cell walls
 Prokaryotic single celled organisms
 Microscopic
c. Eukarya - Animal, Plant, Fungi, Protista
 All have organisms made of eukaryotic cells
 Macroscopic

COMMON ANCESTRY OF ALL LIFE FORMS

Elements conserved across all 3 domains:
1. DNA and RNA are carriers of genetic info
2. Universal genetic code (codons → amino acids)
3. Conserved metabolic pathways

Conserved elements in Eukaryotes

1. Cytoskeleton
2. Membrane-bound organelles
3. Linear chromosomes
4. Endomembrane systems (+ nuclear envelope)

 Horizontal Gene Transfer

  Movement of genes bet. different domains
 Xchange of transposable elements, plasmids, viral infections, fusion of organisms

CO5: PLANT AND ANIMAL TISSUES

A. Kingdom Plantae
Plants are composed of cells with contain:
a. Cell wall
b. Central vacuole
c. Chloroplasts
 Autotroph (photosynthesis)
 Multicellular
 Angiosperms (Flowering plants): Flowers, Fruits, Double Fertilization (by 2 sperm) →
Unique Features
a. ~90% plants
b. Produce seeds within a fruit
c. Key adaptations: flowers and fruits
B. Plant tissue types

Dermal Tissue Vascular Tissue Ground Tissue Meristematic

Tissue

 “Epidermis”,  Transport  Photosynthesis,  Produces

Dermis H2O, food storage, most of a
 Single layer throughout secretion, support plant’s
 Closely packed plant  Found throughout new cells
cells that cover  Types: plant  Located
entire plant a. Xylem -  Anything that isn’t in regions
 Protect against transports H2O dermal or of actively
water loss & from roots to plant vascular dividing
invasion by - composed of  Pith: inside cells
pathogens tracheids (tubular vascular tissue
(Viruses and cells tapered at  Cortex: outside
bacteria) each end) vascular tissue
 Cuticle: waxy b. Phloem -  Parenchyma (thin
layer transports sugars cell wall),
 Located are: to all parts of plant Collenchyma
a. Stomata: -made up of (uneven
opening in leaf tubular cells joined thickening of cell
tissue, help end to end; wall),
control H2O loss - 2 cell types: Sclerenchyma
from plant SIEVE TUBES (even thickening
b. Guard cells: and COMPANION of cell wall)
controls CELLS
opening/closing
of stomata
c. Trichomes:
Hairlike
projections on
stem and leaf;
 reduces
evaporation of
H2O from plant

C. Plant cell types

D. Plant growth

Types of Flowering Plants

Annuals Biennials Perennials

1 yr life cycle 2 yrs Continuous life cycle for many years

Meristem: perpetually embryonic tissues

 Cells divide for plant growth
a. Apical meristem: tips of roots and buds of shoots
: primary growth (increase length)
: divide and elongate
b. Lateral meristem: thickens shoots and roots
: Secondary growth (increase diameter)
 Vascular cambium: secondary xylem (wood)
 Cork cambium: tough covering, replace epidermis
 All tissues outside vascular cambium = BARK

ROOT ANATOMY
 Zone of Maturation: primary growth → functionally mature
 Zone of Elongation: cells elongate, push root tip ahead
 Zone of Cell Division: apical meristem; mitosis
 Root Cap: protects meristem, pushing it through soil

E. Plant organs and organ system

Roots Stems Leaves

 Anchor, absorb  Support leaves & flowers  Photosynthesis

nutrients, contain  Contains vascular tissue for  Solar energy and
vascular tissue for transportation CO2 collectors of
transportation  Arrangement of vascular plants
 short/ long, tissue:  Some are joined
thick/thin a. Monocots: Xylem & Phloem directly to a stem
 Have root hairs: scattered throughout stem  In some, petiole joins
tiny extensions, b. Dicots: Xylem & phloem in the leaf blade to
a circle, forms ring stem
 increase surface  Sometimes modified to  Simple leaf:
area of root store food/ water undivided blade
 Types  Succulents: plants that  Compound leaf:
a. Taproot: 1 thick, store water in stem/leaves blade divided into
vertical root (cacti) leaflets
 Many lateral  Rhizomes: horizontal  Transpiration: loss of
(branch) roots growth; underground, can H2O through
 Firmly anchors produce new shoots and stomata
 Stores food roots  Leaf venation:
b. Fibrous root: mat  Stolons: aboveground, run a. Parallel
of thin roots across soil surface, b. Pinnate
spread just below horizontal growth; produce c. Palmate
surface new shoots/roots  Leaf Anatomy:
 Shallow  Bulbs: underground;  Epidermis of
 Increased surface Tunicate (w/ papery underside
area covering) / Scaly interrupted by
c. Modified roots:  Types: stomate (pores),
“strangling” aerial a. Herbaceous flanked by guard
roots b. Woody stems cells
 Mesophyll: ground
tissue bet. upper/
lower epidermis
 Parenchyma: sites of
photosynthesis
Pollination: transfer pollen from anther to stigma
 Self pollination
 Cross pollination
 Self-incompatibility: plant rejects own pollen/ closely related plant (maximize genetic
variation)
 Pin and thrum reduce self fertilization

Fruit
 Egg cell → plant embryo
 Ovules inside ovary → seeds
 Ripe ovary → fruit
 Protects seed
 Aids in dispersal by wind, water, or animals
 Types:
a. Simple
b. Aggregate
c. Multiple

Seeds
Mature seed → dormancy (resting)
 Low metabolic rate
 growth/development suspended
 Resumes growth when environmental conditions are suitable for germination
Germination - seed take up water (imbibition) → trigger metabolic changes to begin growth
 Very hazardous for plants due to vulnerability
 F. Animal tissue types
1. Structure
Anatomy: study of biological form (STRUCTURE) of an organism
Structure dictates function!
2. Function
Physiology: study of biological FUNCTIONS an organism performs
3. Classification

CO6:
Sensory Organs (5 senses)
 Mechanoreceptors: physical stimuli - pressure, touch, stretch, motion, sound
 Thermoreceptors: detect heat/cold
 Chemoreceptors: transmit solute conc. Info - taste (gustatory), smell (olfactory)
 Electromagnetic receptors: detect EM energy - light (photoreceptors), electricity,
magnetism
 Pain receptors: respond to excess heat, pressure, chemicals

 Reception: receptor detects a stimulus

* Sensation = action potentials reach brain via sensory neurons
 Perception: information processed in brain
 Equilibrium in the inner ear: Semicircular canals (fluid-filled chambers) detect head
movements through hairs of receptor cells
 Vision
 Compound eyes: several thousand ommatidia (light detectors) with its own lens;
insects & crustaceans
 Vertebrates:
a. Rods: sense light
b. Cones: color vision
c. Rhodopsin: light-absorbing pigment that triggers signal
transduction pathway that leads to sight
 Types of Skeletons
a. Hydrostatic: fluid held under pressure in closed body compartment
: Hydra, nematodes, annelids
b. Exoskeletons: hard encasements on surface of animal
: insects, mollusks, crustaceans
c. Endoskeleton: hard supporting elements buried within soft tissues
:human bony skeleton
 Muscles ALWAYS contract
 Muscles work in ANTAGONISTIC pairs to move parts of body

SKELETAL MUSCLE STRUCTURE

 Attached to bones by TENDONS
 Types of muscle:
a. Smooth (internal organs)
b. Cardiac (heart)
c. Skeletal (striated)
 Each muscle fiber = bundle of myofibrils, composed of
  Actin: thin filaments
 Myosin: thick filaments

Sarcomere: basic contractile unit of the muscle

Z lines - border
I band - thin actin filaments
A band - thick myosin filaments

Muscle Contraction:
1. Sarcomere relaxed: actin & myosin overlap
2. Contracting:
 Muscle fiber stimulated by motor neuron
 Length of sarcomere is reduced
 Actin slides over myosin
3. Fully contracted: actin & myosin completely overlap

Sliding-filament model: thick & thin filaments slide past each other to increase overlap (Note:
filaments do NOT shorten!)

 Muscle fibers only contract when stimulated by a motor neuron

 Synaptic terminal of motor neuron releases acetylcholine → Muscle fiber depolarizes →
Ca2+ released → Initiate sliding of filaments
 Depolarization of muscle cell releases Ca2+ ions → binds to troponin → expose myosin
sites on actin
 Hydrolysis of ATP by myosin → cross-bridge formed → thin filament pulled toward
center of sarcomere

SPEED OF MUSCLE CONTRACTION:

 Fast fibers - brief, rapid powerful contractions
 Slow fibers - sustain long contractions (posture)

PROBLEMS
 ALS (Lou Gehrig’s disease): degeneration of motor neurons, muscle fibers atrophy
 Botulism: block release of acetylcholine, paralyzes muscles
 Myasthenia gravis: autoimmune disorder, produce antibodies to acetylcholine
 Calcium deficiency: muscle spasms and cramps
 Rigor mortis (after death): no ATP to break actin/myosin bonds; sustained muscle
contraction until breakdown (decomposition)
_______________________________________________________________________
NERVOUS SYSTEM
 Central Nervous System (CNS)
 Brain
 Spinal cord

 Peripheral Nervous System (PNS)

 Cranial nerves
 Ganglia outside CNS
 Spinal nerves
Reflexes
 Simple, automatic response to stimulus
 Conscious thought not required
 Reflex arc:
1. Stimulus detected by receptor
2. Sensory neuron
3. Interneuron (spinal cord or brain stem)
4. Motor neuron
5. Response by effector organ (muscles, glands)

Vertebrate Brain is regionally specialized

Major regions:
 1. Forebrain
 Cerebrum → Information processing (learning, emotion, memory, perception, voluntary
movement)
→ Right and left cerebral hemisphere
→ Corpus callosum: connect hemispheres
 Thalamus
 Hypothalamus

2. Midbrain
 Brainstem → Oldest evolutionary part
→ Basic, autonomic survival behaviors
→ Medulla oblongata - breathing, heart & blood vessel activity, digestion, swallowing,
vomiting
→ transfer info between PNS & CNS

3. Hindbrain
 Pons
 Medulla oblongata
 Cerebellum → coordinate movement and balance
→ motor skill learning

Grey matter: neuron cell bodies, unmyelinated axons

White matter: fatty, myelinated axons

Neurons, Synapses, and Signaling

 Central nervous system (CNS) - brain and spinal cord
 Peripheral nervous system (PNS) - nerves throughout body
 Sensory receptors: collect info from the world (rods and cones in eye, skin receptors,
chemoreceptors, thermoreceptors)
 Neuron - functional unit of nervous system
= dendrite + cell body + axon
a. Cell body: contains nucleus and organelles
b. Dendrites: receive incoming messages
c. Axons: transmit messages away to other cells
d. Myelin Sheath: fatty insulation covering axon, speeds up nerve impulses
e. Synapse: gap between 2 neurons
f. Neurotransmitter: chemical messengers sent across synapse
g. Glia: cells that support neurons [eg. Schwann cells (forms myelin sheath)]
 Membrane Potential: difference in electrical charge across cell membrane
 The Na+/K+ pump (using ATP) maintains a negative potential inside the neuron
 Action potential (nerve impulses) are the signals conducted by axons
a. Resting potential: membrane potential at rest; polarized
 ↑Na+ outside, ↑K+ inside cell
 Maintained by sodium-potassium pumps
 Voltage-gated Na+ channel = CLOSED

b. Nerve impulse: stimulus causes a change in membrane potential

 Action potential: neuron membrane depolarizes
 All-or-nothing response
 Na+ channels open → Na+ enters cell → K+ channels open → K+ leaves
cell
 Saltatory conduction: nerve impulse jumps between nodes of Ranvier (unmyelinated
gaps) → speeds up impulse
  Neurotransmitter released at synapses
Axon (presynaptic cell) → Synaptic cleft → Dendrite (postsynaptic cell) → cell response
 Neurotransmitters
 Chemicals released from vesicles by exocytosis into synaptic cleft
 Diffuse across synapse
 Bind to receptors on neurons, muscle cells, or gland cells
 Broken down by enzymes or taken back up into surrounding cells
 Types of neurotransmitters:
a. Excitatory: speed up impulses by causing depolarization of postsynaptic membrane
b. Inhibitory: slow impulses by causing hyperpolarization of postsynaptic membrane
 Examples of neurotransmitters:
 Acetylcholine (ACh): stimulates muscles, memory formation, learning
 Epinephrine: (adrenaline) fight-or-flight
 Norepinephrine: fight-or-flight
 Dopamine: reward, pleasure (“high”)
: Loss of Dopamine → Parkinson’s Disease
 Serotonin: well-being, happiness
: Low levels → Depression
 GABA: inhibitory NT
: Affected by alcohol
 Nervous system disorders:
 LSD/mescaline - bind to serotonin and dopamine receptors → hallucinations
 Prozac - enhances effect of serotonin by inhibiting uptake after release
 Morphine, heroin - bind to endorphin receptors → decrease pain perception
 Viagra - increase NO (nitric oxide) effects → maintain erection
 Alzheimer’s Disease (AD) - develop senile plaques, shrinkage of brain tissue

Types of Neurons
 Sensory neurons: info from body sensors → CNS
 Interneurons: connect sensory + motor neurons or local connections between brain +
spinal cord
 Motor neurons: CNS → body (effectors = muscles, glands)
* Nerves = bundles of neurons
 Contains motor neurons +/or sensory neurons
_________________________________________________________________________

CIRCULATORY SYSTEM (“CARDIOVASCULAR SYSTEM”)

Transport systems (circulation) linked with gas exchange (respiration)
 Diffusion of gases only rapid across small distances

Basic Gastrovascular Cavity Circulatory System

 Cells in direct  For digestion and  Moves fluid to

contact with distribution tissues and cells for
environment substances exchange
 Sponges  Jellies, flatworms  Larger animals

Circulatory System = Blood + Vessels + Heart

Open circulatory system Closed Circulatory System

 Blood bathes organs directly  Blood contained in vessels & pumped

 Blood + lymph = hemolymph around body
 Heart pumps hemolymph into  Blood and fluid separate
sinuses  Annelids, cephalopods, vertebrates
 Arthropods, mollusks

Types of Blood Vessels

Arteries Capillaries Veins

 Blood AWAY from  Connect  Blood BACK to heart

heart arteries/veins  Low pressure
 High pressure  Single-cell thick  Thin-walled, large
 Thick, strong walls walls diameter
 Pulse  Exchange of  Valves prevent
O2/CO2 backflow

 Blood enters through an ATRIUM and is pumped out through a VENTRICLE

 Fish = single circulation pathway, 2 chambers
 Double circulation: amphibians, reptiles, mammals
 Cardiac cycle
 Systole: contraction of pumping phase
 Diastole: relaxation or filling phase
 Heart rate: #beats/minute (72 bpm resting)
 Stroke volume: amount of blood pumped by Left ventricle during contraction (~70
ml)
 Valves: prevent backflow of blood
 Atrioventricular (AV) valves (tricuspid, bicuspid) separate each atrium and
ventricle
 Semilunar valves control blood flow to the aorta and the pulmonary artery
 “Lub-dup” sound = blood against closed AV valves (lub) / the semilunar (dup)
valves
 Heart murmur: backflow of blood through a defective valve
 Sinoatrial (SA) node: pacemaker of heart (in right atrium)
a. Two portions of nervous system that regulates the pacemaker:
I. Sympathetic division - speeds up the pacemaker
II. Parasympathetic division - slows down the pacemaker
b. It is also regulated by hormones (epinephrine) and temperature

 Blood pressure
 BP = systolic/ diastolic
: Systolic = heart contracts
: Diastolic = heart relaxed
: Normal: 120/70
 Pulse: rhythmic bulging of artery walls with each heartbeat

 Blood
 Plasma (55%) - water, ions, proteins, gases, nutrients, wastes, hormones
  Cells (45%) - RBC, WBC, platelets
a. Develop from stem cells in bone marrow
b. RBCs (erythrocytes): O2 transport via hemoglobin
c. WBCs (leukocytes): fight infection
d. Platelets (cell fragments): blood clotting
 Cardiovascular Disease
a. Atherosclerosis: buildup of plaque deposits within arteries
b. Heart attack (myocardial infarction): blockage of one or more coronary
arteries
c. Stroke: rupture or blockage of arteries in the head
d. Hypertension: high blood pressure; promotes atherosclerosis and
increases the risk of heart attack and stroke
_________________________________________________________

REPRODUCTIVE SYSTEM (MALE AND FEMALE)

 Types of Reproduction

Asexual Sexual

 Clone  Genetic Diversity

Advantage: FAST, if environment is stable Advantage: ability to change
 Fission: parent separates into 2+ individuals of population when environment
same size (e.g, sea anemone) changes
 Budding: outgrowths from parent (e.g, cnidarians,  Fusion of haploid
tunicates) gametes
 Fragmentation: breaking of body into pieces, form Egg (Ovum) + Sperm →
into adults by regeneration (e.g, sea stars, Zygote
sponges, cnidarians)
 Parthenogenesis: female produces eggs that
develop w/o fertilization (e.g, male bees - haploid;
female blacktip shark - egg fuses with a polar
body)

 Reproductive Cycles and Patterns

1. Ovulation: release of mature eggs
 Young produced when survival is most likely
 Hormonal changes influenced by day length, season temperature, rainfall or lunar
cycles

2. Hermaphroditism: both M/F systems

 Sessile/burrowing animals - barnacles, parasites (tapeworms), earthworms

3. Sex reversal: sex change during its lifetime

 Bluehead wrasse (reef fish)

Fertilization = Sperm + Egg

 Types of Fertilization

EXTERNAL FERTILIZATION INTERNAL FERTILIZATION

 Egg shed by female,  Sperm deposited in female reproductive tract

fertilization by male in
water
 Environmental cues/
courtship behavior
 Large # gametes → low
survival
 Fish, amphibians
 Cooperative behavior
 Dry environment
 Fewer gametes, fewer zygotes → greater
survival
a. External Development: Tough
eggshell (Reptiles, Birds, Platypus)
b. Internal Development: High
parental care (Placentals, Sharks,
some reptiles)

EVOLUTION OF SEXUAL REPRODUCTION

Least Complex -------------------------------------------------------> Most Complex
* No Gonads * Distinct gonads (organs that
* Egg/Sperm develop in produce gametes)
undifferentiated cells * Delivery systems
* Released into coelom,
shed into environment

HUMAN REPRODUCTIVE SYSTEM

MALE FEMALE

Function Produce and deliver 1. Produce Eggs

sperm 2. Development of
baby

Main Reproductive Organs Testes (sing., testis) Ovaries

Reproductive Cells (gametes) Spermatogenesis → Oogenesis → EGGS

SPERM

Main hormone Testosterone Estrogens

Role of FSH (follicle-stimulating Sperm Formation Egg development (in

hormone) follicle)

Role of LH (luteinizing hormone) Produces testosterone Release of egg (ovulation)

FEMALE ANATOMY
 Ovaries - produce eggs, sex hormones
 Follicles - contain oocyte (egg); release 1/month; produce estrogens
 Ovulation - release of egg from follicle
 Remaining follicle → corpus luteum (↑ hormones)
  Egg → Oviduct (fallopian tube) → Uterus (baby) → Cervix → Vagina
 Mammary Glands - secrete milk through nipples in breast

MALE ANATOMY
 Testes (inside scrotum) - produce sperm, sex hormones
 Seminiferous tubules - make sperm
 Seminiferous tubules → epididymis → Vas deferens → Urethra (penis)
 Semen - alkaline fluid with nutrients, enzymes
 100 - 650 million sperm/ ejaculation
MEIOSIS

SPERMATOGENESIS OOGENESIS

 Sperm production  Ova production

 Stem cells → Spermatids in
seminiferous tubules
 Mature & add tail in
epididymis
 4 motile sperm
 Before birth: oogonia → meiosis - STOP at
Prophase I (primary oocytes)
 Puberty: each month, egg in follicle →
Meiosis I (secondary oocytes) →
Fertilization → Meiosis II
 1 ovum + 3 polar bodies

 Menstrual cycle - humans & other primates

 Prepare and release egg for fertilization
 Prepare uterus to receive a fertilized egg
 Estrous cycle - other mammals; no menstruation

FOUR PHASES OF MENSTRUAL CYCLE

1. Follicular Phase: low estrogen, ↑FSH = egg develops in ovary
2. Ovulation (Day 14): ↑LH = egg released into fallopian tube
3. Luteal Phase:
 ↑progesterone, ↑estrogen = lining of uterus thickens to prepare for pregnancy
 Egg travels down into Fallopian tube, waits for fertilization
4. Menstruation (no fertilization:
 ⬇P/⬇E = lining of uterus breaks down
 Blood and unfertilized egg discharged

HUMAN EMBRYONIC DEVELOPMENT

 Conception: in oviduct
 Implantation: in uterus
 Hormones:
 Human Chorionic Gonadotropin (hCG): maintain estrogens in early pregnancy;
pregnancy test
 Human gestation (pregnancy) = 40 weeks
 Rodents (21 days); Dogs (60 days); Cows (270 days); Elephants (600 days)
 Egg lodged in oviduct = ectopic (tubal) pregnancy

FORMATION OF ZYGOTE
1. Ovulation
 2. Fertilization occurs
3. Cleavage starts
4. Cleavage continues
5. The blastocyst implants

 Estradiol (from ovaries) - activates oxytocin receptors on uterus

 Oxytocin (from fetus and mother’s posterior pituitary) - stimulates uterus to contract
 Stimulates placenta to make Prostaglandins
 Prostaglandins - stimulate more contractions of uterus

THREE STAGES OF LABOR

1. Dilation of the Cervix
2. Expulsion: delivery of the infant
3. Delivery of the placenta
_________________________________________________________________________

BIOLOGICAL DEVELOPMENT (INCLUDING LIFE STAGES)

MAMMALIAN FERTILIZATION
1. Sperm binds to receptors in zona pellucida (extracellular matrix of egg)
2. Acrosomal reaction: sperm releases hydrolytic enzymes to digest zona pellucida
(Sea Urchins) Depolarization of membrane: prevent other sperm from binding = fast
block to polyspermy
3. Sperm + Egg Fuse
4. Cortical Reaction: sperm + egg fusion triggers release of Ca^2+
- cortical granules fuse with zona pellucida → zona pellucida hardens to form fertilization
envelope = slow block to polyspermy
5. Ca^2+ release also triggers activation of the egg

Cleavage: Rapid mitotic cell division

 /Zygote cytoplasm partitioned into smaller cells (blastomeres)
 Solid ball of cells = morula
 Blastula (hollow ball of cells) filled with fluid (blastocoel)
 Blastocyst (human)
Gastrulation: rearrange cells to form 3-layered embryo w/ primitive gut

Three Embryonic Germ Layers

ECTODERM MESODERM ENDODERM

 Skin, nails, teeth  Skeletal, muscular  Epithelial linings of

 Lens of eye systems digestive,
 Nervous system (brain,  Notochord respiratory,
spinal cord)  Excretory, excretory tracts
 Sensory systems Circulatory  Liver, pancreas
 Pituitary gland, adrenal  Reproductive  Thymus, thyroid,
medulla system (except and parathyroid
 Jaws and teeth germ cells) glands
 Germ cells  Dermis of skin
  Epidermis of skin and
its derivatives (including
sweat glands, hair
follicles)
 Outer layer of embryo
 Adrenal cortex  Inner layer of
 Blood, bone, embryo
muscle
 Middle layer of
embryo

Organogenesis: development of 3 germ layers into organs

 Notochord - stiff dorsal skeletal rod, forms from mesoderm
 Neural plate → neural tube → brain and spinal cord
 Neurulation - forms hollow dorsal nerve cord
 Somites - blocks of mesoderm arranged along notochord; sign of segmentation

EARLY HUMAN EMBRYONIC DEVELOPMENT

1. Blastocyst reaches uterus
2. Blastocyst implants (7 days after fertilization)
3. Extraembryonic membranes start to form (10 - 11 days) and gastrulation begins (13
days)
4. Gastrulation has produced a three-layered embryo with four extraembryonic membranes

Amniotic embryos (reptile, birds, mammals)

 Develop in fluid-filled sac within a shell or uterus
 Amnion: fluid protects embryo - prevent dehydration, cushions mechanical shock
 Yolk: nutrients in egg
 Mammalian eggs: little stored food
Patterns of development
 Cytoplasmic determinants: chemical signals such as mRNAs and transcription factors,
influence pattern of cleavage
 Induction: interaction among cells that influences their fate, cause changes in gene
expression
 Totipotent cells: capable of developing into all the different cell types
- all cells of mammalian embryos are totipotent until the 16-cell stage
_________________________________________________________________________
NUTRITION
Essential Nutrients - required by cells, obtained through food
 Four classes of essential nutrients:
a. Essential Amino Acids (8)
b. Essential Fatty Acids
c. Vitamins (13) - Fat-soluble, Water-soluble
d. Minerals
Dietary Deficiencies
 Undernourished: diet is deficient in calories, not enough energy
 Malnourishment: missing 1+ essential nutrients
Main stages of food processing:
1. Ingestion: Eating
2. Digestion: Breakdown of food into small molecules
 Mechanical (chewing, grinding)
 Chemical (enzymes)
3. Absorption: Cells take up nutrients
4. Elimination: Pass undigested materials from digestive system

Ingestion → Mechanical Digestion → Chemical Digestion → Nutrient molecules enter body cells
→ Elimination of undigested material

DIGESTIVE COMPARTMENTS
 Most animals process food in specialized compartments
 Intracellular: digestion of food inside cells by food vacuoles
: phagocytosis, pinocytosis, sponges

 Extracellular: food broken down outside of cells

 Compartments are outside of the animal’s body
: Gastrovascular cavity (simple animals; single opening, two-way digestion: food in,
waste out) or
: alimentary canal (more complex, one-way tubes with mouth and anus)
Specialized organs for digestion in Humans
 Digestive system = alimentary canal + glands
 Glands = salivary glands, pancreas, liver, and gallbladder
 Organs of the human alimentary canal (in order): mouth, pharynx, esophagus,
stomach, small intestine, large intestine, anus.
 Peristalsis: push food through rhythmic contractions of muscles in the wall of the
canal
 Sphincters: valves regulate the movement of material between compartments
 Digestion of macromolecules:
 Mouth = carbs
 Stomach = proteins
 Small intestine = carbs, proteins, fats, nucleic acids

Digestion in the mouth

 Oral cavity: mechanical, chemical digestion
 Salivary glands: saliva lubricates food
 Teeth: chew food into smaller particles
 Salivary amylase: breakdown glucose polymers
 Saliva: contains mucus, a viscous mixture of water, salts, cells, and
glycoproteins
 Pharynx: back of throat
 Epiglottis: flap of cartilage, covers trachea when swallowing
 Esophagus: food tube (pharynx → stomach)

Digestion in the Stomach

 The stomach stores food and secretes gastric juice, which converts a meal to
chyme
  HCl: ph 2, kills bacteria & denatures proteins
 Pepsin: enzyme (protease) that hydrolyze proteins into smaller peptides
:Pepsinogen (inactive) → Pepsin (active) by HCl
 Mucus: protects lining of stomach
 Gastric ulcers: lesions in the lining, caused by bacterium Heliobacter pylori

Digestion in the Small Intestine

 Small Intestine = major organ of digestion and absorption
 Duodenum: 1st section, digestive juices, major chemical digestion
 Digestive juices:
 Pancreas: bicarbonate (basic), trypsin & chymotrypsin (proteases); lipase
(fats); amylase (carbs); nuclease (DNA, RNA)
 Bile: made in liver, stored in gallbladder
: Emulsify fats (make smaller droplets)

Hormones that coordinate digestion:

 Gastrin: produced by stomach, ↑ production of gastric juices
 Entrogastrin: produced by small intestine (duodenum), ↓ peristalsis to allow time
for fat digestion
 Secretin & CCK (cholesystokinin): secreted by Small intestine (duodenum), ↑ flow
of digestive juices from pancreas & gall bladder

Absorption in the Small Intestine

 Villi and microvilli increase surface area
 Villi → capillaries → hepatic portal vein → liver → heart
 Liver: distribute nutrients, detox, glucose storage (glycogen)

Absorption in the Large Intestine

 Large Intestine = colon
 Function = compact waste, reabsorb water
 Cecum: pouch where Small Intestine and Large Intestine meet, ferment plant
material
: Appendix = extension of cecum, role in immunity
 Rectum: end of Large intestine; Feces stored until elimination

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IMMUNE SYSTEM
 Types of Immunity
1. Innate Immunity
 Non-specific
 All plants & Animals
 Recognition of traits shared by broad ranges of pathogens, using a small set of
receptors
 Rapid response
 Barrier Defenses: Skin, Mucous membranes, Secretions
 Internal defenses:
  Phagocytic WBCs:
a. Neutrophils - engulf
b. Macrophage - “big eaters”
c. Eosinophils - parasites
d. Dendritic cells - adaptive response
 Natural killer cells
a. Virus-infected and cancer cells
 Antimicrobial proteins
a. Interferons - inhibit viral reproduction
b. Complement system - ~30 proteins, membrane attack complex
 Inflammatory response
a. Mast cells release histamine
b. Blood vessels dilate, increase permeability (redness, swelling)
c. Deliver clotting agents, phagocytic cells
d. Fever

2. Adaptive Immunity
 Pathogen-specific
 Only in vertebrates
 Involves B and T cells
a. T Cells: mature in thymus
: helper T, cytotoxic T
b. B Cells: stay and mature in bone marrow
: plasma cells → antibodies
 Recognition of traits specific to particular pathogens, using a vast array of receptors
 Slower response
 Humoral response: Antibodies defend against infection in body fluids
 Cell-mediated response: Cytotoxic cells defend against against infection in body cells

 Lymphatic System: involved in adaptive immunity

 Lymphoid tissue (lymph nodes, spleen, blood, and lymph)

 Plant Defenses
 Nonspecific responses
 Receptors recognize pathogen molecules and trigger defense responses
a. Thicken cell wall, produce antimicrobial compounds, cell death
 Localize effects

 Antigen: substance that elicits lymphocyte response

 Antibody (immunoglobulin - lg): protein made by B cell that binds to antigens
 Major Histocompatibility Complex (MHC)
 Proteins displayed on cell surface
 Responsible for tissue/organ rejection (“self” vs. “nonself”)
 B and T cells bind to MHC molecule in adaptive response
 Class I: all body cells (except RBCs)
 Class II: displayed by immune cells; “non-self”
  Immunological Memory
 Primary immune response: 1st exposure to antigen
 Memory cells:
a. Secondary immune response: repeat exposure → faster, greater response
 Adaptive immunity defends against infection of body fluids and body cells
 Two branches of acquired immunity:
a. Humoral Immune response: antibodies help neutralize or eliminate toxins and pathogens
in the blood and the lymph
b. Cell-mediated immune response: specialized T cells destroy affected host cells
 Helper T cells: A response to nearly all antigens
 Helper T cell triggers both the humoral and cell-mediated immune responses
 Signals from helper T cells initiate production of antibodies that neutralize
pathogens and activate T cells that kill infected cells
 Antigen-presenting cells have class I and class II MHC molecules on their
surfaces
 Cytotoxic T Cells: A response to infected cells
 Cytotoxic T cells are the effector cells in the cell-mediated immune response
 It recognize fragments of foreign proteins produced by infected cells and possess
an accessory protein that binds to class I MHC molecules
 Activated cytotoxic T cell secretes proteins that disrupt the membranes of target
cells and trigger apoptosis
 B Cells and Antibodies: a response to extracellular pathogens
 Humoral response is characterized by secretion of antibodies by B cells
 In response to cytokines from helper T cells and an antigen, a B cell proliferates
and differentiates into memory B cells and antibody secreting effector cells called
Plasma cells
 Antibody Function
 Antibodies do not kill pathogens; instead they mark pathogens for destruction
 [Neutralization] antibodies bind to viral surface proteins preventing infection of a host
cell
 They may also bind to toxins in body fluids and prevent them from entering body cells
  [Opsonization] antibodies bind to antigens on bacteria creating a target for macrophages
or neutrophils, triggering phagocytosis
 Antigen-antibody complexes may bind to a complementary protein - which triggers a
cascade of complement protein activation

 Immunizations/vaccines: induce immune memory to nonpathogenic microbe or toxin

 Passive immunity: via antibodies in breast milk
 Allergies - hypersensitive responses to harmless antigens
 Autoimmune Diseases - Lupus, rheumatoid arthritis, Type I diabetes, multiple sclerosis
 HIV: infect Helper T cells
 AIDS = severely weakened immune system

_________________________________________________________________________
RESPIRATORY SYSTEM

 Gas exchange supplies O2 for cellular respiration and disposes of CO2

 Partial pressure = pressure exerted by a particular gas in a mixture of gases
 Gases always diffuses from higher partial pressure → lower partial pressure
 Respiratory media: O2 in air or water
 Respiratory surface: body wall, skin, gills, trachea, lungs
 Characteristics:
a. Moist
b. Large surface area-to-volume ratio
c. Larger animals: associated with vascular system

 Pathway of O2
a. Nose/mouth: filtered, warmed, humidified
b. Pharynx
c. Larynx: contains vocal cords
d. Trachea: windpipe, lined with cartilage
e. Bronchi: branches to lungs
f. Bronchioles:
g. Alveoli: air sacs for gas exchange
h. Mucus: traps particles
i. Cilia: sweeps particles up to pharynx
  Diaphragm: dome shaped muscle separating thoracic/abdominal cavities
1. Inhalation: Rib cage expands
2. Exhalation: Rib cage gets smaller (contracts)

 Control of breathing in Humans

 Control center = medulla oblongata
 Responds to pH changes in blood
 High CO2 → carbonic acid forms → lowers pH
 Sensors in the aorta and carotid arteries

 How CO2 is transported

1. Bicarbonate ions (70%)
2. Hemoglobin (23%) Dissolved in plasma (7%)

 Respiratory Disorders
a. Asthma: airways constricted
b. Bronchitis: bronchi swollen and clogged
c. Pneumonia: inflammation of lung caused by infection
d. Tuberculosis: infectious disease caused by M. tuberculosis
e. Emphysema: lose elasticity of lung tissue
f. Lung Cancer: abnormal cell growth in lungs