Table of Contents

Carbon and theCellular

Molecular
Respiration
Diversity
Mendelofand
Life
the The
GeneOrganization
Idea Early
andEarth
Control
andof
AnThe
Eukaryotic
Introduction
Origin of
Ge

An IntroductionCell
to Metabolism
Communi-cation
The Molecular Basis
DNAofTechnology
Inheritance
The
& Origins
Genomicsof Eukaryotic
The Body’s Dive
Defe

A Tour of the Cell

The Cell CycleFrom Gene to Protein
The Genetic Basis
Plants
of Development

PhotosynthesisMeiosis The Genetics of Descent

Viruses and
withBacteria
Modification:
Fungi A Darwi
Index
 Organic chemistry
 Biological thought:
 Vitalism (life force outside
physical & chemical laws)
Berzelius
 Mechanism (all natural
phenomena are governed by
physical & chemical laws) Miller
 Carbon tetravalence
tetrahedron shape determines
function
Hydrocarbons
 Only carbon & hydrogen
(petroleum; lipid ‘tails’)
 Covalent bonding; nonpolar
 High energy storage
 Isomers (same molecular
formula, but different
structure & properties)
 structural~differing covalent
bonding arrangement
 geometric~differing spatial
arrangement
 enantiomers~mirror images
pharmacological industry
(thalidomide)
Functional Groups, I
Attachments that Hydroxyl Group
replace one or more H bonded to O;
of the hydrogens alcohols; polar
bonded to the carbon (oxygen); solubility in
water
skeleton of the
hydrocarbon Carbonyl Group
C double bond to O;
Each has a unique At end of HC:
property from one aldehyde Otherwise:
organic to another ketone
 Functional Groups, II
 Carboxyl Group O
double bonded to C to hydroxyl; carboxylic Sulfhydral Group
acids; covalent bond between O
and H;
ion
polar; dissociation, H sulfur bonded to H;
thiols
 Amino Group N to 2 H atoms;
amines; acts as a base (+1)

Phosphate Group
phosphate ion;
covalently attached by
1 of its O to the C
skeleton;
Polymers
Covalent monomers
Condensation reaction
(dehydration reaction):
One monomer provides a
hydroxyl group while the other
provides a hydrogen to form a
water molecule
Hydrolysis: bonds
between monomers are broken
by adding water (digestion)
Carbohydrates, I
Monosaccharides
√ CH2O formula;
√ multiple
hydroxyl (-OH) groups
and 1 carbonyl (C=O)
group:
aldehyde (aldoses) sugar
ketone sugar
√ cellular respiration;
√ raw
material for amino acids
and fatty acids
Carbohydrates, II
Disaccharides
√ glycosidic
linkage (covalent bond)
between 2
monosaccharides;
√ covalent bond by
dehydration
reaction
Sucrose (table
sugar) √ most
common disaccharide
Disaccharides
 Carbohydrates, III
 Polysaccharides  Polysaccharides Structural:
Storage: Starch~ glucose Cellulose~
monomers Plants: most abundant organic
compound; Chitin~
plastids Animals: glycogen
exoskeletons; cell walls of
fungi; surgical thread
 Lipids
 No polymers; glycerol and fatty acid
 Fats, phospholipids, steroids
 Hydrophobic; H bonds in water exclude fats
 Carboxyl group = fatty acid
 Non-polar C-H bonds in fatty acid ‘tails’
 Ester linkage: 3 fatty acids to 1 glycerol
(dehydration formation)
 Triacyglycerol (triglyceride)
 Saturated vs. unsaturated fats; single vs.
double bonds
Lipids, II
Phospholipids
2 fatty acids instead of
3 (phosphate group)
‘Tails’ hydrophobic;
‘heads’ hydrophilic
Micelle (phospholipid
droplet in water)
Bilayer (double layer);
cell membranes
 Steroids

Lipids with 4 fused carbon

rings
Ex: cholesterol:
cell membranes;
precursor for other
steroids (sex
hormones);
atherosclerosis
 Proteins
Importance: instrumental in nearly everything organisms do;
50% dry weight of cells; most structurally sophisticated molecules
known
Monomer: amino acids (there are 20) ~ carboxyl (-
COOH) group, amino group (NH2), H atom, variable group (R)….
Variable group characteristics: polar (hydrophilic),
nonpolar (hydrophobic), acid or base
Three-dimensional shape (conformation)
Polypeptides (dehydration reaction): peptide
bonds~ covalent bond; carboxyl group to amino group (polar)
 Primary Structure
Conformation:
Linear structure
Molecular Biology:
each type of protein has a unique
primary structure of amino acids
Ex: lysozyme
Amino acid
substitution: hemoglobin;
sickle-cell anemia
 Secondary Structure
Conformation:
coils & folds
(hydrogen bonds)
Alpha Helix:
coiling; keratin
Pleated Sheet:
parallel; silk
Tertiary Structure

Conformation:
irregular contortions
from R group bonding
√hydrophobic
√disulfide
bridges √hydrogen
bonds √ionic
bonds
Quaternary Structure
Conformation:
2 or more
polypeptide chains
aggregated into 1
macromolecule
√collagen
(connective
tissue)
√hemoglobin
 Nucleic Acids, I
 Deoxyribonucleic acid (DNA)
 Ribonucleic acid (RNA)
 DNA->RNA->protein
 Polymers of nucleotides
(polynucleotide):
nitrogenous base
pentose sugar
phosphate group
 Nitrogenous bases:
pyrimidines~cytosine,
thymine, uracil
purines~adenine, guanine
 Nucleic Acids, II
Pentoses:
√ribose (RNA)
√deoxyribose (DNA)
√nucleoside (base +
sugar)
Polynucleotide:
√phosphodiester
linkages (covalent);
phosphate + sugar
 Nucleic Acids, III
Inheritance based on
DNA replication
Double helix (Watson &
Crick - 1953)
H bonds~ between
paired bases van der
Waals~ between stacked
bases
A to T; C to G pairing
Complementary
Index
Metabolism/Bioenergetic
s
Metabolism: The totality of an organism’s
chemical processes; managing the material
and energy resources of the cell
Catabolic pathways: degradative process
such as cellular respiration; releases energy
Anabolic pathways: building process such as
protein synthesis; photosynthesis; consumes
energy
 Thermodynamics
 Energy (E)~ capacity to do work; Kinetic energy~ energy of motion;
Potential energy~ stored energy
 Thermodynamics~ study of E transformations
 1st Law: conservation of energy; E transferred/transformed, not
created/destroyed
 2nd Law: transformations increase entropy (disorder, randomness)


Combo: quantity of E is constant, quality is not
 Free energy
Free energy: portion of system’s E that can perform work (at a constant
T)
Exergonic reaction: net release of free E to surroundings
Endergonic reaction: absorbs free E from surroundings
 Energy Coupling & ATP
E coupling: use of
exergonic process to drive
an endergonic one (ATP)
Adenosine triphosphate
ATP tail: high negative
charge
ATP hydrolysis: release of
free E
Phosphorylation
(phosphorylated
intermediate)~ enzymes
 Enzymes
Catalytic proteins: change
the rate of reactions w/o
being consumed
Free E of activation
(activation E): the E required
to break bonds
Substrate: enzyme reactant
Active site: pocket or groove
on enzyme that binds to
substrate
Induced fit model
 Effects on Enzyme
Activity
Temperature
pH
Cofactors: inorganic,
nonprotein helpers; ex.:
zinc, iron, copper
Coenzymes: organic
helpers; ex.: vitamins
 Enzyme Inhibitors
Irreversible (covalent);
reversible (weak bonds)
Competitive: competes for
active site (reversible);
mimics the substrate
Noncompetitive: bind to
another part of enzyme
(allosteric site) altering its
conformation (shape);
poisons, antibiotics
Index
Cytology: science/study of
cells
 Light microscopy •resolving power~ measure of clarity
 Electron microscopy •TEM~ electron beam to study cell
ultrastructure •SEM~ electron beam to study cell surfaces
 Cell fractionation~ cell separation; organelle study
 Ultracentrifuges~ cell fractionation; 130,000 rpm
Cell Types: Prokaryotic
Nucleoid: DNA
concentration
No organelles with
membranes
Ribosomes: protein
synthesis
Plasma membrane (all
cells); semi-permeable
Cytoplasm/cytosol (all
cells)
Cell size
As cell size increases, the surface area
to volume ratio decreases
Rates of chemical exchange may then
be inadequate for cell size
Cell size, therefore, remains small
Nucleus
Genetic material...
•chromatin
•chromosomes
•nucleolus: rRNA;
ribosome synthesis
Double membrane
envelope with pores
Protein synthesis (mRNA)
Ribosomes
Protein manufacture
Free •cytosol; •protein function in cell
Bound •endoplasmic reticulum; •membranes,
organelles, and export
Endomembrane
system, I
 Endoplasmic reticulum (ER)
 Continuous with nuclear
envelope
 Smooth ER •no
ribosomes; •synthesis of
lipids, •metabolism of
carbohydrates;
•detoxification of drugs and
poisons
 Rough ER •with ribosomes;
•synthesis of secretory
proteins (glycoproteins),
membrane production
Endomembrane
system, II
Golgi apparatus•ER products are modified,
stored, and then shipped
Cisternae: flattened membranous sacs
trans face (shipping) & cis face (receiving)
Transport vesicles
Endomembrane
system, III
Lysosomes •sac
of hydrolytic enzymes;
digestion of
macromolecules
Phagocytosis
Autophagy: recycle cell’s
own organic material
Tay-Sachs disease~
lipid-digestion disorder
Endomembrane
system, IV
Vacuoles
•membrane-bound
sacs (larger than
vesicles)
Food (phagocytosis)
Contractile (pump
excess water)
Central (storage in
plants) •tonoplast
membrane
Other membranous
organelles, I
Mitochondria
• quantity in cell
correlated with
metabolic activity;
•cellular respiration;
•double membranous
(phospholipid);
•cristae/matrix;
•intermembrane space;
•contain own DNA
Other membranous
organelles, II
Chloroplast
•type of plastid; •double membranous;
•thylakoids (flattened disks); •grana (stacked
thylakoids); •stroma; •own DNA
Peroxisomes
Single membrane
Produce hydrogen
peroxide in cells
Metabolism of fatty
acids; detoxification of
alcohol (liver)
Hydrogen peroxide
then converted to
water
The Cytoskeleton
 Fibrous network in cytoplasm
 Support, cell motility, biochemical
regulation
 Microtubules: •thickest;
•tubulin protein;
•shape, support, transport,
chromosome separation
 Microfilaments : •thinnest;
•actin protein filaments;
•motility, cell division, shape
 Intermediate filaments:
middle diameter; •keratin;
•shape,
nucleus anchorage
Centrosomes/centrioles
Centrosome: region near nucleus
Centrioles: 9 sets of triplet microtubules in a
ring; used in cell replication; only in
animal cells
Cilia/flagella
Locomotive appendages
Ultrastructure: “9+2”
•9 doublets of
microtubules in a ring
•2 single
microtubules in center
•connected by
radial spokes •anchored
by basal body
•dynein protein
Cell surfaces &
junctions
 Cell wall: •not in
animal cells •protection,
shape, regulation
 Plant cell: •primary cell
wall produced first •middle
lamella of pectin
(polysaccharide); holds
cells together •some
plants, a secondary cell
wall; strong durable matrix;
wood (between plasma
membrane and primary
wall)
Extracellular matrix
(ECM)
 Glycoproteins: •
proteins covalently bonded to
carbohydrate
 Collagen (50% of protein in
human body) •embedded in
proteoglycan (another
glycoprotein-95%
carbohydrate)
 Fibronectins •bind to
receptor proteins in plasma
membrane called integrins
(cell communication?)
Intracellular junctions
 PLANTS:
 Plasmodesmata:
cell wall perforations;
water and solute passage
in plants
 ANIMALS:
 Tight junctions~ fusion of
neighboring cells; prevents
leakage between cells
 Desmosomes~ riveted,
anchoring junction; strong
sheets of cells
 Gap junctions~
cytoplasmic channels;
allows passage of materials
or current between cells
 Membrane traffic
Diffusion~ tendency of any
molecule to spread out into
available space
Concentration gradient
Passive transport~ diffusion of
a substance across a biological
membrane
Osmosis~ the diffusion of
water across a selectively
permeable membrane
 Water balance
Osmoregulation~
control of water balance
Hypertonic~ higher
concentration of solutes
Hypotonic~ lower
concentration of solutes
Isotonic~ equal
concentrations of
solutes
Cells with Walls:
Turgid (very firm)
Flaccid (limp)
Plasmolysis~ plasma
membrane pulls away
from cell wall
Specialized Transport
 Transport proteins
 Facilitated diffusion~
passage of molecules and
ions with transport proteins
across a membrane down
the concentration gradient
 Active transport~ movement
of a substance against its
concentration gradient with
the help of cellular energy
 Types of Active
Transport
Sodium-potassium pump
Exocytosis~ secretion of
macromolecules by the fusion
of vesicles with the plasma
membrane
Endocytosis~ import of
macromolecules by forming
new vesicles with the plasma
membrane
•phagocytosis
•pinocytosis
•receptor-mediated
endocytosis
(ligands)
Index
 Photosynthesis in
nature
 Autotrophs:
biotic producers;
photoautotrophs;
chemoautotrophs; obtains
organic food without eating
other organisms
 Heterotrophs:
biotic consumers;
obtains organic food by
eating other organisms or
their by-products (includes
decomposers)
The chloroplast
Sites of photosynthesis
Pigment: chlorophyll
Plant cell: mesophyll
Gas exchange: stomata
Double membrane
Thylakoids, grana, stroma
Photosynthesis: an
overview
 Redox process
 H2O is split, e- (along w/ H+)
are transferred to CO2,
reducing it to sugar
 2 major steps:
• light
reactions (“photo”) √
NADP+ (electron
acceptor) to NADPH
√Photophosphorylation:
ADP ---> ATP • Calvin
cycle (“synthesis”) √
Carbon fixation:
carbon into organics
Photosystems
 Light harvesting units of the
thylakoid membrane
 Composed mainly of protein
and pigment antenna
complexes
 Antenna pigment molecules
are struck by photons
 Energy is passed to reaction
centers (redox location)
 Excited e- from chlorophyll is
trapped by a primary e-
acceptor
 Noncyclic electron flow
 Photosystem II (P680): √
photons excite chlorophyll e- to an
acceptor
√ e- are replaced by splitting of H2O
(release of O2)
√ e-’s travel to Photosystem
I down an electron transport chain
(Pq~cytochromes~Pc) √
as e- fall, ADP ---> ATP (noncyclic
photophosphorylation)
 Photosystem I (P700): √
‘fallen’ e- replace excited e- to
primary e- acceptor √
2nd ETC ( Fd~NADP+ reductase)
transfers e- to NADP+ ---> NADPH
(...to Calvin cycle…)
 These photosystems produce equal
amounts of ATP and NADPH
The Calvin cycle
 3 molecules of CO2 are
‘fixed’ into glyceraldehyde
3-phosphate (G3P)
 Phases:
1- Carbon fixation~
each CO2 is attached to
RuBP (rubisco enzyme)
2- Reduction~
electrons from NADPH
reduces to G3P; ATP used
up 3-
Regeneration~ G3P
rearranged to RuBP; ATP
used; cycle continues
Calvin Cycle, net
synthesis
For each G3P (and for 3 CO2)…….
Consumption of 9 ATP’s & 6 NADPH
(light reactions regenerate these molecules)
G3P can then be used by the plant to make
glucose and other organic compounds
Cyclic electron flow
Alternative cycle when ATP
is deficient
Photosystem I used but
not II; produces ATP but no
NADPH
Why? The Calvin cycle
consumes more ATP than
NADPH…….
Cyclic
photophosphorylation
Alternative carbon fixation
methods, I
 Photorespiration: hot/dry
days; stomata close; CO2
decrease, O2 increase in
leaves; O2 added to rubisco;
no ATP or food generated
 Two Solutions…..
 1- C4 plants: 2
photosynthetic cells, bundle-
sheath & mesophyll; PEP
carboxylase (instead of
rubisco) fixes CO2 in
mesophyll; new 4C molecule
releases CO2 (grasses)
Alternative carbon fixation
methods, II
2- CAM plants: open
stomata during night,
close during day
(crassulacean acid
metabolism); cacti,
pineapples, etc.
67of photosynthesis
Index
 Principles of Energy
Harvest
Catabolic pathway
√ Fermentation
√Cellular Respiration
C6H12O6 + 6O2 ---> 6CO2 +
6H2O + E (ATP + heat)
Redox reactions
Oxidation-reduction
OIL RIG (adding e- reduces +
charge)

Oxidation is e- loss;
reduction is e- gain
Reducing agent: e-
donor
Oxidizing agent: e-
acceptor
Oxidizing agent in
respiration
NAD+ (nicotinamide
adenine dinucleotide)
Removes electrons
from food (series of
reactions)
NAD + is reduced to
NADH
Enzyme action:
dehydrogenase
Oxygen is the eventual
e- acceptor
Electron transport
chains
 Electron carrier molecules
(membrane proteins)
 Shuttles electrons that
release energy used to make
ATP
 Sequence of reactions that
prevents energy release in 1
explosive step
 Electron route: food--->
NADH ---> electron transport
chain ---> oxygen
Cellular respiration
Glycolysis: cytosol;
degrades glucose into
pyruvate
Kreb’s Cycle:
mitochondrial matrix;
pyruvate into carbon
dioxide
Electron Transport
Chain: inner membrane
of mitochondrion;
electrons passed to
oxygen
Glycolysis
 1 Glucose ---> 2 pyruvate
molecules
 Energy investment phase: cell
uses ATP to phosphorylate fuel
 Energy payoff phase: ATP is
produced by substrate-level
phosphorylation and NAD+ is
reduced to NADH by food
oxidation
 Net energy yield per glucose
molecule: 2 ATP plus 2 NADH;
no CO2 is released; occurs
aerobically or anaerobically
Kreb’s Cycle
 If molecular oxygen is present…….
 Each pyruvate is converted into
acetyl CoA (begin w/ 2): CO2 is
released; NAD+ ---> NADH;
coenzyme A (from B vitamin),
makes molecule very
reactive
 From this point, each turn 2 C atoms
enter (pyruvate) and 2 exit (carbon
dioxide)
 Oxaloacetate is regenerated (the
“cycle”)
 For each pyruvate that enters: 3
NAD+ reduced to NADH; 1
FAD+ reduced to FADH2
(riboflavin, B vitamin); 1 ATP
molecule
Electron transport chain
 Cytochromes carry electron
carrier molecules (NADH &
FADH2) down to oxygen
 Chemiosmosis:
energy coupling mechanism
 ATP synthase:
produces ATP by using the H+
gradient (proton-motive force)
pumped into the inner
membrane space from the
electron transport chain; this
enzyme harnesses the flow of
H+ back into the matrix to
phosphorylate ADP to ATP
(oxidative phosphorylation)
Review: Cellular
Respiration
 Glycolysis: 2 ATP
(substrate-level phosphorylation)

 Kreb’s Cycle: 2 ATP

(substrate-level phosphorylation)
 Electron transport & oxidative
phosphorylation: 2
NADH (glycolysis) = 6ATP 2
NADH (acetyl CoA) = 6ATP 6
NADH (Kreb’s) = 18 ATP 2
FADH2 (Kreb’s) = 4 ATP
 38 TOTAL ATP/glucose
Related metabolic
processes
Fermentation:
alcohol~ pyruvate to
ethanol lactic acid~
pyruvate to lactate
Facultative anaerobes
(yeast/bacteria)
Beta-oxidation lipid
catabolism
Index
Signal-transduction
pathway
 Def: Signal on a cell’s surface is converted into a
specific cellular response
 Local signaling (short distance):
√ Paracrine (growth factors)
√ Synaptic (neurotransmitters)
 Long distance: hormones
Stages of cell signaling
 Sutherland (‘71)
 Glycogen depolymerization by epinephrine
 3 steps: •Reception: target cell detection
•Transduction: single-step or series of changes •Response:
triggering of a specific cellular response
Protein phosphorylation
Protein activity regulation
Adding phosphate from ATP to
a protein (activates proteins)
Enzyme: protein kinases (1%
of all our genes)
Example: cell reproduction
Reversal enzyme: protein
phosphatases
Second messengers
 Non-protein signaling
pathway (
 Example: cyclic AMP (cAMP)
 Ex: Glycogen breakdown
with epinephrine
 Enzyme: adenylyl cyclase
 G-protein-linked receptor in
membrane (guanosine di-
or tri- phosphate)
Cellular responses to
signals

Cytoplasmic
activity regulation
Cell metabolism
regulation
Nuclear
transcription
regulation
Index
Cell Division: Key Roles
Genome: cell’s genetic information

Somatic (body cells) cells

Gametes (reproductive cells): sperm and egg cells

Chromosomes: DNA molecules

Diploid (2n): 2 sets of chromosomes

Haploid (1n): 1 set of chromosomes

Chromatin: DNA-protein complex

Chromatids: replicated strands of a chromosome

Centromere: narrowing “waist” of sister chromatids

Mitosis: nuclear division

Cytokinesis: cytoplasm division

Meiosis: gamete cell division

 The Cell Cycle
Interphase (90% of cycle)• G1 phase~ growth • S phase~
synthesis of DNA • G2 phase~ preparation for cell division
Mitotic phase • Mitosis~ nuclear division • Cytokinesis~ cytoplasm
division
Mitosis
Prophase
Prometaphase
Metaphase
Anaphase
Telophase
 Prophase
Chromosomes visible
Nucleoli disappear
Sister chromatids
Mitotic spindle forms
Centrosomes move QuickTime™ and a
Cinepak decompressor
are needed to see this picture.
 Prometaphase
Nuclear membrane fragments
Spindle interaction with chromosomes
Kinetochore develops
 Anaphase
Paired centromeres separate; sister chromatids liberated
Chromosomes move to opposite poles
Each pole now has a complete set of chromosomes
Telophase
Daughter nuclei form
Nuclear envelopes arise
Chromatin becomes less coiled
Two new nuclei complete mitosis
Cytokinesis
Cytoplasmic division

Animals: cleavage furrow

Plants: cell plate
Cell Cycle regulation

Growth factors
Density-dependent inhibition
Anchorage dependence
Cancer
Transformation
Tumor: benign or malignant
Metastasis
Index
Heredity
 Heredity: the transmission of traits from
one generation to the next
 Asexual reproduction: clones
 Sexual reproduction: variation
 Human life cycle: •
23 pairs of homologous
chromosomes (46); • 1 pair of
sex and 22 pairs of autosomes; •
karyotype; • gametes are haploid (1N)/
all other cells are diploid (2N);
•fertilization (syngamy) results in
a zygote
 Meiosis: cell division to produce
haploid gametes
Alternative life cycles
Fungi/some algae
•meiosis produces 1N
cells that divide by mitosis
to produce 1N adults
(gametes by mitosis)
Plants/some algae
•Alternation of
generations: 2N
sporophyte, by meiosis,
produces 1N spores; spore
divides by mitosis to
generate a 1N
gametophyte; gametes
then made by mitosis
which then fertilize into 2N
sporophyte
Meiosis
Preceded by
chromosome
replication, but is
followed by 2 cell
divisions (Meiosis I
& Meiosis II)
4 daughter cells;
1/2 chromosome
number (1N);
variation
Meiosis vs. mitosis
 Synapsis/tetrad/chiasmata
(prophase I)
 Homologous vs. individual
chromosomes (metaphase
I)
 Sister chromatids do not
separate (anaphase I)
 Meiosis I separates
homologous pairs of
chromosomes, not sister
chromatids of individual
chromosomes.
Origins of Genetic
Variation, I
Independent assortment:
homologous pair of
chromosomes position
and orient randomly
(metaphase I) and
nonidentical sister
chromatids during
meiosis II
Combinations possible:
2 ; with n the haploid
number of the organism
n
Origins of Genetic
Variation, II
 Crossing over (prophase I):
• the reciprocal exchange of
genetic material between
nonsister chromatids during
synapsis of meiosis I
(recombinant chromosomes)
 Random fertilization:
• 1 sperm (1 of 8 million
possible chromosome
combinations) x 1 ovum (1 of 8
million different possibilities) =
64 trillion diploid combinations!
Index
Mendelian genetics
 Character (heritable feature, i.e.,
fur color)
 Trait (variant for a character, i.e.,
brown)
 True-bred (all offspring of
same variety)
 Hybridization (crossing of 2
different true-breds)
 P generation (parents)
 F1 generation (first filial generation)
Leading to the Law of
Segregation
 Alternative versions of genes
(alleles) account for variations
in inherited characteristics
 For each character, an organism
inherits 2 alleles, one from each
parent
 If the two alleles differ, then
one, the dominant allele, is fully
expressed in the organism’s
appearance; the other, the
recessive allele, has no
noticeable effect on the
organism’s appearance
 The alleles for each character
segregate (separate) during
gamete production (meiosis).
 Mendel’s Law of Segregation
Genetic vocabulary…….
 Punnett square: predicts the
results of a genetic cross
between individuals of known
genotype
 Homozygous: pair of identical
alleles for a character
 Heterozygous: two different
alleles for a gene
 Phenotype: an organism’s traits
 Genotype: an organism’s
genetic makeup
 Testcross: breeding of a
recessive homozygote X
dominate phenotype (but
unknown genotype)
The Law of Independent
Assortment
Law of Segregation involves 1
character. What about 2 (or
more) characters?
Monohybrid cross vs. dihybrid
cross
The two pairs of alleles
segregate independently of
each other.
Mendel’s Law of
Independent Assortment
Non-single gene
genetics, I
 Incomplete dominance:
appearance between the
phenotypes of the 2 parents.
Ex: snapdragons
 Codominance: two alleles
affect the phenotype in
separate, distinguishable
ways. Ex: Tay-Sachs
disease
 Multiple alleles: more than 2
possible alleles for a gene.
Ex: human blood types
Index
The Chromosomal Theory
of Inheritance

Genes have
specific loci on
chromosomes and
chromosomes
undergo
segregation and
independent
assortment
Chromosomal Linkage
 Morgan
 Drosophilia melanogaster
 XX (female) vs. XY (male)
 Sex-linkage: genes located on
a sex chromosome
 Linked genes: genes located
on the same chromosome that
tend to be inherited together
Genetic recombination
 Crossing over
Genes that DO NOT assort
independently of each other
 Genetic maps The further
apart 2 genes are, the higher the
probability that a crossover will
occur between them and
therefore the higher the
recombination frequency
 Linkage maps Genetic
map based on recombination
frequencies
Human sex-linkage
 SRY gene: gene on Y chromosome that triggers the development of testes
 Fathers= pass X-linked alleles to all daughters only (but not to sons)
 Mothers= pass X-linked alleles to both sons & daughters
 Sex-Linked Disorders: Color-blindness; Duchenne muscular dystropy (MD);
hemophilia

 X-inactivation: 2nd X chromosome in females condenses into a Barr body
(e.g., tortoiseshell gene gene in cats)
Chromosomal errors, I
 Nondisjunction:
members of a pair of
homologous chromosomes
do not separate properly
during meiosis I or sister
chromatids fail to separate
during meiosis II
 Aneuploidy: chromosome
number is abnormal •
Monosomy~ missing
chromosome • Trisomy
~ extra chromosome
(Down syndrome)
• Polyploidy~ extra
sets of chromosomes
Chromosomal errors, II
 Alterations of chromosomal structure:
 Deletion: removal of a chromosomal segment
 Duplication: repeats a chromosomal segment
 Inversion: segment reversal in a chromosome
 Translocation: movement of a chromosomal segment to another
Genomic imprinting
Def: a parental effect on
gene expression
Identical alleles may
have different effects on
offspring, depending on
whether they arrive in
the zygote via the ovum
or via the sperm.
Fragile X syndrome:
higher prevalence of
disorder and retardation
in males
Index
Searching for Genetic
Material, I
 Mendel: modes of heredity in pea plants
 Morgan: genes located on chromosomes
 Griffith: bacterial work; transformation: change in
genotype and phenotype due to assimilation of external
substance (DNA) by a cell
 Avery: transformation agent was DNA
Searching for Genetic
Material, II
Hershey and Chase
√ bacteriophages (phages)
√ DNA, not protein, is the
hereditary material √ Expt: sulfur(S) is
in protein, phosphorus (P) is in DNA;
only P was found in host cell
DNA Structure
 Chargaff ratio of nucleotide
bases (A=T; C=G)
 Watson & Crick (Wilkins,
Franklin)
 The Double Helix √
nucleotides: nitrogenous base
(thymine, adenine, cytosine,
guanine); sugar deoxyribose;
phosphate group
 *Franklin died without knowing
her contribution to DNA
DNA Bonding
Purines: ‘A’ & ‘G’
Pyrimidines: ‘C’ & ‘T’
(Chargaff rules)
‘A’ H+ bonds (2) with
‘T’ and ‘C’ H+ bonds
(3) with ‘G’
Van der Waals
attractions between
the stacked pairs
DNA Replication
 Watson & Crick strands are complementary; nucleotides line up on
template according to base pair rules (Watson)

 Meselson & Stahl replication is semiconservative; Expt: varying

densities of radioactive nitrogen
DNA Replication: a
closer look
 Origin of replication (“bubbles”): beginning of replication
 Replication fork: ‘Y’-shaped region where new strands of
DNA are elongating
 Helicase:catalyzes the untwisting of the DNA at the
replication fork
 DNA polymerase:catalyzes the elongation of new DNA
DNA Replication, II
Antiparallel nature:
• sugar/phosphate
backbone runs in opposite
directions (Crick);
• one strand runs 5’
to 3’, while the other runs 3’
to 5’; • DNA polymerase
only adds nucleotides at the
free 3’ end, forming new
DNA strands in the 5’ to 3’
direction only
DNA Replication, III
 Leading strand: synthesis
toward the replication fork
(only in a 5’ to 3’ direction
from the 3’ to 5’ master
strand)
 Lagging strand: synthesis
away from the replication fork
(Okazaki fragments); joined by
DNA ligase (must wait for 3’
end to open; again in a 5’ to 3’
direction)
 Initiation: Primer
(short RNA
sequence~w/primase
enzyme), begins the
replication process
DNA Repair

Mismatch repair:
DNA polymerase
Excision repair:
Nuclease
Telomere ends:
telomerase
Index
Protein Synthesis:
overview
 One gene-one enzyme
hypothesis (Beadle and
Tatum)
 One gene-one polypeptide
(protein) hypothesis
 Transcription:
synthesis of RNA under
the direction of DNA (mRNA)
 Translation:
actual synthesis of a
polypeptide under the
direction of mRNA
The Triplet Code
The genetic
instructions for a
polypeptide chain are
‘written’ in the DNA
as a series of
3-nucleotide
‘words’
Codons
‘U’ (uracil) replaces
‘T’ in RNA
Transcription, I
 RNA polymerase: pries DNA
apart and hooks RNA
nucleotides together from the
DNA code
 Promoter region on DNA:
where RNA polymerase
attaches and where initiation
of RNA begins
 Terminator region: sequence
that signals the end of
transcription
 Transcription unit: stretch
of DNA transcribed into an
RNA molecule
Transcription, II
 Initiation~ transcription
factors mediate the binding
of RNA polymerase to an
initiation sequence (TATA
box)
 Elongation~ RNA
polymerase continues
unwinding DNA and adding
nucleotides to the 3’ end
 Termination~ RNA
polymerase reaches
terminator sequence
mRNA modification
 1) 5’ cap: modified guanine; protection; recognition site for
ribosomes
 2) 3’ tail: poly(A) tail (adenine); protection; recognition; transport
 3) RNA splicing: exons (expressed sequences) kept,introns
(intervening sequences) spliced out; spliceosome
Translation, I
mRNA from nucleus is
‘read’ along its codons
by tRNA’s anticodons
at the ribosome
tRNA anticodon
(nucleotide triplet);
amino acid
Translation, II
rRNA
site of mRNA codon &
tRNA anticodon coupling
P site
holds the tRNA carrying
the growing polypeptide
chain
A site
holds the tRNA carrying
the next amino acid to be
added to the chain
E site discharged
tRNA’s
Translation, III
Initiation~
union of mRNA, tRNA, small
ribosomal subunit; followed
by large subunit
Elongation~
•codon recognition
•peptide bond formation
•translocation
Termination~
‘stop’ codon reaches ‘A’ site
Polyribosomes:
translation of mRNA by
many ribosomes (many
copies of a polypeptide very
quickly)
 Mutations: genetic material changes in a
cell
 Point mutations….
 Changes in 1 or a few base pairs
in a single gene
 Base-pair substitutions: •silent
mutations no
effect on protein •missense
∆ to a
different amino acid
(different protein)
•nonsense
∆ to a stop codon and a
nonfunctional protein
 Base-pair insertions or deletions:
additions or losses of
nucleotide pairs in a gene; alters
the ‘reading frame’ of
triplets~frameshift mutation
 Mutagens: physical and chemical
agents that change DNA
Index
Viral structure
Virus: “poison”
(Latin); infectious
particles consisting
of a nucleic acid in a
protein coat
Capsid; (viral
envelopes); DNA or
RNA
Bacteriophages
(phages)
Viral reproduction: Lytic
Cycle
 Host range: infection of a
limited range of host cells
(receptor molecules on the
surface of cells)
 The lytic cycle:
1- attachment
2- injection
3- hydrolyzation
4- assembly
5- release
 Results in death of host cell
 Virulent virus (phage
reproduction only by the
lytic cycle)
Viral reproduction: Lysogenic
Cycle

Genome replicated w/o

destroying the host cell
Genetic material of virus
becomes incorporated into the
host cell DNA (prophage DNA)
Temperate virus (phages
capable of using the lytic and
lysogenic cycles)
May give rise to lytic cycle
RNA viruses
Retroviruses:
transcribe DNA from
an RNA template
(RNA--->DNA)
Reverse transcriptase
(catalyzing enzyme)
HIV--->AIDS
Viroids and prions
Viroids: tiny, naked
circular RNA that infect
plants; do not code for
proteins, but use
cellular enzymes to
reproduce; stunt plant
growth
Prions: “infectious
proteins”; “mad cow
disease”; trigger chain
reaction conversions; a
transmissible protein
Bacterial genetics
Nucleoid:
region in bacterium
densely packed with
DNA (no membrane)
Plasmids:
small circles of
DNA
Reproduction:
binary fission
(asexual)
 Bacterial DNA-transfer
processes
 Transformation: genotype alteration
by the uptake of naked, foreign DNA
from the environment (Griffith expt.)
 Transduction: phages that carry
bacterial genes from 1 host cell to
another •generalized~
random transfer of host cell
chromosome •specialized~
incorporation of prophage DNA into
host chromosome
 Conjugation: direct transfer of
genetic material; cytoplasmic
bridges; pili; sexual
 Bacterial Plasmids
 Small, circular, self-replicating DNA separate from the bacterial
chromosome
 F (fertility) Plasmid: codes for the production of sex pili (F+ or F-)
 R (resistance) Plasmid: codes for antibiotic drug resistance
 Transposons: transposable genetic element; piece of DNA that can move
from location to another in a cell’s genome (chromosome to
plasmid, plasmid to plasmid, etc.); “jumping genes”
 Def: Unit of genetic function consisting

Operons, I of coordinately related clusters of genes

with related functions (transcription unit)

 Repressible (trp operon):

 tryptophan (a.a.) synthesis
 promoter: RNA polymerase binding
site; begins transcription
 operator: controls access of RNA
polymerase to genes
(tryptophan not present)

 repressor: protein that binds to

operator and prevents
attachment of RNA polymerase ~
coded from a regulatory gene
(tryptophan present ~ acts as a
corepressor)
 transcription is repressed when
tryptophan binds to a
regulatory protein
 Def: Unit of genetic function
consisting of coordinately related
Operons, II clusters of genes with related
functions (transcription unit)

 Inducible (lac operon):

 lactose metabolism
 lactose not present:
repressor active, operon off;
no transcription for lactose
enzymes
 lactose present: repressor
inactive, operon on; inducer
molecule inactivates protein
repressor (allolactose)
 transcription is stimulated when
inducer binds to a regulatory protein
Index
 Chromatin
 Def: complex of DNA and proteins
 DNA Packing •histone protein (+
charged amino acids ~ phosphates of
DNA are - charged)
 Nucleosome •”beads on a
string”; basic unit of DNA packing
 Heterochromatin •highly condensed
interphase DNA (can not be
transcribed)
 Euchromatin •less compacted
interphase DNA (can be transcribed)
 Molecular Biology of
Cancer
 Oncogene •cancer-causing genes
 Proto-oncogene •normal
cellular genes
 How? 1-movement
of DNA; chromosome fragments that
have rejoined incorrectly
2-amplification; increases the
number of copies of proto-oncogenes
3-proto-oncogene point mutation;
protein product more active or more
resistant to degradation
 Tumor-suppressor genes
•changes in genes that prevent
uncontrolled cell growth (cancer growth
stimulated by the absence of suppression)
Index
Recombinant DNA
 Def: DNA in which
genes from 2 different
sources are linked
 Genetic engineering:
direct manipulation of
genes for practical
purposes
 Biotechnology:
manipulation of
organisms or their
components to perform
practical tasks or
provide useful products
 DNA Cloning
 Restriction enzymes (endonucleases): in
nature, these enzymes protect bacteria
from intruding DNA; they cut up the DNA
(restriction); very specific
 Restriction site: recognition
sequence for a particular restriction
enzyme
 Restriction fragments: segments of DNA
cut by restriction enzymes in a
reproducable way
 Sticky end: short extensions of
restriction fragments
 DNA ligase: enzyme that can join the
sticky ends of DNA fragments
 Cloning vector: DNA molecule that
can carry foreign DNA into a cell and
replicate there (usually bacterial
plasmids)
Steps for eukaryotic gene
cloning
 Isolation of cloning vector
(bacterial plasmid) & gene-
source DNA (gene of interest)
 Insertion of gene-source DNA into
the cloning vector using the same
restriction enzyme; bind the
fragmented DNA with DNA ligase
 Introduction of cloning vector into
cells (transformation by bacterial
cells)
 Cloning of cells (and foreign
genes)
 Identification of cell clones
carrying the gene of interest
DNA Analysis &
Genomics
PCR (polymerase
chain reaction)
Gel electrophoresis
Restriction fragment
analysis (RFLPs)
Southern blotting
DNA sequencing
Human genome
project
Polymerase chain reaction
(PCR)
Amplification of any
piece of DNA without
cells (in vitro)
Materials: heat, DNA
polymerase,
nucleotides, single-
stranded DNA primers
Applications: fossils,
forensics, prenatal
diagnosis, etc.
 DNA Analysis
 Gel electrophoresis: separates nucleic acids or proteins on the basis of size or electrical charge creating DNA bands
of the same length
Restriction fragment
analysis
Restriction fragment length polymorphisms
(RFLPs)
Southern blotting: process that reveals
sequences and the RFLPs in a DNA sequence
DNA Fingerprinting
DNA Sequencing
Determination of
nucleotide sequences
(Sanger method,
sequencing machine)
Genomics: the study
of genomes based on
DNA sequences
Human Genome
Project
Practical DNA Technology
Uses

 Diagnosis of disease
 Human gene therapy
 Pharmaceutical
products (vaccines)
 Forensics
 Animal husbandry
(transgenic organisms)
 Genetic engineering in
plants
 Ethical concerns?
Index
From fertilized egg to
multicellular organism

 Cell Division:
increase in
cell number
 Differentiation:
cells becoming
specialized in
structure and function
 Morphogenesis;
physical processes
giving an organism
shape
Morphogenesis: plants vs.
animals
 Animals:
 movements of cells and tissues are
necessary for 3-D form of the
organism

 ongoing development in adults

restricted to differentiation of cells
continually replenished throughout
lifetime
 Plants:
 morphogenesis and growth of
overall size occur throughout
lifetime of plant; apical meristems
(perpetually embryonic regions),
responsible for plant’s continual
growth
 Differential gene
expression
 Differences between cells come
from differences in gene
expression (genes turned on or
off), not from differing genomes.
 Evidence:
 1- Genomic equivalence: all
the cells of an organism have the
same genes
 2- Totipotency: cells that can
retain the zygote’s potential to
form all parts of the mature
organism (plant cells; cloning)
 3- Determination: restriction of
developmental potential causing
the possible fate of each cell to
become more limited as the
embryo develops; noted by the
appearance of mRNA
Determination---
>Differentiation
 Determination: as the embryo
develops the possible fate of
each cell becomes more limited
 Differentiation: specialization of
cells dependent on the control of
gene expression
 Induction: the ability of one
group of embryonic cells to
influence the development of
another; cytoplasmic
determinants that regulate gene
expression
 Homeotic genes: genes that
control the overall body plan of
animals by controlling the
developmental fate of groups of
cells
Genetic cell death
Apoptosis programmed
cell death (“suicide genes”)
 1. Programmed cell death is as
needed for proper development as
mitosis is.
 Ex: Reabsorption of the tadpole tail;
formation of the fingers and toes of
the fetus requires the removal of the
tissue between them; sloughing off
of the endometrium at the start of
menstruation; formation of the
proper connections (synapses)
between neurons in the brain
requires that surplus cells be
eliminated.
Apoptosis, Pt. II
2. Programmed cell death is needed to destroy
cells that represent a threat to the integrity of
the organism.
Ex: Cells infected with viruses; waning cells of
the immune system; cells with DNA damage;
cancer cells
Index
Evolution
 Evolution: the change
over time of the genetic
composition of populations
 Natural selection: populations
of organisms can change over
the generations if individuals
having certain heritable traits
leave more offspring than others
(differential reproductive
success)
 Evolutionary adaptations: a
prevalence of inherited
characteristics that enhance
organisms’ survival and
reproduction

November 24, 1859

Evolutionary history
 Linnaeus: taxonomy  Lyell: uniformitarianism
 Hutton: gradualism  Darwin: evolution
 Lamarck: evolution  Mendel: inheritance
 Malthus: populations  Wallace: evolution
 Cuvier: paleontology
Descent with
Modification, I
5 observations:
1- Exponential fertility
2- Stable population size

3- Limited resources

4- Individuals vary
5- Heritable variation
Descent with
Modification, II
3 Inferences:

1- Struggle for

existence
2- Non-random
survival
3- Natural selection
(differential success in
reproduction)
Evolution evidence:
Biogeography

Geographical
distribution of
species
Examples:
Islands vs.
Mainland Australia
Continents
Evolution evidence:
The Fossil Record

Succession of
forms over time
Transitional links
Vertebrate
descent
Evolution evidence:
Comparative Anatomy
Homologous
structures
(homology)
Descent from a
common ancestor
Vestigial organs
Ex: whale/snake
hindlimbs; wings on
flightless birds
 Comparative
Embryology

Pharyngeal
pouches, ‘tails’ as
embryos
Evolution evidence:
Molecular Biology

Similarities in
DNA, proteins,
genes, and gene
products
Common genetic
code
Final words…...
“Absence of
evidence is not
evidence of
absence.”
Index
Population genetics
Population: a localized group of individuals belonging
to the same species
Species: a group of populations whose individuals have
the potential to interbreed and produce fertile offspring
Gene pool: the total aggregate of genes in a
population at any one time
Population genetics: the study of genetic changes in
populations
Modern synthesis/neo-Darwinism
“Individuals are selected, but populations evolve.”
Hardy-Weinberg
Theorem
 Serves as a model for the
genetic structure of a
nonevolving population
(equilibrium)
 5 conditions:
 1- Very large population
size;
 2- No migration;
 3- No net mutations;
 4- Random mating;
 5- No natural selection
Hardy-Weinberg Equation
p=frequency of one allele (A); q=frequency of
the other allele (a);
p+q=1.0 (p=1-q &
q=1-p)
P2=frequency of AA genotype; 2pq=frequency
of Aa plus aA genotype; q2=frequency of aa
genotype;
p2 + 2pq + q2 = 1.0
Microevolution, I
A change in the
gene pool of a
population over a
succession of
generations
1- Genetic drift:
changes in the
gene pool of a
small population
due to chance
(usually reduces
genetic variability)
Microevolution, II
The Bottleneck
Effect: type of
genetic drift resulting
from a reduction in
population (natural
disaster) such that the
surviving population is
no longer genetically
representative of the
original population
Microevolution, III
Founder Effect:
a cause of
genetic drift
attributable to
colonization by a
limited number of
individuals from a
parent population
Microevolution, IV
2- Gene Flow:
genetic exchange
due to the migration
of fertile individuals
or gametes between
populations (reduces
differences between
populations)
Microevolution, V
3- Mutations:
a change in
an organism’s DNA
(gametes; many
generations); original
source of genetic
variation (raw
material for natural
selection)
Microevolution, VI
4- Nonrandom
mating:
inbreeding and
assortive mating
(both shift
frequencies of
different
genotypes)
Microevolution, VII
5- Natural
Selection:
differential success
in reproduction;
only form of
microevolution that
adapts a population
to its environment
Population variation
Polymorphism:
coexistence of 2 or
more distinct forms
of individuals
(morphs) within the
same population
Geographical
variation:
differences in genetic
structure between
populations (cline)
Variation preservation
 Prevention of natural selection’s
reduction of variation
 Diploidy 2nd set
of chromosomes hides variation in
the heterozygote
 Balanced polymorphism 1-
heterozygote advantage (hybrid
vigor; i.e., malaria/sickle-cell
anemia); 2-
frequency dependent selection
(survival & reproduction of any 1
morph declines if it becomes too
common; i.e., parasite/host)
Natural selection
Fitness:
contribution an
individual makes
to the gene pool
of the next
generation
3 types:
A. Directional
B. Diversifying
C. Stabilizing
Sexual selection
Sexual dimorphism:
secondary sex
characteristic distinction

Sexual selection:
selection towards
secondary sex
characteristics that
leads to sexual
dimorphism
Index
Macroevolution: the origin of new taxonomic
groups
Speciation: the origin of new
species
1- Anagenesis (phyletic
evolution): accumulation of
heritable changes

2- Cladogenesis (branching

evolution): budding of new species
from a parent species that continues
to exist (basis of biological diversity)
 What is a species?
Biological species
concept (Mayr): a
population or group of
populations whose members
have the potential to
interbreed and produce viable,
fertile offspring (genetic
exchange is possible and that
is genetically isolated from
other populations)
Reproductive Isolation (isolation of gene
pools), I
 Prezygotic barriers: impede mating
between species or hinder the
fertilization of the ova
 Habitat (snakes;
water/terrestrial)
 Behavioral (fireflies; mate
signaling)
 Temporal (salmon; seasonal
mating)
 Mechanical (flowers; pollination
anatomy)
 Gametic (frogs; egg coat
receptors)
 Reproductive Isolation,
II
 Postzygotic barriers: fertilization
occurs, but the hybrid zygote does
not develop into a viable, fertile
adult
 Reduced hybrid viability (frogs;
zygotes fail to develop or reach
sexual maturity)
 Reduced hybrid fertility (mule;
horse x donkey; cannot
backbreed)
 Hybrid breakdown (cotton; 2nd
generation hybrids are sterile)
Modes of speciation
(based on how gene flow is
interrupted)
Allopatric:
populations segregated
by a geographical
barrier; can result in
adaptive radiation
(island species)
Sympatric:
reproductively isolated
subpopulation in the
midst of its parent
population (change in
genome); polyploidy in
plants; cichlid fishes
 Punctuated equilibria
Tempo of speciation:
gradual vs. divergence
in rapid bursts; Niles
Eldredge and Stephen
Jay Gould (1972); helped
explain the non-gradual
appearance of species
in the fossil record
Index
Phylogeny: the evolutionary history of
a species
Systematics:
the study of biological
diversity in an
evolutionary context
The fossil record:
the ordered array of
fossils, within layers,
or strata, of
sedimentary rock
Paleontologists
 The fossil record
 Sedimentary rock: rock formed
from sand and mud that once
settled on the bottom of seas,
lakes, and marshes
 Dating:
 1- Relative~ geologic time scale;
sequence of species
 2- Absolute~ radiometric dating;
age using half-lives of radioactive
isotopes
 Biogeography: the study of the
past and present distribution of
species

Pangaea-250 mya √
Permian extinction
Geographic isolation-180
mya √ African/South
American reptile fossil
similarities √ Australian
marsupials
 Mass extinction
Permian
(250 million years
ago): 90% of marine
animals; Pangea
merge
Cretaceous
(65 million years
ago): death of
dinosaurs, 50% of
marine species; low
angle comet
 Phylogenetics
The tracing of
evolutionary relationships
(phylogenetic tree)
Linnaeus
Binomial
Genus, specific epithet
Homo sapiens
Taxon (taxa)
 Phylogenetic Trees
 Cladistic Analysis: taxonomic
approach that classifies organisms
according to the order in time at
which branches arise along a
phylogenetic tree (cladogram)
 Clade: each evolutionary branch in a
cladogram
 Types:
 1- Monophyletic single ancestor that
gives rise to all species in that taxon
and to no species in any other taxon;
legitimate cladogram
 2- Polyphyletic members of a taxa are
derived from 2 or more ancestral
forms not common to all members;
does not meet cladistic criterion
 3- Paraphyletic lacks the common
ancestor that would unite the species;
does not meet cladistic criterion
 Constructing a
Cladogram
 Sorting homology vs. analogy...
 Homology:
likenesses attributed to
common ancestry
 Analogy:
likenesses attributed to
similar ecological roles and
natural selection
 Convergent evolution:
species from different
evolutionary branches that
resemble one another due
to similar ecological roles
A Cladogram
Index
Early history of life
 Solar system~ 12 billion years
ago (bya)
 Earth~ 4.5 bya
 Life~ 3.5 to 4.0 bya
 Prokaryotes~ 3.5 to 2.0 bya
stromatolites
 Oxygen accumulation~ 2.7 bya
photosynthetic cyanobacteria
 Eukaryotic life~ 2.1 bya
 Muticelluar eukaryotes~ 1.2 bya
 Animal diversity~ 543 mya
 Land colonization~ 500 mya
The Origin of Life
Spontaneous generation vs.
biogenesis (Pasteur)
The 4-stage Origin of life
Hypothesis:
1- Abiotic synthesis of
organic monomers
2- Polymer formation
3- Origin of Self-replicating
molecules
4- Molecule packaging
(“protobionts”)
Organic monomers/polymer
synthesis
Oparin (Rus.)/Haldane (G.B.)
hypothesis (primitive earth):
volcanic vapors (reducing
atmosphere) with lightning & UV
radiation enhances complex
molecule formation (no O2)
 Miller/Urey experiment:
 water, hydrogen, methane,
ammonia
 all 20 amino acids, nitrogen
bases, & ATP formed
 Fox proteinoid formation (abiotic
polypeptides) from organic
monomers dripped on hot sand,
clay or rock
 Oparin (coacervates) protobionts
(aggregate macromolecules;
abiotic) surrounded by a shell of
H2O molecules coated by a
protein membrane
Abiotic genetic
replication
First genetic material
Abiotic production of
ribonucleotides
Ribozymes (RNA
catalysts)
RNA “cooperation”
Formation of short
polypeptides
(replication enzyme?)
RNA~ DNA template?
Index
Classification
Kingdom: Monera?
Domain: Bacteria
Domain: Archaea

Shape
•cocci (sphere)
•bacilli (rod)
•helical (spiral)
Structural
characteristics
 Cell wall~ peptidoglycan
(sugars & proteins);
√ Gram +: w/peptidoglycan
penicillin action
√ Gram -: little
peptidoglycan,
lipopolysaccharides; most
pathogens; impede drug
action
 Capsule: adherence;
protection
 Pili: adherence;
conjugation
Motility
1- Flagella
2- Helical shape
(spirochetes) QuickTime™ and a
Cinepak decompressor
are needed to see this picture.
3- Slime
4-Taxis
(movement away
or toward a
stimulus)
Form & Function
 Nucleoid region (genophore: non-
eukaryotic chromosome)
 Plasmids
 Asexual reproduction: binary
fission (not mitosis)
 “Sexual” reproduction (not meiosis):
transformation~ uptake of genes
from surrounding environment
conjugation~ direct gene transfer
from 1 prokaryote to another
transduction~ gene transfer by
viruses
 Endospore: resistant cells for harsh
conditions (250 million years!)
Nutrition & Metabolism
 Photoautotrophs: photosynthetic; harness light
to drive the synthesis of organics
(cyanobacteria)
 Chemoautotrophs: oxidation of inorganics for
energy; get carbon from CO2
 Photoheterotrophs: use light to generate ATP
but get carbon in an organic form
 Chemoheterotrophs: consume organic molecules
for both energy and carbon saprobes-
dead organic matter decomposers
parasites- absorb nutrients from living hosts
 Nitrogen fixation: conversion of atmospheric
nitrogen (N2) to ammonium (NH4+)
 Oxygen relationships: obligate aerobes;
facultative anaerobes; obligate anaerobes
Prokaryotic ecology
 Decomposers: unlock organics from
corpses and waste products
 Symbiosis~ •symbiont/host
•mutualism (+, +) •parasitism (+, -)
•commensalism (+, 0)
 Disease •opportunistic: normal
residents of host; cause illness when
defenses are weakened •Koch’s
postulates: criteria for bacterial disease
confirmation •exotoxins: bacterial
proteins that can produce disease w/o the
prokaryote present (botulism)
•endotoxins: components of gram -
membranes (Salmonella)
Index
Protists
Ingestive
(animal-like);
protozoa

Absorptive
(fungus-like)

Photosynthetic
(plant-like);
alga
The Endosymbionic
Theory
Mitochondria and chloroplasts were
formerly from small prokaryotes living
within larger cells (Margulis)
Protist Systematics &
Phylogeny, I

1- Groups lacking mitochondria;

early eukaryotic link; Giardia
(human intestinal parasite;
severe diarrhea); Trichomonas
(human vaginal infection)
2- Euglenoids; autotrophic &
heterotrophic flagellates;
Trypanosoma (African sleeping
sickness; tsetse fly)
Protist Systematics &
Phylogeny, II
 Alveolata: membrane-
bound cavities (alveoli)
under cell surfaces;
dinoflagellates
(phytoplankton);
Plasmodium (malaria);
ciliates
(Paramecium)
Protist Systematics &
Phylogeny, III
 Stamenophila: water molds/mildews and
heterokont (2 types of flagella) algae;
numerous hair-like projections on the
flagella; most molds are decomposers
and mildews are parasites; algae include
diatoms, golden, and brown forms
Protist Systematics &
Phylogeny, IV
Rhodophyta: red
algae; no flagellated
stages; phycobilin
(red) pigment
Chlorophyta: green
algae; chloroplasts;
gave rise to land
plants; volvox, ulva
Protist Systematics &
Phylogeny, V
 Affinity uncertain:
 Rhizopods: unicellular
with pseudopodia; QuickTime™ and a
Cinepak decompressor
are needed to see this picture.

amoebas
 Actinopods: ‘ray foot’
(slender pseudopodia;
heliozoans, radiolarians
Protist Systematics &
Phylogeny, VI
Mycetozoa: slime
molds (not true QuickTime™ and a

fungi); use Cinepak decompressor

are needed to see this picture.

pseudopodia for
locomotion and
feeding;
plasmodial and
cellular slime
molds
Index
 Plant Evolution
bryophytes (mosses),
pteridophytes (ferns),
gymnosperms (pines and
conifers); angiosperms (flowering
plants)
Plants: multicellular, eukaryotic,
photosynthetic autotrophs
Terrestrial colonization:
Vascular tissue
The seed
The flower
Plant origins
Charophytes: green algae
(closest plant ancestor)
Similarities:
 1-Homologous chloroplasts:
chlorophyll a & b
 2- Biochemical similarity cellulose
composition; peroxisomes
 3- Cell division similarity mitosis;
cytokinesis
 4- Sperm similarity
ultrastructure
 5- Genetic relationship nuclear
genes; rRNA
Characteristics that separate plants from
algae ancestors

Apical meristems: localized

regions of cell division
Multicellular, dependent
embryos (embryophytes)
Alternation of generations
Walled spores produced in
sporangia
Multicellular gametangia
Other terrestrial
adaptations

Cuticle
Stomata
Xylem and
phloem
Secondary
compounds
 Bryophytes
 Mosses, liverworts, and
hornworts
 1st to exhibit the embryonic
condition (male = antheridium;
female = archegonium)
 Flagellated (water) sperm
 No vascular tissue (imbibe
water)
 No lignin (short stature)
 Haploid gametophyte is the
dominant generation
 Pteridophytes: seedless vascular
plants
 Ferns, club ‘moss’, horsetails
 True roots and leaves
 Roots have lignified vascular tissue
 Sporophyte-dominant life cycle
 Homosporous plants: a single type
of spore….
 Sporophyte---->Single type of
spore ---->Bisexual gametophyte
---->Eggs; sperm
(flagellated; damp locations)
 Carboniferous period plants
Index
Seed Plant Reproductive
Adaptations
 Reduction of the gametophyte: shift from haploid to diploid condition;
female gametophyte and embryo remain in sporangia (protection against
drought and ionizing radiation on land?)
 Advent of the seed multicellular sporophyte embryo with food supply and
protective coat; heterosporous (two types of spores): megaspores--->female
gametophyte--->eggs; microspores---> male gametophyte--->sperm
 Evolution of pollen: develop from microspores which mature into the male
gametophytes; resistant and airborne for a terrestrial environment; eliminated
water (sporopollenin coats)
Gymnosperms
 Cone-bearing plants
 Lack enclosed chambers
(ovaries) for seeds
 Ovules and seeds develop
on specialized leaves called
sporophylls
 Ginkgo, cycads, and conifers
 All are “evergreens”
 Needle-shaped leaves
 Vascular tissue refinement:
tracheids~ water
conducting and supportive
element of xylem
 Angiosperms
 Most diverse and geographically widespread of all plants
 “Flowering plants”(Phy: Anthophyta)
 Monocots: 1 embryonic seed leaf (lilies, palms, grasses, grain
crops)
 Dicots: 2 embryonic seed leaves (roses, peas, sunflowers, oaks,
maples)
 Vascular tissue refinement: vessel elements/fiber cells
 The flower: the defining structure of
angiosperms

Reproductive structure:
pollen transfer; specialized
shoot with modified leaves
Sepals: enclose flower before
it opens
Petals: attract pollinators
Stamens: male; anther
(produces pollen), filament
Carpels: female; stigma,
style, ovary, ovules
 Angiosperm life cycle
Fruit (mature ovary); seeds
from ovules
Pollen grains: 2 haploid cells
(immature male gametophytes)
Ovules (female gametophyte~
embryo sac)
Double fertilization: 1 sperm w/
egg = diploid zygote; other
sperm w/ 2 nuclei in center of
sac = triploid endosperm
Beginning of Plants Index
Angiosperm structure
 Three basic organs:
 Roots (root system)
 fibrous: mat of thin roots
 taproot: one large, vertical root
 Stems (shoot system)
 nodes: leave attachment
 internodes: stem segments
 axillary bud: dormant, vegetative
potential
 terminal bud: apex of young shoot
 apical dominance: inhibits axillary buds
 Leaves (shoot system)
 blade
 petiole
Plant Organ Systems
 Dermal (epidermis): single layer
of cells for protection
 cuticle
 Vascular (material transport)
 xylem: water and dissolved
minerals roots to shoots
 tracheids & vessel elements:
xylem elongated cells
dead at maturity
 phloem: food from leaves to roots
and fruits
 sieve-tube members: phloem
tubes alive at maturity
capped by sieve plates;
companion cells
(nonconducting) connected by
plasmodesmata
 Ground (photosynthesis, storage,
support): pith and cortex
Plant Tissue Cell Types
 Parenchyma primary walls thin and
flexible; no secondary walls; large
central vacuole; most metabolic
functions of plant (chloroplasts)
 Collenchyma unevenly thick primary
walls used for plant support (no
secondary walls ; no lignin)
 Sclerenchyma support
element strengthened by secondary
cell walls with lignin (may be dead;
xylem cells); fibers and sclereids for
support
Plant Growth
 Life Cycles
 annuals: 1 year (wildflowers; food
crops)
 biennials: 2 years (beets; carrots)
 perennials: many years (trees;
shrubs)
 Meristems
 apical: tips of roots and buds;
primary growth
 lateral: cylinders of dividing cells
along length of roots and stems;
secondary growth (wood)
Primary growth
 Roots
 root cap~ protection of
meristem
 zone of cell division~
primary (apical) meristem
 zone of elongation~ cells
elongate; pushes root tip
 zone of maturation~
differentiation of cells
(formation of 3 tissue
systems)
Primary Tissues of
Roots
 Stele~ the vascular bundle where both xylem and phloem
develop
 Pith~ central core of stele in monocot; parenchyma cells
 Cortex~ region of the root between the stele and epidermis
(innermost layer: endodermis)
 Lateral roots~ arise from pericycle (outermost layer of stele);
just inside endodermis, cells that may become meristematic
Primary Tissues of
Stems
Vascular bundles (xylem and phloem)
Surrounded by ground tissue (xylem faces pith
and phloem faces cortex)
Mostly parenchyma; some collenchyma and
sclerenchyma for support
Primary Tissues of
Leaves
 Epidermis/cuticle (protection; desiccation)
 Stomata (tiny pores for gas exchange and
transpiration)/guard cells
 Mesophyll: ground tissue between upper and lower
epidermis (parenchyma with chloroplasts); palisade
(most photosynthesis) and spongy (gas circulation)
Secondary Growth
 Two lateral meristems
 vascular cambium ~
produces secondary xylem
(wood) and secondary phloem
(diameter increase; annual growth
rings)
 cork cambium ~
produces thick covering that
replaces the epidermis; produces
cork cells; cork plus cork cambium
make up the periderm; lenticels
(split regions of periderm) allow
for gas exchange; bark~ all
tissues external to vascular
cambium (phloem plus periderm)
 PRIMARY PRIMARY LATERAL SECONDARY
MERISTEMS TISSUES MERISTEM TISSUES

Protoderm Epidermis Secondary

phloem
Apical Primary phloem Vascular
meristem Procambium cambium Secondary
of stem Primary xylem xylem

Ground
Periderm
meristem Ground Pith &
tissue: Cortex Cork
cambium Cork
Index
Transport Overview
1- uptake and loss of water
and solutes by individual
cells (root cells)
2- short-distance transport
from cell to cell (sugar
loading from leaves to
phloem)
3- long-distance transport of
sap within xylem and phloem
in whole plant
Whole Plant Transport
 1- Roots absorb water and dissolved minerals
from soil
 2- Water and minerals are transported upward
from roots to shoots as xylem sap
 3- Transpiration, the loss of water from leaves,
creates a force that pulls xylem sap upwards
 4- Leaves exchange CO2 and O2 through
stomata
 5- Sugar is produced by photosynthesis in
leaves
 6- Sugar is transported as phloem sap to roots
and other parts of plant
 7- Roots exchange gases with air spaces of soil
(supports cellular respiration in roots)
 Cellular Transport
 Water transport √ Osmosis;
hyper-; hypo-; iso-
 Cell wall creates physical pressure:
√water potential solutes decrease;
pressure increase
 Water moves from high to low water
potential
 Flaccid (limp, iostonic);
 Plasmolysis (cell loses water in a
hypertonic environment; plasma
membrane pulls away);
 Turgor pressure (influx of water due to
osmosis; hypotonic environment)
Transport within
tissues/organs
 Tonoplast vacuole
membrane
 Plasmodesmata (components)
cytosolic connection
 Symplast route (lateral)
cytoplasmic continuum
 Apoplast route (lateral)
continuum of cell walls
 Bulk flow (long distance)
movement of a fluid by pressure
(xylem)
Transport of Xylem Sap
Transpiration: loss of water
vapor from leaves pulls water
from roots (transpirational pull);
cohesion and adhesion of water
Root pressure: at night (low
transpiration), roots cells
continue to pump minerals into
xylem; this generates pressure,
pushing sap upwards; guttation
 Transpirational Control

Photosynthesis-Transpiration compromise….
Guard cells control the size of the stomata
Xerophytes (plants adapted to arid environments)~
thick cuticle; small spines for leaves
Translocation of Phloem
Sap
 Translocation: food/phloem transport
 Sugar source: sugar production organ (mature
leaves)
 Sugar sink: sugar storage organ (growing roots,
tips, stems, fruit)
 1- loading of sugar into sieve tube at source
reduces water potential inside; this causes tube
to take up water from surroundings by osmosis
 2- this absorption of water generates pressure
that forces sap to flow alon tube
 3- pressure gradient in tube is reinforced by
unloading of sugar and consequent loss of water
from tube at the sink
 4- xylem then recycles water from sink to source
Index
Nutrients
 Essential: required for the plant life cycle
 Macro- (large amounts) carbon, oxygen, hydrogen, nitrogen, sulfur,
phosphorus, potassium, calcium, magnesium
 Micro- (small amounts; cofactors of enzyme action) chlorine, iron, boron,
manganese, zinc, copper, molybdenum, nickel
 Deficiency • chlorosis (lack of magnesium; chlorophyll production)
Soil
Determines plant growth &
variety (also climate)
Composition/horizons:
•topsoil (rock particles, living
organisms, humus-partially
decayed organic material)
•loams (equal amounts of
sand, silt, and clay)
Nitrogen Fixation
Atmosphere, 80% N2
Conversion to: ammonium (NH4+) or nitrate
(NO3-)
Bacteria types: Ammonifying (humus
decomposition); nitrogen-fixing (atmospheric
N2); nitrifying (convert NH4+ to NO3-);
denitrifying (convert NO3- to N2)
Nitrogen fixation; crop rotation
Plant symbiosis, I
Rhizobium bacteria
(found in root nodules
in the legume family)
Mutualistic: legume
receives fixed N2;
bacteria receives
carbohydrates &
organic materials
Plant symbiosis, II
 Mycorrhizae (fungi); modified roots
 Mutualistic: fungus receives sugar;
plant receives increased root surface
area and increased phosphate uptake
 Two types: ectomycorrhizae •
ensheaths the root endomycorrhizae
(90% of plants) •through cell
wall but not cell membrane
Plant parasitism &
predation
Mistletoe (parasite)
Epiphytes
Carnivorous plants

Q u ic k T im e ™ a n d a
C in e p a k d e c o m p r e s s o r
a r e n e e d e d t o s e e t h is p ic t u r e .
Index
Sexual Reproduction
 Alternation of generations:
haploid (n) and diploid (2n)
generations take turns
producing each other
 Sporophyte (2n): produces
haploid spores by meiosis;
these spores divide by
mitosis giving rise to male
and female haploid plants
called….
 Gametophytes (n): develop
and produce gametes
Floral variations
 Floral organs: sepals, petals,
stamens (male ), carpels (female)
 •complete: all 4 floral organs
 •incomplete: lacking 1 or more floral
organs
 •perfect: both stamens and carpels
on 1 flower
 •imperfect: lacking either a stamen
or carpel
 •monoecious: staminate and
carpellate flowers on 1 plant)

 •dioecious: staminate and

carpellate flowers on separate
plants
Gametophyte
development
Male gametophyte:
microsporocyte (in pollen sacs of anther)
divides by meiosis into 4-1N microspores;
mitosis produces a generative cell (sperm)
and a tube cell (pollen tube)= a pollen grain

Female gametophyte:
megasporocyte (in ovule) divides by meiosis
to 4 cells, only 1 survives to a 1-N
megaspore; 3 mitotic divisions forms the
embryo sac; includes: 1 egg cell (female
gamete) and 2 polar nuclei (synergids)
Double fertilization
 Pollination (pollen grain
lands on a receptive stigma)
 Tube cell (pollen tube
produced down the style)
 Generative cell (2 sperm by
mitosis)
 Enters ovary through
micropyle
 1 sperm fertilizes egg to
form zygote; other sperm
combines with 2 polar nuclei
to form 3n endosperm
(food-storing tissue)
The seed
From fertilized ovule…..
The mature seed:
•seed coat (protection)
•cotyledons (seed leaves)
•hypocotyl (lower embryonic axis)
•radicle (embryonic root)
•epicotyl (upper embryonic axis)
•plummule (shoot tip)
•coleoptile (sheath for embryonic
shoot)
The fruit
 From ovary….
 Fruit protects seeds and aids in their dispersal
 Pericarp (thickened wall of fruit from ovary wall)
 Fruit types:
 •simple (1 ovary/1 flower)~ cherry, soybean
 •aggregate (1 flower with many carpels/ovaries)~ blackberry
 •multiple (inflorescence; group of flowers/ovaries) ~ pineapple
Seed germination
Seed dormancy (low metabolic rate and
growth suspension)
Imbibition (uptake of water)
Radicle 1st, then shoot tip (hypocotyl);
stimulated by light
Germination
Index
Plant hormones
 Hormone: chemical signals that
coordinate parts of an organism;
produced in one part of the body
and then transported to other
parts of the body; low
concentrations
 Tropism: movement toward or
away from a stimulus
 Went experiments (phototropism)
 Hormone: auxin
 Others: gravitropism,
thigmotropism
 Auxin
IAA (indoleacetic acid)
Location: seed embryo; meristems of
apical buds and young leaves
Function: stem elongation; root growth,
differentiation, branching; fruit
development; apical dominance; tropisms

QuickTime™and a
Cinepak decompressor
areneeded toseethis picture.
Cytokinins
Zeatin
Location: roots (and actively growing
tissues)
Function: root growth and
differentiation; cell division and growth;
germination; delay senescence (aging);
apical dominance (w/ auxin)
Gibberellins
GA3
Location: meristems of apical buds and
roots, young leaves, embryo
Function: germination of seed and
bud; stem elongation; leaf growth;
flowering (bolting); fruit development;
root growth and differentiation
Abscisic acid
ABA
Location: leaves, stems, roots, green
fruit
Function: inhibits growth; closes
stomata during stress; counteracts
breaking of dormancy
Ethylene
Gaseous hormone
Location: ripening fruit tissue; stem
nodes; aging leaves and flowers
Function: fruit ripening; oppositional
to auxin (leaf abscission);
promotes/inhibits: growth/development of
roots, leaves, and flowers; senescence
Daily and Seasonal
Responses
 Circadian rhythm (24 hour periodicity)
 Photoperiodism (phytochromes)
 Short-day plant: light period shorter than a critical length to flower
(flower in late summer, fall, or winter; poinsettias, chrysanthemums)
 Long-day plant: light period longer than a critical length to flower
(flower in late spring or early summer; spinach, radish, lettuce, iris)
 Day-neutral plant: unaffected by photoperiod (tomatoes, rice,
dandelions)
 Critical night length controls flowering
Phytochromes
Plant pigment
that measures
length of darkness
in a photoperiod
(red light)
Pr (red absorbing)
660nm
Pfr (far-red
absorbing) 730nm
Index
 Fungi
Heterotrophic by absorption
(exoenzymes)
Decomposers (saprobes), parasites,
mutualistic symbionts (lichens)
Hyphae: body filaments
•septate (cross walls)
•coenocytic (no cross walls)
Mycelium: network of hyphae
Chitin cell walls (polysaccharide)
Fungi Diversity, I
Phy: Chytridiomycota
•aquatic fungi; chytrids
•lineage closest to protists
(flagella)
Phy: Zygomycota •Rhizopus
(food mold) •mycorrhizae:
mutualistic with plant roots
•zygosporangia: resistant
structure (freezing and drying)
Fungi Diversity, II
Phy.: Ascomycota •sac fungi
• yeasts, truffles,
morels, Sordaria
•asci: sexual spores
•conidia: asexual spores
Phy.: Basidiomycota • club
fungus •mushrooms, puffballs,
shelf fungus, rusts
•basidiocarps: produce sexual
spores
Specialized Lifestyles, I
Molds
•only the asexual stage
(asexual spores)
•Penicillium (antibiotic,
cheese)

Yeasts
•unicellular, asexual
budding
•Saccharomyces (bread,
alcohol)
 Specialized Lifestyles, II
 Lichens •
symbiotic association held in a hyphae
mesh •alga provides food,
fungus provides physical
environment •pioneer organisms
•air pollution detection
 Mycorrhizae •root
and fungi mutualism •found in 95% of
vascular plants
•exchange of organic minerals •increases
absorptive surface of roots
Index
Tissues: groups of cells with a
common structure and function (4
types)
 Anatomy: structure
 Physiology: function
 1- Epithelial: outside of body and
lines organs and cavities; held
together by tight junctions
 basement membrane: dense mat
of extracellular matrix
 Simple: single layer of cells
 Stratified: multiple tiers of cells
 Cuboidal (like dice)
 Columnar (like bricks on end)
 Squamous (like floor tiles)
 mucous membrane
 Tissues, II
 2- Connective: bind and support other tissues; scattered cells through matrix; 3 kinds:
 A-Collagenous fibers (collagen protein) B-Elastic fibers (elastin protein) C-Reticular fibers
(thin branched collagen fibers)
 Loose connective tissue: binds epithelia to underlying tissue; holds organs
 1-Fibroblasts- secretes extracellular proteins 2-Macrophages- amoeboid WBC’s;
phagocytosis 3-Adipose tissue- fat storage; insulation
 Fibrous connective tissue: parallel bundles of cells
 1-Tendons- muscles to bones 2-Ligaments- bones to bones; joints (BOBOLI)
 Cartilage: collagen in a rubbery matrix (chondroitin); flexible support
 Bone: mineralized tissue by osteoblasts
 Blood: liquid plasma matrix; erythrocytes (RBC’s) carry O2; leukocytes (WBC’s) immunity
Tissues, III
3-Nervous: senses stimuli and
transmits signals from 1 part
of the animal to another
Neuron: functional unit that
transmits impulses
Dendrites: transmit impulses
from tips to rest of neuron
Axons: transmit impulses
toward another neuron or
effector
Tissues, IV
 4- Muscle: capable of
contracting when stimulated
by nerve impulses; myofibrils
composed of proteins actin
and myosin; 3 types:
 A- Skeletal: voluntary
movement (striated)
 B- Cardiac: contractile wall of
heart (branched striated)
 C- Smooth: involuntary
activities (no striations)
Organ systems
Organ: organization of
tissues
Mesentaries: suspension of
organs (connective tissue)
Thoracic cavity (lungs and
heart)
Abdominal cavity
(intestines)
Diaphragm (respiration)
Organ systems…...
 Digestive-food processing
 Circulatory-internal distribution
 Respiratory-gas exchange
 Immune/Lymphatic-defense
 Excretory-waste disposal;
osmoregulation
 Endocrine-coordination of body
activities
 Reproductive-reproduction
 Nervous-detection of stimuli
 Integumentary-protection
 Skeletal-support; protection
 Muscular-movement; locomotion
Internal regulation
 Interstitial fluid: internal fluid
environment of vertebrates;
exchanges nutrients and wastes
 Homeostasis: “steady state” or
internal balance
 Negative feedback: change in a
physiological variable that is being
monitored triggers a response that
counteracts the initial fluctuation;
i.e., body temperature
 Positive feedback: physiological
control mechanism in which a change
in some variable triggers
mechanisms that amplify the change;
i.e., uterine contractions at childbirth
Metabolism: sum of all
energy-requiring biochemical
reactions
 Catabolic processes of cellular
respiration
 Calorie; kilocalorie/C
 Endotherms: bodies warmed by
metabolic heat
 Ectotherms: bodies warmed by
environment
 Basal Metabolic Rate (BMR):
minimal rate powering basic
functions of life (endotherms)
 Standard Metabolic Rate (SMR):
minimal rate powering basic
functions of life (ectotherms)
Index
Embryonic
development/fertilization
 Preformation~ until 18th century; miniature infant in sperm or egg
 At fertilization/conception:
 Acrosomal reaction~ hydrolytic enzyme action on egg jelly coat….
 Fast block to polyspermy~ membrane depolarization prevents
multiple fertilizations….
 Cortical reaction~ release of calcium causes hardening of egg outer
layer and creates a...
 Slow block to polyspermy and...
 Egg activation~ increases metabolic activity; protein synthesis
The Fertilized Egg &
Cleavage
Blastomeres~ resultant cells
of cleavage/mitosis
Yolk~ nutrients stored in the egg
Vegetal pole~ side of egg with
high yolk concentration
Animal pole ~ side of egg with
low yolk concentration
Morula~solid ball of cells
Blastocoel~fluid-filled cavity in
morula
Blastula~hollow ball stage of
development
 Gastrulation
Gastrula~ 2 layered, cup-shaped
embryonic stage
3 Embryonic germ layers:
 Ectoderm~ outer layer; epidermis;
nervous system, etc.
 Endoderm~ inner layer; digestive tract
and associated organs; respiratory, etc.
 Mesoderm~skeletal; muscular;
excretory, etc.
Invagination~ gastrula buckling
process to create the...
Archenteron~ primitive gut
Blastopore~ open end of
archenteron
Organogenesis: organ
formation
Blastodisc~ cap of
cells on top of yolk
Primitive streak~
invagination of blastodisc
Neural tube~
beginning of spinal cord
Somites~ vertebrae
and skeletal muscles
Neural crest~ bones
and muscles of skull
 Amniote embryos
Extraembryonic
membranes: •yolk sac
(support; circulatory function)

•amnion (fluid-filled sac;

protection) •chorion
(placenta formation) •allantois
(nitrogenous waste)
Index
Def: an•i•mal (n)
 Unique characteristics:
 Heterotrophic eukaryotes; ingestion
 Lack cell walls; collagen
 Nervous & muscular tissue
 Sexual; diploid; cleavage; blastula; gastrulation; larvae;
metamorphosis
 Regulatory genes: Hox genes
 Animal phylogeny &
diversity, I
 Monophyletic; colonial flagellated
protist ancestor
 1- Parazoa-Eumetazoa dichotomy:
sponges (Parazoa)~ no true tissues;
all other animals (Eumetazoa)~ true
tissues
 2- Radiata-Bilateria dichotomy:
Cnidaria (hydra; ‘jellyfish’; sea
anemones) & Ctenophora (comb
jellies)~ radial body symmetry; all
other animals~ bilateral body
symmetry (also: cephalization)
 Animal phylogeny &
diversity, II
 3- Gastrulation: germ layer development;
ectoderm (outer), mesoderm (middle),
endoderm (inner); radiata are diploblastic-2
layers; no mesoderm; bilateria are
triploblastic-all 3 layers
 4- Acoelomate, Pseudocoelomate, and
Coelomate Grades: triploblastic animals~
solid body, no body cavity called
acoelomates (Platyhelminthes-flatworms);
body cavity, but not lined with mesoderm
called pseudocoelomates (Rotifers); true
coelom (body cavity) lined with mesoderm
called coelomate
Animal phylogeny &
diversity, III
 5- Protostome-Deuterostome
dichotomy among coelomates:
protostomes (mollusks, annelids,
arthropods); deuterostomes
(echinoderms, chordates)
 a) cleavage: protostomes~ spiral and
determinate; deuterotomes~ radial
and indeterminate
 b) coelom formation: protostomes~
schizocoelous; deuterostomes~
enterocoelous
 c) blastopore fate: protostomes~
mouth from blastopore;
deuterostomes~ anus from blastopore
Index
Parazoa
Invertebrates: animals
without backbones
Closest lineage to
protists
Loose federation of
cells (unspecialized); no
tissues
Phy.: Porifera (sponges)
Phylum: Porifera (“pore
bearer”)
Sessile (attached to bottom)
Spongocoel (central cavity)
Osculum (large opening)
Choanocytes (flagellated collar cells)
Hermaphroditic (produce both sperm and eggs)
The Radiata, I
 Diploblastic
 Radial symmetry
 Phy: Cnidaria (hydra, jellies, sea
anemones, corals)
 No mesoderm; GVC
gastrovascular cavity (sac with a
central digestive cavity)
 Hydrostatic skeleton (fluid held
under pressure)
 Polyps and medusa
 Cnidocytes (cells used for
defense and prey capture)
 Nematocysts (stinging capsule)
The Radiata, II
Phy: Ctenophora
(comb jellies)
8 rows of comblike
plates of fused cilia
(largest animals that
use cilia for
locomotion)
Tentacles with
colloblasts (adhesive
structures that
capture prey)
Eumetazoa: The Acoelomates
Phy: Platyhelminthes
(flatworms, flukes, tapeworms)
Bilateral; no body cavity
Predators, scavengers,
parasites
Triplobastic; mesoderm but,
GVC with only one opening
Some cephalization
Many pathogens
(Schistosoma, Cestodidias)
Eumetazoa: Pseudocoelomates,
I
Body cavity partially
derived from mesodermally
derived tissue
Phy: Rotifera
1st with a complete
digestive tract
Hydrostatic skeleton
Parthenogenesis: type of
reproduction in which
females produce offspring
from unfertilized eggs
Eumetazoa: Pseudocoelomates,
II

Phy: Nematoda
(roundworms)
 Very widespread group of
animals (900,000 sp. ?)
 Cuticle (tough exoskeleton)
 Decomposition and nutrient
cycling
 Complete digestive track;
no circulatory system
 Trichinella spiralis
The Coelomates:
Protostomes, I
 Phylogenetics debated….
 Phy: Nemertea (proboscis and
ribbon worms)
 Complete digestion and closed
circulatory system (blood)
 Phy: the lophophorates (sea
mats, tube worms, lamp shells)
 Lophophore: Circular shaped
body fold with ciliated tentacles
around the mouth
The Coelomates:
Protostomes, II
 Phy: Mollusca (snails,
slugs, squid, octopus,
clams, oysters, chiton)
 Soft body protected by a
hard shell of calcium
carbonate
 Foot (movement), visceral
mass (internal organs);
mantle (secretes shell);
radula (rasp-like scraping
organ)
 Ciliated trochophore larvae
(related to Annelida?)
The Coelomates: Protostomes,
III

 Phy: Annelida (earthworms,

leeches, marine worms)
 True body segmentation
(specialization of body
regions)
 Closed circulatory system
 Metanephridia: excretory
tubes
 “Brainlike” cerebral ganglia QuickTime™ and a
Cinepak decompressor
are needed to see this picture.

 Hermaphrodites, but cross-

fertilize
The Coelomates: Protostomes,
IV
 Phy: Arthropoda trilobites
(extinct); crustaceans (crabs,
lobsters, shrimps); spiders,
scorpions, ticks (arachnids); insects
(entomology)
 2 out of every 3 organisms (most
successful of all phyla)
 Segmentation, hard exoskeleton
(cuticle)~ molting, jointed
appendages; open circulatory
system (hemolymph); extensive
cephalization
Insect characteristics
 Outnumber all other forms of life
combined
 Malpighian tubules: outpocketings
of the digestive tract (excretion)
 Tracheal system: branched tubes
that infiltrate the body (gas
exchange)
 Metamorphosis…...
 •incomplete: young resemble
adults, then molt into adulthood
(grasshoppers)
 •complete: larval stages (looks
different than adult); larva to QuickTime™ and a
Cinepak decompressor
are needed to see this picture.

adult through pupal stage

 The Coelomates:
Deuterostomes, I
 Phy: Echinodermata (sea stars,
sea urchins, sand dollars, sea
lilies, sea cucumbers, sea daisies)
 Spiny skin; sessile or slow moving
 Often pentaradial
 Water vascular system by
hydraulic canals (tube feet)

QuickTime™ and a
Cinepak decompressor
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Index
 Chordates
 Notochord: longitudinal, flexible
rod located between the digestive
and the nerve cord
 Dorsal, hollow nerve cord;
eventually develops into the brain
and spinal cord
 Pharyngeal slits; become modified
for gas exchange, jaw support,
and/or hearing
 Muscular, postanal tail
Invertebrate chordates
 Both suspension feeders…..
 Subphy: Urochordata (tunicates; sea squirt); mostly sessile & marine
 Subphy: Cephalochordata (lancelets); marine, sand dwellers
 Importance: vertebrates closest relatives; in the fossil record, appear
50 million years before first vertebrate
 Paedogenesis: precocious development of sexual maturity in a larva
(link with vertebrates?)
Subphylum: Vertebrata
 Retain chordate characteristics with
specializations….
 Neural crest: group of embryonic
cells near dorsal margins of closing
neural tube
 Pronounced cephalization:
concentration of sensory and neural
equipment in the head
 Cranium and vertebral column
 Closed circulatory system with a
ventral chambered heart
Vertebrate diversity
Phy: Chordata
Subphy: Vertebrata
Superclass: Agnatha~
jawless vertebrates
(hagfish, lampreys)
Superclass: Gnathostomata~
jawed vertebrates with 2
sets of paired
appendages; including
tetrapods (‘4-footed’) and
amniotes (shelled egg)
Superclass Agnatha
Jawless vertebrates
Most primitive, living
vertebrates
Ostracoderms (extinct);
lamprey and hagfish
(extant)
Lack paired appendages;
cartilaginous skeleton;
notochord throughout life;
rasping mouth
Superclass
Gnathostomata, I
 Placoderms (extinct): first with hinged jaws and paired appendages
 Class: Chondrichthyes~ Sharks, skates, rays
 Cartilaginous fishes; well developed jaws and paired fins; continual water
flow over gills (gas exchange); lateral line system (water pressure
changes)
 Life cycles:
 Oviparous- eggs hatch outside mother’s body
 Ovoviviparous- retain fertilized eggs; nourished by egg yolk; young born
live
 Viviparous- young develop within uterus; nourished by placenta
Superclass Gnathostomata,
II
 Class: Osteichthyes
 Ossified (bony) endoskeleton; scales operculum(gill covering);
swim bladder (buoyancy)
 Most numerous vertebrate
 Ray-fined (fins supported by long, flexible rays): bass, trout,
perch, tuna, herring
 Lobe-finned (fins supported by body skeleton extensions):
coelocanth
 Lungfishes (gills and lungs): Australian lungfish (aestivation)
III
 Class: Amphibia
 1st tetrapods on land
 Frogs, toads, salamanders, caecilians
 Metamorphosis; lack shelled egg;
moist skin for gas exchange
Superclass Gnathostomata,
IV
 Class: Reptilia
 Lizards, snakes, turtles, and crocodilians
 Amniote (shelled) egg with extraembryonic membranes (gas exchange,
waste storage, nutrient transfer); absence of feathers, hair, and
mammary glands; ectothermic; scales with protein keratin (waterproof);
lungs; ectothermic (dinosaurs endothermic?)
Superclass Gnathostomata,
V
Class: Aves
Birds
Flight adaptations: wings
(honeycombed bone); feathers (keratin);
toothless; one ovary
Evolved from reptiles (amniote egg and
leg scales); endothermic (4-chambered
heart)
Archaeopteryx (stemmed from an
ancestor that gave rise to birds)
Superclass Gnathostomata,
VI
Class: Mammalia
Mammary glands; hair (keratin);
endothermic; 4-chambered heart;
large brains; teeth differentiation
Evolved from reptilian stock
before birds
Monotremes (egg-laying):
platypus; echidna
Marsupials (pouch): opossums,
kangaroos, koalas
Eutherian (placenta): all other
mammals
Order: Primates (evolution)
 Characteristics: hands & feet for
grasping; large brains, short jaws, flat
face; parental care and complex social
behaviors
 Suborder: Prosimii •lemurs, tarsiers
 Suborder: Anthropoidea •monkeys,
apes, humans (opposable thumb)
 45-50 million years ago
 Paleoanthropology: study of human
origins
 Hominoid: great apes & humans
 Hominid (narrower classification): √
australopithecines (all extinct) √
genus Homo (only 1 exant, sapiens)
Human evolution
Misconceptions:
1- Chimp ancestor (2 divergent branches)
2- Step-wise series (coexistence of human species)
3- Trait unison vs. mosaic evolution (bipedalism,
upright, enlarged brain)
The first humans
 Ape-human split (5-7 mya)
 Australopithecus; “Lucy” (4.0 mya)
 Homo habilis; “Handy Man” (2.5 mya)
 Homo erectus; first to migrate (1.8
mya)
 Neanderthals (200,000 ya)
 Homo sapiens (1.0 mya?)
 Multiregional model
(parallel evolution)
 “Out of Africa”
(replacement evolution)
 Regulatory systems
 Hormone~ chemical signal secreted
into body fluids (blood)
communicating regulatory messages
 Target cells~ body cells that respond
to hormones
 Endocrine system/glands~ hormone
secreting system/glands (ductless);
exocrine glands secrete chemicals
(sweat, mucus, enzymes) through
ducts
 Neurosecretory cells~ actual cells
that secrete hormones
 Feedback mechanisms ~ negative
and positive
Local regulators: cells adjacent to or near point
of secretion

Growth factors ~ proteins for

cell proliferation
Nitric oxide (NO) ~ neurotransmitter;
cell destruction; vessel dilation
Prostaglandins ~ modified
fatty acids secreted by placenta and
immune system; also found in semen
Mode of Action: Chemical
Signaling
 1- Plasma membrane reception
• signal-transduction pathways
(neurotransmitters, growth factors, most hormones)
 2- Cell nucleus reception
• steroid hormones, thyroid hormones, some
local regulators
Vertebrate Endocrine
System
 Tropic hormones ~
a hormone that has
another endocrine gland as
a target
 Hypothalamus~pituitary
 Pituitary gland
 Pineal gland
 Thyroid gland
 Parathyroid glands
 Thymus
 Adrenal glands
 Pancreas
 Gonads (ovary, testis)
The hypothalamus &
pituitary, I
 Releasing and inhibiting hormones
 Anterior pituitary:
 Growth (GH)~bones
√gigantism/dwarfism
√acromegaly
 Prolactin (PRL)~mammary glands;
milk production
 Follicle-stimulating (FSH) &
 Luteinizing (LH)~ovaries/testes
 Thyroid-stimulating (TSH)~ thyroid
 Adrenocorticotropic (ACTH)~ adrenal
cortex
 Melanocyte-stimulating (MSH)
 Endorphins~natural ‘opiates’; brain
pain receptors
The pituitary, II

The posterior
pituitary:
Oxytocin~
uterine and
mammary gland cell
contraction
Antidiuretic (ADH)~
retention of water by
kidneys
The pineal, thyroid, &
parathyroid
Melatonin~ pineal
gland; biological rhythms
Thyroid
hormones:
Calcitonin~
lowers blood calcium
Thyroxine~
metabolic processes
Parathyroid
(PTH)~ raises blood
calcium
 The pancreas
Islets of Langerhans
Alpha cells: •glucagon~
raises blood glucose levels

Beta cells:
•insulin~ lowers blood glucose levels

Type I diabetes mellitus

(insulin-dependent; autoimmune
disorder)

Type II diabetes mellitus

(non-insulin-dependent; reduced
responsiveness in insulin targets)
 The adrenal glands
Adrenal medulla (catecholamines): •epinephrine &
norepinephrine~ increase basal metabolic rate (blood glucose and
pressure)
Adrenal cortex (corticosteroids): •glucocorticoids
(cortisol)~ raise blood glucose •mineralocorticoids
(aldosterone)~ reabsorption of Na+ and K+
The gonads
Steroid hormones:
precursor is cholesterol

androgens
(testosterone)~ sperm formation;
male secondary sex
characteristics; gonadotropin

estrogens
(estradiol)~uterine lining growth;
female secondary sex
characteristics; gonadotropin
Q u ic k Tim e™ an d a
C in ep ak d ec om p ressor
are n eed ed to see t h is p ic t u re.

progestins
(progesterone)~uterine lining
growth
Steroid Hormone Action

QuickTime™ and a
Cinepak decompressor
are needed to see this picture.
Index
 Overview
Asexual (one parent)
fission (parent separation)
budding (corals)
gemmules (porifera)
fragmentation &
regeneration (inverts)
Sexual (fusion of haploid gametes)
gametes (sex cells)
zygote (fertilized egg)
ovum (unfertilized egg)
spermatozoon (male gamete)
Reproductive cycles
Parthenogenesis unfertilized
egg development; haploid, sterile adults
(honeybees)
Hermaphroditism both
male & female reproductive systems;
sessile & burrowing organisms
(earthworms)
Sequential hermaphroditism
reversal of gender during lifetime
•protogynous (female 1st)
•protandrous (male 1st)
Mechanisms of sexual
reproduction
Fertilization
(union of sperm and egg)
• external
• internal
Pheromones
chemical signals that
influence the behavior of
others (mate attractants)
Mammalian
reproduction, I
The Human Male
 Testes~ male gonads
 Seminiferous tubules~ sperm
formation
 Leydig cells~ hormone production
 Scrotum~ outside body temp.
 Epididymis~ sperm development
 Vas deferens~ sperm propulsion
 Seminal vesicles~ semen
 Prostate gland~ anticoagulant;
nutrients
 Bulbourethral glands~ acid
neutralizer
 Penis/urethra~ semen delivery
Mammalian
reproduction, II
The Human Female
Ovaries~ female gonads
Follicle~ egg capsule
Corpus luteum~ hormone
secretion

Oviduct~ fertilization
Uterus/endometrium
~ womb/lining

Cervix/vagina~ sperm
receptacle
Spermatogenesis
 Puberty until death!
 Seminiferous tubules~ location
 Primordial germ cell (2N)~
differentiate into….
 Spermatogonium (2N)~ sperm
precursor
 Repeated mitosis into….
 Primary spermatocyte (2N)
 1st meiotic division
 Secondary spermatocyte (1N)
 2nd meiotic division
 Spermatids (1N)~Sertoli cells….
 Sperm cells (1N)
Oogenesis
 As embryo until menopause...
 Ovaries
 Primordial germ cells (2N)
 Oogonium (2N)
 Primary oocyte (2N)
 Between birth & puberty;
prophase I of meiosis
 Puberty; FSH; completes
meiosis I
 Secondary oocyte (1N); polar
body
 Meiosis II; stimulated by
fertilization
 Ovum (1N); 2nd polar body
The female pattern

 Estrous cycles/estrus
(many mammals)
 Menstrual cycle (humans
and many other primates):

 Ovarian/Menstrual
cycles~ •follicular
phase~follicle growth
•ovulation~ oocyte
release •luteal phase~
hormone release
Embryonic & fetal
development
Gestation~ pregnancy
1st trimester:
organogenesis
fetus (week 8; all adult features)
HCG hormone (menstruation
override; pregnancy test detection)

Parturition~birth
Labor~uterine contractions
Lactation~prolactin & oxytocin
Modern technologies
Index
 Nutritional
requirements
 Undernourishment: caloric deficiency
 Overnourishment (obesity): excessive
food intake
 Malnourishment: essential nutrient
deficiency
 Essential nutrients: materials that must
be obtained in preassembled form
 Essential amino acids: the 8 amino
acids that must be obtained in the diet
 Essential fatty acids: unsaturated fatty
acids
 Vitamins: organic coenzymes
 Minerals: inorganic cofactors
Food types/feeding
mechanisms
 Opportunistic
 Herbivore: eat autotrophs
 Carnivore: eat other animals
 Omnivore: both
 Feeding Adaptations
 Suspension-feeders: sift food
from water (baleen whale)
 Substrate-feeders: live in or on
their food (leaf miner)
(earthworm: deposit-feeder)
 Fluid-feeders: suck fluids from a
host (mosquito)
 Bulk-feeders: eat large pieces of
food (most animals)
 Overview of food
processing
 1-Ingestion: act of eating
 2-Digestion: process of food break down
 enzymatic hydrolysis
 intracellular: breakdown within cells (sponges)
 extracellular: breakdown outside cells (most animals)
 alimentary canals (digestive tract)
 3- Absorption: cells take up small molecules
 4- Elimination: removal of undigested material
 Mammalian digestion, I
 Peristalsis: rhythmic waves of contraction by smooth
muscle
 Sphincters: ring-like valves that regulate passage of
material
 Accessory glands: salivary glands; pancreas; liver; gall
bladder
Mammalian digestion, II
 Oral cavity
•salivary amylase
•bolus
 Pharynx
•epiglottis
 Esophagus
 Stomach
•gastric juice
•pepsin/pepsinogen
(HCl) •acid chyme
•pyloric
sphincter
Mammalian digestion,
III
 Small intestine •duodenum •bile
 Intestinal digestion: a-carbohydrate b-protein c-
nucleic acid d-fat
Mammalian digestion,
IV
 Villi / microvilli
 Lacteal (lymphatic)
 Chylomicrons (fats mixed with cholesterol)
 Hepatic portal vessel
Mammalian digestion, V
 Hormonal Action:  Large intestine (colon)
 Gastrin food---> stomach wall  Cecum
---> gastric juice
 Appendix
 Enterogastrones (duodenum)
 Feces
 1-Secretin
acidic chyme---> pancreas  Rectum/anus
to release bicarbonate
 2-Cholecystokinin (CCK)
amino/fatty acids---> pancreas
to release enzymes and gall
bladder to release bile
 Evolutionary
adaptations
Dentition: an animal’s assortment of
teeth
Digestive system length
Symbiosis
Ruminants
Overview of Mammalian Digestive Enzymes
Index
 Circulation system
evolution, I
 Gastrovascular cavity (cnidarians, flatworms)
 Open circulatory •hemolymph (blood & interstitial fluid)
•sinuses (spaces surrounding organs)
 Closed circulatory: blood confined to vessels
 Cardiovascular system •heart (atria/ventricles)
•blood vessels (arteries, arterioles, capillary beds,
venules, veins) •blood (circulatory fluid)
 Circulation system
evolution, II
Fish: 2-chambered heart; single circuit of blood flow
Amphibians: 3-chambered heart; 2 circuits of blood flow-
pulmocutaneous (lungs and skin); systemic (some mixing)
Mammals: 4-chambered heart; double circulation; complete
separation between oxygen-rich and oxygen poor blood
Double circulation
 From right ventricle to lungs via
pulmonary arteries through
semilunar valve (pulmonary
circulation)
 Capillary beds in lungs to left
atrium via pulmonary veins
 Left atrium to left ventricle
(through atrioventricular valve)
to aorta
 Aorta to coronary arteries; then
systemic circulation
 Back to heart via two venae
cavae (superior and inferior);
right atrium
The mammalian heart
 Cardiac cycle: sequence of
filling and pumping
 Systole- contraction
 Diastole- relaxation
 Cardiac output: volume of blood
per minute
 Heart rate- number of beats per
minute
 Stroke volume- amount of blood
pumped with each contraction
 Pulse: rhythmic stretching of
arteries by heart contraction
The heartbeat
 Sinoatrial (SA) node (“pacemaker”): sets rate and timing
of cardiac contraction by generating electrical signals
 Atrioventricular (AV) node: relay point (0.1 second delay)
spreading impulse to walls of ventricles
 Electrocardiogram (ECG or EKG)
Blood vessel structural
differences
Capillaries
•endothelium; basement
membrane
Arteries •thick connective
tissue; thick smooth muscle;
endothelium; basement
membrane
Veins •thin connective
tissue; thin smooth muscle;
endothelium; basement
membrane
The lymphatic system
 Lymphatic system: system
of vessels and lymph nodes,
separate from the
circulatory system, that
returns fluid and protein to
blood
 Lymph: colorless fluid,
derived from interstitial fluid
 Lymph nodes: filter lymph
and help attack viruses and
bacteria
 Body defense / immunity
 Blood
 Plasma: liquid matrix of blood in which cells are suspended (90%
water)
 Erythrocytes (RBCs): transport O2 via hemoglobin
 Leukocytes (WBCs): defense and immunity
 Platelets: clotting
 Stem cells: pluripotent cells in the red marrow of bones
 Blood clotting: fibrinogen (inactive)/ fibrin (active); hemophilia;
thrombus (clot)
Cardiovascular disease
 Cardiovascular disease (>50% of
all deaths)
 Heart attack- death of cardiac
tissue due to coronary blockage
 Stroke- death of nervous tissue in
brain due to arterial blockage
 Atherosclerosis: arterial plaques
deposits
 Arteriosclerosis: plaque hardening
by calcium deposits
 Hypertension: high blood pressure
 Hypercholesterolemia: LDL,
HDL
Gas exchange
CO2 <---> O2
Aquatic: •gills •ventilation •countercurrent
exchange
Terrestrial: •tracheal systems •lungs
 Mammalian respiratory
systems
 Larynx (upper part of  Bronchi (tube to lungs)
respiratory tract)  Bronchioles
 Vocal cords (sound  Alveoli (air sacs)
production)  Diaphragm (breathing
 Trachea (windpipe) muscle)
 Breathing
 Positive pressure breathing: pushes air into lungs (frog)
 Negative pressure breathing: pulls air into lungs (mammals)
 Inhalation: diaphragm contraction; Exhalation: diaphragm
relaxation
 Tidal volume: amount of air inhaled and exhaled with each
breath (500ml)
 Vital capacity: maximum tidal volume during forced
breathing (4L)
 Regulation: CO2 concentration in blood (medulla oblongata)
Respiratory pigments: gas
transport
 Oxygen transport-
 Hemocyanin: found in hemolymph
of arthropods and mollusks (Cu)
 Hemoglobin: vertebrates (Fe)
 Carbon dioxide transport-
 Blood plasma (7%)
 Hemoglobin (23%)
 Bicarbonate ions (70%)
 Deep-diving air-breathers-
 Myoglobin: oxygen storing protein
Index
Lines of Defense

Nonspecific Defense Mechanisms……

Phagocytic and Natural Killer
Cells
 Neutrophils 60-70% WBCs;
engulf and destroy microbes at
infected tissue
 Monocytes 5% WBCs; develop
into….
 Macrophages enzymatically
destroy microbes
 Eosinophils 1.5% WBCs;
destroy large parasitic invaders (blood
flukes)
 Natural killer (NK) cells destroy
virus-infected body cells & abnormal
cells
The Inflammatory
Response
 1- Tissue injury; release of chemical signals~ • histamine (basophils/mast cells): causes Step 2... • prostaglandins: increases
blood flow & vessel permeability
 2/3- Dilation and increased permeability of capillary~ • chemokines: secreted by blood vessel endothelial cells mediates
phagocytotic migration of WBCs
 4- Phagocytosis of pathogens~ • fever & pyrogens: leukocyte-released molecules increase body temperature
Specific Immunity
Lymphocyctes •pluripotent stem
cells... • B Cells (bone marrow)
• T Cells (thymus)
Antigen: a foreign molecule that
elicits a response by lymphocytes
(virus, bacteria, fungus, protozoa,
parasitic worms)
Antibodies: antigen-binding
immunoglobulin, produced by B cells
Antigen receptors: plasma
membrane receptors on b and T
cells
Clonal selection
 Effector cells: short-lived cells that
combat the antigen
 Memory cells: long-lived cells that
bear receptors for the antigen
 Clonal selection: antigen-driven
cloning of lymphocytes
 “Each antigen, by binding to
specific receptors, selectively
activates a tiny fraction of cells
from the body’s diverse pool of
lymphocytes; this relatively small
number of selected cells gives rise
to clones of thousands of cells, all
specific for and dedicated to
eliminating the antigen.”
Induction of Immune
Responses
Primary immune response: lymphocyte proliferation and
differentiation the 1st time the body is exposed to an antigen
Plasma cells: antibody-producing effector B-cells
Secondary immune response: immune response if the
individual is exposed to the same antigen at some later time~
Immunological memory
Self/Nonself Recognition
 Self-tolerance: capacity to distinguish self from non-self
 Autoimmune diseases: failure of self-tolerance; multiple sclerosis, lupus,
rheumatoid arthritis, insulin-dependent diabetes mellitus
 Major Histocompatability Complex (MHC): body cell surface antigens
coded by a family of genes
 Class I MHC molecules: found on all nucleated cells
 Class II MHC molecules: found on macrophages, B cells, and activated T
cells
 Antigen presentation: process by which an MHC molecule “presents’ an
intracellular protein to an antigen receptor on a nearby T cell
 Cytotoxic T cells (TC): bind to protein fragments displayed on class I
MHC molecules
 Helper T cells (TH): bind to proteins displayed by class II MHC molecules
Types of immune
responses
 Humoral immunity
 B cell activation
 Production of antibodies
 Defend against bacteria,
toxins, and viruses free in
the lymph and blood plasma
 Cell-mediated immunity
 T cell activation
 Binds to and/or lyses cells
 Defend against cells infected
with bacteria, viruses, fungi,
protozoa, and parasites;
nonself interaction
Helper T lymphocytes
 Function in both humoral & cell-mediated immunity
 Stimulated by antigen presenting cells (APCs)
 T cell surface protein CD4 enhances activation
 Cytokines secreted (stimulate other lymphocytes):
a) interleukin-2 (IL-2): activates B cells and cytotoxic
T cells b) interleukin-1 (IL-1): activates helper T cell
to produce IL-2
 Cell-mediated:
cytotoxic T cells
 Destroy cells infected by intracellular pathogens and cancer cells
 Class I MHC molecules (nucleated body cells) expose foreign proteins
 Activity enhanced by CD8 surface protein present on most cytotoxic T cells
(similar to CD4 and class II MHC)
 TC cell releases perforin, a protein that forms pores in the target cell
membrane; cell lysis and pathogen exposure to circulating antibodies
Humoral response: B
cells
Stimulated by T-dependent
antigens (help from TH cells)
Macrophage (APCs) with
class II MHC proteins
Helper T cell (CD4 protein)
Activated T cell secretes IL-2
(cytokines) that activate B
cell
B cell differentiates into
memory and plasma cells
(antibodies)
Antibody Structure &
Function
Epitope: region on antigen surface recognized by
antibodies
2 heavy chains and 2 light chains joined by
disulfide bridges
Antigen-binding site (variable region)
5 classes of
Immunoglobins
 IgM: 1st to circulate; indicates
infection; too large to cross placenta
 IgG: most abundant; crosses walls of
blood vessels and placenta; protects
against bacteria, viruses, & toxins;
activates complement
 IgA: produced by cells in mucous
membranes; prevent attachment of
viruses/bacteria to epithelial surfaces;
also found in saliva, tears, and
perspiration
 IgD: do not activate complement and
cannot cross placenta; found on
surfaces of B cells; probably help
differentiation of B cells into plasma
and memory cells
 IgE: very large; small quantity;
releases histamines-allergic reaction
Antibody-mediated Antigen
Disposal
 Neutralization (opsonization): antibody binds to and blocks antigen
activity
 Agglutination: antigen clumping
 Precipitation: cross-linking of soluble antigens
 Complement fixation: activation of 20 serum proteins, through
cascading action, lyse viruses and pathogenic cells
Immunity in Health &
Disease
 Active immunity/natural: conferred
immunity by recovering from disease
 Active immunity/artificial: immunization and
vaccination; produces a primary response
 Passive immunity: transfer of immunity from
one individual to another • natural: mother to
fetus; breast milk •
artificial: rabies antibodies
 ABO blood groups (antigen presence)
 Rh factor (blood cell antigen); Rh- mother vs.
an Rh+ fetus (inherited from father)
function
 Allergies (anaphylactic shock): hypersensitive responses to
environmental antigens (allergens); causes dilation and blood
vessel permeability (antihistamines); epinephrine
 Autoimmune disease: multiple sclerosis, lupus, rheumatoid
arthritis, insulin-dependent diabetes mellitus
 Immunodeficiency disease: SCIDS (bubble-boy); A.I.D.S.
Overview of Human Immune System Function
Index
Homeostasis: regulation of internal
environment

Thermoregulation
internal temperature
Osmoregulation
solute and water balance
Excretion
nitrogen containing waste
Regulation of body
temperature
 Thermoregulation
 4 physical processes:
 Conduction~transfer of heat between
molecules of body and environment
 Convection~transfer of heat as
water/air move across body surface
 Radiation~transfer of heat produced
by organisms
 Evaporation~loss of heat from liquid
to gas
 Sources of body heat:
 Ectothermic: determined by
environment
 Endothermic: high metabolic rate
generates high body heat
Regulation during environmental
extremes
 Torpor~ low activity;
decrease in metabolic rate

 1- Hibernation
long term or winter torpor
(winter cold and food
scarcity); bears, squirrels
 2- Estivation
short term or summer
torpor (high temperatures
and water scarcity); fish,
amphibians, reptiles
 Both often triggered by
length of daylight
Water balance and
waste disposal
 Osmoregulation:
management of the body’s water
content and solute composition
 Nitrogenous wastes:
breakdown products of proteins and
nucleic acids; ammonia-very toxic
 Deamination~
 Ammonia: most aquatic animals,
many fish
 Urea: mammals, most amphibians,
sharks, bony fish (in liver;
combo of NH3 and CO2)
 Uric acid: birds, insects, many
reptiles, land snails
Osmoregulators
 Osmoconformer: no active adjustment of internal
osmolarity (marine animals); isoosmotic to environment
 Osmoregulator: adjust internal osmolarity (freshwater,
marine, terrestrial)
 Freshwater fishes (hyperosmotic)- gains water, loses;
excretes large amounts of urine salt vs. marine fishes
(hypoosmotic)- loses water, gains salt; drinks large
amount of saltwater
Excretory Systems
 Production of urine by 2 steps: • Filtration (nonselective) •
Reabsorption (secretion of solutes)
 Protonephridia ~ flatworms (“flame-bulb” systems)
 Metanephridia ~ annelids (ciliated funnel
system)
 Malpighian
tubules ~ insects
(tubes in digestive tract)
 Kidneys ~ vertebrates
Kidney Functional Units
 Renal artery/vein: kidney blood flow
 Ureter: urine excretory duct
 Urinary bladder: urine storage
 Urethra: urine elimination tube
 Renal cortex (outer region)
 Renal medulla (inner region)
 Nephron: functional unit of kidney
 Cortical nephrons (cortex; 80%)
 Juxtamedullary nephrons (medulla;
20%)
hormones
 Antidiuretic hormone (ADH) ~ secretion
increases permeability of distal tubules and
collecting ducts to water (H2O back to body);
inhibited by alcohol and coffee
 Juxtaglomerular apparatus (JGA) ~
reduced salt intake--->enzyme renin initiates
conversion of angiotension (plasma protein) to
angiotension II (peptide); increase blood
pressure and blood volume by constricting
capillaries
 Angiotension II also stimulates adrenal
glands to secrete aldosterone; acts on distal
tubules to reabsorb more sodium, thereby
increasing blood pressure (renin-angiotension-
aldosterone system; RAAS)
 Atrial natriuretic factor (ANF) ~ walls of
atria; inhibits release of renin, salt
reabsorption, and aldosterone release
Overview of Mammalian Nephron Function
Index
Nervous systems
Effector cells~
muscle or gland cells
Nerves~ bundles of
neurons wrapped in
connective tissue
Central nervous
system (CNS)~ brain
and spinal cord
Peripheral nervous
system (PNS)~
sensory and motor neurons
 Structural Unit of Nervous
System
 Neuron~ structural and functional unit
 Cell body~ nucelus and organelles
 Dendrites~ impulses from tips to neuron
 Axons~ impulses toward tips
 Myelin sheath~ supporting, insulating layer
 Schwann cells~PNS support cells
 Synaptic terminals~ neurotransmitter releaser
 Synapse~ neuron junction
 Simple Nerve Circuit
 Sensory neuron: convey information
to spinal cord
 Interneurons: information integration
 Motor neurons: convey signals to
effector cell (muscle or gland)
 Reflex: simple response; sensory to
motor neurons
 Ganglion (ganglia): cluster of nerve
cell bodies in the PNS
 Supporting cells/glia: nonconductiong
cell that provides support, insulation,
and protection
 Neural signaling, I
 Membrane potential (voltage differences across the plasma membrane)
 Intracellular/extracellular ionic concentration difference
 K+ diffuses out (Na+ in); large anions cannot follow….selective
permeability of the plasma membrane
 Net negative charge of about -70mV
 Neural signaling, II
 Excitable cells~ cells that can change membrane potentials (neurons, muscle)
 Resting potential~ the unexcited state of excitable cells
 Gated ion channels (open/close response to stimuli): photoreceptors; vibrations in air
(sound receptors); chemical (neurotransmitters) & voltage (membrane potential changes)
 Graded Potentials (depend on strength of stimulus):
 1- Hyperpolarization (outflow of K+); increase in electrical gradient; cell becomes more
negative
 2- Depolarization (inflow of Na+); reduction in electrical gradient; cell becomes less
negative
 Neural signaling, III
 Threshold potential: if stimulus reaches a
certain voltage (-50 to -55 mV)….
 The action potential is triggered….
 Voltage-gated ion channels (Na+; K+)
 1-Resting state •both channels
closed
 2-Threshold •a stimulus opens some Na+
channels
 3-Depolarization •action potential
generated •Na+ channels open; cell
becomes positive (K+ channels closed)
 4-Repolarization •Na+ channels close,
K+ channels open; K+ leaves •cell
becomes negative
 5-Undershoot •both gates close, but K+
channel is slow; resting state restored
 Refractory period~ insensitive to
depolarization due to closing of Na+ gates
 Neural signaling, IV
 “Travel” of the action potential is self-propagating
 Regeneration of “new” action potentials only after refractory
period
 Forward direction only
 Action potential speed:
 1-Axon diameter (larger = faster; 100m/sec)
 2-Nodes of Ranvier (concentration of ion channels); saltatory
conduction; 150m/sec
 Synaptic
communication
 Presynaptic cell: transmitting cell
 Postsynaptic cell: receiving cell
 Synaptic cleft: separation gap
 Synaptic vesicles:
neurotransmitter releasers
 Ca+ influx: caused by action
potential; vesicles fuse with
presynaptic membrane and
release….
 Neurotransmitter
Neurotransmitters
Acetylcholine (most common) •skeletal muscle
Biogenic amines (derived from amino acids)
•norepinephrine •dopamine •serotonin
Amino acids
Neuropeptides (short chains of amino acids)
•endorphin
 Vertebrate PNS
Cranial nerves (brain origin)
Spinal nerves (spine origin)
Sensory division
Motor division
•somatic system
voluntary, conscious control
•autonomic system
√parasympathetic
conservation of energy
√sympathetic
increase energy consumption
 The Vertebrate Brain
 Forebrain •cerebrum~memory, learning,
emotion •cerebral cortex~sensory and
motor nerve cell bodies •corpus
callosum~connects left and right hemispheres
•thalamus; hypothalamus
 Midbrain •inferior (auditory) and
superior (visual) colliculi
 Hindbrain •cerebellum~coordination of
movement •medulla
oblongata/ pons~autonomic, homeostatic
functions
Index
Vertebrate Skeletal
Muscle
 Contract/relax: antagonistic
pairs w/skeleton
 Muscles: bundle of….
 Muscle fibers: single cell w/ many nuclei
consisting of….
 Myofibrils: longitudinal bundles
composed of….
 Myofilaments: •Thin~ 2
strands of actin protein and a regulatory
protein •Thick~ myosin
protein
 Sarcomere: repeating unit of muscle
tissue, composed of….
 Z lines~sarcomere border
 I band~only actin protein
 A band~actin & myosin protein overlap
 H zone~central sarcomere; only myosin
Sliding-filament model
Theory of muscle contraction
Sarcomere length reduced
Z line length becomes shorter
Actin and myosin slide past each other (overlap
increases)
 Actin-myosin interaction
 1- Myosin head hydrolyzes ATP to ADP and inorganic phosphate
(Pi); termed the “high energy configuration”
 2- Myosin head binds to actin; termed a “cross bridge”
 3- Releasing ADP and (Pi), myosin relaxes sliding actin; “low
energy configuration”
 4- Binding of new ATP releases myosin head
 Creatine phosphate~ supplier of phosphate to ADP
Muscle contraction regulation,
I

Relaxation:
tropomyosin blocks
myosin binding sites on
actin
Contraction:
calcium binds to toponin
complex; tropomyosin
changes shape, exposing
myosin binding sites
Muscle contraction regulation,
II
Calcium (Ca+)~ concentration
regulated by the….
Sarcoplasmic reticulum~ a
specialized endoplasmic reticulum
Stimulated by action potential in
a motor neuron
T (transverse) tubules~ travel
channels in plasma membrane for
action potential
Ca+ then binds to troponin
I am the Lorax.
I speak for the trees.
I speak for the trees,
for the trees have no tongues.

Index
Ecology
Components:
•abiotic~nonliving chemical &
physical factors
•biotic~living factors
Population~group of
individualsof the same species in
a particular geographical area
Community~assemblage of
populations of different species
Ecosystem~all abiotic factors
and the community of species in
an area
Rachel Carson, 1962,
Silent Spring
Abiotic factors
Biosphere~the sum of all
the planet’s ecosystems
Biome~ areas of
predominant flora and fauna

Temperature
Water
Sunlight
Wind
Rocks & Soil
Periodic Ecotone: biome grading areas

disturbances
Global climate
• Precipitation & Winds
Lake stratification &
turnover
Thermal stratification~ vertical temperature layering
Biannual mixing~ spring and summer
Turnover~ changing water temperature profiles; brings
oxygenated water from the surface to the bottom and nutrient
rich water form the bottom to the surface
Aquatic biomes
Vertical
stratification: •photic
zone~ photosynthetic light
•aphotic zone~ little light
•thermocline~ narrow
stratum of rapid
temperature chang •benthic
zone~ bottom substrate
Benthos~ community of
organisms
Detritus~ dead organic
matter; food for benthic
organisms
Freshwater biomes
Littoral zone~ shallow, well-lit
waters close to shore
Limnetic zone~ well-lit, open
water farther from shore
Profundal zone~ deep, aphotic
waters
Lake classification:
•oligotrophic~ deep, nutrient poor
•eutrophic~ shallow, high nutrient
content •mesotrophic~
moderate productivity
Wetland~ area covered with
water
Estuary~ area where freshwater
merges with ocean
Marine biomes
Intertidal zone~ area
where land meets water
Neritic zone~ shallow
regions over continental shelves

Oceanic zone~ very deep

water past the continental shelves
Pelagic zone~ open water
of any depth
Benthic zone~ seafloor
bottom
Abyssal zone~ benthic
region in deep oceans
 Terrestrial biomes
 Tropical forests~ equator; most complex; constant temperature and rainfall;
canopy
 Savanna~ tropical grassland with scattered trees; occasional fire and drought;
large herbivores
 Desert~ sparse rainfall (<30cm/yr)
 Chaparral~ spiny evergreens at midlatitudes along coasts
 Temperate grassland~ all grasses; seasonal drought, occasional fires; large
mammals
 Temperate deciduous forest~ midlatitude regions; broad-leaf deciduous trees
 Coniferous forest~ cone-bearing trees
 Tundra~ permafrost; very little precipitation
Index
 Behavior
Ethology~ study of animal behavior
Causation: •proximate~
physiological & genetic mechanisms of
behavior •ultimate~
evolutionary significance of behavior
Sign stimulus~ external sensory
stimulus
Fixed action pattern (FAP)~
sequence of acts; unchangeable; carried
to completion
Ex: 3-spined stickleback
(Tinbergen ‘73 Nobel)

Supernormal stimulus
 Learning?
 Maturation~ behavior due to developing physiological changes
 Habituation~ loss of responsiveness to stimuli that convey
 no information; simple learning
 Imprinting~ limited learning within a specific time period
•critical period (Lorenz, ‘73 Nobel)
 Associative learning:
•classical conditioning~ Pavlov’s dogs
•operant conditioning (trial and
error)~ “Skinner’s box”
 Social behavior
Sociobiology~ evolutionary theory
applied to social behavior (Hamilton) QuickTime™ and a
Cinepak decompressor
are needed to see this picture.

Agonistic behavior~ contest behavior

determining access to resources
Dominance hierarchy~ linear
“pecking order”
Territoriality~ an area an individual
defends excluding others
Mating systems:
•promiscuous~ no strong pair bonds
•monogamous~ one male/one
female •polygamous~ one with
many •polygyny~ one
male/many females •polyandry~ one
female/many males
Altruistic behavior
Inclusive fitness~ total effect
an individual has on proliferating its
genes by its own offspring and aid
to close relatives
Coefficient of relatedness~
proportion of genes that are
identical because of common
ancestors
Kin selection~ aiding related
individuals altruistically
Reciprocal altruism~
exchange of aid; humans?
Index
 Population
characteristics
Density~ # of individuals per unit of area
•counts •sample size
estimate •indirect
indicators •mark-
recapture
Dispersion~ pattern of spacing
•random~ unpredictable, patternless
spacing (a)
•clumped~ patchy aggregation (b)
•uniform~ even spacing (c)
Demography: factors that affect growth & decline of
populations
 Birthrate (natality, fecundity)~ # of offspring produced
 Death rate (mortality)
 Age structure~ relative number of individuals of each age
 Survivorship curve~ plot of numbers still alive at each age
 Population Growth
Models
Exponential model (red)
• idealized population in an
unlimited environment (J-
curve); r-selected species (r=per
capita growth rate)

Logistic model (blue)

•carrying capacity (K):
maximum population size that a
particular environment can support (S-
curve); K-selected species
Population life history
“strategies”
r-selected K-selected
(opportunistic) (equilibrial)

Short maturation & Long maturation &

lifespan lifespan
Many (small) Few (large) offspring;
usually several (late)
offspring; usually 1
reproductions;
(early) reproduction; extensive parental
no parental care care
High death rate Low death rate
 Population limiting
factors

Density-dependent
factors •competition
•predation
•stress/crowding
•waste accumulation

Density-independent
factors •weather/climate
•periodic
disturbances
Index
 Community structure
Community~ an assemblage of
populations living close enough
together for potential interaction
Richness (number of species)
& abundance…….
Species diversity
Hypotheses:
•Individualistic~ chance
assemblage with similar abiotic
requirements
•Interactive~ assemblage
locked into association by mandatory
biotic interactions
Interactions
Interspecific (interactions
between populations of different
species within a community):
•Predation
including parasitism; may
involve a keystone
species/predator
•Competition
•Commensalism
•Mutualism
Predation
defense
Cryptic (camouflage)
coloration
Aposematic (warning)
coloration
Mimicry~ superficial resemblance
to another species
√ Batesian~ palatable/
harmless species mimics an
unpalatable/ harmful model √
Mullerian~ 2 or more unpalatable,
aposematically colored species
resemble each other
Competition: a closer
look
Interference~ actual fighting
over resources

Exploitative~ consumption or
use of similar resources

Competitive Exclusion
Principle (Lotka / Volterra)~ 2
species with similar needs for the
same limiting resources cannot
coexist in the same place
√Gause experiment
Competition evidence
Resource Character
partitioning~ sympatric displacement~
species consume slightly sympatric species tend to
different foods or use other diverge in those
resources in slightly different characteristics that overlap
ways

Ex: Anolis lizard sp. perching sites in the Ex: Darwin’s finch beak size on the
Dominican Republic Galapagos Islands
 The Niche
Ecological niche~ the sum total of an
organism’s use of biotic and abiotic resources in
its environment; its “ecological role”
√ fundamental~ the set of resources
a population is theoretically capable of using
under ideal conditions √ realized~
the resources a population actually uses
Thus, 2 species cannot coexist in a
community if their niches are
identical

Ex: Barnacle sp. on the coast of Scotland

 Succession
Ecological
succession~ transition in
species composition over
ecological time
Primary~ begun in lifeless
area; no soil, perhaps volcanic
activity or retreating glacier
Secondary~ an existing
community has been cleared by
some disturbance that leaves the
soil intact
Index
 Relationships, I
Trophic structure / levels~ feeding
relationships in an ecosystem
Primary producers~ the trophic level
that supports all others; autotrophs
Primary consumers~ herbivores
Secondary and tertiary
consumers~ carnivores
Detrivores/detritus~ special
consumers that derive nutrition from non-
living organic matter
Food chain~ trophic level food pathway
Relationships, II

Food webs~
interconnected feeding
relationship in an
ecosystem
 Energy Flow, I
 Primary productivity (amount of light energy converted to chemical
energy by autotrophs) •Gross (GPP): total energy
•Net (NPP): represents the
storage of energy available to consumers •Rs:
respiration
 NPP = GPP - Rs
 Biomass: primary productivity reflected as dry weight of organic material
 Secondary productivity: the rate at which an ecosystem's consumers
convert chemical energy of the food they eat into their own new biomass
 Energy Flow,
Ecological efficiency
II : % of E
transferred from one trophic level
to the next (5-20%)
Pyramid of productivity:
multiplicative loss of energy in
trophic levels
Biomass pyramid: trophic
representation of biomass in
ecosystems
Pyramid of numbers:
trophic representation of the
number of organisms in an
ecosystem
Chemical Cycling
 Biogeochemical cycles: the various nutrient circuits, which involve
both abiotic and biotic components of an ecosystem
 Water
 Carbon
 Nitrogen
 Phosphorus
 Human Impact
Biological magnification: trophic
process in which retained substances
become more concentrated at higher
levels
Greenhouse effect: warming of
planet due to atmospheric accumulation
of carbon dioxide
Ozone depletion: effect of
chlorofluorocarbons (CFC’s) released
into the atmosphere
Rainforest destruction
Cause: Overpopulation?
Index
Biodiversity crisis
 Extinction ~ natural phenomenon,
however, rate is of concern…..
 50% loss of species when 90% of
habitat is lost
 Major Threats:
 Habitat destruction ~ single
greatest threat; cause of 73% of
species designation as extinct,
endangered, vulnerable, rare; 93% of
coral reefs
 Competition by exotic (non-
native) species ~ cause of 68% of
species designation as extinct,
endangered, vulnerable, rare; travel
 Overexploitation ~ commercial
harvest or sport fishing; illegal trade
Biodiversity: Human
welfare
25% of all medical
prescriptions
Genetic variability
Aesthetic and
ethical reasons
Species survival
 Conservation biology
focus
Preservationism: setting side
select areas as natural and
underdeveloped
Resource conservation:
public lands to meet the needs of
agriculture and extractive
industries, i.e., ”multiple use”
Evolutionary / ecological
view: natural systems result from
millions of years of evolution and
ecosystem processes are necessary
to maintain the biosphere
Geographic distribution
of biodiversity
Energy availability ~
solar radiation
Habitat heterogeneity
~ environmental patchiness
Niche specialization ~
narrow resource range
specialization
Population
interactions ~ complex
population interactions
 Population & species level
conservation

Biodiversity hot spot:

small area with an exceptional
concentration of species
Endemic species: species
found nowhere else
Endangered species:
organism “in danger of extinction”
Threatened species: likely
to become endangered in the
foreseeable future
Bioremediation: use of living
organisms to detoxify polluted
systems