Midterm Final Review
Part I
Ecology: the scientific study of the interactions between
organisms and the environment
• The ecological study of species involves biotic
and abiotic influences.
– Biotic = living (organisms)
– Abiotic = nonliving (temp, water, salinity, sunlight,
soil)
Heirarchy
• Organisms
• Population: group of individuals of same
species living in a particular geographic
area
• Community: all the organisms of all the
species that inhabit a particular area
• Ecosystem: all the abiotic factors +
community of species in a certain area
• Biosphere: global ecosystem
Learning is experience-based modification of
behavior
• Learning ranges from simple behavioral
changes to complex problem solving
– Learning: a change in behavior
resulting from experience
– Social learning involves
changes in behavior that result
from the observation and
imitation of others
Vervet alarm call
Innate behavior is developmentally fixed
• Unlearned behavior
• Environmental indifference - performed the
same way by all members of a species
• Fixed action patterns (FAPs): innate
behaviors that exhibit unchangeable
sequences; carried to completion
• Triggered by sign stimulus
• Ensures that activities essential to survival
are performed correctly without practice
Directed Movements
• Kinesis: simple change in activity or turning rate in response to a
stimulus
Kinesis increases the chance that a sow bug will encounter and stay
in a moist environment.
• Taxis: automatic movement, oriented movement +/- from
stimulus; i.e. Phototaxis, chemotaxis, and geotaxis.
Positive rheotaxis keeps trout facing into the current, the direction
from which most food comes.
Types of Learning
1. Habituation: loss of responsiveness to
stimuli that convey little or no
information
– Simple form of learning
2. Imprinting: learning + innate
components
– Limited to sensitive period in
life, generally irreversible
– ie. Lorenz’ imprinting in greylag
geese
Types of Learning
3. Associative learning: ability to associate one
stimulus with another
– Also called classical conditioning
– Fruit fly (drosophila): trained to respond to odor +
shock
Types of Learning
Operant conditioning: another type of
associative learning
– Trial-and-error learning
– Associate its own behavior with reward or
punishment
Types of Learning
4. Cognition: the ability of an animal’s nervous
system to:
– Perceive, store, process, and use information
gathered by sensory receptors
– Problem-solving behavior relies on cognition
Territorial Behavior
• Territorial behavior parcels space and resources
–
Animals exhibiting this behavior mark and defend their
territories
Patterns of
Dispersal:
Clumped. For many animals, such as these wolves,
living in groups increases the effectiveness of hunting,
spreads the work of protecting and caring for young,
and helps exclude other individuals from their territory.
Uniform. Birds nesting on small islands, such as these
king penguins on South Georgia Island in the South
Atlantic Ocean, often exhibit uniform spacing, maintained
by aggressive interactions between neighbors.
Random. Dandelions grow from windblown seeds that
land at random and later germinate.
1. Clumped – most common; near
required resource
2. Uniform – usually antagonistic
interactions
3. Random – not common in
nature
Demography: the study of vital statistics that
affect population size
• Additions occur through birth, and subtractions occur
through death.
• A life table is an age-specific summary of the survival
pattern of a population.
• A graphical way of representing the data is a
survivorship curve.
– This is a plot of the number of individuals in a cohort
still alive at each age.
Survivorship Curves:
• Type I curve: low death rate early in life (humans)
• Type II curve: constant death rate over lifespan (squirrels)
• Type III curve: high death rate early in life (oysters)
• Zero population growth: B = D
• Exponential population growth: ideal
conditions, population grows rapidly
2,000
Population size (N)
dN
dt = 1.0N
1,500
dN
dt = 0.5N
1,000
500
0
0
5
10
Number of generations
15
• Unlimited resources are rare
• Logistic model: incorporates carrying capacity (K)
– K = maximum stable population which can be
sustained by environment
• dN/dt = rmax((K-N)/K)
• S-shaped curve
• K-selection: pop. close to carrying capacity
• r-selection: maximize reproductive success
K-selection
r-selection
Live around K
Exponential growth
High prenatal care
Little or no care
Low birth numbers
High birth numbers
Good survival of young
Poor survival of young
Density-dependent
Density independent
ie. Humans
ie. cockroaches
Factors that limit population growth:
• Density-Dependent factors: population matters
– i.e. Predation, disease, competition, territoriality,
waste accumulation
• Density-Independent factors: population not a factor
– i.e. Natural disasters: fire, flood, weather
Age-Structure Diagrams
Interspecific interactions
• Can be positive (+), negative (-) or neutral (0)
• Includes competition, predation, and symbiosis
• Interspecific competition for resources can
occur when resources are in short supply
• Species interaction is -/• Competitive exclusion principle: Two species
which cannot coexist in a community if their
niches are identical.
– The one with the slight reproductive advantage will
eliminate the other
Ecological niche: the sum total of an organism’s use
of abiotic/biotic resources in the environment
• Fundamental niche = niche potentially occupied
by the species
• Realized niche = portion of fundamental niche
the species actually occupies
Chthamalus
Balanus
High tide
High tide
Chthamalus
realized niche
Chthamalus
fundamental niche
Balanus
realized niche
Ocean
Low tide
Ocean
Low tide
Predation (+/-)
Defensive adaptations include:
– Cryptic coloration – camouflaged by coloring
– Aposematic or warning coloration – bright color of
poisonous animals
– Batesian mimicry – harmless species mimic color
of harmful species
– Mullerian mimicry – 2 bad-tasting species
resemble each other; both to be avoided
– Herbivory – plants avoid this by chemical toxins,
spines, & thorns
Community Structure
Species diversity = species richness (the number
of different species they contain), and the
relative abundance of each species.
• Dominant species: has the highest biomass or
is the most abundant in the community
• Keystone species: exert control on community
structure by their important ecological niches
– Ex: loss of sea otter  increase sea urchins,
destruction of kelp forests
Disturbances influences species diversity and
composition
• A disturbance changes a community by
removing organisms or changing resource
availability (fire, drought, flood, storm, human
activity)
• Ecological succession: transitions in species
composition in a certain area over ecological
time
Primary Succession
• Plants & animals invade where soil
has not yet formed
– Ex. colonization of volcanic island or
glacier
Secondary Succession
• Occurs when existing community is cleared by
a disturbance that leaves soil intact
– Ex. abandoned farm, forest fire
Soon after fire. As this photo taken soon after the fire
shows, the burn left a patchy landscape. Note the
unburned trees in the distance.
One year after fire. This photo of the same general area
taken the following year indicates how rapidly the community began to recover. A variety of herbaceous plants,
different from those in the former forest, cover the ground.
Invasive Species
• Organisms that become established outside
native range
• Kudzu – vine plant from Japan, noxious weed that
kills trees & shrubs
Ecosystems
Ecosystem = sum of all the organisms living
within its boundaries (biotic community) +
abiotic factors with which they interact
Involves two unique processes:
1. Energy flow
2. Chemical cycling
Tertiary
consumers
Microorganisms
and other
detritivores
Detritus
Secondary
consumers
Primary consumers
Primary producers
Heat
Key
Chemical cycling
Energy flow
Sun
Trophic Structures
• The trophic structure of a community is
determined by the feeding relationships
between organisms.
• Trophic levels = links in the trophic structure
• The transfer of food energy from plants 
herbivores  carnivores  decomposers is
called the food chain.
• Two or more food chains
linked together are called
food webs.
• A given species may
weave into the web at
more than one trophic
level.
Primary Production
• Total primary production is known as gross
primary production (GPP).
– This is the amount of light energy that is
converted into chemical energy.
• The net primary production (NPP) is equal to
gross primary production minus the energy used
by the primary producers for respiration (R):
– NPP = GPP – R
• NPP = storage of chemical energy available to
consumers in an ecosystem
Net primary production of different ecosystems
Open ocean
Continental shelf
Estuary
Algal beds and reefs
Upwelling zones
Extreme desert, rock, sand, ice
Desert and semidesert scrub
Tropical rain forest
Savanna
Cultivated land
Boreal forest (taiga)
Temperate grassland
Woodland and shrubland
Tundra
Tropical seasonal forest
Temperate deciduous forest
Temperate evergreen forest
Swamp and marsh
Lake and stream
5.2
0.3
0.1
0.1
4.7
3.5
3.3
2.9
2.7
2.4
1.8
1.7
1.6
1.5
1.3
1.0
0.4
0.4
0
Key
Marine
Terrestrial
125
360
65.0
10 20 30 40 50 60
Percentage of Earth’s
surface area
Freshwater (on continents)
24.4
5.6
1,500
2,500
1.2
0.9
0.1
0.04
0.9
500
3.0
90
22
2,200
7.9
9.1
9.6
5.4
3.5
900
600
800
600
700
140
0.6
7.1
4.9
3.8
2.3
0.3
1,600
1,200
1,300
2,000
250
0
500 1,000 1,500 2,000 2,500
Average net primary
production (g/m2/yr)
0
10 15 20 25
5
Percentage of Earth’s net
primary production
• Primary production affected by:
– Light availability (↑ depth, ↓ photosynthesis)
– Nutrient availability (N, P in marine env.)
• Key factors controlling primary production:
– Temperature & moisture
• A nutrient-rich lake that supports algae growth
is eutrophic.
Energy transfer between trophic levels is typically
only 10% efficient
• Production efficiency:
only fraction of E stored
in food
• Energy used in
respiration is lost as heat
• Energy flows (not cycle!)
within ecosystems
Feces
Plant material
eaten by caterpillar
200 J
67 J
100 J
33 J
Growth (new biomass)
Cellular
respiration
Tertiary
consumers
Secondary
consumers
Primary
consumers
Primary
producers
10 J
10% transfer of
energy from one
level to next
100 J
1,000 J
10,000 J
1,000,000 J of sunlight
Pyramids of energy or biomass or numbers
gives insight to food chains
• Loss of energy
limits # of top-level
carnivores
Pyramid of Numbers
• Most food webs
only have 4 or 5
trophic levels
Pyramid of Biomass
Matter Cycles in Ecosystem
• Biogeochemical cycles: nutrient cycles that
contain both biotic and abiotic components
• organic  inorganic parts of an ecosystem
• Nutrient Cycles: water, carbon, nitrogen,
phosphprus
Carbon Cycle
CO2 in atmosphere
Photosynthesis
Cellular
respiration
Burning of
fossil fuels
and wood
Higher-level
Primary consumers
consumers
Carbon compounds
in water
Detritus
Decomposition
• CO2 removed by
photosynthesis,
added by burning
fossil fuels
Nitrogen Cycle
• Nitrogen fixation:
– N2  plants by bacteria
N2 in atmosphere
• Nitrification:
Assimilation
Denitrifying
– bacteria
NO3
Nitrogen-fixing
bacteria in root Decomposers
nodules of legumes
Nitrifying
Ammonification
bacteria
Nitrification
NH3
Nitrogen-fixing
soil bacteria
NO2–
NH4+
Nitrifying
bacteria
– ammonium  nitrite 
nitrate
– Absorbed by plants
• Denitrification:
– Release N to atmosphere
Acid Precipitation
• Acid precipitation: rain, snow, or fog with a pH less
than 5.6
• Caused by burning of wood & fossil fuels
– Sulfur oxides and nitrogen oxides released
– React with water in the atmosphere to produce
sulfuric and nitric acids
• These acids fall back to earth as acid
precipitation, and can damage ecosystems
greatly.
• The acids can kill plants, and can kill aquatic
organisms by changing the pH of the soil and
water.
Concentration of PCBs
Biological Magnification
Herring
gull eggs
124 ppm
Smelt
1.04 ppm
Zooplankton
0.123 ppm
• Toxins become more
concentrated in
successive trophic levels
of a food web
Lake trout
Toxins can’t be broken
4.83 ppm •
down & magnify in
concentration up the food
chain
• Problem: mercury in fish
Phytoplankton
0.025 ppm
Greenhouse Effect
– Greenhouse Effect: absorption of heat the Earth
experiences due to certain greenhouse gases
• CO2 and water vapor causes the Earth to retain
some of the infrared radiation from the sun that
would ordinarily escape the atmosphere
– The Earth needs this heat, but too much could be
disastrous.
Rising atmospheric CO2
– Since the Industrial Revolution, the concentration
of CO2 in the atmosphere has increased greatly
as a result of burning fossil fuels.
Global Warming
• Scientists continue to construct models to predict
how increasing levels of CO2 in the atmosphere
will affect Earth.
• Several studies predict a doubling of CO2 in the
atmosphere will cause a 2º C increase in the
average temperature of Earth.
• Rising temperatures could cause polar ice cap
melting, which could flood coastal areas.
– It is important that humans attempt to stabilize
their use of fossil fuels.
Human activities are depleting the
atmospheric ozone
• Life on earth is protected from the damaging affects of
ultraviolet radiation (UV) by a layer of O3,
or ozone.
• Chlorine-containing compounds erode the ozone layer
The four major threats to biodiversity:
1. Habitat destruction
– Human alteration of habitat is the single
greatest cause of habitat destruction.
2. Introduced species: invasive/nonnative/exotic
species
3. Overexploitation: harvest wild plants/animals
4. Food chain disruption: extinction of keystone
species
Elements of Life
• 25 elements
• 96% : C, O, H, N
• ~ 4% : P, S, Ca, K & trace
elements (ex: Fe, I)
Hint: Remember CHNOPS
II. Atomic Structure
• Atom = smallest unit of matter that
retains properties of an element
• Subatomic particles:
Mass
Location
Charge
(dalton or AMU)
neutron
1
nucleus
0
proton
1
nucleus
+1
electron
negligible
shell
-1
Bonds
Covalent
Ionic
Hydrogen
All important to life
Form cell’s
molecules
Quick reactions/
responses
H bonds to other
electronegative
atoms
Strong bond
Weaker bond
(esp. in H2O)
Even weaker
Made and broken by chemical reactions
Weaker Bonds:
Van der Waals Interactions: slight, fleeting
attractions between atoms and molecules
close together
– Weakest bond
– Eg. gecko toe hairs + wall surface
1. Polarity of H2O
• O- will bond with H+ on a different molecule of
H2O = hydrogen bond
• H2O can form up to 4 bonds
H2O Property
Chemical
Explanation
Examples of
Benefits to Life
Cohesion
•polar
•H-bond
•like-like
↑gravity plants, trees
transpiration
Adhesion
•H-bond
•unlike-unlike
plants xylem
bloodveins
Surface Tension
•diff. in stretch
•break surface
•H-bond
bugswater
Specific Heat
•Absorbs & retains E
•H-bond
oceanmoderates
temps protect
marine life (under ice)
Evaporation
•liquidgas
•KE
Cooling
Homeostasis
•Polarityionic
Good dissolver
Universal Substance
4. Solvent of life
• “like dissolves like”
Hydrophilic
Hydrophobic
Affinity for H2O
Appears to repel
Polar, ions
Nonpolar
Cellulose, sugar, salt
Oils, lipids
Blood
Cell membrane
Acids and Bases
Acid: adds H+ (protons); pH<7
Bases: removes protons, adds OH-; pH>7
Buffers = substances which minimize changes
in concentration of H+ and OH- in a solution
(weak acids and bases)
• Buffers keep blood at pH ~7.4
• Good buffer = bicarbonate
Figure 3.9 The pH of some aqueous solutions
Functional Groups
Functional Group
Molecular Formula
Names & Characteristics
Draw an Example
Hydroxyl
-OH
Alcohols
Ethanol
Carbonyl
>CO
Ketones (inside skeleton)
Aldehydes (at end)
Acetone
Propanol
Carboxyl
-COOH
Carboxylic acids (organic
acids)
Acetic acid
Amino
-NH2
Amines
Glycine
Sulfhydryl
-SH
Thiols
Ethanethiol
Phosphate
-OPO32- / -OPO3H2
Organic phosphates
Glycerol phosphate
Monomers
•Small organic
•Used for building
blocks of polymers
•Connects with
condensation reaction
(dehydration
synthesis)
Polymers
Macromolecules
•Long molecules of
•Giant molecules
monomers
•2 or more polymers
•With many identical
bonded together
or similar blocks linked
by covalent bonds
ie. amino acid  peptide  polypeptide 
protein
smaller
larger
Dehydration Synthesis
(Condensation Reaction)
Hydrolysis
Make polymers
Breakdown polymers
Monomers  Polymers
Polymers  Monomers
A + B  AB
AB  A + B
+
+ H2O
+ H2O
+
I. Carbohydrates
• Fuel and building
• Sugars are the smallest carbs
 Provide fuel and carbon
• monosaccharide  disaccharide 
polysaccharide
• Monosaccharides: simple sugars (ie. glucose)
• Polysaccharides:
Differ in
 Storage (plants-starch, animals-glycogen)
 Structure (plant-cellulose, arthropod-chitin)
position &
orientation of
glycosidic
linkage
II. Lipids
A.Fats: store large amounts of energy
– saturated, unsaturated, polyunsaturated
B.Steroids: cholesterol and hormones
C.Phospholipids: cell membrane
– hydrophilic head, hydrophobic tail
– creates bilayer between cell and external
environment
Hydrophilic head
Hydrophobic tail
Four Levels of Protein Structure:
1. Primary
– Amino acid sequence
– 20 different amino acids
– peptide bonds
2. Secondary
– Gains 3-D shape (folds, coils) by H-bonding
– α helix, β pleated sheet
3. Tertiary
– Bonding between side chains (R groups) of amino acids
– H & ionic bonds, disulfide bridges
4. Quaternary
– 2+ polypeptides bond together
amino acids  polypeptides  protein
• Protein structure and function are sensitive to
chemical and physical conditions
• Unfolds or denatures if pH and temperature
are not optimal
IV. Nucleic Acids
Nucleic Acids = Information
Monomer: nucleotide
DNA
•Double helix
•Thymine
•Carries genetic code
•Longer/larger
•Sugar = deoxyribose
RNA
•Single strand
•Uracil
•Messenger (copies),
translator
•tRNA, rRNA, mRNA, RNAi
•Work to make protein
•Sugar = ribose
Comparisons of Scopes
Light
Electron
• Visible light passes through
specimen
• Light refracts light so
specimen is magnified
• Magnify up to 1000X
• Specimen can be
alive/moving
• color
• Focuses a beam of electrons
through specimen
• Magnify up to 1,000,000
times
• Specimen non-living and in
vacuum
• Black and white
Prokaryote Vs. Eukaryote
•
•
•
•
•
“before” “kernel”
No nucleus
DNA in a nucleoid
Cytosol
No organelles other
than ribosomes
• Small size
• Primitive
• i.e. bacteria
• “true” “kernel”
• Has nucleus and nuclear
membrane
• Cytosol
• Has organelles with
specialized structure
and function
• Much larger in size
• More complex
• i.e. plant/animal cell
Parts of plant & animal cell p 108-109
• Cells must remain small to maintain a large
surface area to volume ratio
• Large S.A. allows increased rates of chemical
exchange between cell and environment
Animal cells have intercellular junctions:
• Tight junction = prevent leakage
• Desomosome = anchor cells together
• Gap junction = allow passage of material
Cell Membrane
6 types of membrane proteins
Passive vs. Active Transport
• Little or no Energy
• Moves from high to low
concentrations
• Moves down the
concentration gradient
• i.e. diffusion, osmosis,
facilitated diffusion
(with a transport
protein)
• Requires Energy (ATP)
• Moves from a low
concentration to high
• Moves against the
concentration gradient
• i.e. pumps,
exo/endocytosis
hypotonic / isotonic / hypertonic
Exocytosis and Endocytosis transport large
molecules
3 Types of Endocytosis:
• Phagocytosis (“cell eating” solids)
• Pinocytosis (“cell drinking” fluids)
• Receptor-mediated
endocytosis
• Very specific
• Substances bind to
receptors on cell surface
• Catabolic pathways release energy by breaking
down complex molecules into simpler
compounds
• C6H12O6 +6O2
6H2O + 6CO2 +E
• Anabolic pathways consume energy to build
complex molecules from simpler ones
• 6H20+6CO2 + E
C6H12O6 +6O2
Concept 8.3 ATP powers cellular work by coupling exergonic
reactions to endergonic reactions
• A cell does three main kinds of work:
– Mechanical
– Transport
– Chemical
• To do work, cells manage energy resources by energy
coupling, the use of an
exergonic (energy releasing) process to drive an
endergonic (energy absorbing) one
Concept 8.4: Enzymes speed up metabolic
reactions by lowering energy barriers
A catalyst is a chemical agent that speeds up a reaction
without being consumed by the reaction
An enzyme is a catalytic protein
Hydrolysis of sucrose by the enzyme sucrase is an example
of an enzyme-catalyzed reaction
Substrate Specificity of Enzymes
• The reactant that an enzyme acts on is called the
enzyme’s substrate
• The enzyme binds to its substrate, forming an enzymesubstrate complex
• The active site is the region on the enzyme where the
substrate binds
Cofactors
Cofactors are nonprotein enzyme helpers such as
minerals
Coenzymes are organic cofactors such as vitamins
Enzyme Inhibitors
Allosteric Regulation
• a protein’s function at
one site is affected by
binding of a
regulatory molecule
at another site
• Allosteric regulation
may either inhibit or
stimulate an enzyme’s
activity
Feedback
Inhibition
• In feedback inhibition,
the end product of a
metabolic pathway
shuts down the
pathway
Energy Harvest
• Energy is released as electrons “fall” from
organic molecules to O2
• Broken down into steps:
Food  NADH  ETC  O2
– Coenzyme NAD+ = electron acceptor
– NAD+ picks up 2e- and 2H+  NADH (stores E)
– NADH carries electrons to the electron transport
chain (ETC)
– ETC: transfers e- to O2 to make H2O ; releases
energy
Cellular Respiration
Mitochondrion Structure
Citric Acid
Cycle
(matrix)
ETC
(inner membrane)
Glycolysis
Without O2
Fermentation
• Occurs in plants and
animals
• Occurs in cytosol
• Keep glycolysis going
• No oxygen needed
• Creates alcohol [+ CO2] or
lactic acid
O2 present
Respiration
• Release E from breakdown
of food with O2
• Occurs in mitochondria
• O2 required (final electron
acceptor)
• Produces CO2, H2O and up
to 38 ATP (NADH, FADH2)
Types of Fermentation
Alcohol fermentation
Lactic acid fermentation
• Pyruvate  Ethanol + CO2
• Ex. bacteria, yeast
• Used in brewing,
winemaking, baking
• Pyruvate  Lactate
• Ex. fungi, bacteria, human
muscle cells
• Used to make cheese,
yogurt, acetone, methanol
• Note: Lactate build-up does
NOT causes muscle fatigue
and pain (old idea)
PURPOSE = NAD+ recycled for glycolysis
Various sources of fuel
• Carbohydrates, fats and
proteins can ALL be
used as fuel for cellular
respiration
• Monomers enter
glycolysis or citric acid
cycle at different points
ENERGY
aerobic
(with O2)
glycolysis
anaerobic
(without O2)
(cytosol)
Respiration
(mitochondria)
Krebs cycle
(citric acid cycle)
electron
transport
chain
chemiosmosis
fermentation
Oxidative
Phosphorylation
ethanol + CO2
(yeast, some bacteria)
lactic acid
(animals)
Leaf cross section
Sites of Photosynthesis
Vein
Mesophyll
• mesophyll: chloroplasts
mainly found in these cells of
leaf
• stomata: pores in leaf (CO2
enter/O2 exits)
• chlorophyll: green pigment in
thylakoid membranes of
chloroplasts
Stomata
CO2 O2
Mesophyll cell
Chloroplast
5 µm
Outer
membrane
Thylakoid
Thylakoid
Stroma Granum
space
Intermembrane
space
Inner
membrane
1 µm
Photosynthesis = Light Reactions + Calvin Cycle
“photo”
“synthesis”
Light Reactions
Both respiration and photosynthesis use
chemiosmosis to generate ATP
Calvin Cycle = produce 3C sugar (G3P)
Photorespiration: low carbon-fixation when
stomata closed in hot, dry climate
C3
C4
CAM
C fixation & Calvin C fixation & Calvin in C fixation & Calvin at
together
different cells
different TIMES
Rubisco
PEP carboxylase
Organic acid
(normally fixes CO2)
fixes CO2
Mesophyll: fix CO2 Night: fix CO2 in 4C
Mesophyll cells
Bundle Sheath:
acids
Calvin Cycle
Day: Calvin Cycle
Ex. rice, wheat,
soybeans
Ex. sugarcane, grass
Ex. cacti, pineapple,
succulent
Comparison
RESPIRATION
PHOTOSYNTHESIS
• Plants + Animals
• Needs O2 and food
• Produces CO2, H2O and ATP,
NADH
• Occurs in mitochondria
membrane & matrix
• Oxidative phosphorylation
• Proton gradient across
membrane
• Plants
• Needs CO2, H2O, sunlight
• Produces glucose, O2 and ATP,
NADPH
• Occurs in chloroplast
thylakoid membrane &
stroma
• Photorespiration
• Proton gradient across
membrane