Midterm Final Review

1
Midterm Final Review

• Part I

2
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)

3
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

4
(No Transcript)
5
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
6
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

7
Directed Movements

• Kinesis simple change in activity or turning
  rate in response to a stimulus
• Taxis automatic movement, oriented movement /-
  from stimulus i.e. Phototaxis, chemotaxis, and
  geotaxis.

Kinesis increases the chance that a sow bug will
encounter and stay in a moist environment.
Positive rheotaxis keeps trout facing into the
current, the direction from which most food comes.
8
Types of Learning

• Habituation loss of responsiveness to stimuli
  that convey little or no information
• Simple form of learning
• Imprinting learning innate components
• Limited to sensitive period in life, generally
  irreversible
• ie. Lorenz imprinting in greylag geese

9
Types of Learning

• Associative learning ability to associate one
  stimulus with another
• Also called classical conditioning
• Fruit fly (drosophila) trained to respond to
  odor shock

10
Types of Learning

• Operant conditioning another type of associative
  learning
• Trial-and-error learning
• Associate its own behavior with reward or
  punishment

11
Types of Learning

• Cognition the ability of an animals nervous
  system to
• Perceive, store, process, and use information
  gathered by sensory receptors
• Problem-solving behavior relies on cognition

12
Territorial Behavior

• Territorial behavior parcels space and resources
• Animals exhibiting this behavior mark and defend
  their territories

13
Patterns of Dispersal

1. Clumped most common near required resource
2. Uniform usually antagonistic interactions
3. Random not common in nature

14
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.

15

• 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)

16

• Zero population growth B D
• Exponential population growth ideal conditions,
  population grows rapidly

17

• 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

18

• 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
19
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

20
Age-Structure Diagrams
21
Interspecific interactions

• Can be positive (), negative (-) or neutral (0)
• Includes competition, predation, and symbiosis

22

• 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

23
Ecological niche the sum total of an organisms
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

24
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

25
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

26
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

27
Primary Succession

• Plants animals invade where soil has not yet
  formed
• Ex. colonization of volcanic island or glacier

28
Secondary Succession

• Occurs when existing community is cleared by a
  disturbance that leaves soil intact
• Ex. abandoned farm, forest fire

29
Invasive Species

• Organisms that become established outside native
  range
• Kudzu vine plant from Japan, noxious weed that
  kills trees shrubs

30
Ecosystems

• Ecosystem sum of all the organisms living
  within its boundaries (biotic community)
  abiotic factors with which they interact
• Involves two unique processes
• Energy flow
• Chemical cycling

31
Tertiary consumers
Microorganisms and other detritivores
Secondary consumers
Primary consumers
Detritus
Primary producers
Heat
Key
Chemical cycling
Sun
Energy flow
32
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.

33

• 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.

34
(No Transcript)
35
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

36
Net primary production of different ecosystems
Open ocean Continental shelf
125
65.0
24.4
360
5.2
5.6
Estuary Algal beds and reefs
1,500
0.3 0.1 0.1
1.2
2,500
0.9
Upwelling zones Extreme desert, rock, sand, ice
0.1
500
4.7
3.0
0.04
Desert and semidesert scrub Tropical rain forest
3.5
90
0.9
22
3.3
2,200
Savanna Cultivated land
2.9
7.9
900
2.7
600
9.1
Boreal forest (taiga) Temperate grassland
2.4
800
9.6
1.8
600
5.4
Woodland and shrubland Tundra
1.7
700
3.5
1.6
140
0.6
Tropical seasonal forest
1.5
1,600
7.1
Temperate deciduous forest Temperate evergreen
forest
1.3
1,200
4.9
1.0
1,300
3.8
Swamp and marsh Lake and stream
0.4 0.4
2,000
2.3
250
0.3
60
50
40
20
0
20
15
0
30
10
2,500
2,000
1,500
1,000
500
0
25
10
5
Key
Percentage of Earths surface area
Average net primary production (g/m2/yr)
Percentage of Earths net primary production
Marine
Terrestrial
Freshwater (on continents)
37

• 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.

38
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

39
10 transfer of energy from one level to next
Tertiary consumers
10 J
Secondary consumers
100 J
Primary consumers
1,000 J
Primary producers
10,000 J
1,000,000 J of sunlight
40
Pyramids of energy or biomass or numbers gives
insight to food chains

• Loss of energy limits of top-level carnivores
• Most food webs only have 4 or 5 trophic levels

Pyramid of Numbers
Pyramid of Biomass
41
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

42
Carbon Cycle

• CO2 removed by photosynthesis, added by burning
  fossil fuels

43
Nitrogen Cycle

• Nitrogen fixation
• N2 ? plants by bacteria
• Nitrification
• ammonium ? nitrite ? nitrate
• Absorbed by plants
• Denitrification
• Release N to atmosphere

44
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.

45
Biological Magnification

• Toxins become more concentrated in successive
  trophic levels of a food web
• Toxins cant be broken down magnify in
  concentration up the food chain
• Problem mercury in fish

46
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.

47
Rising atmospheric CO2

• Since the Industrial Revolution, the
  concentration of CO2 in the atmosphere has
  increased greatly as a result of burning fossil
  fuels.

48
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.

49
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

50
The four major threats to biodiversity

• Habitat destruction
• Human alteration of habitat is the single
  greatest cause of habitat destruction.
• Introduced species invasive/nonnative/exotic
  species
• Overexploitation harvest wild plants/animals
• Food chain disruption extinction of keystone
  species

51
Elements of Life

• 25 elements
• 96 C, O, H, N
• 4 P, S, Ca, K trace elements (ex Fe, I)
• Hint Remember CHNOPS

52
II. Atomic Structure

• Atom smallest unit of matter that retains
  properties of an element
• Subatomic particles

Mass (dalton or AMU) Location Charge
neutron 1 nucleus 0
proton 1 nucleus 1
electron negligible shell -1
53
Bonds
Covalent Ionic Hydrogen
All important to life All important to life All important to life
Form cells 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 Made and broken by chemical reactions Made and broken by chemical reactions
54

• Weaker Bonds
• Van der Waals Interactions slight, fleeting
  attractions between atoms and molecules close
  together
• Weakest bond
• Eg. gecko toe hairs wall surface

55
1. Polarity of H2O

• O- will bond with H on a different molecule of
  H2O hydrogen bond
• H2O can form up to 4 bonds

56
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
Universal Substance Polarity?ionic H-bond Good dissolver solvent
57
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
58
Acids and Bases

• Acid adds H (protons) pHlt7
• Bases removes protons, adds OH- pHgt7
• 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

59
Figure 3.9 The pH of some aqueous solutions
60
(No Transcript)
61
Functional Groups
Functional Group Molecular Formula Names Characteristics Draw an Example
Hydroxyl -OH Alcohols Ethanol
Carbonyl gtCO 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
62
Monomers Polymers Macromolecules
Small organic Used for building blocks of polymers Connects with condensation reaction (dehydration synthesis) Long molecules of monomers With many identical or similar blocks linked by covalent bonds Giant molecules 2 or more polymers bonded together
ie. amino acid ? peptide ? polypeptide ? protein
larger
smaller
63
Dehydration Synthesis (Condensation Reaction) Hydrolysis
Make polymers Breakdown polymers
Monomers ? Polymers Polymers ? Monomers
A B ? AB AB ? A B

64
I. Carbohydrates

• Fuel and building
• Sugars are the smallest carbs
• Provide fuel and carbon
• monosaccharide ? disaccharide ? polysaccharide
• Monosaccharides simple sugars (ie. glucose)
• Polysaccharides
• Storage (plants-starch, animals-glycogen)
• Structure (plant-cellulose, arthropod-chitin)

Differ in position orientation of glycosidic
linkage
65
II. Lipids

• Fats store large amounts of energy
• saturated, unsaturated, polyunsaturated
• Steroids cholesterol and hormones
• Phospholipids cell membrane
• hydrophilic head, hydrophobic tail
• creates bilayer between cell and external
  environment

66

• Four Levels of Protein Structure
• Primary
• Amino acid sequence
• 20 different amino acids
• peptide bonds
• Secondary
• Gains 3-D shape (folds, coils) by H-bonding
• a helix, ß pleated sheet
• Tertiary
• Bonding between side chains (R groups) of amino
  acids
• H ionic bonds, disulfide bridges
• Quaternary
• 2 polypeptides bond together

67
amino acids ? polypeptides ? protein
68

• Protein structure and function are sensitive to
  chemical and physical conditions
• Unfolds or denatures if pH and temperature are
  not optimal

69
IV. Nucleic Acids

• Nucleic Acids Information
• Monomer nucleotide

DNA RNA
Double helix Thymine Carries genetic code Longer/larger Sugar deoxyribose Single strand Uracil Messenger (copies), translator tRNA, rRNA, mRNA, RNAi Work to make protein Sugar ribose
70
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

71
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

72
Parts of plant animal cell p 108-109
73
(No Transcript)
74

• 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

75
(No Transcript)
76
(No Transcript)
77
(No Transcript)
78

• Animal cells have intercellular junctions
• Tight junction prevent leakage
• Desomosome anchor cells together
• Gap junction allow passage of material

79
Cell Membrane
80
6 types of membrane proteins
81
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

82
hypotonic / isotonic / hypertonic
83
(No Transcript)
84
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

85

• 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
• 6H206CO2 E C6H12O6 6O2

86
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

87
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

88
Substrate Specificity of Enzymes

• The reactant that an enzyme acts on is called the
  enzymes substrate
• The enzyme binds to its substrate, forming an
  enzyme-substrate complex
• The active site is the region on the enzyme where
  the substrate binds

89
(No Transcript)
90
(No Transcript)
91
Cofactors

• Cofactors are nonprotein enzyme helpers such as
  minerals
• Coenzymes are organic cofactors such as vitamins
• Enzyme Inhibitors

92
Allosteric Regulation

• a proteins function at one site is affected by
  binding of a regulatory molecule at another site
• Allosteric regulation may either inhibit or
  stimulate an enzymes activity

93
Feedback Inhibition

• In feedback inhibition, the end product of a
  metabolic pathway shuts down the pathway

94
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

95
Cellular Respiration
96
Mitochondrion Structure
Citric Acid Cycle (matrix)
ETC (inner membrane)
97
Glycolysis
O2 present
Without O2

• Fermentation

• Respiration

• Occurs in plants and animals
• Occurs in cytosol
• Keep glycolysis going
• No oxygen needed
• Creates alcohol CO2 or lactic acid

• 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)

98
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
99
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

100
ENERGY
aerobic (with O2)
anaerobic (without O2)
glycolysis (cytosol)
Respiration (mitochondria)
substrate-level phosphorylation
Krebs cycle (citric acid cycle)
fermentation
electron transport chain
Oxidative Phosphorylation
ethanol CO2 (yeast, some bacteria)
lactic acid (animals)
chemiosmosis
101
Sites of Photosynthesis

• 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

102
Photosynthesis Light Reactions Calvin Cycle
photo
synthesis
103
Light Reactions
104
(No Transcript)
105
Both respiration and photosynthesis use
chemiosmosis to generate ATP
106
Calvin Cycle produce 3C sugar (G3P)
107
Photorespiration low carbon-fixation when
stomata closed in hot, dry climate
C3 C4 CAM
C fixation Calvin together C fixation Calvin in different cells C fixation Calvin at different TIMES
Rubisco (normally fixes CO2) PEP carboxylase fixes CO2 Organic acid
Mesophyll cells Mesophyll fix CO2 Bundle Sheath Calvin Cycle Night fix CO2 in 4C acids Day Calvin Cycle
Ex. rice, wheat, soybeans Ex. sugarcane, grass Ex. cacti, pineapple, succulent
108
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