Download Final Review Study Guide BIOCHEMISTRY Chapter 3 Water and the

Final Review Study Guide
BIOCHEMISTRY
Chapter 3 Water and the Fitness of the Environment
Vocabulary:
 Polar (molecule)
 Hydrogen bonding
 Electronegative
 cohesion
 adhesion
 surface tension
 kinetic energy
 heat
 temperature
 calorie (cal)
 joule (J)
 mole (mol)
 Molarity
 specific heat
 heat of vaporization
 evaporative cooling
 crystalline lattice
 solution
 solvent
 solute
 aqueous solution
 hydration shell
 hydrophilic
 hydrophobic
 hydrogen ion
 hydroxide ion
 acid
 base
 pH/pH scale
 buffer
I.
THE EFFECTS OF WATER’S POLARITY
a. Polarity of water results in hydrogen bonding
i. Water structure: 2 hydrogen, 1 hydrogen w/ single covalent bond
1. Oxygen is more electronegative than Hydrogen electrons spend
more time closer to the Oxygen resulting in the “bent” shape
2. POLAR MOLECULE  opposite ends of the molecule have opposite
charges
a. Due to electronegativity
b. more negative (-) towards oxygen and more positive (+)
towards hydrogen
c. “Like attracts like”  polar molecules are attracted to one
another due to the partial charges.
i. Hydrogen bond  holds two water molecules
together (one water molecule can form 4 hydrogen
bonds)
1. Hydrogen bonding causes the extraordinary
and unusual qualities of water
2. Hydrogen bonds are only 1/20th as strong as
a covalent bond
(NOTE! Polar WILL NOT be attracted to nonpolar)
b. Organisms depend on the cohesion of water molecules
i. COHESION  the attraction of one substance to the same substance
1. Contributes to the transport of water against gravity in plant veins
ii. ADHESION the clinging of one substance to another
iii. SURFACE TENSION  a measure of how difficult it is to stretch or break the
surface of a liquid
1. Due to cohesion
2. Water has a stronger surface tension than other liquids
3. Allows insects to “walk on water”
c. Water moderates temperatures on earth
i. KINETIC ENERGY  anything that moves has this energy of motion
ii. HEAT  the measure of the total quantity of kinetic energy of molecules
1. CALORIE (cal)  the amount of heat energy it takes to raise the
temperature of 1 gram of water by 1⁰C
2. JOULE (J)  one joule equals 0.239 cal
iii. TEMPERATURE  measures the intensity of heat due to the average kinetic
energy of the molecules
1. Difference between heat and temperature:
a. A swimmer crossing the ocean has a higher temperature
than the water, but the ocean contains far more heat
because of its greater volume
2. Whenever two objects of different temperature come together,
temperature goes from the warmer object to the cooler object
3. CELSIUS SCALE
iv. SPECIFIC HEAT  the amount of heat that must be absorbed or lost for 1
gram of that substance to change its temperature by 1⁰C
1. Specific heat can be thought of as the measure of how well a
substance resists changing its temperature when it absorbs or
releases heat
2. Specific heat of water: 1 cal/g/⁰C (unusually high)
v. HEAT OF VAPORIZATION the quantity of heat a liquid must absorb for 1
gram of it to be converted from a liquid to a gas
1. Water has a high heat of vaporization
vi. EVAPORATIVE COOLING  as a liquid evaporates, the surface of the liquid
that remains behind cools down because the ‘hottest’ molecules (with the
greatest kinetic energy)are leaving with the gas
d. Oceans and lakes don’t freeze solid because ice floats
i. Water is less dense as a solid than it is as a liquid. In other words, ice floats
1. At 4⁰C, the molecules aren’t moving as fast and the liquid begins to
freeze
2. At 0⁰C, the molecules AREN’T MOVING
a. They lock into a ‘crystalline lattice’ and since each molecule
is bent, they don’t fit together so the solid form is more
“spread out” or more dense
ii. The ability of water to float is important in the fitness of the environment. If
ice sank, during the winter, lakes, oceans, rivers (etc) would freeze solid
making it impossible to live.
1. When a deep body of water cools, the floating ice insulates the
liquid water below preventing it from freezing and allowing to
sustain life
e. Water is the solvent of life
i. SOLUTION  a liquid that is a completely homogeneous mixture of two OR
MORE substances
1. SOLVENT  the dissolving agent
2. SOLUTE  the substance that is dissolved
a. EX: sugar is mixed in water. Water is the solvent and sugar
is the solute. The entire mixture would be the solution
b. HYDROPHILIC any substance that has an affinity for water
c. HYDROPHOBICany substance that has a phobia or repels
water
3. AQUEOUS SOLUTION  a solution in which water is the SOLVENT
II.
4. HYDRATION SHELL when a substance dissolves or dissociates in
water, the sphere of water molecules that will surround each
dissolved ion
5. MOLE(mol)  equal to the molecular weight of a substance “but
upscaled from units of Daltons to units of grams”
a. MOLARITY  the number of moles of solute per liter of
solution (mol solute/L soln)
i. Used to measure the concentration of aqueous
solutions
6. MOLECULAR WEIGHT the sum of the weights of all the atoms in a
molecule
THE DISSOCIATION OF WATER MOLECULES
i. HYDROGEN ION  a single proton with a charge of +1 (H+)
ii. HYDROXIDE ION a water molecule that has lost a proton (OH-)
1. When water dissociates, it splits into hydrogen and hydroxide ions
b. Organisms are sensitive to changes in pH
i. ACID a substance that increases the hygrogen ion concentration of a
solution
1. Hydrogen donor
ii. BASE a substance that reduces the hydrogen ion concentration of a
solution
1. Hydrogen acceptor
iii. pH  the negative logarithm (base 10) of the hydrogen ion concentrations:
1. pH = -log (H+)
2. PH SCALE  ranges from 0 to 14; 0 is most acidic, 14 is most basic
and 7 is neutral
iv. BUFFERS  substances that minimize changes in the concentrations of H+
and OH- in a solution
1. Maintains neutrality
c. Acid precipitation threatens the fitness of the environment
i. ACID PRECIPITATION rain snow or fog that is more acidic that a pH of 5.6
1. Caused by the presence of sulfur oxides and nitrogen oxides in the
atmosphere. These react with the air to form strong acids which fall
to the earth in precipitation form
Chapter 5 The Structure and Function of Macromolecules



Macromolecules are large biological polymers, such as nucleic acids and proteins,
which are made up of small monomers linked together.
Polymer- a long molecule consisting of many similar or identical building blocks
linked by covalent bonds
The three polymers are carbohydrates, proteins, and nucleic acids.




Monomers: the small units that serve as the building blocks in polymers.
Condensation reaction- monomers connected by a reaction and two molecules are
bonded together through loss of water- thus called dehydration synthesis because
the molecule lost is water.
Hydrolysis- how polymers are disassembled to monomers; bonds between
monomers are broken by the addition of water molecules.
CARBOHYDRATES (sugars and their polymers)
Monosaccharaides- simplest carbohydrates: CH2O=general molecular formula;
Glucose is the most common monosaccharide
Structure- carbonyl group(C=O) and multiple hydroxyl groups (OH−).
-can have linear or ring structures, a ring is more favored.

Disaccharide- two monosaccharaides joined by glycosidic linkage, which is a
covalent bond formed between two monosaccharaides by a dehydration synthesis.

Polysaccharides- macromolecules, polymers with a few hundred or a few thousand
monosaccharaides joined by glycosidc linkage.
Functions
1. Polysaccharides serve as storage material (starch)- in plants- the sugar can later
be withdrawn from this carbohydrate by hydrolysis.
Glycogen- polysaccharide animals store, mainly in liver and muscle cells.
2. Structure. Cellulose- major component of tough cell walls of plants.
Chitin- used by arthropods(insects, spiders, crustaceans) to build their
exoskeletons. Also found in many fungi. Chitin has a nitrogen containing
appendage unlike cellulose. Also used for surgical use.





LIPIDS (diverse hydrophobic molecules)
DO NOT INCLUDE POLYMERS. They consist mostly of hydrocarbons.
Waxes, certain pigments, fats, phospholipids, steroids.
Fat is constructed from glycerol( an alcohol with three carbons) and fatty acids(
have long carbon skeleton)
In making a fat, three fatty acids each join to glycerol by an ester linkage(bond
between a hydroxyl group and a carboxyl group)
The resulting fat is called triacylglycerol, three fatty acids (tails) and one glycerol
molecule (head).
Saturated and unsaturated Fats
 Saturated fatty acids- no double bonds between carbon atoms (NO KINKS). As many
hydrogen atoms as possible are bonded to the carbon skeleton.
-most animal fats, stays solid at room temperature.
 Unsaturated- has one or more double bonds, formed by removal of hydrogen atom
from carbon skeleton, a kink forms where there is double bond between carbon
atoms.
Phospholipids
 Have only two fatty acid tails rather than three.
 Third hydroxyl group of glycerol attached to phosphate group, which is negative in
electrical charge.


Hydrocarbon tails are hydrophobic, phosphate group end of the molecule is
hydrophilic because of the oxygens with all of their pairs of unshared electrons, and
thus phospholipids are soluble in both water and oil.
Phospholipids form the cell membrane, which is composed of two layers, each
composed of trillions of Phospholipid molecules.
Steroids are lipids with four fused rings.
 Different steroids vary in functional groups attached to this ensemble of rings.
 Cholesterol (a steroid) common component of animal cell membranes, and is
the precursor from which all steroids are synthesized.
 Many hormones including vertebrate sex hormones are steroids produced from
cholesterol.



PROTEINS
POLYPEPTIDES- polymers of amino acids(building blocks of proteins.)
Protein- consists of one or more polypeptides folded or coiled into specific
conformations.
General formula of amino acids(amino group, side chin and carboxyl group)
Protein functions
 Antibodies - white blood cells.
 Contractile Proteins for movement. actin and myosin, involved in muscle
contraction and movement.
 Enzymes - facilitate biochemical reactions; catalysts. Ex. lactase and pepsin.
 Hormonal Proteins - are messenger proteins Ex. insulin, oxytocin, and



Structural Proteins - are fibrous and stringy and provide support Ex. keratin,
collagen, and elastin
Storage Proteins - store amino acids. Ex. ovalbumin
Transport Proteins - are carrier proteins which move molecules from one place to
another Ex. hemoglobin and cytochromes
Peptide bond-bond formed between the carboxyl groups and amino groups of neighboring
amino acids: through Dehydration synthesis
Fibrous proteins are elongated molecules in which the secondary structure (either a-helices
or b-pleated sheets) forms the dominant structure- Keratin, Fibroin, Collagen
Globular proteins are a highly diverse group of proteins that are soluble and form compact
spheroidal molecules in water. All have tertiary structure and some have quaternary
structure in addition to secondary structure; Enzymes, some hormones such as insulin,
antibodies and haemoglobin
Four levels of protein structure
1. Primary structure: linear arrangement of amino acids in a protein and the location
of covalent linkages.
-can become cross-linked, most commonly by disulfide bonds
2. Secondary structure:
 Coils and folds made by hydrogen bonds at regular intervals along the
polypeptide backbone. Only atoms of the backbone are involved, not the
amino acid chains.
 One type of secondary structure is α helix- coil held together by hydrogen
bonding every fourth amino acid.

Beta pleated sheet-individual protein chains are aligned side-by-side with
every other protein chain aligned in an opposite direction. The protein
chains are held together by intermolecular hydrogen bonding.
3. Tertiary structure Interactions between side chains(R groups) of the various amino acids.
 Hydrophobic interactions, disulfide bridges, van der Waals interactions,
hydrogen bonds, and ionic bonds contribute to tertiary interactions.
 Hydrogen bonds, ionic bonds, and van der Waals interactions are all weak
interactions between the side chains.
 Hydrophobic interactions- as a polypeptide folds into its functional
conformation, amino acids with hydrophobic (non- polar) side chains usually
end up in clusters at the core of the protein, out of contact with water.
 Disulfide bridge(strong covalent bonds)- form where two cysteine
monomers, amino acids with sulfhydryl groups( SH) on their side chains, are
brought together by the folding of the protein.
4. Quaternary structure- Aggregation of two or more polypeptide chains
 Ex. Collagen(fibrous), and Hemoglobin(globular)
Denaturation- is loss of native conformation due to change in pH, temperature, salinity, or
other environmental factors.
Chaparonins- are protein molecules that assist in the proper folding of other proteins.
NUCLEIC ACIDS- informational polymers
Gene- unit of inheritance consists of DNA, a polymer belonging to nucleic acids.
Two types of nucleic acids are DNA and RNA.
DNA provides directions for its own replication, and directs RNA synthesis, thus controls
protein synthesis.
Nucleotides- building blocks of nucleic acids.
A nucleotide consists of a nitrogenous base, a pentose(5 carbon sugar) and a phosphate
group.
Two families of nitrogenous bases – pyrimidines and purines.
Pyrimidine has six-membered ring of carbon and nitrogen atoms: consist of cytosine,
thymine and uracil (in RNA)
Purines(larger) have six membered ring fused to a five membered ring: consist of adenine
and Guanine.
Remember!! Pure Gold. Purines Ag
RNA molecules consist of a single polynucleotide, while DNA molecules have two
polynucleotides that spiral on an axis- double helix.
Chapter 6 Metabolism 
CELLS
Chapter 7 A Tour of the Cell
I.
II.
Microscopes
 Resolving power- image density

Minimum distance two points can be separated and distinguishable
 Light microscopes- visible light passes through specimen

Bad resolution.

Live cells.
 Electron microscope- beam of electrons through specimen

Better resolution.

Dead cells.
 Transmission electron microscope- electron beam through section of specimen

Uses electromagnets

Internal ultrastructure
 Scanning electron microscopes- electron beam scans surface

Surface usually covered in gold

See surface structures
Isolating organelles
 Cell fractionation- separate organelles to study individually
 Use ultracentrifuges (machines that spin particles)
III. Prokaryotes vs. Eukaryotes
 Cytosol- semi fluid substance in membrane
 Cytoplasm- region between nucleus and plasma membrane
Prokaryotes
Both
DNA in nucleoid
Have chromosomes
(genes)
No membrane bound
Have ribosomes
organelles
Single circular chromosome
Typically smaller in size
Eukaryotes
Chromosomes in nucleus with nuclear
envelope
Membrane bound organelles
Typically larger in size
 Volume increases faster than surface area  can’t have a very
large bacteria
 More surface area more exchange across membrane  more
efficient
 Internal membranes in eukaryotic cell separate different
processes  more efficient
IV. Nucleus
 Contains genetic library
 In eukaryotes
 Double membrane (both with lipid bilayer)
 Pores in nuclear envelope regulate what enters/exits nucleus
 Nuclear lamina- netlike array of protein filaments

Keeps shape of nucleus
 Nuclear matrix- framework of fibers in the nucleus
 Chromatin- fibrous material in nucleus made of DNA and proteins
 Before the cell divides, chromatin condenses form chromosomes
 Nucleolus- inside nucleus

Ribosomal RNA synthesized here
V. Ribosomes
 Ribosome- carry out protein synthesis
 Made of ribosomal RNA and protein
 Free ribosomes- in cytosol
 Bound ribosomes- attached to endoplasmic reticulum or nuclear envelope

Usually make proteins that are used for insertion into membranes, packaging within
organelles, or export from the cell
 Bound and free ribosomes have identical structures
VI. Endomembrane system
 Vesicles- sacs made of membrane
 Consist of nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, vacuoles,
plasma membrane
VII. Endoplasmic reticulum
and
 Manufactures
membranes+
performs other
biosynthetic
functions
 Network of
membranous tubules
cisternae (sacs)
 Cisternal spaceinternal
compartment of the
ER
 Smooth ER- cytoplasmic surface lacks ribosomes
 Rough ER- ribosomes on cytoplasmic surface
 Smooth ER-:

Synthesize lipids, metabolism of carbohydrates, detoxify drugs and poisons
 Rough ER:

Makes secretory proteins

Most secretory proteins= glycoproteins

Glycoproteins- proteins covalently bonded to carbohydrates

Transport vesicles- transport from one part of cell to another
VIII. Golgi apparatus
 Finish, sort, and ship cell products
 Products of the ER stored+ shipped here
 Contains cisternae- flattened membranous sacs
 Two poles of Golgi stack:

Cis face- near ER

Trans face- forms vesicles
IX. Lysosomes
 Think digestion
 Hydrolytic enzymes digest macromolecules
 Maintain low pH by pumping hydrogen ions from cytosol into lysosome
 Phagocytosis- engulf smaller particles
 Autophagy- use hydrolytic enzymes to recycle cell’s organic material
X. Vacuoles
 Cell maintenance
 Food vacuoles- phagocytosis
 Contractile vacuoles- pump excess water out of cell
 Central vacuole- plant cells

Enclosed by tonoplast

Holds organic compounds, disposal site, provide defense (poisonous to predators), growth
XI. Mitochondria and chloroplasts
 Mitochondria: cellular respiration site
 Chloroplasts: photosynthesis site
 Both not part of endomembrane system b/c their membrane proteins are made by ribosomes in
the cytosol and in the organelles themselves rather than the ER
 Both contain a small amount of DNA
 Semiautonomous organelles
 Each have double membrane
 Mitochondria:

Outer membrane: smooth

Inner membrane: cristae- infoldings

Intermembrane space

Mitochondrial matrix- enclosed by inner membrane
 Chloroplasts=plastid (type of plant organelle)
 Chloroplast:

Thylakoids- flattened sacs

Granum-stacks of thylakoids

Stroma- fluid outside thylakoids
XII. Peroxisome
 Metabolic compartment
 Single membrane
 Contain enzymes that transfer hydrogen from substrates to oxygen produce hydrogen
peroxide
 Some detoxify alcohol
XIII. Cytoskeleton
 Network of fibers through cytoplasm
 Provide structural support and cell motility
and regulation
 Can be dismantled and reassembled
 Manipulates plasma membrane to form food
vacuoles





Microtubules- thickest fiber in cytoskeleton
Microfilament- thinnest fiber
Intermediate filaments-middle
Centrosome- region near nucleus from which microtubules come out of
Centrioles- in the centrosome

Composed of nine sets of triplet microtubules in a ring
 Flagella+ cilia= locomotor appendages
 Flagella- undulating motion
 Cilia- alternating power. Like an oar
 Both have microtubule cores
 Basal body- anchors the flagella and cilia in a cell
 Dynein-large protein that makes up motor molecules

Responsible for bending movements of cilia and flagella
 Microfilaments, also called actin filaments

Built from actin- globular protein

Bears tension

Semi solid consistency

Microvilli- increase surface area

Actin+ myosin slide past one another, move muscles

Pseudopodia- cellular extension that extends and contracts

Cytoplasmic streaming- circular flow of cytoplasm in cells to distribute materials faster
 Intermediate filaments- keratin

Permanent, fixed position of organelles
XIV. Cell wall
 Protect, shape, prevent excess water intake
 Primary cell wall- thin and flexible
 Middle lamella- between primary walls of adjacent cells

Glues the cells together
 Secondary cell wall- between plasma membrane and primary wall

Cell protection and support
XV. Extracellular matrix
 Support, adhesion, movement, regulation
 Contains glycoproteins
 Animal cells- contain collagen (a glycoprotein)
 Collagen fibers embedded into network made of proteoglycans (another glycoprotein)
 Fibronectin- another glycoprotein

Binds to integrins (receptor protein)
 Changes in cytoskeleton trigger chemical signaling
XVI. Intercellular junctions
 Plasmodesmata- channels in plant cell walls

Cytosol passes through, unifies cells
 Tight junctions- membranes of neighboring cells are fused
 Desmosomes- fasten cells together into strong sheets
 Gap junctions- provide cytoplasmic channels between adjacent animal cells
Chapter 8 Membrane Structure and Function
MEMBRANE STRUCTURE
Phospholipid bilayer
Fluid-mosaic model
 Fluid structure
o Phospholipids and most proteins in membrane – amphipathic molecules (have both
hydrophobic and hydrophilic regions)
o Lateral movement of molecules
 Proteins
o Proteins embedded in or attached phospholipids
o Integral proteins (trans-membrane proteins)
 Completely span the membrane
o Peripheral proteins
 Loosely bound to membrane surface
 Often attached to exposed part of integral proteins
o Proteins responsibilities: transport, enzyme activity, signal transduction, intercellular
joining, cell-cell recognition, and attachment to cytoskeleton and extracellular matrix
 Carbohydrates
o On outside of membrane
o Oligosaccharides -- short polysaccharides (fewer than 15 sugar units)
o Glycolipids – some carbohydrates are covalently bonded to lipids
o Glycoproteins – most carbohydrates are covalently bonded to proteins
TRAFFIC ACROSS MEMBRANES
Selective permeability
 Hydrophobic molecules cross membrane easily (hydrocarbons, oxygen, carbon dioxide)
 Polar/hydrophilic molecules and large molecules don’t pass easily
 Transport proteins
o Help polar molecules (like water) and ions pass through membrane
o Some have a hydrophilic channel
o Others hold on to molecules and physically move them across
o Proteins are specific to molecules they translocate
Passive transport
 Molecules diffuse down their own concentration gradients (high to low concentration)
 Cell does not expend energy
 Concentration gradient creates potential energy
 Osmosis – passive transport of water
Osmosis
 Hypertonic – refers to solution with higher solute concentration
 Hypotonic – refers to solution with lower solute concentration
 Isotonic – equal solute concentrations
 Cells without walls (animal)
o In hypertonic environment  cell loses water, shrivels, dies
o In hypotonic environment  cell absorbs too much water, lyses (bursts)
o Osmoregulation – control of water balance
 Cells with walls (plant)
o In hypertonic environment  cell plasmolysizes (membrane pulls away from cell wall)
o In hypotonic environment  cell absorbs water, elastic cell wall expands until the cell
wall puts pressure back on the inside; cell becomes turgid (firm); healthy state
o In isotonic environment  water doesn’t enter, cell becomes flaccid (limp), plant wilts
Facilitated Diffusion
 Passive transport with help of transport proteins (still no energy expended)
 Molecules move through channel proteins
o Some form hydrophilic tunnels
 Aquaporin – water channel protein
o Some are gated channels
 Stimulus causes them to open and close
 Some transport proteins are not channel proteins (instead they alter their own shape to allow
passage)
Active Transport
 Cell expends energy to move molecules against concentration gradient
 Energy from ATP
o One way ATP powers transport is by transferring phosphate group to transport protein
and causing change in protein conformation
Ion Pumps
 Membrane potential – voltage (electrical potential energy) across membrane
 Electrochemical gradient – diffusion of ions driven by both chemical and electric forces
 Electrogenic pump – transport protein that generates voltage across membrane
o
Eg. proton pump
Cotransport
 As molecule diffuses (passive) across membrane, it helps transport other molecules
Exocytosis
 Cell secretes macromolecules by fusing vesicle with plasma membrane
Endocytosis
 Cell takes in macromolecules by forming new vesicles from the plasma membrane
o Phagocytosis (“cellular eating”) – cell engulfs particle in large vesicle
o Pinocytosis (“cellular drinking”) – cell takes in extracellular fluids in tiny vesicles
o Receptor-mediated endocytosis –extracellular substances called “ligands” bind to
external receptor site (specific to molecule) and trigger formation of vesicle
CELLULAR RESPIRATION AND PHOTOSYNTHESIS
Chapter 9 Cellular Respiration
Cellular respiration (aerobic respiration) is a means to extract energy from food and transfer the energy
to ATP. This reaction is aerobic and exergonic. It is composed of 3 processes: glycolysis, Krebs Cycle,
electron transport chain.
-C6H12O6 + 6O2 ---> 6CO2 + 6H2O + energy (ATP + heat)
In the mitochondria, the Krebs Cycle and oxidation of pyruvate occur in the matrix while the electron
transport chain takes place in the folded inner cristae
membrane.
ATP--Adenosine Triphosphate (ribose sugar+adenine+3 phosphates)
As one phosphate group is removed from ATP by hydrolysis, ADP results and releases energy
Anaerobic Respiration (Fermentation)- Three types of fermentation: alcohol fermentation, lactic acid
fermentation, and acetic acid fermentation.
With each fermentation process, glycolysis occurs, breaking down glucose into 2 pyruvate releasing 2
NADH and 2 ATP
Alcohol Fermentation (yeast and bacteria)
2 pyruvate + 2 NADH -----> 2 ethyl alcohol + 2 CO2 + 2 NAD+
Lactic Acid Fermentation (fungi, human muscle cells, bacteria)
2 pyruvate + 2 NADH -----> 2 lactic acid + 2 NAD+
Acetic Acid Fermentation (bacteria)
2 pyruvate + NADH ----->2 acetic acid + 2 CO2 + 2 NAD +
1. Glycolysis is anaerobic (does NOT require oxygen in order to occur), occurs in the cytoplasm. During
this process, the cell regulates ATP production through allosteric inhibition of phosphofructokinase
-glucose + 2 ATP -----> 4 ATP + 2 pyruvate (3C) + 2 NADH (2 net ATP)
NAD+(nicotinamide adenine dinucleotide) and FAD+ (flavin adenine
dinucleotide) are coenzymes that carry protons, electrons, and hydrogens from glycolysis and Krebs to
electron transport chain.
oxidized form: NAD+ reduced form: NADH 1 proton and 2 eoxidized form: FAD
reduced form: FADH2
2. In aerobic respiration, the Krebs Cycle begins when pyruvate enters the matrix of the mitochondria.
Before the Krebs Cycle is the oxidation of pyruvate (which occurs twice for 1 molecule of glucose):
- pyruvate acid + coenzyme A (vitamin)------> acetyl CoA + 1 NADH + CO2 (waste)
In Krebs Cycle, acetyl CoA combines with oxaloacetatic acid to produce citric acid. The Krebs Cycle
produces, 3 NADH, 1 ATP, 1 FADH, and 2 CO2 before becoming oxaloacetatic acid, ready to accept
another acetyl CoA.
1 glucose produces 2 turns of Krebs cycle
3. Electron Transport Chain (ETC) occurs in cristae membrane of mitochondrion. ETC has a proton
pump, using energy from exergonic flow of electrons (as electrons go from a high energy state to a low
energy state), to pump protons from matrix to outer compartment, creating a proton gradient.
ETC carries electrons from glycolysis and Krebs to oxygen, the final electron acceptor (with 1/2 oxygen
with 2 electrons and 2 protons, forming water). Redox reactions occur in ETC as proteins (also known
as cytochromes) in ETC gain electrons through reduction and lose electrons through oxidation
(OIL/RIG). The electronegative oxygen pulls electrons down ETC. With NADH and FADH2 each NADH
produces 3 ATPs; each FAD H2 produces 2 ATPs.
ATP is not produced in the ETC but through oxidative phosphorylation and chemiosmosis. Oxidative
phosphorylation occurs through phosphorylation of ADP into ATP by oxidation of coenzyme hydrogen
carrier molecules NADH and FADH2. ETC couples the exergonic flow of electrons with endergonic
pumping of protons across the cristae membrane. Thus, there results in the pH of outer compartment
more acidic than in matrix.
Chemiosmosis occurs as the protons flow down the concentration gradient through ATP synthase
channels (energy generated phosphorylates ADP---->ATP)
Summary of ATP Production
In substrate phosphorylation kinase transfers a phosphate from substrate directly to ADP, producing
a small amount ATP in glycolysis and Krebs Cycle.
With oxidative phosphorylation, chemiosmosis occurs. 90 % of all ATP produced in through this
process with ETC. NAD and FAD lose protons, electrons, and hydrogens, oxidized by ETC, which pumps
protons to outer compartment, creating proton gradient, which powers phosphorylation of ATP.
- Glucose---> NAD + FAD----->ETC------> chemiosmosis---->ATP
1 NADH produces 3 ATP
1 FADH produces 2 ATP
ATP produced from 1 glucose:
i. Glycolysis (substrate phosphorylation)
-----> 2 ATP \
8 Glycolysis
ii. Glycolysis (oxidative phosphorylation)
2 NADH------> 6 ATP /
iii. pyruvate oxidation
2 NADH------->6 ATP
iv. Krebs (oxidative phosph.)
2 FADH2------>4 ATP
\ 24 Krebs
v. Krebs (oxidative phosph.)
6 NADH------->18 ATP /
vi. Krebs (substrate phosphorylation)
------->2 ATP /
Total 38 ATP
Diagram of Cellular Respiration
Chapter 10 Photosynthesis
I. Photosynthesis in Nature
 Autotrophs: Producers; sustains themselves without eating other organisms
1. Photoautotrophs: use light energy to help synthesis organic molecules
2. Chemoautotrophs: oxidize organic compounds like sulfur and ammonia
 Chloroplasts: Found in cells of mesophyll tissue (spongy); green from chlorophyll
Structure: Double membrane; stacks (grana) of thylakoids inside each chloroplast;
Stroma: dense fluid surrounding the grana.
II. The Pathways of Photosynthesis
 General equation for photosynthesis:
6CO2 + 12 H2O + Light energy  C6H12O6 + 6O2 + 6H2O
The oxygen molecule comes from the splitting of water (photolysis). 6H2O can be subtracted
from both sides to form a net equation.
 Sunlight and pigments:
Electromagnetic spectrum: entire range of radiation including visible light (380 [violet]-750 [red]
nm).
Wavelength: distance between crests of electromagnetic waves. Longer the wavelength = lower
energy
Photons: discrete particles with fixed amount of energy; the amount of energy is inversely
related to the wavelength.
Spectrophotometer: directs beams of light of certain wavelength through pigment solution and
measures the fraction of light transmitted
Absorption spectrum: fraction of light absorbed/not transmitted/not reflected
Action spectrum: Effectiveness of different wavelengths of light in driving photosynthesis
Pigments
Chlorophyll a
Color
Blue green
Chlorophyll b
Yellow green
Carotenoids
Xanthophyll
Anthocyanin
Yellow and orange
Yellow
Red, purple, blue
Description
Best with blue and red light, works directly in light
reactions, has CH3 in the molecule
Transfers energy to chlorophyll a, has CHO in the
molecule
Transfers energy to chlorophyll a
Transfers energy to chlorophyll a
Transfers energy to chlorophyll a



Chlorophyll: porphyrin ring (light absorbing head, hydrophilic, contains Mg in the middle)
Hydrocarbon tail (hydrophobic)
Factors that affect the rate of photosynthesis:
1. Light intensity: more light = higher rate; too much light = lower rate
2. Light wavelength: best = red and blue; least effective = green
3. Temperature of environment: warmer temperature = higher rate; too high = denatured
enzymes, shriveled
4. Level of CO2: more CO2 = higher rate
5. Level of H2O: too much = mesophyll tissue does not have enough room for oxygen
A. Light Reactions
Photosystems: collection of chlorophyll, proteins and other smaller organic molecules on
thylakoid membrane
Antenna complex: clusters of chlorophyll a, chlorophyll b, and carotenoids that gather light and
transmitted to a chlorophyll a molecule in the reaction center
Reaction center: special chlorophyll a loses one election (excited) to the primary electron
acceptor
Noncyclic electron flow: produces ATP and NADPH in equal amounts, noncyclic
photophosphorylation
Photosystem I: discovered first, takes wavelength of 700nm
Photosystem II: discovered second, takes wavelength of 680nm
The two photosystems occur at the same time.
1. Photolysis: water is split to give off 2 electrons and an oxygen atom which forms O2 with
another oxygen atom.
2. Electrons are excited and kept in the excited state by the primary acceptor.
3. Electron is passed down the electron transport chain (Pq  Cytochrome complex  Pc).
Chemiosmosis: the energy from the electrons powers the proton pumps to create a H+ gradient
(higher in thylakoid space, lower in stroma). When proton is diffused through ATP synthase, ATP
is created.
4. The electron transport chain from Photosystem I produces NADPH.

Cyclic electron flow: produces no NADPH and does not release oxygen, cyclic
photophosphorylation
Goal: increases ATP level because Calvin cycle uses more ATP than NADPH
Some Similarities and Differences between Mitochondrion and Chloroplast
Similarities
Mitochondrion
Chloroplast
Double membrane bound
Cellular respiration
Photosynthesis
Use chemiosmosis to generate ATP; creates
high H+ concentration in the “smaller” space
(intermembrane space and thylakoid space)
Oxidative and
substrate
phosphorylation
Cyclic and noncyclic
phosphorylation
Contains own DNA; can replicate by itself
(could be prokaryotes)
Uses NADH and FADH2
Uses NADPH
B. Calvin Cycle: “dark reactions”: light independent; 1 glucose molecule = 6 CO2 + 2 Calvin
cycles
 Location: Stroma
 Phase 1: Carbon fixation
3 CO2 molecules joins 5-carbon RuBP and enzyme Rubisco
 Phase 2: Reduction
ATP (6) and NADPH (6) from light reactions are used to form PGAL (G3P)
Output for one cycle = 1 PGAL (G3P)
 Phase 3: Regeneration of CO2 acceptor (RuBP)
5 3-carbon G3P + 3 ATP = 3 5-carbon RuBP
C. C4 and CAM Plants
Problem: When stomata close because of intense light and heat, O2 levels rise while CO2
levels decrease. Rubisco starts to take in O2 which causes photorespiration (decrease
efficiency)
1. C4 plants: steps are separated structurally: bundle sheath cell around vascular tissue have
chloroplasts
Examples: sugar cane, corn, crab grass
Solution: CO2 is “stored” in oxaloacetic acid (4-carbon acid) to use in Calvin Cycle ( in
bundle-sheath cell)
2. CAM plants: Steps are separated by time (day and night)
Examples: succulents like cacti and pineapple
Solution: CO2 is “stored” during the night in crassulacean acid system to use during the day;
water is conserved in the process
D. Overview
ECOLOGY
Chapter 50 An Introduction to Ecology and the Biosphere
I.
Introduction
a. Ecology: the scientific study of interactions between organisms and their environments
II. The Scope of Ecology
a. The interactions between organisms and their environments determine distribution and
abundance of organisms.
i. Abiotic components: nonliving chemical and physical factors in the environment – e.g.
temperature, light, and water
ii. Biotic components: living factors in the environment of an individual
b. Ecology and evolutionary biology are closely related sciences.
i. Ecological time: minutes, months, years
ii. Evolutionary time: decades, centuries, millennia
c. Ecological research ranges from adaptations of individual organisms to biosphere dynamics.
i. Organismal ecology: morphological, physiological, behavioral ways in which an individual
meets environmental challenges
ii. Population: a group of individuals of same species in a particular area
iii. Population ecology: the number of individuals of a species living in an area
iv. Community: all of the species in a particular area
v. Ecosystem: all of the abiotic factors in addition to the entirety of the community – e.g. a lake
vi. Ecosystem ecology: energy flow and the cycling of components among abiotic and biotic
factors
vii. Landscape ecology: arrays of ecosystems and their arrangement in a geographic region
viii. Landscape/seascape: several different ecosystems linked by organisms, materials, and
energy exchanges
ix. Biosphere: global ecosystem – the sum of the environments of the planet
d. Ecology provides a scientific context for evaluating environmental issues.
i. Precautionary principle: the idea of “looking before you leap” – environmental damage
might be greater by action than by inaction
III. Factors Affecting the Distribution of Organisms
a. Biogeography: the study of the past and present distributions of individual species.
b. Species dispersal contributes to the distribution of organisms.
i. Dispersal: the critical process for understanding geographic isolation and distribution
ii. The Tens Rule: one out of ten species become established
c. Behavior and habitat selection contribute to the distribution of organisms.
d. Biotic factors affect the distribution of organisms.
e. Abiotic factors affect the distribution of organisms.
f. Temperature and water are major climatic factors that determine the distribution of organisms.
i.
ii.
iii.
iv.
Climate: the prevailing weather conditions at a locality
Biomes: major types of ecosystems which occupy broad regions
Tropics: regions that are between 23°5 N and 23°5 S latitude
Microclimate: climate variations on a very fine scale
IV. Aquatic and Terrestrial Biomes
a. Aquatic biomes occupy most of the biosphere.
i. Photic zones vs. aphotic zones: areas of light vs. areas without light for photosynthesis
ii. Thermocline: narrow stratum of rapid temperature change
iii. Benthic zone: the bottom-most of aquatic biomes
iv. Benthos: communities in the Benthic zone
v. Detritus: dead organic matter
vi. Littoral zone: shallow, well-lit water near the shore. Farther out is the limnetic zone.
vii. Profundal zone: a deep, aphotic region
viii. Oligotrophic zone: a deep, nutrient-poor region
ix. Eutrophic zone: shallower region with many nutrients
x. Mesotrophic zone: moderate amount of nutrients and phytoplankton productivity
xi. Wetland: an area that is covered with water and that supports aquatic plants
xii. Estuary: where a freshwater stream or river merge with the ocean
xiii. Intertidal zone: area where land meets water
xiv. Neritic zone: a shallow region over the continental shelf
xv. Oceanic zone: the great depths of the ocean
xvi. Pelagic zone: open water at any depth
xvii. Oceanic pelagic biome: most of the water of the ocean far from the shore
xviii. Abyssal zone: very deep benthic communities
xix. Deep-sea hydrothermal vents: volcanic origins in mid-ocean ridges
b. Geographic distribution of terrestrial biomes is based on regional climate variations.
i. Canopy: low tree stratum
ii. Permafrost: permanently frozen stratum
V. Spatial Scale of Distributions
a. Different factors determine the distribution of species on different scales.
b. Most species have small ranges.
Chapter 51 Behavior
I. Introduction to Behavior and Behavioral Ecology.
A. What is behavior?
-Behavior - What an animal does and how it does it.
B. Behavior has both proximate and ultimate causes.
C. Behavior results from both genes and environmental factors.
D. Innate behavior is developmentally fixed.
E. Classical ethology presaged an evolution any approach to behavioral biology.
-Ethology - The study of animal behavior in natural conditions.
-Fixed action pattern (FAP) - A sequence of behavioral acts that is essentially
unchangeable and usually carried to completion once initiated.
-Sign Stimulus - An external sensory stimulus that triggers a FAP.
F. Behavioral ecology emphasizes evolutionary hypotheses.
-Behavioral ecology - heuristic approach based on the expectation that Darwinian
fitness (reproductive success) is improved by optimal behavior.
-Foraging - Behavior necessary to recognize, search for, capture, and consume food.
-Optimal foraging theory - The basis for analyzing behavior as a compromise of feeding
costs versus feeding benefits.
II. Learning.
A. Learning is experience - based modification of behavior
-Learning - A behavioral change resulting from experience.
-Maturation - Ongoing developmental changes in neuromuscular systems.
-Habituation - A very simple type of learning that involves a loss of reponsiveness to
stimuli that convey little or no info.
B. Imprinting is learning limited to a sensitive period.
-Imprinting - A type of learned behavior with a significant innate component, acquired
during a limited critical period.
-Sensitive Period - A limited phase in individual animal's development when learning of
particular behavior can take place.
C. Bird song provides a model system for understanding the development of behavior.
D. Many animals can learn to associate one stimulus with another.
-Associative learning - The acquired ability to associate one stimulus with another.
-Classical conditioning - A type of associative learning; the association of a normally
irrelevant stimulus with a fixed behavioral response.
-Operant Conditioning - A type of associative learning in which an animal learns to
associate one of its own behaviors with a reward or punishment and then tends to repeat or
avoid that behavior.
E. Practice and Exercise may explain the ultimate basis of play
-Play - Behavior with no apparent external goal but involves movements closely
associated with goal-directed behaviors.
III. Animal Cognition
A. The study of cognition connects nervous system function with behavior.
-Cognition - The ability of an animal's nervous system to perceive, store, process, and
use info obtained by its sensory receptors.
-Cognitive ethology - The scientific study of cognition.
B. Animals use various cognitive mechanisms during movement through space
-Kinesis - A change in activity or turning rate in response to stimulus.
-Landmark - A point of reference for orientation during navigation
-Cognitive map - A representation within the nervous system of spatial relations among
objects in an animal's environment.
-Migration - movement of organisms.
C. The study of consciousness poses a unique challenge for scientists.
IV. Social Behavior and Sociology.
A. Sociology places social behavior in an evolutionary context
-Social behavior - Any kind of interaction between two or more animals or same species.
-Sociology - The study of social behavior based on evolutionary theory.
B. Competitive social behaviors often represent contests for resources.
-Agonistic behavior - A type of behavior involving a contest of some kind that
determines which competitor gains access to some resource.
-Ritual - A type of symbolic activity.
-Reconciliation behavior - Post-conflict behavior that renews friendly relations.
-Dominance hierarchy - A linear "pecking order" of animals, where position dictates
characteristic social behavior.
-Territory - An area that an individual lives in.
C. Natural selection favors mating behavior that maximizes the quantity or quality of mating
partners.
-Courtship - Behavior patterns that lead up to copulation or gamete release.
-Parental investment - The time and resources an individual must spend to produce and
nurture offspring
-Promiscuous - With no strong pair-bonds or lasting relationships.
-Monogamous - One male mating with one female.
-Polygamous - An individual of one sex mating with several of the other.
-Polyandry - A single female mates with several males.
D. Social interactions depend on diverse modes of communication.
-Signal - A behavior that cause change in another organism's behavior.
-Communication - Transmission of, reception of, and response to signals.
-Pheromes - Chemical odors emit by animals that act as signals.
E. The concept of inclusive fitness can account for most altruistic behavior.
-Altruism - Behavior that reduces an individual's fitness while increasing the fitness of
another individual.
-Coefficient - of Relatedness
-Hamilton's rule - rB>C
-Kin selection
-Reciprocal altruism - Altruistic behavior between unrelated individuals, whereby the
current altruistic individual benefits in the future when the current beneficiary reciprocates.
Chapter 52 Populations
Vocabulary
Characteristics of Populations
 population: group of individuals of a single species that simultaneously occupy the same
general area
A. Two important characteristics of any population are density and the spacing of individuals
 density: number of individuals per unit area or volume
 dispersion: pattern of spacing among individuals within the geographic boundaries of
the population
1. Measuring density
 mark-recapture method: number of recaptures in second catch / total number in second
catch = number marked in first catch / total population N
2. Patterns of Dispersion
 clumped: individuals aggregated in patches where
factors are favored
 uniform: evenly spaced from direct interactions
between individuals
 random spacing: unpredictable dispersion occurs in the
absence of strong attractions or repulsions among individuals
B. Demography is the study of factors that affect the growth and decline of populations
 Demography: study of the vital statistics that
affect population size
1. Life Tables and Survivorship Curves
 life table: age-specific summary of the survival
pattern of a population
 cohort: a group of individuals of the same age
from birth until all are dead
 survivorship curve: plot of the proportion or
numbers in a cohort still alive at each age
2. Reproductive Rates
 reproductive table: fertility schedule, agespecific summary of the reproductive rates in a
population
II.
Life histories
 life history: traits that affect an organism’s schedule of reproduction and survival
A. Life histories are highly diverse, but they exhibit patterns in their variability
 big-bang reproduction (semelparity): grows without reproducing for several years and
then produces a large quantity in a single reproductive opportunity and then they die
 repeated reproduction (iteroparity): adults produce offspring over many years
III.
Population Growth
A. The exponential model of population growth describes an idealized population in an
unlimited environment
 Zero population growth (ZPG): the per capita birth rates and death rates are equal
 exponential growth: population increase under ideal conditions
 intrinsic rate of increase: maximum growth rate for species
B. The logistic model of population growth incorporates the concept of carrying capacity
 carrying capacity: maximum population size that a particular
environment can support at a particular time with no degradation
of the habitat
1. The logistic growth equation
 logistic population growth: incorporates the effect of
population density on the per capita rate of increase
2. The logistic population growth model and life histories
 K-selection: density-dependent
 r-selection: density-independent
IV.
Population-limiting factors
 density dependent: death rate that rises as population density rises
 negative feedback: output of a system acts to oppose changes to the input of the
system
 density independent: birth rate or death rate that doesn’t change with population
density
V. Human Population growth
A. The human population has been growing almost exponentially for three centuries but
cannot do so indefinitely
1. The demographic transition
 demographic transition: movement from the first toward the
second state
2. Age structure
 age structure: the relative number of individuals of each age
B. Estimating the Earth’s carrying capacity for humans is a complex
problem
 Ecological footprint: using multiple constraints to estimate
human carrying capacity
Equations:
I. Characteristics of Populations
 Number of recaptures in second catch / total number in second catch = Number
marked in first catch / Total population N
 N = Number marked in first catch X Total number in second catch / Number of
recaptures in second catch
II. Population Growth

Change in population size during time interval = Births during time interval –
Deaths during time interval
 ΔN/Δt = B – D
o ΔN = change in population size
o Δt = time interval
o B = number of births in population during time interval
o D = number of deaths
 Exponential population growth: dN/dt = rmaxN
o d = per capita death rate
o rmax = instrinsic rate of increase
 Logistic Population growth: dN/dt = rmaxN (K – N / K)
o K = carrying capacity
o N = population size
III.
Human Population growth
 Zero population growth = High birth rates – High death rates
 Zero population growth = Low birth rates – Low death rates
Summary of Key Concepts
I. Characteristics of Populations
A.
Two important characteristics of any population are density and the spacing of
individuals
 Dispersion may range from clumped (most common) to uniform to random, as
determined by various environmental and social factors.
B.
Demography is the study of factors that affect the growth and decline of populations
 Populations increase from births and immigration and decrease from deaths and
emigration.
II. Life histories
A. Life histories are highly diverse, but they exhibit patterns in their variability
 Life history traits represent trade-offs between conflicting demands for limited time,
energy, and nutrients.
B. Limited resources mandate trade-offs between investments in reproduction and survival
 Clutch size and age at first reproduction involve trade-offs between current and future
fecundity and adult survival, or fecundity and survival of the offspring.
III. Population Growth
A. The exponential model of population growth describes an idealized population in an
unlimited environment
 If we can ignore immigration and emigration, a populations growth rate is determined
by the birth rate minus the death rate. The larger a population becomes, the faster it
grows.
B.
The logistic model of population growth incorporates the concept of carrying capacity
 Exponential growth cannot be sustained for long in any population. A more realistic
population model limits growth by incorporating carrying capacity (K), the maximum
population size that can be sustained by available resources. For many natural
populations, there is no stable carrying capacity, and populations fluctuate regularly or
irregularly around some long term average density. Natural selection will favor traits
that allow survival and reproduction with few resources in populations that live at
densities near carrying capacity.
IV. Population-limiting factors
A. Negative feedback prevents unlimited population growth
 Density-dependent changes in birth and death rates act to curb population increase and
can eventually stabilize a population near its carrying capacity. Mandy densitydependent factors produce negative feedback, including intraspecific competition for
limited food or space, increased predation, disease, stress due to crowding, or buildup
of toxins.
B.
Population dynamics reflect a complex interaction of biotic and abiotic influences
 Carrying capacities can vary in space, providing good and poor habitats for a species, or
in time, producing population fluctuations. Most natural populations are characterized
by instability
C.
Some populations have regular boom-and-bust cycles
 Snowshoe hares have 10-year cycles, and field experiments have shown that intensive
predation coupled with food shortage in winter drives these cycles.
V. Human Population growth
A. The human population has been growing almost exponentially for three centuries but
cannot do so indefinitely
 Human population growth has been sustained by such factors as improved nutrition,
medical care, and sanitation, which have lowered death rates rapidly but birth rates
more slowly.
B. Estimating the Earth’s carrying capacity for humans is a complex problem
 We can estimate the ecological footprints of nations as one measure of how close we
are to the carrying capacity of Earth.
Chapter 53 Community Ecology
I. What is a Community?
•
•
A community is an assemblage of species living close enough together for potential
interaction
Communities differ dramatically in species richness, which is the number of species they
contain, and the relative abundance of those species.
II. Contrasting Views of Communities are Rooted in the Individualistic and Interactive Hypothesis
•
•
How can we account for the species found together as members of a community?
The individualistic hypothesis depicts plant communities as a chance assemblage of species
found in the same area simply because of similar abiotic requirements.
•
•
The interactive hypothesis depicts communities as a closely linked assemblage of species,
locked into association by mandatory biotic interaction that cause the community to
function as an integrated unit, or super organism
Actual observations support the individualistic hypothesis, because plant species are often
able to survive on their own without the other species in their community.
III. The Debate Continues with the Rivet and Redundancy Models
•
•
The rivet model suggests that most species in a community are tightly associated with one
another in a web of life. Thus, reducing or increasing the abundance of one species in the
community affects many other species.
The redundancy model suggests that most species in a community are not tightly associated
with one another and the web of life is very loose. Thus increasing or reducing the
abundance of one species in the community has little effect on the other species which
operate independently.
IV. Interspecific Interactions and Community Structure
•
•
•
•
Populations may be linked by competition, predation, mutualism, and commensalism.
Interspecific competition for recourses occurs when recourses are in short supply.
The competitive exclusion principle states that even a slight reproductive advantage will
eventually lead to local elimination of an inferior competitor.
The sum total of a species use of biotic and abiotic recourses in its environment is called the
specie’s ecological niche.
Recourse partitioning is when similar species have different niches, reducing competition,
and allowing the species to coexist.
V. Character Displacement
•
•
•
When two species evolve in the same area, i.e. allopatric speciation, those species are often
far more different than when speciation is caused by physical separation, i.e. sympatric
speciation.
The tendency of allopatric speciation to cause more divergence than sympatric speciation is
called character displacement.
Species that evolve in the same area must diverge in order to avoid competition, or else
one of the species will be wiped out, and this causes character displacement.
VI. Predation
•
•
•
•
Predation is when any organism feeds of another. This includes herbivory, the eating of
plants, and parasitism, when an organism uses a host as its home and source of nutrition.
Cryptic coloration is the use camouflage adapted to prey species.
Aposematic coloration is when poisonous species are brightly colored to warn predators.
Batesian mimicry is when a perfectly edible species mimics a harmful species in order to
scare off predators.
•
Müllerian mimicry is when two or more unpalatable species resemble one another,
meaning predators learn more quickly not to eat them.
VII. Commensalism and Coevolution
•
•
VIII.
•
•
•
•
Commensalism is an interaction between species that benefits only one of the species
involved. An example is barnacles on whales.
Coevolution is when an adaptation in one species drives selection to cause adaptations in
another species. Examples include a faster rabbit selecting for a faster fox species to catch
that rabbit.
Trophic structure is a key factor in community dynamics.
The trophic structure of a community is the feeding relationships of the community.
The food chain is the transfer of energy from plants to herbivores to consumers to
decomposers.
Trophic levels are the links in a food chain, and often there are no more than five levels.
Food chains are hooked together into a giant food web, which shows the feeding
relationships of a community.
IX. What limits the length of a Food Chain?
•
•
•
The energetic hypothesis suggest that the inefficiency of energy transfer along a food chain
limits the length of the food chain.
The dynamic stability hypothesis states that fluctuations at lower trophic levels are
magnified as they go up the food chain making it more likely a species will go extinct the
farther along a food chain it is.
Most data supports the energetic hypothesis.
X. Dominant species and keystone species exert strong control on community structure.
•
•
•
Dominant species are the species with the most biomass in a community.
Keystone species are species with a niche that is very important to their community.
Example: when starfish are removed, mussels, the prey of the starfish, expand their
population rapidly and eliminate many other species in their communities.
XI. The structure of a community may be controlled bottom-up by by nutrients or top-down by
•
•
predators
The bottom up model postulates that mineral nutrients control community organization;
because nutrients control the number of plants, upon which herbivores and predators rely.
The top down model states that predators control the number of herbivores, which control
the number of plants, which control the amount of nutrients.
XII. Disturbance and Community Structure
•
Stability is the tendency of a community to reach and maintain an equilibrium.
•
•
•
XIII.
•
•
XIV.
•
•
•
•
Most ecologist now favor the nonequilibrium model where communities are seen as
constantly changing after being buffeted by disturbances.
Most communities are in a state of nonequilibrium owing to disturbances such as storms,
fires, floods, droughts, overgrazing, or human activities.
Humans are the most widespread agents of disturbance and use 60% of the Earth’s land in
one way or another.
Ecological Succession is the sequence of Changes after a disturbance
Primary succession is when a virtually lifeless area without soil is colonized by species such
as lichens and mosses which create soil allowing for grasses, shrubs, and trees.
Secondary succession is when a disturbance clears an existing community but leaves the soil
in the area intact.
Biogeographic Factors Affecting the Biodiversity of Communities
Community biodiversity measures the number of species and their relative abundance in the
community.
Species richness generally declines as as you move north or southward away from the
equator.
The species area curve shows that the larger the area of land a community occupies, the
more species in that community.
Generally the larger an island is and the closer that island is to the mainland, the higher that
island’s species richness.
EVOLUTION
Chapter 22: Descent with Modification
People:








Plato: believes real world (ideal and eternal) and illusory world (imperfection)
Aristotle: believes in ladder of increasing complexity (scala naturae)
Linnaeus: specialized in taxonomy (genus and species)
Cuvier: developed paleontology (study of fossils), and advocated catastrophism (each boundary
between strata correspond in time to catastrophe)
Hutton: explained theory of gradualism (slow, but continuous change)
Lyell: incorporated gradualism w/ uniformitarianism (his idea is that geologic process have not
changed)
Lamark: lines of descent (chronological) on fossils and evolved two ideas:
1. use and disuse: part of the body coping with the environment became stronger
while the other deteriorate
2. inheritance of acquired characteristics: modifications are passed to offspring
*there’s no evidence that characteristics can be inherited*
Maithus: studied population growth

Wallace: had a theory of natural selection before Darwin; however, Darwin published the
bookOrigin of Species because Darwin had more support and evidence
 Darwin: he published Origin of Species because he had great evidence and logic.
1. Darwin read Lyell’s book, Principles of Geology, and combined both their ideas that
Earth has also evolved.
2. species on Galapagos differ from everywhere else; even from South America
3. Darwin noticed that the bird’s beaks are adapted to the type of food they eat
information/facts:
 fossils mostly found in sedimentary rocks; the new layer of sediments on top of the old layer is
called strata
 Darwinian: concept of natural selection as the cause of adaptive evolution
 Darwinism: life’s unity and diversity
 Major taxonomic categories:
1. Kindgom
2. Phylum
3. Class
4. Order
5. Family
6. Genus
7. Species
*Kids Playing Cups On Freeways Get Squished*
 Natural selection:
1. differential success in reproduction
2. occurs through interaction between environment and variability inherent among
individuals
 Examples of Natural Selection:
1. Insecticide resistance - the insects that are immune to the insecticide passes their
resistance genes to their offspring, and so on.
2. Drug resistance HIV - resistance to a drug evolves rapidly in HIV population

Over reproduction causes struggle for existence because of the limited resources
 Descent with modification supported by fossil records
 Homology (Common Ancestry have similarities):
1. Artificial Selection: breeding of domesticated plants and animals (selecting desired
traits)
2. Anatomical Homology: descent with modification evident in anatomical similarities
between species grouped in the same taxonomic category
3. Homologous Structures: anatomical signs of evolution
4. Vestigial organs: historical remnants of structures that had important functions in
ancestors
5. Embryological homologies: embryonic structures develop into homologies structures
6. Molecular homologies: molecularly similar
 Biogeography:


1. species tend to be more closely related to other species from the same area than to
other species in other areas
2. endemic: found nowhere else in the world
Divergent evolution: common ancestry, then changes occur; hence, diverge.
Convergent evolution: different background, but similar geographic areas causing similarities
Chapter 23 Evolution of Populations
Microevolution is defined as the change in the allele frequencies of a population over time.
Population Genetics
The Modern Evolutionary Theory integrates Darwinian Selection and Mendelian Inheritance
Population Genetics emphasizes the extensive genetic variation within populations and recognizes the
importance of quantitative characters.
Modern Synthesis – a comprehensive theory of evolution because it combines ideas from biogeography,
population genetics, paleontology, and taxonomy. The population is the unit of evolution, natural
selection is the most important mechanism of evolution, and gradualism explains who large changes
can occur as a result of many small changes.
A Population’s Gene Pool is Defined by Allele Frequencies
Population – a localized group of individuals belonging to the same species
Species – A group of a population whose individuals can interbreed and produce fertile offspring in
nature
Gene Pool – the total aggregate of genes in a population at any one time
Ploidy – the number of sets of chromosome contained in a cell
Diploid – humans two sets of chromosomes, one inherited from each parent
Dominant alleles are expressed over recessive alleles (R vs. r) (p vs. q).
The Hardy-Weinberg Theorem Describes a Nonevolving Population
Hardy-Weinberg Theorem – frequencies of alleles and genotypes in a population’s gene pool remain
constant over the generations unless acted upon by agents other than Mendelian segregation
and recombination of alleles. Meiosis and random fertilization has no effect on the overall
gene pool of a population.
Hardy-Weinberg Equilibrium – when the gene pool reaches a state of equilibrium, the
population is no longer evolving
Hardy-Weinberg Equation:
Natural Selection requires genetic variation, but the Hardy-Weinberg theorem explains how
Mendelian inheritance preserves genetic variation from one generation to the next in a
genetically uniform population
Assumptions of the Hardy-Weinberg Theorem:
1) Very large population size
2) No migration
3) No net mutations
4) Random mating
5) No natural selection
Causes of Microevolution
Microevolution is a Generation to Generation Change in a Population’s Allele Frequencies
Microevolution affects a gene pool on the smallest scale. Over a succession of generations, if only some
allele frequencies are changing, evolution is still occurring.
The Two Main Causes of Microevolution are Genetic Drift and Natural Selection
Causes of Microevolution: *are the most common causes of change in allele frequencies
1)* Genetic Drift – a change in a population’s allele frequencies due to chance sampling error
(usually of a small population. The Bottleneck Effect reduces the overall genetic variability in a
population because at least some alleles are likely to be lost from the gene pool (due to a
sudden loss in population). The Founder Effect occurs when individuals from a larger
population colonize an isolated island, lake, or new habitat – and genetic variability is reduced.
2)* Differential Survival – allows for differential reproductive success, and therefore allows
natural selection to take place in a population.
3) Gene Flow – genetic change due to the migration of fertile individuals or gametes between
populations: such as pollen moving from one nearby population to another
4) Mutation – a change in an organisms DNA – could affect a population as a whole over a long
period of time. Mutations are the original source of genetic variation that serve as the raw
material for natural selection.
Genetic Variation – The Substrate for Natural Selection
Genetic Variation Occurs Within and Between Populations
Variation within Populations:
Quantitative Characteristics – vary along a continuum (height)
Discrete Characteristics – classified on an either or basis (distinct phenotypes with no blends)
Polymorphism – applies to discrete characteristics: when multiple, distinct forms are
represented in a population (blood type)
Gene Diversity – the average percent of loci that are heterozygous
Nucleotide Diversity – the nucleotide sequence differences of DNA samples from two individuals
Variation between Populations:
Geographic Variation – differences in gene pools between populations or subgroups of
populations due to differing environmental factors
Cline – a graded change in some trait along a geographic axis – i.e. due to interbreeding
between neighboring populations, for example plant height changes in a population along
from the base to the peak of a mountain
Mutation and Sexual Recombination Generate Genetic Variation
Mutations:
Point mutations are typically only beneficial when the environment is changing, and the
reproductive success of the individual might improve.
Chromosomal mutations that disrupt gene loci are usually negative, but the effect could be
neutral.
Chromosomal duplication is nearly always harmful, but it could be neutral, and later benefit the
population after a point mutation.
Sexual Recombination:
Reproduction shuffles alleles and deals them at random, and this allows gametes from a single
individual to vary extensively. Reproduction recombines old alleles into fresh assortments
every generation.
Diploidy and Balanced Polymorphism Preserve Variation
Diploidy – hides genetic variation from selection as recessive alleles. Heterozygote protection maintains
a huge pool of alleles that may not be suitable for present conditions, but could bring benefits
when the environment changes.
Balanced Polymorphism – the ability of natural selection to maintain stable frequencies of two or more
phenotypic forms.
Heterozygote Advantage – heterozygotes have better changes at survival, and have better
reproductive success.
Frequency-Dependent Selection – the survival and reproduction of any one allele declines if the
phenotypic form becomes too common in the population
Neutral Variation - variation that seems to confer no selective advantage for some individuals over
others
A Closer Look at Natural Selection as the Mechanism of Adaptive Evolution
Evolutionary Fitness
Darwinian Fitness – the contribution an individual makes to the gene pool of the next generation
relative to the contributions of other individuals.
Relative Fitness – the contribution to the genotype of the next generation compared to the
contributions of alternative genotypes for the same locus. If RR produces the most offspring, its
relative fitness is the standard, at 1; and rr would be scaled to that (ie an arbitrarily assigned 0.8).
The Effect of Selection on a Varying Characteristic can be Directional, Diversifying, or Stabilizing
Directional Selection – shifts the makeup of a population to one phenotypic extreme
Diversifying Selection – shifts the makeup of a population to both phenotypic extremes
Stabilizing Selection – favors a population that has an intermediate phenotype
Sexual Selection may lead to Pronounced Secondary Differences Between the Sexes
Sexual Dimorphism – secondary sex characteristics
Intrasexual Selection – direct competition among individuals of one sex for mates of the
opposite sex
Intersexual Selection – individuals of one sex are choosy in selecting mates of the other sex
Natural Selection Cannot Fashion Perfect Organisms
Evolution is limited by historical constraints – by mixing structures, evolution may be better, but not
perfect (human back problems)
Adaptations are often compromises – humans are not built for seas, but we can manage
Not all evolution is adaptive – alleles preserved after adversity are not always the ones best suited for an
environment
Selection can only edit existing variations – natural selection can only occur from available phenotypes
Chapter 24 Origin of Species
Macroevolution- The origin of new taxonomic groups (i.e. evolutionary changes above the
species level)
Microevolution- change in allele frequencies over time (genetic drift and natural selection)
Speciation- origin of new species
Anagenesis- (phyletic evolution) = the accumulation of heritable changes in a population
transforming that population into a new species
Cladogenesis- (branching evolution)- new species develops for a populations which branches
out from a parent species. This is the basis for biological diversity
Biology Species Concept- species= pop. Or group of pop. whose members have the potential to
interbreed with one another to produce viable, fertile offspring, but who cannot produce viable,
fertile offspring with members of other species
-Limitations of this concept:
1) No way to check interbreeding in the extinct forms represented by fossils
2) No utility at all for org. which are entirely asexual like bacteria (Biologists assign an
asexual org. to a species based mainly on structural/biochemical characteristics)
A biological species= largest set of pop. In which genetic exchange is possible and that is
genetically isolated from other such populations
Prezygotic
Barriers
Types of Isolation
-Reproductive: can’t interbreed even if population ranges overlap
-Habitat: (Ex: two species of parasites living of different hosts will not have a chance to meet)
-Behavioral: some species have elaborate courtship rituals
-Temporal: Species breed at different times
-Mechanical: Reproductive organs don’t fit together
-Gametic: sperm of one species may not be able to survive in the female reproductive tract of
another species
Postzygotic Barriers
- isolating mechanisms that prevent hybrids from developing into viable, fertile adults
-Reduced Hybrid Viability- development of the hybrid aborts at an embryonic stage
-Reduced Hybrid Fertility- hybrid is sterile (ex: mule)
-Hybrid Breakdown: offspring of hybrids have reduced viability or fertility
Alternative Concepts of Species
-Ecological Species Concept- Ecological roles (niche) define species (this concept can include
asexual organisms w/in its premise.)
-Pluralistic Species Concept- The Factors that are most important for the cohesion of individuals
as a species vary. (herding, schools of fish, pacts)
-Morphological Species Concept- organisms are defined by their structural features
-Genealogical Species Concept- species = a set of org. with a unique genetic history.
Allopatric Speciation
- a pop. forms a new species while geographically isolated
- ring species = distributed around some geographic barrier (Salamanders in
California)
- adaptive radiation- the emergence of numerous species from a common
ancestor introduced into an environment, presenting a diversity of new
opportunities and problems (this happens on island chains)
- Fruit Fly Diet Lab- flies do not show much mating preference for the flies from their own pop.
compared to like-adapted flies from other populations
- Monkey Flower Experiment- there is no selection pressure keeping the genomes of such
distant pops. compatible enough for successful interbreeding
Sympatric Speciation
- a small pop. becomes a new species w/o geographic separation from its parent population
- Polyploid Speciation in Plants
- Polyploidy- a chromosomal alteration in which the organism possesses more than two
complete chromosome sets
-Autopolyploid- an individual that has more than two chromosomal sets, all derived
from from a single species
- Allopolyploid- contribution of two diff. species to a polyploid hybrid
Punctuated Equilibrium Model- A theory of evolution advocating spurts of relatively rapid
change followed by long periods of stasis
Exaptations- structures that evolve and function in one environmental context that can perform
additional functions when place in some new environment
“Evo-devo”(environmental developmental biology) - the interface b/w evolutionary biology and
the study of how organisms develop
allometric growth- proportioning that helps give a body its specific form (diff growth rates for
diff parts of the body)
heterochrony- evolutionary change in the rate or timing of developmental events
Paedomorphesis- the retention in an adult organism of the juvenile features of its evolutionary
ancestors
Species Selection- a theory maintaining that species living the longest and generating the
greatest # of species determine the direction of major evolutionary trends
Chapter 25 Phylogeny
I. The Fossil Record and Geologic Time
 Phylogeny: evolutionary history of a species or group of related species.
 Systematics: study of biological diversity in an evolutionary context.
 Fossils: preserved remnants let by organisms of the past.
A. Sedimentary rocks are the richest source of fossils.
 For from layers of minerals
 Most common fossilized plant material is pollen, which has a hard organic case that resists
degradation.
 Locomotion: pattern of leg movement, stride length, and speed.
B. Paleontologists use a variety of methods to date fossils.
 Relative Dating: trapping of dead organisms in sediments freezes fossils in time.
 Geologic Time scale: time scale established by geologists that reflects a consistent sequence of
historical periods, grouped into 4 eras:- Precamrian, Paleozoic, Mesozoic, Cenozoic.
 Mesozoic: time of the reptiles.
 Epoch: period within each era subdivided.
 Series of sedimentary rocks do not tell the absolute ages of embedded fossils.
 Absolute Dating- ages is given in years instead of relative terms such as before and after, early
and late.
 Radiometric dating: measurement of certain radioactive isotopes in fossils or rocks. In more
simple terms, it determines the ages of rocks and fossils.
 Half-life: number of years it takes 50% of the original sample to decay. It remains unaffected by
temperature, pressure, and other environmental variables.
 Amino acids esits in isomers with either left-handed or right-handed symmetry, designed for the
L and D forms.
 Organisms synthesize only amino acids, which are incorporated into proteins.

Racemization: chemical conversion. Used to determine how long the organism has been dead.
Temperature sensitive.
C. The fossil record is a substantial, but incomplete, chronicle of evolutionary history.
 A substantial fraction of species that have lived probably left no fossils, most fossils that have
formed have been destroyed, and only a fraction of existing fossils have been discovered.
 Fossil record favors species that existed for a long time, were abundant and widespread, and
had shells or hard skeletons.
D. Phylogeny has a biogeographic basis in continental drift
 The drifting of continents is the major geographic factor correlated with this partial distribution
of life and with such evolutionary episodes as mass extinctions increase in biological diversity.
 250 million years ago
plate=landmasses together
Pangaea environment impact.
 Mezoic era
Pangea break up
geographic isolation
E. History of life is punctuated by mass extinctions.
 Extinction is inevitable in a changing world.
 Larger comet or small asteroid crashed into earth 65 million years ago causing Cetacean’s
extinctions.
 Reduced temperature differences between the equator and the poles would have slowed the
mixing of ocean water, which in turn would have reduced amounts of oxygen available to
marine organisms.
II. Systematics: Connecting Classification to Phylogeny
 Systematics: study of biological diversity in an evolutionary context.
 Taxonomy = system of nature.
A. Taxonomy employs a hierarchical system of classification.
 Linnaean system: two part name and hierarchical classification.
 Binomial: taxonomists assign each species a two-part latinized name.
 Genus: first part of a binomial to which species belong.
 Specific epithet: second part of binomial referring to one species within a genus.
 Taxon: taxonomic unit at any level.
 Only genus name and specific epithet are italicized.
 Phylogenetic trees: systematics reflects the hierarchical classification of taxonomic
groups nested within more inclusive groups.
B. Modern Phylogenetic systematics is based on cladistics analysis.
 Cladogram: phylogenetic diagram based on cladistics. Each branch represents the divergence of
2 species from a common ancestor. A chronological sequence of branching during evolutionary
history of a set of organisms. Analysis of the taxonomic distribution of homologies.
 Clade: each evolutionary branch in a cladogram. Monophyletic: means “single tribe” which
consists of an ancestral species and all of its descendants.












Homology: likeness attributed to shared ancestry.
Convergent evolution: species from different evolutionary branches may come to resemble one
another if they have similar ecological roles.
Analogy: similarity due to convergence.
The more the number of homologous parts between 2 species, the more closely the species is
related.
Backbone is a homology for the vertebrae tree.
Shared primitive character: a character that is shared by species beyond the taxon of interest.
Shared derived character: a trait that evolved in the ancestor of a group and is present in all its
descendants
Among vertebrates, backbone is a shared primitive character since it’s evolved in the ancestor
common to all vertebrates.
Outgroup comparison: differentiated shared characters that are derived from those that are
primitive. They are based on assumption that homologies present in both the outgroup and
ingroup must be primitive characters that were already present in the ancestors common to
both groups.
Outgroup: species or groups of species that is closely related to the species we are studying.
Ingroup: group of taxa that is actually being analyzed.
Phylocode: having clades without the hierarchical tags, such as class, order and family. Each
diagram of phylogeny represents a hypothesis or a set of hypothesis about how the organisms in
the tree are related.
C. Systematists can infer phylogeny from molecular data.
 Molecular systematics trace evolutionary relationships of species that are so different that there
is very little homology.
 Each nucleotide position along a stretch of DNA represents an inherited character in one of the
DNA bases: Adenine, Guanine, Cytosine, or Thymine.
 Aligning DNA sequences: 1) align homologous DNA sequence from the 2 species that are being
compared. 2) Compare the bases and lengths. 3) Convert data to phylogenetic trees.
D. The principle of Parsimony helps systematics reconstruct.
 Parsimony: method for estimating phylogenies.
 The most parsimony tree is one that requires the fewest evolutionary events in the form of
shared derived characters.
E. Phylogenetic trees are hypotheses.
 Point mutations occasionally change a base with a DNA sequence at molecular level.
 The best phylogenetic hypotheses are those that incorporate extensive molecular and
morphological data.
 The practice of parsimony in molecular systematics is more reliable if a
phylo genetic tree
is based on a large database of DNA sequence comparisons for the set of species in the tree.
F. Molecular clocks may keep track of evolutionary time.
 Timing of evolutionary history based mainly on fossil record.
 Molecular clocks: evolutionary timing methods based on the observation that at least some
regions of genomes evolve at constant rates.
 No genes mark time with precise accuracy.
 The regularity of some genes as molecular clocks implies that much of the change in DNA
sequences is due to genetic drift and that the changes are mostly neutral--neither adaptive nor
detrimental. Molecular evolution due to natural selection favoring certain DNA changes over
others would probably be too irregular to mark time accurately.
 The base sequences of some regions of DNA change at a rate consistent enough to serve as
clocks to date episodes in past evolution.
G. Modern systematics is flourishing with lively debate.
 phylogenetic fuse hypothesis: Perhaps the modern mammalian orders originated about 100
million years ago, but did not proliferate extensively enough to be noticeable in the fossil record
until after the extinction of the dinosaurs almost 40 million years later.