1

Go to View > Show document outline for an overview of topics

May 2020 Update: GOOD LUCK

MY CORONA CHILDREN!! Ace
those AP Exzooms
Carbon and Macromolecules

Identifying Compounds

Carbs and Lipids == C, H, O

Protein == C, H, O, N, S
Nucleic Acid == C, H, N, O, P

Carbs ratio = C1H2O1

Lipids ratio = high high amount of hydrogen and carbon (not as much oxygen, hydrocarbons)

Radioactive tracers to identify each, Tag phosphorus to identify nucleic acids, tag sulfur to
identify proteins

CARBON

● Carbon is essential to life

● Organic compound == carbon
● Inorganic compound != include carbon
● Carbon leads to diversity
● Determining factors of organic molecules’ properties
○ Carbon Backbone - gives structure shape, function
○ Functional Groups - part of molecule that participates in reactions
■ Backbone is unchanged, functional groups that react
● Tetravalence
○ Has four valence (outer shell) electrons (covalent)
■ Can bond with 4 other atoms
● Create wide array of molecules
 2

○ Atom unstable unless valence shell is full, reacts with other atoms
● Organic Chemistry
○ Branch of chem that studies carbon compounds
● Carbon Backbone
○ Central part of an organic molecule, determines structure (and
function/properties) of molecule
■ Rings, linear, branching, and double bonds
■ Shape determines function -- variety of different molecules
● Hydrocarbons
○ Long chains containing carbon and hydrogen
○ Make up lipids
■ Contains lots of energy (lots of bonds, for ex. fat)
■ Nonpolar (Hydrophobic) - only polar if distribution of charge with an
electronegative charge
● (No O, Su, N -- electronegative atoms)
● Isomers
○ Structure leads to function
○ Compounds with same formula but different arrangement of atoms
○ Structural
■ Carbon backbone is different
○ Geometric
■ Groups branching off backbone are different (functional groups)
■ Carbons are double bonded
■ Functional groups on opposite sides = trans
■ Functional groups on same side = cis
○ Enantiomers/Stereoisomers
■ Mirror images of structure
■ Example: L-Dopa and D-Dopa - only difference is structure
● L-Dopa treats Parkinson’s, D-Dopa inactive
● Functional Groups - branch off Carbon Backbone
○ Participates in chemical reactions***
○ Hydroxyl
■ Alcohols (OH-)
○ Carbonyl
■ Ketones (acetone) (carbon double bonded with oxygen)
■ Aldehydes (propanol)
○ Carboxyl
■ Carboxylic acids, ie. acetic acid
 3

■ Carbon double bonded to oxygen oxygen single bonded to another

oxygen
● Can be ionized or nonionized
● Donate H+ ions to solution, acidic
○ Amino
■ Amines (glycine)
■ Neutral by itself
■ NH2 - can Ionize and become NH3+, accepts H+ ions (base)
○ Sulfhydryl
■ Thiols (ethanethiol)
■ SH-
○ Phosphate
■ Organic phosphates i.e. glyceral phosphate (PO4)
■ Phosphorus bonded to four oxygens two oxygens have negative charges
● In DNA, ATP, GTP etc.
● Important phosphate groups

MACROMOLECULES

● Polymer
○ Large molecule consisting of many identical/similar building blocks
(monomers)
● Monomer
○ A single repeating subunit
● Reactions:
○ Hydrolysis
■ Addition of H2O to break bonds
○ Dehydration Synthesis (Condensation) chemical bonds are always made
this way
■ Removal of H2O to make bonds
○ Stomach acid does not actually digest food, hydrolysis does (in intestines)
● First macromolecules
○ Building blocks for life
○ Volcanoes on earth released gasses like Carbon oxides, water vapor,
methane, etc.
■ Water formed primordial seas, location of first macromolecules
and first living organisms - 3.6 billion years ago
■ Stromatolites
 4

● Stanley Miller made experiment simulate conditions on early earth, to create

macromolecules abiotically
○ Included gasses, rain, and electricity
■ Gases reacted with one another
■ Water condensed and formed “sea” found monomers, the first
macromolecules
■ Abiotic synthesis of monomers → chemical reactions
● Earth covered in volcanoes, volatile, releasing gasses in atmosphere → formed
primordial seas where sea meets land is where life started.
● Start of life - took 1 billion years
○ Have right elements - CHNOPS
○ Elements come together to form the first monomers (amino acids, fatty
acids, glycerol, monosaccharides, etc. building blocks)
○ Form polymers (proteins, triglycerides, nucleic acids, etc.)
○ Form cells → bacterial life
● DNA (bases) and Proteins (amino acids) compare amounts that organisms share
in common, more in common the more similar the organisms are
○ Molecular homology - things shared in common due to common ancestry
● Monomers are repeating sub units in polymers
○ Fused by dehydration synthesis (remove water) and defused using
hydrolysis (add water)
● Carbohydrates - main energy source for ATP and cellular respiration
○ Monosaccharides -(ready energy) monomers subunits (glucose, -ose)
means “one sugar”
■ Similar formulas: (CH2O)n where n is number of carbons
○ Polysaccharides -energy storage and structural support, polymers
■ Energy storage/Long term energy:
● Starch storage carbs for plants
○ quick energy in animals
● Glycogen storage found in stomach and liver cells animals
○ After glycogen reservoirs are full then stored as fat
● Cellulose - major structural molecule in plants
○ Fiber in humans
● Chitin - structural support in exoskeletons and fungi
■ Starch vs. Cellulose
● Long chains of glucose
○ Direction of bonds is different
 5

■ Starch Alpha Glucose (hydroxyl group is

down) and Cellulose Beta Glucose (hydroxyl
group is up)
● (Alpha) Starch can be digested as energy
○ Alpha bonds can be broken down
● (Beta) Cellulose cannot == fiber
○ No enzymes to break down beta bonds
○ Goes through digestive system unbroken, cleans
colon dead bacteria and rotten food on inside of
intestines, fiber cleans it
■ Structural support
● Cellulose
○ Structural component of plants
● Chitin
○ exoskeleton of arthropods
○ Always has ring structure (hexagon (gluc) and pentagon (fruc))
■ Glucose and Fructose are isomers
■ Glucose + Glucose = Maltose
■ Glucose + Fructose = Sucrose
○ Disaccharides - two monosaccharides held by one bond
○ Monosaccharides provide immediate energy
■ Already broken down unlike polysaccharides
● No need for hydrolysis
■ Maltose
■ Sucrose (sugar)
● Glucose + Fructose (thru Dehydration Synthesis)
○ Glycosidic Bonds link monosaccharides in to disaccharides
○ Glycogen
■ Energy storage in liver and muscles
■ Eat more energy than needed first stored as glycogen
■ When energy storage of glycogen is full, then fat storage begins
● Lipids
○ Hydrophobic (nonpolar)
○ 4 cal/gram for proteins and carbs, 9 cal/gram for lipids
○ Triglyceride fats (three fatty acids and a glycerol) makeup hydrocarbon
chains
■ Fatty acids to glycerol bonded by dehydration synthesis
● Formed by an ester bond
 6

■ Sat fats
● No double bonds between carbons
● Bad for you (butter & lard)
● Solid at room temperature (dense)
○ Remain solid in bloodstream, create plaques in
blood stream
○ Molecules can be compacted together, no kinks in
each chain → dense and solid
● ALL single bonds (max amount of hydrogen)
■ Unsat fats
● Have some carbon double bonds (removal of two
hydrogens, not saturated in hydrogen)
○ Create kinks in fatty acid chain
● Liquid at room temp (oils) less dense Kinks don’t stack well
● Mono vs Poly unsat fats = 1 double bond, and two double
bonds
○ Mono is healthier, least dense
● Hydrogens on same side (cis)
■ Trans Fats (technically unsat)
● If hydrogens in an unsat fat are trans (opposite sides) no
more kinks in bond → solid at room temperature →
contribute to plaque
● Hydrogens near double bond are on opposite sides, no
kink
○ Hydrogenated Oils
■ Make unsaturated fats → saturated fats with hydrogen
■ No more stirring of unsat fat oils in peanut butter, unhealthy
○ Evil Hierarchy:
■ Trans
■ Hydrogenated/Sat
■ Unsat
○ Used in membranes (only phospholipids), insulation, protection and fat
long term energy storage
○ Phospholipids
■ Make up cell membrane (with cholesterol a steroid)
● Hydrophilic head
● Hydrophobic tails
● Has glycerol and two fatty acids (unsat and sat→ nonpolar)
 7

● Third fatty acid replaced by phosphate group (polar)

■ Amphipathic Molecule partially hydrophilic and hydrophobic
■ When placed in water, create double layer, where nonpolar tails
face each other and polar tails face water on both sides →
membrane structure
○ No energy made to create cell membrane, beginnings of life, occurs
naturally
○ Steroids - hormones for protein synthesis
■ Cholesterol
● Found in cell membranes and myelin sheath
● 4 carbon ring structure
● Solid
● Used in nervous system and cell membranes
○ Insulates neurons
● Good except excess
■ Estrogen and Testosterone
● Made using Cholesterol
● Proteins
○ Most important macromolecule
○ pH remains constant
○ Made up of amino acids (20 different types)
■ Contains amino group, R variable group, and carboxyl group
■ Peptide bonds link amino acids
■ Central Carbon (one C) backbone attached to H
■ Carboxyl group (Carbon double bonded to Oxygen and OH)
● Acid in “amino acid”
● Donates H+, acidic
■ Amino group (N bonded to two H’s)
● Accepts H+, basic
● Amino in “amino acid”
■ R group
● “Random group”
● What makes the amino acid special
● Polar R groups have (N, S, or O)
● Nonpolar R groups have carbon and hydrogen
■ React through dehydration synthesis
● Peptide bonds form
● OH from carboxyl and H from amino groups react
 8

○ Four levels of protein structure

■ Primary
● Unique sequence of amino acids (most important)
○ Held by peptide bonds
○ Determined by DNA
● Takes place inside a chaperonin protein
○ If misfolding, → parkinson's and alzheimer's mad
cow disease (prions)
■ Secondary
● One of two three dimensional shapes that are the result of
hydrogen bonding between amino acids
○ Alpha helix - coil (like DNA)
○ Beta pleated sheet - accordion
■ BOTH determined by amino sequence
■ Tertiary
● Structure results as of R group reactions final foldings
○ Disulfide bridges
○ Hydrophobic interactions
○ Ionic bonds
● Makes single polypeptide subunit
■ Quaternary
● The 3D shape is a polypeptide subunit
● Two or more polypeptide chains into one large protein.
● Creates full protein
● Multiple tertiary structures put together
● Hemoglobin is a globular protein with structure
○ Collagen most important and abundant protein
■ Made of 3 polypeptides
○ Hemoglobin made up of 4 subunits
■ SCA caused by one amino acid mutation glutamine → valine
○ Dimer - protein with two tertiary structures (polypeptides)
○ Shape of the protein determines function
○ Structural/Fibrous Protein - strong proteins (collagen, keratin, silk, elastin
etc.)
○ Globular -
■ Like a glob
■ Microtubules
■ Enzymes
 9

■ Antibodies
■ hemoglobin
○ Chaperonins
■ Aid in proper folding of proteins
○ Disrupting protein structure:
■ Change in pH
■ Temperature change (boiling point)
● Chemical bonds in protein are broken, unfolded
○ Denaturing - proteins become ineffective
■ Can renature but rare
■ Salinity (NaCl concentration)
○ Denaturation - when protein loses shape in function due to some
disturbance (temperature, change in pH)
○ Functions
■ Enzymes - speed chemical reactions
■ Defensive proteins - antibodies destroy invaders
■ Storage - used to store amino acids
■ Transport - transport substances around body and within cells
■ Hormonal - transmit information
■ Contractile/Motor - movement within or whole cell movement
■ Structural Proteins - collagen, connective tissue
● Nucleic Acids
○ Nucleotides composed of
■ Pentose sugar
■ Phosphate group (PO4)
■ Nitrogenous base (adenine, thymine, guanine, cytosine, and uracil)
● Purines AG
● Pyrimidines CT (U) Cing Tut
○ Nucleotides strung together are called polynucleotides
○ DNA - carrier of genetic messages, construction of chromosomes
■ Has deoxyribose sugar
○ RNA - transcribes genes in DNA and translates into proteins
■ Has ribose sugar
Cellular Respiration

Jess Notes:
Alcohol fermentation (yeast)
Pyruvate converted to ethanol (2 carbon, releases CO2)
Brain cells = purely aerobic
 10

Obligate anaerobes = die in the presence of O2 (bacteria), carry out fermentation/anerobic respiration
Denitrifying bacteria
Anaerobic respiration: use sulfates as final electron activity instead of O2 and substrate level
phosphorylation not the electron transport chain

Glycolysis
Oldest process
Before mitochondria, glycolysis took place
Oldest prokaryotes used this for energy

Cell respiration
Regulated by feedback inhibition
When ATP builds up, pathway is turned off
Utilizes allosteric enzymes
Turns off Phosphofructokinase (first enzyme in pathway)
AMP turns back on, forces pathway on

● Fats and proteins can also be used in cellular respiration (triglycerides), not
just glucose and carbohydrates
○ Fats provide more energy than carbohydrates, therefore more ATP
○ Glycerol (3 carbon molecule) and three fatty acids
● Monomers of fatty acids/glycerol can enter cellular respiration
● Glycerol has the same amount of carbons as a glucose pyruvate, enters
process at pyruvate oxidation no need for glycolysis, more energy
● Beta Oxidation
○ Fatty acids from lipids need to break down long chains of carbons in
order to enter cellular respiration
○ Breaks the fatty acid chain and breaks it down into two-carbon
molecules
○ Feeds directly into the Kreb Cycle
● If you don’t have enough carbs or lipids, or too much protein, protein can
be used in cellular respiration
○ Proteins have an atom that cannot enter cellular respiration, have to
get rid of nitrogen in order to enter, stomach and small intestines
break down proteins into amino acids
 11

■ The amino acids can go into cellular respiration

● Deamination
○ The process by which the amino group (NH2)
leaves the amino acid to enter cell respiration
■ Amino acid can enter multiple levels of the cellular respiration
● Cellular Respiration refers to both aerobic and anerobic respiration but is
mainly the aerobic respiration
○ Respiration usually tracked with glucose because it starts at the first
step
● Fermentation partial degradation of sugars that occur without O2
○ Keeps pyruvate happening?
● Aerobic respiration consumes organic molecules and O2 and yields ATP
● Anerobic Respiration similar to aerobic respiration but consumes
compounds other than O2
● Glycolysis occurs whether or not O2 is present
● Ecosystem - all living communities and abiotic factors (nonliving components, pH, water)
● Trophic Levels - troph = food
○ Primary producers
■ Autotroph - plants protists, cyanobacteria
■ Chemosynthesis and photosynthesis, produce their own food
■ Convert light energy to chemical energy, all consumers depend on plants
○ Primary Consumers
■ Herbivores, eat the primary producers
○ Secondary Consumers
■ Omnivores, primary carnivores
○ Tertiary consumers
■ Secondary carnivores
○ Detritivores
■ Decomposers (fungi, bacteria, earthworms, insects, scavengers, vultures)
● Food Chain - linear chart which shows who eats who
○ Grass → zebra → lion → vulture
○ Top down model (top of the food chain controls the autotrophs) and bottom up model
(grass controls the rest of the chain)
 12

● Food Webs - nonlinear expanded chart showing multiple relationships between each organism
● Keystone species
○ Most important role within the ecosystem, disproportionate effect on ecosystem
● Productivity - amount of solar energy converted into chemical energy (photosynthesis) in a
community by autotrophs (amount of photosynthesis)
○ More producers → more energy
○ Most productive ecosystem - open ocean → productivity is low but so much ocean is the
most productive biome on planet because of algae
■ Per square unit, tropical rainforests are most productive (dense plants)
○ Gross Productivity total amount of organic compounds that were created through
photosynthesis
■ Ocean by surface is more productive → need sunlight
○ Net Productivity Gross amount MINUS the amount of consumed by respiration -
producers still respirate and consume energy
○ Factors
■ Amount of sunlight
■ Limiting Nutrients limit the amount of productivity that can take place, very
small quantity in water
● More nutrients == more productivity
○ Mutually exclusive, either nitrogen xor phosphorus limits an
ecosystem
● Nitrogen (Ammonium) and Phosphorous
○ Excessive amounts (thru pollution) can create a lot of algae
(algal bloom) cuts off marine life underwater from nutrients
above water, taken by algae cuts off oxygen from water
ecosystem
○ Formed by eutrophication materials with nitrogen or
phosphorus leech into a river/lake through sewage lots of algae
● Ecological Efficiency amount of energy moving through an ecosystem, transferred from one
trophic level to the next == 10% ***90% of energy is lost through moving from each level, heat,
cell respiration, growth, waste, etc.
○ Number of organisms also decrease from one level to the next, not enough energy to
support upper levels
○ Energetic Hypothesis limit put on food chain because of ecological efficiency, after 4-5
organisms there is no more energy left
○ Dynamic Stability Hypothesis longer food chains are less stable
 13

Enzymes
● Catalyst - a chemical agent that speeds up a reaction without being consumed by the
reaction
● Enzyme - catalytic protein. Recycled
○ All enzymes are catalysts, but not all catalysts are enzymes
● Hydrolysis of sucrose by the enzyme sucrase (end with -ase)
● Activation Energy Barrier ( E A )- initial amount of energy needed to kickstart a chemical
reaction
○ Often from heat/thermal energy from surroundings
○ Exergonic - lost energy as products (spontaneous)
○ Endergonic - gained energy as products
○ Enzymes catalyze chemical reactions by lowering the activation energy, reactions
occur at lower temperatures
■ Do not have effect on amount of energy produced from reaction (Δ G)
● Substrate - reactant an enzyme acts on
○ Enzyme binds to substrate forming enzyme-substrate complex
■ Active site - region on the enzyme where the substrate binds
● Enzymes are like lock and key, very specific
● Orienting substrates
● Straining substrate bonds
● Providing favorable microenvironment
● Covalently bonding to the substrate
○ Induced fit - substrate brings chemical groups of the active site into positions
that enhance their ability to catalyze the reaction
● Local conditions
○ Optimal temperature and optimal pH (37 C, heat bacteria use 77 C)
■ If not optimal, would denature
■ Decreasing temperature does not denature, just slows down reaction
○ Cofactors
■ Non Protein enzyme helpers
■ May be inorganic (metals in ionic form) or organic (carbon)
■ Organic cofactors called coenzymes bound to enzyme
● Include vitamins, w/o vitamins, some enzymes cannot function
● Inhibitors - stop an enzyme from functioning
○ Competitive inhibitors - resembles substrate, competes with substrate for active
site, reversible → reverse action by adding more substrate, then substrate can
outcompete inhibitor.
 14

○ Noncompetitive inhibitors - bind to different region of enzyme, change shape of

active site, then substrate can no longer bind to enzyme, nonreversible
■ Penicillin - antibiotic, binds to bacteria enzymes → cannot function, kills
bacteria
■ DDT, nerve gas, etc.
○ Regulates enzyme activity → control metabolism
■ Chemical chaos would result if cell metabolic pathways were not tightly
regulated
■ Cell does this by switching on or off the genes that encode specific
enzymes or by regulating activity of enzymes
■ Allosteric regulation - enzymes that can be turned on and off
● Inactive and active forms
○ Activators - lock enzyme to be active
○ Inhibitors - lock enzyme to be inactive
○ Change in shape
● Cooperativity form of allosteric regulation that can amplify
enzyme activity
○ One substrate molecule primes an enzyme to act on
additional substrate molecules more readily
○ Allosteric because binding by a substrate to one active site
affects catalysis in a different active site
● Allosteric regulators are good for drugs because of enzyme
specificity
○ Inhibitions of proteolytic enzymes called caspases manage
inflammatory responses act as inhibitor
■ Feedback Inhibition
● Regulate and shut down metabolic pathways, end product used to
inhibit first step in pathway
● Prevents cell from wasting chemical resources by synthesizing
more product than is needed
● Evolution
○ Proteins formed by amino acid sequence, encoded by DNA
○ Mutations in DNA cause mutations in amino acids and in enzyme
● Localization
○ Structures within cell help bring order to metabolic pathways
○ Some enzymes act as structural components of membrane
○ In Eukaryotic cells, some enzymes reside in specific organelles for example
enzymes for cellular respiration are located in the mitochondria
 15

Metabolism
● Living organisms require a constant input of energy. Biological systems constantly transform this
energy from one form to another in order to carry out all life functions.
● First Law of Thermodynamics- energy cannot be created or destroyed, only transformed from
one form to another.
○ Law of conservation of energy
● Second Law of Thermodynamics- during energy conversions, the universe becomes more
disordered→ entropy increases
● Gibb’s free energy- the way to calculate how much free energy is available to do work within a
cell (G)
○ If energy is released, the reaction is said to be exergonic or exothermic and delta G is
negative
■ Exergonic reactions power the endergonic ones.
○ If energy is absorbed, the reaction is said to be endergonic or endothermic and delta G
is positive
● Metabolism- the sum of all chemical reactions that take place in cells
○ Some reactions break down molecules→ catabolism
○ Other reactions build up molecules→ anabolism
○ Metabolic reactions take place in a series of pathways
■ Each of which serves a specific function.
■ Controlled by enzymes
● Enzymes do not provide energy for a reaction, and they do not enable a reaction to occur that
would not occur on its own.
● Catalytic proteins- speed up chemical reactions by lowering the energy of activation EA
○ What enzymes serve as
○ Energy of activation- amount of energy needed to begin a reaction
● When potential energy of the products is less than the potential energy of the reactants, energy
is released and the reaction is exergonic
● When potential energy of the products is greater than the potential energy of the reactants,
energy is absorbed and the reaction is endergonic
● Transition state- reactive (unstable) condition of the substrate after sufficient energy has been
absorbed to initiate the reaction
● Characteristics of Enzymes
○ Globular proteins that exhibit a tertiary structure
○ Substrate specific
○ Induced-fit model- as the substrate enters the active site, it induces the enzyme to alter
its shape slightly so the substrate fits better.
○ Enzyme-substrate complex- when enzyme binds to its substrate
○ Enzymes are not destroyed in a reaction, they are reused
○ Enzymes are named after their substrate. The enzyme ends with a suffix of “ase”
○ Enzymes catalyze reactions in both directions
 16

○ Enzymes often require assistance from cofactors (inorganic) or coenzymes (vitamins)

○ Efficiency of enzyme is affected by temperature, pH, concentration, and substrate
concentration
● Control of Enzyme Activity
○ Cell metabolism is tightly regulated by controlling when and where different enzymes
are active.
■ This is expressed by switching on and off (the genes) that code for enzymes.
■ Enzymes that have been produced already are regulated by competitive or
noncompetitive inhibition
● Competitive Inhibition
○ Some compounds resemble the substrate molecules and compete for the same active
site on the enzyme
■ Competitive inhibitors (mimics) reduce the amount of product by preventing or
limiting the substrate from binding to the enzyme
● This kind of inhibition can be overcome by increasing the concentration
of substrate
■ Enzymes are allosteric- a change in shape alters their efficiency
● Noncompetitive Inhibition
○ Molecules called noncompetitive inhibitors or allosteric regulators bind to a site
distinct and separate from the active site of the enzyme
○ This binding of the inhibitor to the alternate site causes the enzyme to change shape in
a way that inhibits the enzyme from catalyzing substrate into product
○ Other allosteric enzymes toggle between two different conformations (shapes)
■ One active
■ The other inactive
○ The binding of either an activator or an inhibitor locks or stabilizes the allosteric enzyme
in either the active or inactive form
○ Feedback inhibition- where the end product of the pathway is the allosteric inhibitor for
an enzyme that catalyzes an early step in the pathway
● Cooperativity
○ Type of allosteric activation
○ The binding of one substrate molecule to one active site of one subunit of the enzyme
causes a change in the entire molecule and locks all subunits in an active position.
■ Amplifies the response of an enzyme to its substrates

Metabolism
● Cells have thousands of chemical reactions
● Speed metabolism
○ Balanced meals
○ King in the morning (activate metabolism) prince at noon, pauper at night
● Cell extracts energy and applies energy to perform work
 17

● Catalysis - acceleration of a chemical reaction by a catalyst

● Metabolism transforms matter and energy subject to thermodynamics
● Metabolism - totality of an organism’s chemical reactions
○ Metabolic pathway - begins with a specific molecule (reactant, substrate) and
ends with a product
○ Each step catalyzed by an specific enzyme
● Catabolic Pathway release energy by breaking down complex molecules into simpler
compounds to do work
○ E.g. cell respiration, glucose breakdown, etc.
● Anabolic pathways - consume energy to build complex molecules from simpler ones
○ Protein synthesis e.g. of anabolism
● Bioenergetics - study of how organisms manage their energy resources (metabolic
pathways)
● Chemical reactions
○ Exergonic Reaction
■ High energy reactants and low energy products, net release of energy,
spontaneous negative Δ G
● Break bonds, hydrolysis, catabolic
● Difference between exergonic and catabolic
○ Exergonic is a specific reaction
○ Catabolic is a pathway that’s made up of multiple
exergonic reactions
○ Endergonic Reaction
■ Absorbs free energy from surroundings, nonspontaneous stored in bonds
● Energy from food
● Builds bonds, dehydration synthesis, anabolic
● Forms of Energy
○ Energy is the capacity to cause change, some forms of energy can perform work
○ Kinetic energy associated by motion
○ Heat (thermal energy) kinetic energy associated with random movement of
molecules
■ Heat is not usable energy, wasted
○ Potential energy - energy that matter possesses bec. location and structure
○ Chemical energy potential energy released in chemical reactions (bonds)
○ Energy is converted from one form or another, never appears/disappears
■ Matter and energy can not be created/destroyed
 18

● Free energy - energy that can be used to perform work (needs input = endergonic,
spontaneous = exergonic) usable
○ Delta G (result energy) = G (final) - G (initial) ← net energy
■ == positive → endergonic
■ == negative → exergonic (spontaneous)
● Spontaneous
○ No energy is invested to make reaction happen
● Laws of Energy Transformation
○ Thermodynamics study of energy transformations
○ In an open system (organisms) energy and matter can be transferred between
the system and its surroundings
○ 1st law “Principle of conservation of energy”
■ Energy can be transferred and transformed by it cannot be created or
destroyed
○ 2nd law “Law of Entropy”
■ Every energy transfer or transformation increases the entropy (disorder)
of the universe
● Some energy is unstable, lost as heat
● Evolution of complex organisms does not defy 2nd law of entropy,
as organism becomes more organized, entropy of universe
increases, not within organism bec. Heat is released
○ Living cells unavoidably convert unorganized energy into heat
○ Energy flows into an ecosystem in the form of light and exits as heat
● Spontaneous processes occur without energy input, (quickly or slowly)
○ Occurs without initial energy input to kickstart
○ Free Energy Change = Δ G
■ Δ G= ΔH- Temperature * Delta Entropy
● Delta H = Enthalpy, change in total energy
● Delta Entropy (S), whats lost as heat
● Same as Δ G(result energy) = G (final) - G (initial) ← net energy
○ IF Delta G is negative, it’s a spontaneous process, releases
energy for work
■ A measure of a system’s instability, tendency to change to a more stable
state (high energy)
○ Equilibrium is a state of maximum stability (low energy)
■ System always works towards it in spontaneous process
 19

■ Closed systems can reach equilibrium, then system can no longer be used
for work (matter and energy cannot be transferred between system and
its surroundings)
● Living organisms are all open systems

ATP - (adenosine triphosphate)

● The body’s only usable energy source converted by enzymes
● Energy coupling - put together endergonic and exergonic reaction
○ Energy released by exergonic reaction, endergonic reaction uses released energy
○ Exergonic reaction makes ATP and endergonic reaction uses ATP
● Three types of work (only types)
○ Chemical Work - making chemical bonds
○ Transport Work - transporting materials in/out cells
○ Mechanical Work - physical movement (e.g. muscle contractions)
● Fast metabolism - body efficient to make food → ATP, less likely to store as fat (fast
metabolism → less body fat), more efficient at biosynthesis building
● Structure
○ Has nitrogenous base (adenine) attached to
○ Ribose (carbohydrate)
○ Three phosphate groups
■ All negative charged groups → VERY unstable
■ Lots of potential energy
● Releases energy by hydrolyzing the last (terminal) phosphate group, lots of energy (7.3
cal)
○ Factors: energy is released
○ Phosphate group (more important than energy)
○ Phosphorylation activates things
■ Turns on chemical reactions
■ When phosphate group attaches to reactant from ATP, turns on a
chemical reaction
○ Powers endergonic reactions
● ATP cannot be made by the body, ATP is converted or recycled in the body, regeneration
○ Carbs and lipids regeneration ATP, take in phosphate groups to add back to ADP
(adenosine diphosphate)
■ ATP - full battery
■ ADP (+P) - low battery (little energy) when P is added, create another ATP
● Cell respiration adds phosphate to ADP → ATP
 20

● Extra P brought back through dehydration synthesis

● ATP is unstable (potential energy) if you had all ATP, you would explode, always some
energy in ADP

Enzymes
● Catalyst - a chemical agent that speeds up a reaction without being consumed by the
reaction
○ Reactions end when equilibrium is reached, not when enzyme is used up
● Enzyme - catalytic protein. Recycled globular
○ All enzymes are catalysts, but not all catalysts are enzymes
○ Enzymes’ functions are determined by sequence of amino acids
● Hydrolysis of sucrose by the enzyme sucrase (end with -ase)
● Enzymes are extremely specific, each enzyme only does one thing
● Activation Energy Barrier ( E A )- initial amount of energy needed to kickstart a chemical
reaction used in transition state, activation energy is needed for both exergonic and
endergonic reactions
○ Often from heat/thermal energy from surroundings/environment
○ Exergonic - lost energy as products (spontaneous)
○ Endergonic - gained energy as products
○ Enzymes catalyze chemical reactions by lowering the activation energy, reactions
occur at lower temperatures
■ Do not have effect on amount of energy produced from reaction (Δ G)
○ Enzymes reduce amount of heat needed from environment
■ Enzymes allow chemical reactions to occur at lower temperatures
■ Chemical reactions in body can occur without enzymes, just would be
slower → lots of more energy
■ Speeds up reactions, does not cause them
■ Amount of energy released (Δ G) is unaffected by enzyme
● Substrate - reactant an enzyme acts on
○ Enzyme binds to substrate forming enzyme-substrate complex
■ Active site - region on the enzyme where the substrate binds (most
important part of the enzyme), specific for one substrate
● Enzymes are like lock and key, very specific
● Orienting substrates correctly to collide (physically)
● Straining substrate bonds (breaking bonds, hydrolysis)
● Providing favorable microenvironment
● Covalently bonding to the substrate
 21

○ Induced fit - substrate brings chemical groups of the active site into positions
that enhance their ability to catalyze the reaction
■ Active site changes shape slightly envelops substrate
● Local conditions
○ Optimal temperature and optimal pH (37 C, heat bacteria use 77 C)
■ If not optimal, would denature most importantly, active site will unravel
■ Decreasing temperature does not denature, just slows down reaction
■ Enzymes work at specific temperatures and specific pHs with specific
substrates
○ Cofactors
■ Non Protein enzyme helpers, bound to enzymes
■ May be inorganic (metals in ionic form, cofactor) or organic (carbon)
■ Organic cofactors called coenzymes bound to enzyme, inorganic ==
cofactor
● Include vitamins, w/o vitamins, some enzymes cannot function
● Vitamins are coenzymes, used in chemical reactions that’s why
vitamins are essential
● Inhibitors - stop an enzyme from functioning
○ Competitive inhibitors - resembles substrate, competes with substrate for active
site, reversible → reverse action by adding more substrate, then the substrate
can outcompete inhibitor.
○ Noncompetitive inhibitors - bind to different region of enzyme, change shape of
active site, then the substrate can no longer bind to enzyme, irreversible, enzyme
becomes useless
■ Penicillin - antibiotic, binds to bacteria enzymes → cannot function, kills
bacteria (drugs)
■ DDT, nerve gas, etc.
○ Regulates enzyme activity → control metabolism
■ Chemical chaos would result if cell metabolic pathways were not tightly
regulated
■ Cell does this by switching on or off the genes that encode specific
enzymes or by regulating activity of enzymes
● Regulation of enzyme activity helps control metabolic pathways
○ Cells - switch on or off the genes that encode specific enzymes or by regulating
the activity of enzymes
■ Realistically without enzymes, your body won’t react
○ Allosteric regulation - enzymes that can be turned on and off (allosteric enzymes
and reversible)
 22

■ Occurs when a regulatory molecule binds to an enzyme changes its shape

and active site
■ Allosteric enzymes have 4 active sites (4 polypeptide subunits)
■ Inactive and active forms (active site is changed)
● Activators - lock enzyme to be active
● Inhibitors - lock enzyme to be inactive
○ Natural bodily inhibitor, not noncompetitive or
competitive
● Change in shape
● If you have enough of the enzyme product, the pathway is turned
off (shut off the first enzyme usually first enzyme is allosteric)
○ If you don’t have enough of the product, then not enough
of the inhibitor, pathway is turned on again
■ Cooperativity form of allosteric regulation that can amplify enzyme
activity and response
● One substrate molecule primes an enzyme to act on, locks into
the active form 3 additional substrates can bind
● Allosteric because binding by a substrate to one active site affects
catalysis in a different active site
■ Allosteric regulators are good for drugs because of enzyme specificity
● Inhibitions of proteolytic enzymes called caspases manage
inflammatory responses act as inhibitor
● Drug companies look for chemicals that would be allosteric
inhibitors to the caspase
○ Feedback Inhibition end product of the metabolic pathway inhibits the pathway
■ Regulate and shut down metabolic pathways, end product used to inhibit
first step in pathway
■ Maintain homeostasis
■ Prevents cell from wasting chemical resources by synthesizing more
product than is needed
● Evolution
○ Proteins formed by amino acid sequence, encoded by DNA
○ Mutations in DNA cause mutations in amino acids and in enzyme
● Localization makes sure chemical reactions occur in set places → control amount of
enzymes and where they are released → compartmentalized enzymes
○ Structures within cell help bring order to metabolic pathways
○ Some enzymes act as structural components of membrane
 23

○ In Eukaryotic cells, some enzymes reside in specific organelles for example

enzymes for cellular respiration are located in the mitochondria

NUTRIENT CYCLING AND WATER

● Ecosystems:
○ Factors:
■ Abiotic: nonliving (pH, sunlight, altitude, sand, rocks, water, etc.)
● Abiotic factors control the living factors
■ Biotic: living (organisms: plants, bacteria, animals, etc.)
○ Ecosystems include both abiotic and biotic factors
● Carbon Cycle
○ RE: In atmosphere through burning fuels,
○ A: Plants take in carbon through photosynthesis
○ A(cont.):Consumers eat the plants
○ R: Consumers have cellular respiration which produced CO2
■ Universal Release: Decomposition
● Phosphorus Cycle:
○ RE: rocks
○ A: plants absorb from soil, consumers
○ R: decomposition, waste excretions
● Major solutes in water: sugar, and sodium 180 g glucose = 1 mol so 180g/1L = 1mol
● Fresh water: 0 mol
● Water gives life to all organisms
○ Oxygen’s electronegativity: pulls electrons towards it
■ What makes water polar
■ Held together by covalent bond (sharing electrons)
● Electrons not shared equally, pulled closer to oxygen in H2O.
● Therefore hydrogens become partial positives and oxygen a
partial negative
○ Polar Covalent Bonds - (strong bonds)
■ Uneven distribution of charge
■ Water’s polarity forms hydrogen bonds - (weak bonds)
● Bond between other molecule’s hydrogen and other water
molecule’s oxygen
■ Collectively a strong force of water molecules, each molecule connected
to four more molecules
■ Cohesion - water sticking to water
● Capillary action - (transpirational pull)
 24

○ Water is pulled up, water molecules at top attracted

higher to other molecules, water attracted to that water
moves up.
○ Xylem cells in trees transport water around the tree
○ Transpiration: water evaporating off of a plant, water
evaporates through plant and up through the tree
■ Adhesion, water sticking to other molecules
■ Water resists temperature change
● High specific heat (H2O = 1 cal/gram to change 1 mL of water by 1
degree (in Celsius) = 4.168 J/gram)
○ 30 mL by 1 degree: 4.168 J * 30 mL * 1 C
○ 30 mL by 30 degrees: 4.168 * 30 mL * 30 C = number in
joules
● Aquatic organisms live in constant environment
○ Land isn’t as stable, more temperature fluctuations
● Animals can maintain constant internal temperature
● High heat of vaporization (evaporation)
○ Temperature a measure of kinetic energy, (energy of
movement) measure of how fast molecules are moving
○ Evaporative cooling - hottest water evaporates first when
sweating, cooling down skin so lower temperature water
remains (negative feedback)
■ Expands on freezing
● Solid has rigid hydrogen bonds, which are larger and farther apart
● Becomes less dense, why ice floats
● Ice on top of water would sink if didn’t happen, aquatic organisms
would die
● Ice insulates lakes
● pH
○ Water doesn’t always stay water, can break down into OH- and H+ (ions) and can
convert back to water
■ Hydrogen H+ ions (protons)
■ Hydroxide OH- ions
○ Acids/Bases affect the ratio of hydrogen ions to hydroxide ions
■ More H+ ions == Acids increases ratio in water
■ More OH- ions == Base decreases ratio in water
○ HCl in water breaks down into H+ and Cl- ions, HCl == acid, increasing H+ ions
■ Donor of protons
 25

■ Strong acid because NOT reversible to HCl, now only H+ and Cl-
○ Strong base == NaOH-
■ Breaks into Na+ and OH-
■ Basic because increases OH- amounts
○ Weak acids vs. strong acids
■ H2CO3 (carbonic acid) - weak acid
● Converts to H+ and HCO3
○ *** weak because reaction is reversible
○ NH3 (ammonia) base
■ NH3 + H+ →← NH4 (ammonium)
● Accepts hydrogen, so it increases ratio of OH- to less H+
● Takes away a H+ from water solution, so less H+, ergo basic
○ Acids == donate H+ ions
○ Bases == donate OH- OR accept H+
■ If H in reactants, must be a base
○ pH is a measure of H+ ions,
○ Pure water = 1/10,000,000 moles of hydrogen ions == ph of 7
■ 0.0000001 mol/L of H+
● 10-7 (neutral)
● Means 10-7 Hydroxide (equal amount) add then == 10^-14
○ pH of 6 (10^-6) has 10 times more hydrogen ions than ph 7,
■ pH 7 == .0000001
■ pH 6 - 10x times (more H+)
■ pH 5 - 100x
■ pH 4 - 1000x
■ pH 3 - 10000x == .001
○ Lower pHs are more acidic
○ If you have (pH 8) 10-8 H+ you have 10-6 OH- (exponents always add to 14)
● Buffers
○ Combinations of H+ donor and H+ acceptor forms of weak acid/bases
■ Keep pH STABLE NOT NEUTRAL
■ Combo of weak acid and weak base
● H2CO3 (carbonic acid) and HCO3 (bicarbonate, base) regulate
blood pH
● H2CO3 →← HCO3- + H+
● Ocean acidification
○ Increased amounts of CO2 in the atmosphere
■ CO2 + H20 → H2CO3, reacts with seawater (creates carbonic acid)
 26

● Making oceans acidic

○ Coral relies on calcium carbonate (CaCO3) for shell making
■ Made by putting together Ca and CO3
● Instead Carbonate reacts with excess H+ and making bicarbonate
○ CO3 + H+ → HCO3
● Coral has less carbonate to make shells, reefs are dying can’t use
bicarbonate

● Photosynthesis - the most important reaction in all of nature, makes food

○ Converts solar energy into chemical energy
○ Directly and indirectly nourishes all living things
● Autotrophs/Producers - organisms that produce their own food through photosynthesis
○ Algae (protist, eukaryotic organism), plants, cyanobacteria - first living organisms to
perform photosynthesis
● Heterotrophs/Consumers - must eat in order to obtain energy, eating products of
photosynthesis
● Energy (light, invested energy) + 6CO2 + 6H2O → C6H12O6 + O2
○ Opposite of cell respiration (which is exergonic, produces ATP), photosynthesis is
endergonic
■ Water is oxidized to O2, CO2 is reduced → glucose
● Photosynthetic part of a plant (organ): Leaf
○ Holes in leaf: stomata, where water evaporates (transpiration) and CO2 enters and O2
leaves
■ Creates transpirational pull from roots
● Xylem are cells that water travels through
■ Plants want water to evaporate out of the plants, no transpirational pull without
evaporation
● Plant would dehydrate if too much water evaporated, need to balance
transpiration
■ Increase transpiration and dehydration
● Heat (temperature)
● Dryness (humidity)
● Wind
○ PHOTORESPIRATION
○ STOMATA CLOSE to balance out environment with the guard
cells
■ Calvin Cycle cannot occur (no CO2) can’t make sugar
■ RuBisCo can ALSO fix O2 to RuBP in place of CO2 → cant
produce G3P
● Wastes NADPH and ATP
 27

■ C3 Plants make 3-Carbon compound, PGA in the calvin

cycle
■ C4 Plants live in dry conditions (midwest), have
adaptations to prevent photorespiration → STORE
CARBON DIOXIDE
● Doesnt matter if stomata are closed or open
● Used stored CO2,
● C4 Plant
○ Uses enzyme PEP Carboxylase → pulls
in CO2 stores carbon as 4 carbon
molecule Oxaloacetate
○ Calvin cycle takes place in Bundle-
sheath cell, but still have mesophyll
cells
■ CAM Plant - the extremes (cacti, desert plants)
● Store carbon as crassulacean acid, organic acid
● CAM Plant opens stomata at night (when it
cools down)
■ More stomata on bottom, if more on top plant would dehydrate
■ Guard cells: flank stomata, control if stomata are open, closed, where gasses
enter and leave, (O2/CO2), water can evaporate out of the stomata →
transpiration (transpirational pull)
○ Mesophyll- part of a leaf that contains lots of photosynthetic cells
■ Cells contain chloroplast - double membrane, inside are pancake shaped discs
called thylakoids, and stacks of thylakoids = granum
■ Fluid in membrane outside thylakoids called stroma
● Two reactions:
○ Light Reactions - light (photo) inside the thylakoids
■ NADP+ and ADP + P, take H2O and oxidize it, produce NADPH, and ATP, O2 as a
byproduct,
■ Light to make ATP - photophosphorylation
○ Calvin cycle (The Dark Reactions)- synthesis (builds molecule) inside stroma
■ Major reactant in cycle: CO2 reduced and given electrons/protons, creates
glucose, given by NADPH gives CO2 the electrons/protons. Electrons - energy
■ Powered by ATP
● Purpose of producing glucose?
○ Glucose is used for everything:
■ Sugar → cell respiration, used to make ATP to grow plant
■ Sugar = structure, cellulose (long chain of glucose)
■ Sugar = energy storage, starch
● Light - electromagnetic radiation
○ Shorter wavelength -- high energy (UV, gamma, X ray)
 28

○ Longer wavelength -- low energy (infared microwaves, radiowaves)

○ Different colors correspond with different wavelengths, visible light in the middle of
spectrum
○ Chlorophyll a is the main photosynthetic pigment
○ Accessory pigments such as chlorophyll b broaden the spectrum used in photosynthesis
○ Xanthophylls - yellow
○ Carotenoids - orange
● Reflect (bounce off) vs Transmitting (go through)
○ No light is absorbed by cell
○ Green light cannot be used by plant, would die
○ Plants absorb red and blue light the best
● Color of sky depends on molecular composition of atmosphere
● Spectrophotometer - put sample of light in, tells level of transmittance or absorption
○ Shoot green light through chlorophyll, high transmittance (low absorption)
○ Shoot blue light through chlorophyll, low transmittance (high absorption)
● Absorption Spectrum - graph plotting a pigment’s light absorption versus wavelength
○ Larger spectrums,
● Action Spectrum - profiles the relative effectiveness of different wavelengths of radiation in
driving a process, totality of spectrums
● Pigment - molecule that will absorb or reflect a wavelength
○ Color determined by what it reflects
● Trees go dormant in winter, chlorophyll dies, only see carotenoids and xanthophylls (yellow +
orange), not enough sunlight
● Engelmann’s Experiment
○ Grew algae under different wavelengths
○ Grew aerobic bacteria on top of the algae, large growth on opposite sides of spectrum,
none in green because algae isn’t photosynthesizing there
● Plants not black because would absorb every wavelength, overheat, proteins denature
● Chlorophyll has a Magnesium center (a vs. b has difference of one func. group)
○ Mg holds on to electrons, electrons from water and NADPH
○ Accepts unit of light - photon, excites electron, gives power to electron

CELL COMMUNICATION + APOPTOSIS

● Cells communicate with each other via chemical signals
○ Intro to nervous and endocrine systems
○ Cell-to-cell communication is essential for all organisms
○ E.g. flight or fight response is triggered by a signaling molecule (epinephrine)
● Signal Transduction Pathway: series of steps that take place when a signal binds to a cell
(message delivered) and converts it into a specific cellular response
○ Ligand binds to receptor → induces series of reactions for cell response
 29

○ Pathway similarities suggest that ancestral signaling molecules evolved in

prokaryotes and were modified later in eukaryotes
● Ligand - things that bind to receptors and trigger signal transduction pathways
○ Neurotransmitters: SYNAPTIC SIGNALING nervous system ligands, how nerves
communicate with target cells thru a synapse, enter synapse through exocytosis,
doesn’t travel a far distance in synaptic cleft (ergo local)
■ Bind to receptors like GPCR (epinephrine), RTK (growth factors), or ligand
gated
○ Hormones: ONLY LONG DISTANCE, sent thru bloodstream
○ Growth Factors: most important ligand PARACRINE SIGNALING trigger cell
division, cause growth and repair. Don’t travel a far distance. Fix damaged parts
of the body. Large role if cancer occurs
● Local Signaling: animal cells may communicate by direct contact, or cell-cell recognition,
info not sent very far
○ Gap junctions: cells are tightly bound and act as one unit (heart pumping)
○ Plasmodesmata: rigid cell walls make diffusion difficult between plant cells, they
have plasmodesmata tubes instead
○ Cell-to-Cell Recognition: can determine if self or nonself using glycoproteins
○ Synaptic signaling- use neurotransmitters for neurons to communicate to target
cells
○ Paracrine signaling- use growth factors, can repair wounds
○ Affect nearby cells, do not enter bloodstream
● Long-distance Signaling:
○ Released in the bloodstream by endocrine system (hormones)
■ Every cell in body is exposed to hormone, only cells with receptors
respond to the hormone
■ Target cell is the cell being communicated wit
■ Growth hormone: grow a lot of cells, growth factors only affect nearby
cells, hormones in the bloodstream
● STEPS
○ Reception: signaling molecule (ligand) binds with protein in membrane
■ Only if the ligand is accepted by the cell’s membrane proteins
○ Transduction: in a pathway to relay the message to the rest of the cell using
protein kinases
○ Response: a response
RECEPTION
● Receptors: specific membrane proteins that receive the ligands and trigger transduction,
ligands that bind to ion channel, GPCR, RTK has to be polar
 30

○ (G protein-coupled receptors) GPCR Receptors: largest family of cell surface

receptors, include epinephrine
■ G-protein normally an inactive protein but activated when ligand binds to
it (epinephrine and using GTP), sent on a mission by receptor to trigger a
cell response
○ (Receptor tyrosine kinases) RTK Receptors: Growth factors, any broken receptors
associated with cancer
■ Responds to ligands like growth factors
■ Causes cell division
■ Malfunctioning RTKs causes cancer
■ Phosphorylates relay proteins
○ Ligand-gated ion channel: acts as a gate when the receptor changes shape, e.g.
neurotransmitters
■ In nervous system: e.g. sodium & calcium channels
■ Have a gate, and the only way to open it is to have a ligand bind to it, K+,
Ca+ or Na+ can enter/leave the cell
○ Intracellular receptors: proteins found in the cytosol or nucleus of target cells,
receives NONPOLAR hormones
■ Small or hydrophobic chemical messengers can readily cross the
membrane and activate receptors
● E.g. testosterone, or estrogen (steroids)
○ Binds to protein in nuclear envelope and initiates
transcription
○ Activated hormone-receptor complex can act as a
transcription factor, turning on specific genes
TRANSDUCTION
● Protein Kinase: 2nd messengers perform transduction where message is relayed
throughout the cell. Proteins that are specialized activated thru phosphorylation
“Passing the baton” (relay message), causes a chain
○ Phosphorylation Cascade: series of activated protein kinases that receive and
transport the relay molecule (using ATP) often involving 2nd messengers
● Message relayed throughout the cell, prompting a cell response
● Using a series of protein kinases using phosphorylation
○ Responsible for passing the message through the cell using a phosphorylation
cascade , passing the relay message as a baton
● Second Messenger: anything not a protein kinase that performs transduction/relay the
message; water-soluble molecules or ions that spread throughout a cell by diffusion.
Participate in pathways initiated by GPCR and RTK.
 31

○ Cyclic AMP (cAMP)

■ Most common 2nd messenger
■ Created using Adenylyl cyclase by taking ATP and cutting off two
phosphates (becomes adenosine monophosphate)
■ E.g. epinephrine binds to GPCR and G protein phosphorylates adenylyl
cyclase and makes cAMP and cAMP activates a protein kinase
○ Ca+++ (calcium ions)
■ Cell can tightly regulate Ca concentration (active transport) in ER and
mitochondria
■ Can activate IP3 or DAG
○ IP3
○ Diacylglycerol (DAG)
RESPONSE
● Cell Response: depends on the pathway within the cell leads to regulation of
transcription or cytoplasmic activities or “output response”
○ Many signaling pathways regulate the synthesis of enzymes or other proteins
usually by turning genes on or off in the nucleus
○ Other pathways regulate the activity of enzymes rather than their synthesis
○ Signal pathways can also affect the overall behavior of a cell, for example,
changes in a cell shape
○ Initiate transcription: begin production of proteins within the cell, control what
happens in the cell
■ E.g. testosterone, estrogen, progesterone
○ Change cell behavior: tell the cell to do something
■ E.g. yeast (fungus) cells mating (making shmoos, induce change in cell
shape) produce actin microfilaments (for cell movement and shape) to
form cortex for changing cell shape (shmoo)
■ Muscle contractions
■ Pheromones: externally released ligands for organism-to-organism
communication
○ Activate enzymes: control what chemical reactions the cell is able to perform
■ Apoptosis (1. DNA mutation, 2. Misfolded protein, 3. Death signal)
○ Active or suppress genes: triggered by growth factors and hormones
● Fine-Tuning of the Response
○ Amplification of the Signal (and response): enzyme cascades amplify the cell’s
response the number of activated products is much greater than in the
preceding step
■ Small amount of ligand create a large response
 32

■ All of the proteins relaying the message can amplify the response, can
activate many enzymes
○ Specificity of the Response: pathway within the cell dictates the response given
from that ligand
■ Cell can only respond if they have the receptor but the pathway
determines what that response is
○ Efficiency of the Response: increased using scaffolding proteins hold many relay
proteins in one location. Have proteins associated with pathway close together
to make pathway faster
○ Termination of the Signal: unbound receptors revert to an inactive state
● Specific Responses
○ Apoptosis: controlled cell death using lysosomes’ hydrolytic proteins (proteases,
amylases [carbs], nucleases, etc.) cells in a vesicle the vesicles are taken in by
white blood cells and digested
■ Lysosomal enzymes are released in the cell and break everything down,
package everything into vesicles and WBC phagocytosis consumes the
vesicles
■ Release of “death-signal” binds to receptor initiation of phosphorylation
cascade and activates nucleases (nucleic acids) and proteases (protein)
that break down the cell
● Activate enzymes mainly caspase
■ Reasons: normal development, selectively killing particular cells (finger
webbing removal, more space between digits) embryonic development
● Triggered by DNA damage (mutation) in the nucleus
● Extracellular death ligands (signals)
● Protein misfolding in the nucleus (e.g. alzheimer's, parkinson's)
■ Mutations cause cancer and disease so it’s better to destroy the cell →
when things go awry apoptosis is the safeguard
■ Evolved in early animal evolution and is essential for development and
maintenance of all animals
■ Interference with apoptosis may cause cancer
■ Caspases are the main proteases (enzymes that cut up proteins that carry
out apoptosis)

BODY SYSTEMS
● Temperature just == average kinetic energy
● Shape and size affect the way an animal interacts with its environment, they are the way that
they are because of their environment
 33

● Materials such as nutrients, waste products, and gases must be exchanged across the cell
membranes of animal cells (organisms contribute to environment, not just take substances from
environment)
○ Digestive System - take in food and drink
○ Respiratory System - take in oxygen for cell respiration
○ Excretory System - get rid of waste
■ ALL have lots of surface area for organs of exchange
● Circulatory System- connects all the organs of exchange with all regions of the body for
transport of substances by vessels, makes organisms large and complex, otherwise just rely on
diffusion to move things in the body
● Rate of exchange is proportional to the cell’s surface area while amount of exchange material
is proportional to a cell’s volume
○ E.g. rabbit as large thin ears full of blood vessels in order to dissipate heat
● Hierarchical Organization of Body Plans
○ Organelle → Cell → Tissue → Organ → Organ System → Organism
○ Tissues perform specific functions for organs
○ All things first originate as things that first happen in your cells
○ Cells are the most basic unit

TISSUES
● Tissue Types every organ contains every tissue type
○ Epithelial - surface tissue, covers every surface of the body for protection
■ Skin is not epithelial tissue, it’s an organ; only outside has epithelium
■ Densely packed cells
○ Nervous - senses stimuli and transmits signals throughout the animal
■ Neurons: transmit nerve impulses
■ Glial Cells outnumber neurons that nourish, replenish and replenish neurons
(insulation, e.g. schwann cells)
○ Muscle - produces movement
■ Skeletal: voluntary movement of bones, striped appearance because of
striations
■ Cardiac: involuntary movement of blood by the heart only muscle the body that
doesn’t get tired
● When you do cardio heart hypertrophizes (gets larger)
■ Smooth: lacks striations, causes movement inside body (involuntary) peristalsis -
wave movement of smooth muscle, lines internal passageways (vessels,
esophagus, intestines, etc.)
○ Connective - gives body support and structure, extremely varied, if they can’t classify it,
put it in connective tissue
■ Binds/connects parts of the body together
 34

■ Has very little actual cells, mainly made up of spacious extracellular matrix
● Collagen - strongest protein in the body (most important)
● Elastin (elastic fibers) - provides for stretchiness, amount of elastin can
determine if you get stretch marks
● Reticular Fibers - bind things together (glue like proteoglycan)
● Fibrous Tissue: strong collagen, tendons (muscle to bone) and ligaments
(bone to bone)
● Loose Tissue: has a lot of reticular fibers, hold thing together (e.g.
fascia) glue
■ Fibroblasts - make components of ECM, cells in connective tissue
■ Cartilage: strong lubricant between bones → fat pads
● Meniscus in knee
■ Bone: made of collagen and calcium and phosphorus
■ Blood: who knows why lel
■ Adipose: fat

THERMOREGULATION
● Regulators: organism that stays constant no matter what
○ ENDOTHERMIC (warm-blooded): generate heat by metabolism
■ Maintains body temperature no matter what
■ Always need food, to maintain body temperature (fuel reactions → heat)
○ Most active species
● Conformer: organism that changes along with environment
○ ECTOTHERMIC (cold-blooded): gain heat from external sources
■ Body temperature conforms to environment
■ Doesn’t have to eat as much as endotherms
○ No set points
○ Often live in warm environments, to keep up with metabolic processes
○ More likely to survive
● Heat Gain and Loss Regulation
○ Integumentary System: involves skin, hair and nails, covers your external body
■ Insulation: skin, hair, fur, blubber, feathers, etc. to reduce the amount of heat
lost to the environment
○ Circulatory System: bloodstream, and holds heat
■ Regulation of blood flow near the body surface significantly affects
thermoregulation
■ In the cold, you constrict blood flow to extremities to conserve heat in your
torso to internal organs, limbs are deprioritized
■ Vasoconstriction: in cold weather, blood goes to the core, constricted from
flowing to extremities
● Give off less heat
 35

■ Vasodilation: blood vessels get larger, and blood flows more to the face and
extremities to cool down the center body
● Give off more heat
■ Countercurrent Exchange:
● Arteries: are thick and take blood away from the body (away from
heart, AAaartery Aaaway) CONTAINS WARM BLOOD, coming directly
from core/heart of the body
● Veins: carry cold blood back to the heart, comes back from extremities
● Arteries and veins run TOGETHER in PAIRS, stops the extremity from
getting too cold by physically heating the vein next to the artery

■ Evaporative Cooling (Sweating):

● Water has a high specific heat (a lot of energy to change the current
temperature of water, amount of mJ 1 ml of water by 1 C), therefore it
takes a lot of energy to make water evaporate, the surface of the object
it evaporates off becomes cooler because all the energy is expended
when evaporating the water
● Reason humans lost their fur, in a Savannah Africa (hot conditions)
● Dogs evaporate through their tongues that why their face is open just
like crocodiles and alligators
○ Behaviors that regulate body temperature (both ecto and endotherms)
■ Lizard when it’s cold will bask in the sun
■ Lizard when it’s hot will go in the cool mud
 36

○ Metabolic Heat Production:

■ Thermogenesis: “shivering” to adjust metabolism, tiny muscle contractions that
produce heat to heat up body
Bioenergetics
● Energy efficiency is 10% so the other 90% is given off as heat (body temperature) → → →
HYDROLYTIC BREAKDOWN OF FOOD THRU DIGESTION
● Basal Metabolic Rate (BMR): metabolic rate at rest, measure of heat
○ Endotherms have a higher resting metabolic rate in order to maintain high body
temperature
○ Slows down in cold conditions and gets faster in hot conditions

NERVOUS AND ENDOCRINE SYSTEMS

● Systems work together in communication. Allow parts of the body to communicate to each
other
● Nervous system response depends upon the pathway (which places in the body are connected)
and neurotransmitters (signal)
● Endocrine system is purely dependent on the chemical messenger
○ Every cell in body comes in contact with that hormone
○ Only cells with a receptor can respond to a receptor
● Homeostasis: stable unchanging internal environment
○ Organisms need to maintain homeostasis, in regards to an ever-changing external
environment
○ Maintained using negative feedback
● Negative Feedback
○ Set point: an original amount or condition, set by hypothalamus, desired condition
■ Fever: hypothalamus changes set point to a high temperature to run immune
system on hyperdrive (speed reactions) to fight illness
○ Stimulus: causes you to move away from the set point
○ Response: attempt to reach back to the set point
○ NOT FEEDBACK INHIBITION, feedback inhibition is where the final product stops the
metabolic pathway, uses allosteric enzymes to control reactions
■ Negative feedback regulates much larger things (blood-sugar levels, and body
temperature)
● Positive Feedback
○ Does not maintain homeostasis
○ Like cooperativity, where one enzyme binds activating more enzymes
○ A stimulus pulls you away from the set point, and then your body keeps going away
from set point
○ E.g. breastfeeding, or uterine contractions

NERVOUS SYSTEM
 37

● Sensory Receptors: detects things from the environment (e.g. olfaction, photoreceptors (light)
transmit using the optic nerve in PNS, pain, thermoreceptors, touch, stretch receptors, etc.)
○ Create Sensory Input take info from PNS receptors and gives it to the Central Nervous
System (spinal cord)
● Integration: processing the information by interneurons in CNS
● Motor Output: outgoing message, information is taken from the CNS (spinal cord) and is taken
to areas of the body called effectors (usually muscles) to generate a response, performed by the
PNS
● Central Nervous System (CNS): receives info from PNS, brain AND spinal cord
● Peripheral Nervous System (PNS): branch off spinal cord, gives info to CNS thru sensory
receptors, receiving information from CNS by motor neurons
○ Sensory Division (Afferent) info to the CNS
■ Can sense from both internal and external environment
○ Motor Division (Efferent e stands for exit) info away from CNS
● Autonomic Nervous System: technically in the motor division of the PNS
○ Have no control over this part of the nervous system
○ Parasympathetic Division: hibernation and conservation, does the opposite, increase
energy conservation, causes metabolism to slow
■ In the face of starvation, or when you need to hibernate
■ Body temperature goes down, e.g. sleep
○ Sympathetic Division: responsible for creating a fight or flight response, activated by
epinephrine/adrenaline
■ Mass release of energy, all other body functions are cut off in order to save your
life
● Each response is initiated by a nerve/wire that physically connects parts of the body
● Neuron types
○ Sensory Neurons (PNS): a lot of dendrites that are rich in sensory receptors, has a long
axon
○ Interneurons (CNS) lots of terminal branches and dendrites, but SHORT AXON, doesn’t
take information long distances INHIBITORY, and prevents nerve impulses--brain tries to
prevent you from doing stupid things
■ Glial Cells: NOT neurons, but are helper cells that aid neurons through
insulation and nourishment, like schwann cells. Outnumber neurons in the
nervous system
○ Motor Neurons (PNS) has few dendrites (doesn’t take a lot of sensory input), has a lot of
terminal branches/dendrites
● Reflex: something automatic and doesn’t require the brain
○ Automatic: much faster response for survival
○ Brain can override reflexes if you think about it
 38

● Knee-Jerk Reflex: to test all three components (motor, sensory, and interneurons are working
properly) of the nervous system. Hits the patellar tendon, and the message is sent to and from
the spinal cord
○ Quadriceps: muscle on top of leg that kicks the leg out
○ Hamstring: pull your leg in muscle
○ Two things happen simultaneously
■ Make quads contract
■ But inhibit the hamstrings (if not inhibited would prevent action from
happening)
○ Sensory neurons in legs synapse with motor neurons in spinal cord, one tells quads to
contract, other tells the hamstrings to contract, the motor neuron to the quads is cut off
○ Reflex Arcs have all three parts of the nervous system working together

NERVE IMPULSES/ACTION POTENTIAL

● Neurons have a membrane potential (difference in charge across a plasma membrane)

○ Electrochemical Gradient: both chemical and electrical gradients
■ Sodium wants to go in, bec. Lots on outside
■ Potassium wants to go out, bec. Lots on inside
■ Negative on inside wants to go to positive on outside
● RESTING POTENTIAL: positive charge on the outside of the neuron and negative on the inside (-
70 mV) created by Na/K pump
● Sodium/Potassium Pump (Active Transport, requires ATP): pumps K+ and Na+ against their
gradients to create gradients
○ Pumps 3 Na out and 2 K in: both positive
■ Pump out more positive than negative, so outside of membrane becomes more
positive (lots of Na) and inside is more negative because of (K)
■ Anions and Chloride are also in there to contribute to negativity
● Excitable Cell: can change its membrane potential (change which side is positive/negative)
○ If the charges flip across the membrane (reversal in membrane polarity/charge) is called
an action potential: electricity is this movement of charge
■ All or none, either it occurs or it doesn’t
○ Gated-ion channels: opened by specific things to allow Na/K thru (two types, Na
channels and K channels so total: 6 types of Na/K gated-ion channels)
■ Ligand-gated: receives neurotransmitters
■ Stretch-gated: opened to physical stretching
■ Voltage-gated: reaching a certain mV (charge)
○ Hyperpolarization: neuron becomes more negative caused by K channels opening and K
leaving the neuron
 39

○ Depolarization: neuron becomes more positive caused by Na channels opening and Na

entering the neuron
■ Can cause an action potential, reach action potential faster
● Falling dominos:
○ When an action potential is triggered, Na+ flows into the membrane and makes
neighboring regions positive, thus those regions reaching the threshold
○ CANNOT TRAVEL BACKWARDS, the previous region is in its refractory period and cannot
be stimulated.
● Saltatory Conduction
○ Action potential jumps from node of ranvier to node, the schwann cells block off large
regions of the axon so the action potential has to occur in jumps, speeds up the action
potential
○ MS (multiple sclerosis) and ALS, schwann cells are deteriorating, nerve impulses slow
down → bad communication
● SEE NERVE AND ACTION POTENTIAL DIAGRAMS

● Signal Conversion
○ At the end of the terminal bulb, Calcium channels instead of sodium channels
open, Ca+ enters the bulb → causes neurotransmitters to enter synaptic cleft
and initiate a signal transduction pathway
○ Vesicles inside of terminal bulb store neurotransmitters (proteins) the golgi
packages the neurotransmitters and it goes to the terminal bulb → uses
exocytosis to leave the bulb and to enter the synapse
○ Can connect to other neurons/target cells (would connect to neuron’s dendrites

NEUROTRANSMITTERS
● Either bind to ligand gated sodium or potassium channels in neuron’s dendrites
○ Inhibitory: If it opens a K channel, becomes more negative by K leaving the cell
(hyperpolarized) inhibit action potential
■ IPSP (Inhibitory Post-Synaptic Potential): inhibits an action potential
○ Excitatory: If it opens a Na channel, becomes more positive by Na entering the
cell (depolarized) toward an action potential
■ EPSP (Excitatory Post-Synaptic Potential) triggers an action potential
○ Neurotransmitters are either inhibitory or excitatory
○ Each neuron is connected via dendrites to many other neurons to receive signals,
and has many terminal bulbs to send signals
● All action potentials are the same, but neurotransmitters (signals) are really what
changes the message
 40

NEUROTRANSMITTERS
Either excitatory (cause action potential) or inhibitory (prevent action potential)
● Epinephrine: excitatory in the CNS (sympathetic response)
○ Causes activation of sympathetic nervous system in the flight or fight response
● Dopamine: excitatory in the CNS (pleasure response, motor systems)
○ Used to tell motor neurons to contract
○ Lack of dopamine → parkinson’s disease cannot tell muscles to contract properly
○ Too much causes schizophrenia: excitatory, can cause parts of the brain to be
excited that aren’t supposed to be excited → hear and see things that aren’t
really there
● Serotonin: inhibitory in the CNS (lack of can make you depressed)
○ A sense of content/fulfillment → satiated
○ Can cause clinical depression when there is a lack of it
○ Mostly released in the digestive system; food = goodt
● GABA: inhibitory in the brain (makes neuron less excitable)
○ Major inhibitory neurotransmitter in the brain
○ Prevents an over-excited brain (anxiety, high-strung, etc.)
■ Ignorance = bliss
○ Opposite of Glutamate
● Acetylcholine: secreted at the neuromuscular junction: triggers muscle contraction,
excitatory.
○ Released at synapse btwn. neuron and muscle, used in controlling muscle
contraction with dopamine
○ Lack of acetylcholine causes alzheimer’s (need it for memory)
● Glutamate: excitatory in CNS (learning)
○ Major excitatory neurotransmitter in the brain
○ Causes learning, too much glutamate causes high-string, anxiety
○ Opposite of GABA
● Endorphins: inhibitory in CNS (blocks pain, pleasure)
○ Part of the fight or flight response or injury
 41

○ You don’t feel pain in that part of the body, it’s part of the brain’s response
○ Part of euphoria (runner’s high, and morphine)
 42

ENDOCRINE SYSTEM
● All about control and homeostasis
● Releases hormones in the bloodstream, so it takes a longer period of time to initiate a
response and is also longer lasting
● Used for regulation rather than coordination like the nervous system
● Endocrine Glands: release hormones into the bloodstream

● Pituitary Gland: part of the brain AND THE NERVOUS SYSTEM (not endocrine) and has
the ability to secrete hormones
○ Made of neurosecretory cells hormone making cells that are the exception and
not part of the endocrine system
 43

● Chemical signals/hormones bind to receptor proteins (polar hormones, proteins) or

within the target cell (nonpolar steroids usually, lipids)
○ Hormones are either proteins or lipids
○ Steroid Hormones: go thru cell membrane and bind to receptors within the cell
■ Control production of proteins and activation of genes
● Local Regulators (NOT hormones)
○ Not hormones because they are released by paracrine glands to nearby cells,
not in the bloodstream
○ Growth Factors: cause cells to divide, to develop tissues and organs
(peptides/proteins)
○ Nitric Oxide (NO): causes blood vessels to dilate especially when exerting
yourself
○ Prostaglandins (PGs): causes pain and inflammation (like during childbirth)
● Major Endocrine Glands
○ Pineal Gland
○ Pituitary Gland
○ Thyroid Gland
○ Parathyroid Glands
○ Thymus
○ Pancreas
○ Adrenal Glands
○ Testes/Ovaries
● Tropic Hormones: released by one gland and travels to another gland
● Pituitary Gland: master gland of the body
○ Controls all of the other glands
○ Releases a lot of tropic hormones
○ Posterior Pituitary Gland
■ ADH antidiuretic hormone causes you to retain water in kidneys, pee less.
Diuretics inhibit ADH production so you dehydrate.
● Regulates blood osmolarity: amount of solute in your blood
○ High osmolarity (too much solute and little water) →
dehydrated
■ Hypothalamus “want center” makes you feel
thirsty
○ Low osmolarity (too little solute and too much water) →
overhydrated
○ Parathyroid Gland: releases PTH to raise blood calcium levels
 44

■ Hyperparathyroidism: too much PTH production causes bones to break

down causes osteoporosis
○ Thyroid Gland: releases calcitonin which lowers blood calcium levels
○ Pancreas: releases insulin which is used to lower blood sugar levels and glucagon
which affects liver and causes stored carbs (glycogen) to be broken down and
released into the bloodstream as glucose
■ Type I Diabetes: cannot produce insulin → autoimmune disorder bec.
Beta cells in pancreas are attacked by immune system. Glucose you eat
stays in your bloodstream.
■ Type II Diabetes: caused by bad diet and lack of exercise, if you
constantly eat sugar, you release more insulin which causes body to
create more insulin receptors. All receptors need to be filled in order to
have the same response (TOLERANCE), eventually the insulin response is
exists no more

CELL CYCLE AND DIVISION (MITOSIS) NOTES

● Function:
○ Reproduction: only unicellular organisms reproduce using this process
○ Growth: multicellular development, get bigger by getting more cells
○ Repair: replace old, dead, and worn-out cells

GENOME
● The Genome: all of your genetic information, every cell has a copy, and all 23,000 genes
○ DNA molecules are packaged into chromosomes, there are 23 pairs of chromosomes,
too condensed for access to DNA
■ DNA wrapped in coils around histones to condense long DNA
● Nucleosomes (beads on a string): DNA (string) wrapped around
histones (beads)
■ Chromatin: a bunch of nucleosomes, it’s the material that makes up
chromosomes, becomes condensed and turns into a chromosome (in mitosis),
only when undergoing mitosis can we have access to DNA because it’s too
condensed to see in chromosomes
● Gets looped when a cell divides, and loops again to condense it →
chromosome
● In interphase, chromatin is loose and open
■ Paired because one half is from dad and one half is from mom
○ Cells need to make a copy of its entire genome to divide
○ Somatic Cells (body cells): contain 46 chromosomes
○ Gametes (sex cells): sperm and eggs have 23 (half) chromosomes
 45

■ When fertilization occurs, makes a zygote, the first cell in a new human, with 46
chromosomes
○ Karyotype: shows all of your chromosomes

CELL CYCLE
● Interphase: any time the cell is not dividing
○ G1 (Growth 1): cell spends the bulk of its time, the cell grows and begins normal
processes
○ S (Synthesis): cell begins to prepare for division. DNA replicates critical to mitosis so
both new daughter cells get a full set of DNA
■ ****The chromosomes make copies and are held together by a centromere
band, the two copies held are called sister chromatids, those chromatids are
identical to each other and are still considered one chromosome, one mitotic
chromosome, when the cell divides, the sister chromatids separate and are now
separate chromosomes, both daughter cells get one copy and have the same
chromosomes as the parent.
■ If DNA replicates it has to divide, a critical point to decide whether or not it will
divide
○ G2 (Growth 2): undergoes more growth, the cell prepares more for division, organelles
begin to replicate
● Mitosis: process of cell division, occurs after the G2 phase, technically only when the nucleus
divides
○ The two daughter cells are identical does not produce variation, purpose = cloning
● Cytokinesis: when the rest of the cell (cytosol) divides after mitosis nuclei divide
○ In animal cells:
■ Cleavage furrow (groove in cell) is formed using a ring of actin microfilaments
(for movement) the ring gets tighter until it cuts through the cytoplasm into two
daughter cells
○ In plant cells:
■ Can’t pinch plant cells into two because of the rigid cell wall
■ Creates cell plates (produces new membrane and cell wall) the vesicles
containing new material form a plate and build new structures to be separated
in two through growth
 46

SEE STAGES OF MITOSIS SHEET (on classroom)

***Mitosis preserve the chromosome count
● Motor proteins move apart chromatids, along spindle fibers
● Spindle fiber behind chromatid as it’s walking down it being destroyed, not pulled along fiber,
using motor proteins

REGULATION
● Checkpoints: points at which the cell checks its function to determine if it will undergo mitosis
or not, using analysis of internal conditions
○ If things go wrong at these checkpoints, the cell will undergo apoptosis
○ If something goes wrong and goes unregulated/undetected, cell will divide out of
control, and this is cancer
○ G1 “Restriction Point”: to replicate or not replicate DNA, ultimatum either to divide or
not divide
■ If the signal is not reached at the restriction point for the go-ahead, the cell
enters:
● G0 Stage: a perpetual state of G1, like neurons and heart cells
■ In order to enter the S Stage, the restriction point go-ahead needs to be reached
using the chemical ligand of growth factors
■ After checkpoint you are committed to divide
○ G2 Checkpoint: point at which cell decides if they should leave interphase
■ Uses internal factors ; chemical messengers in side of the cell
 47

● Cyclin: levels increase and decrease in a cycle, but at G2, its levels are at
its highest and combines with CDK
● Cyclin-dependent Kinase (CDK): levels remain constant
■ Cyclin + CDK come together and form the Maturation Promoting Factor (MPF)
which triggers the end of interphase
○ M Checkpoint (Metaphase Checkpoint): checks if all of the chromosomes are lined up
in the middle of the cell, if they aren’t lined up properly, causes apoptosis
● Conditions: detected using proteins
○ Anchorage Dependence: in order for a cell to divide it needs to be attached to
something
○ Density-dependent Inhibition: if cells get crowded, they stop dividing
○ ***cancer cells do not exhibit either of these conditions, that’s why they keep dividing
out of control.

CANCER

● Cells are unable to regulate mechanisms going thru the process of the cell cycle
○ → cells divide out of control
● Cancer: unregulated and uncontrolled cell division
● Cancer cells do not require growth factors to grow and divide
○ They can make their own growth factors
○ Convey a growth factor signal without the presence of a growth factor
○ ***Abnormal cell cycle control mechanism
■ CDK, cyclin, receptors, growth factors, condition proteins, are all proteins, which
are created using DNA, which codes specifically for proteins
■ If a gene mutates, the protein changes, and when you change a shape of a
protein you change its function, and improper regulation begins
● Proto-oncogenes: genes that code for all of the proteins used in the cell cycle
○ If a gene mutates it causes transformation: proto-oncogenes become, oncogenes which
are cancerous
■ Causes proteins to change shape and no longer work
○ One oncogene is not enough to cause cancer, need 6-9 genes to get cancer
○ Cannot directly inherit cancer, can’t pass down 7 oncogenes, but could pass down a
couple oncogenes, so you’re predisposed
● Tumor suppressor genes: group of genes that stop cancer from developing, can also mutate
○ Can code for proteins that correct mutations and proofread DNA
○ *P53 Gene: codes for p53 protein which triggers apoptosis
■ If the gene mutates, bad cells cannot be stopped from living
■ We normally undergo many mutations on a daily basis, P53 gene prevents these
cells from manifesting
○ 50% of cancers involve a mutation to the P53 gene
 48

○ BRCA1 and BRCA2 genes: genes related to ovarian cancer and breast cancer
○ HER2 gene: codes for growth factor receptors in breast tissue, if it mutates, cells would
divide out of control
■ Found in high concentration in breast/ovarian cancer patients
○ Ras gene: codes for G-protein which relays the signal from growth factors
● Carcinogens: cause proto-oncogenes to mutate (radiation (x-ray), UV light, Nicotine, e.g.)
○
● ***Each cancer is caused by a different set of mutated genes, so there is no possible cure-all
○ Can only treat certain cancers using specific methods, they have to be tailored to that
specific type of cancer
● Tumors:
○ Major difference between the two is a number mutations
○ Benign: have 5 mutations about, generate a mass but do not spread stays at original
site, abnormal cells but are not cancerous
○ Malignant: impairs the functioning of whatever organ it’s in, this is cancerous so about 7
mutations,
■ can metastasize: part breaks off, enters the bloodstream, divides and creates a
tumor elsewhere in the body
■ Release their own growth factors, and cause blood vessels to grow towards it so
it can nourish and spread
● Radiation: high dosage of energy generated to a specific part of the body (lasers) to kill tumor at
location (using an MRI)
○ Usually done in part of chemotherapy
● Chemotherapy: toxin that kills all dividing cells
○ Destroys the spindle fibers that make cells split

CELL ORGANELLES
● Universal Function: COMPARTMENTALIZATION
○ Allow chemical reactions to occur in specific locations by isolating specific enzymes
○ By having highly folded organelles, more surface area, more can happen
● Nucleus
○ Contains genes/DNA of cell for organism (most important function)
○ Control entire cell
○ Nucleolus: produces ribosomes
○ Nucleus enclosed by phospholipid membrane: nuclear envelope
■ Pores: regulate the entry and exit of molecules from the nucleus
○ Nuclear lamina - maintain structure of the nuclear envelope, contain cytoskeleton
○ DNA wrapped around proteins to create chromatin, which is what chromosomes are
made of (46 of them)
● Ribosomes
 49

○ Particles made from ribosomal RNA and protein, carry out the process of protein
synthesis
○ Free RIbosomes found in cytosol, produce proteins for within-cell use
○ Bound Ribosomes attached to endoplasmic reticulum, make proteins that are secreted
from cell
● Endomembrane System
○ Involved in protein synthesis, comprise multiple phospholipid bilayered organelles
■ Nuclear envelope
■ Endoplasmic reticulum
1. Smooth ER
○ Detoxification of drugs and poisons
○ Synthesis of lipids (oils, phospholipids, steroids)
○ Carb metabolism
○ Stores calcium ions
2. Rough ER mainly for protein synthesis and modification (have bumps)
○ Has bound ribosomes, which secrete glycoproteins (proteins
covalently bonded to carbs) and proteins
○ Distributes proteins surrounded by membranes using transport
vesicles to the Golgi apparatus
○ Membrane factory for the cell
■ Golgi apparatus UPS of the cell
1. Ship proteins to their final destination in and out of the cell
2. Two poles
○ Cis face receiving face, where transport vesicles come in from
ER
○ Trans face shipping/exporting face
3. Each piece of golgi is made up of cisternae which are membranes
4. Modify products of the ER in stages as they move through the GOlgi
stack from the cis to the trans face
■ Lysosomes contains digestive enzymes
1. Perform hydrolysis
2. Functions
○ Intracellular digestion - break things down in the cell
○ Autophagy - recycling of cell material
○ Apoptosis - programmed cell death, some cells are programmed
to destroy themselves (embryonic development, webbing in
fingers) or mistakes in cell cycle(, cancer)
○ Phagocytosis cells that can engulf other cells
i. Macrophage a large WBC can engulf and form a vesicle
called the food vacuole, which travels to the lysosome
and digestive enzymes in lysosome destroy that
bacteria
 50

■ Vacuoles storage and cell maintenance

1. Food vacuoles formed by phagocytosis
2. Contractile vacuoles found in many freshwater protists, pump excess
water out of cells
3. Central vacuoles found in mature plant cells, hold organic compounds
and water
■ Peroxisome - perform beta oxidation
1. Fatty acids enter peroxisome, using oxidation the enzyme oxidase
breaks down into two-carbon molecules that can enter cell respiration
and make ATP
2. ***H2O2 is formed on the side, catalase takes toxic H2O2 and breaks it
down into water and O2.
■ Plasma Membrane
○ All components are continuous and can send stuff to eachother by vesicles (a sack of
membrane
● Energy transformers
○ Mitochondria is the organelle used to produce ATP from organic compounds using O2.
Organic compounds cannot be used directly for energy
○ Chloroplasts found in plant cells and algae and converts solar energy into chemical
energy, and are the sites of photosynthesis
○ Evolutionary Origins
■ Mitochondria and chloroplasts were once their own separate prokaryotes
(bacteria) and were engulfed by bacteria and formed a permanent relationship
1. Proof:
○ M and C both have double membranes
○ Contain free ribosomes and circular DNA which only bacteria
have
○ Grow and reproduce somewhat independently in cells
○ Permanent relationship with double benefits
■ Endosymbiont theory
1. Start with ancestor eukaryote, can’t support itself so it uses
phagocytosis to engulf an energy transforming cell
2. Symbiotic relationship: smaller cell gained protection and supply of food
where larger cell got source of ATP, could have also happened with
chloroplast
3. So beneficial became permanent to eukaryotes

● Fundamental units of life (Cell Theory)

1. All organisms are made of cells
2. The cell is the simplest collection of matter that can be alive
3. Cell structure is related to cellular function
4. All cells are related by their descent from earlier cells
 51

● Everything that happens to the body originates from an effect on the cells
● How Cells are Studied
○ Usage of Microscopes
■ Light Microscopes - see most cells, organelles, bacteria, etc.
■ Electron Microscopes - viruses, ribosomes, proteins, etc.
● Scanning Microscope (SEMs) - scans surface of an object, tells what an
object looks like on a surface, use for viruses, proteins
● Transmission Microscope (TEMs) - look inside of an object
○ Cell Fractionation - uses centrifuge (spins fast) to separate contents based upon density
split cell into its components, isolates organelles
■ Begins with homogenization (break apart cell membranes, blenderize)
■ Put in centrifuge and separate contents after spinning, get pellet in bottom
(most dense part) Nucleus of each cell is bottom
■ Pour supernatant on top of nuclei, centrifuge again, find mitochondria and
chloroplasts in pellet
■ Pour out supernatant on top again to find membrane pellet
■ Find Ribosomes in last pellet
● Why are cells so small?
○ Cells take in three things thru membrane: nutrients, O2, and H2O
○ CO2 and waste leave the cells thru the membrane
○ Cells need as much surface area as possible (the amount of membrane you have) more
surface area = faster rate of exchange
○ Smaller cells have more surface area compared to volume (which is amount of stuff in
cell)
■ More efficient at exchange, for respiration and waste excretion
○ Surface area vs. Volume (ratio):
■ Larger the volume of a cell the more surface area it needs to exchange materials
necessary for life to continue
■ Nucleus (brain of the cell) can only control a certain amount of cell processes,
control smaller cell better than bigger cell
● Two categories of cells
○ Prokaryotes
■ Archaea and Bacteria (germs)
○ Eukaryotes
■ Protists (algae, like fungi: slime mold, like animals: protozoans), fungi, animals,
and plants (all descended from protists)
○ All cells have
■ Plasma membrane (made of phospholipids)
■ Semifluid substance called cytosol (glycolysis and fermentation)
■ Chromosomes (carry genes)
■ Ribosomes (make proteins)
○ Every cell is a protein factory, genes code for proteins
 52

○ Every cell needs ribosomes and DNA

● Prokaryotic Cells do NOT have a nucleus, have a general region called nucleoid region very
simple organisms
○ Only have one circular chromosome in nucleoid region
○ Only internal organelle they have are ribosomes
○ Have cell wall made of peptidoglycan (amino acid and sugar combo)
○ First form of life to exist, most successful form
● Eukaryotic Cells DNA in nucleus, possess membrane bound organelles (organelles has
membranes, phospholipids)
○ Much larger than prokaryotes
○ Animal Cells
■ Have centrosome: microtubule (rods) organizing center, constructs these rods
■ Flagella - large tail structure for motility
■ Cilia - hair like projections outside of a cell
○ Plant Cells
■ Have cell wall (cellulose)
■ Chloroplasts - photosynthesis
■ Large central vacuole - holds water for photosynthesis
○ Plant and animal cells both have mitochondria for respiration
● Compartmentalization
○ Organelles isolate specific enzymes and reactions within cell
○ Increase surface area within cell, most organelles are highly folded
○ Purpose of having multiple organelles, separate functions of each organelle, each
organelle holds different enzymes → controls which chemical reactions occur where
● Endosymbiotic Theory: describes the origin of eukaryotic cells
○ Eukaryotic cells are much larger and more complex, and have a lot of membrane bound
organelles
■ Need to have energy in order to support complexity
○ ORIGIN OF MITOCHONDRIA AND CHLOROPLAST
■ Mitochondria and Chloroplasts were once their own separate bacteria
■ Basic eukaryote engulfs the mitochondria thru phagocytosis, and mitochondrion
contains electron transport chains for oxidative phosphorylation, efficient at
making 28 ATP
● No longer have to rely on 2 ATP produced in glycolysis
■ Form a symbiotic relationship
● Small cell gets protection and steady supply of food
● Large cell gets all the ATP
● Permanent relationship of double benefits
○ Mitochondria and Chloroplasts have their own
■ Mitochondrial DNA (bacterial DNA)
■ Ribosomes (identical to bacterial ribosomes)
■ Reproduce separate of cell (identical to bacterial asexual reproduction)
 53

○ Most important event in the evolution of eukaryotic organisms

● CYTOSKELETON - Network of fibers that organize structures and activities in the cell in the
cytoplasm
● Fibers
○ Microtubules (largest) - hollow
■ Made up of spiralled tubulin proteins
■ Form cilia and flagella, and centrioles in centrosome
○ Intermediate Filaments (mediumest)
■ Made of keratin structural proteins (hair, nails, etc.), form nuclear lamina (give
nuclear envelope shape)
○ Microfilaments (smallest) - thinnest fibers also actin filaments
■ Made up of actin subunits contracts, generates movement within the cell
■ Directly underneath cell membrane form cortex give cell shape
■ Movement in the cell and of the cell
● Muscle contraction: actin react with myosin to create reactions
● Amoeba movement: creates pseudopodia extend outward or retract
inward
● Cytoplasmic streaming in plant cells : actin contract cause movement of
cytosol, increase movement of nutrients
● Roles
○ Support the cell and maintain shape
○ Interacts with motor proteins to produce motility (using ATP), move along microtubules
to transport things around the cell
● Centrosome MICROTUBULE organizing center
○ Where microtubules grow from, has a pair of centrioles each with nine triples of
microtubules arranged in a ring
○ Centrioles are used for chromosome movement in mitosis/cell division
● Cilia composed of MICROTUBULES
○ Hair like structures outside cell, used for movement outside
■ E.g. cells in windpipe move mucus and debris
● Flagella locomotive tail independent movement made of MICROTUBULES
○ E.g. sperm
● Cilia and Flagella Structure
○ Core of microtubules sheathed by plasma membrane
○ Basal body that anchors the cilium or flagellum
○ Dynein - motor protein drives the bending movements of cilia and flagella
● How Dynein proteins work
○ Dynein arms alternately grab, move and release outer microtubules
○ Protein cross-links limit sliding
○ Forces exerted by dynein arms cause doublets to curve bending the cilium or flagellum
 54

○ If microtubules were not anchored, one set of microtubules would just be pushed
upward, would not produce movement just back and forth
● Microtubules are an internal highway within cell, or cell motility
● Microfilaments (Actin) cause movement of the cell as a whole , muscle contractions

DNA TECHNOLOGY
● Recombinant DNA: nucleotide sequence from two different sources, often two species, what
DNA tech revolves around
○ All DNA is the same, so it doesn’t matter what organism you put it in, it’s all the same →
evidence of a common ancestor
○ Done in vitro outside of the body (test tube/petri dish), in vivo in the body
● Genetic Engineering: direct manipulation of genes for practical purposes
● Creating Recombinant DNA:
○ Restriction Enzyme: also called a nuclease or an endonuclease
■ Recognizes a specific sequence of DNA and cuts it at a Restriction Site:
palindromic sequence (GAATTC or CTTAAG) where it cuts
■ Each enzyme has a different restriction site
○ Blunt Ends: straight cut thru the DNA, bad for recombination, cannot recombine the
DNA
○ Sticky Ends: staggered cut on a diagonal, can be recombined with new DNA
○ Cut the gene out with a restriction enzyme, then cut the plasmid (where you want to
insert it) with the same enzyme so the sticky ends match, and then use ligase to connect
it to the plasmid → becomes a recombinant plasmid because it takes genes from
multiple sources, and you can insert the plasmid into a bacterium using transformation,
plasmids can only be used in bacteria
○ Vector: a way that is used to insert a gene into an organism (like viral vectors
● DNA Amplification:
○ Amplifying a gene: making copies of that gene
○ DNA/Gene Cloning: amplifies a gene (not an organism) and a protein product
■ Cut the gene out with a restriction enzyme, then cut the plasmid (where you
want to insert it) with the same enzyme so the sticky ends match, and then use
ligase to connect it to the plasmid → becomes a recombinant plasmid because
it takes genes from multiple sources, and you can insert the plasmid into a
bacterium using transformation, plasmids can only be used in bacteria
■ Plasmid enters the bacteria using heat shocking, to create competency
■ Result: recombinant bacterium with a recombinant plasmid
■ When a bacteria replicates, it also replicates the plasmid, and since bacteria
reproduce so fast, every time they reproduce, the plasmid gets passed on.
■ We can now either extract the genes (now a lot of copies) from the bacteria or
we can extract the products (amplify the proteins, like insulin, HGH (growth
 55

hormone), or TPA (for heart attack patients it thins blood and prevent more
heart attacks) which is produced in this method)
■ Bioremediation: inserting genes in ocean bacteria to consume oil and wastes in
the ocean
○ Polymerase Chain Reaction (PCR): used for scanty or impure/trace DNA (like at a crime
scene) fast, easy, and cheap
■ Uses polymerase to replicate DNA
■ PCR runs in cycles, each cycle doubles the amount of DNA
● 1→2→4→8→16...
■ Steps of each cycle:
● Denaturation: pull the DNA hydrogen bonds apart using heat
● Annealing: laying down primers artificially ***primers would be DNA
(not RNA like natural), no need to remove the primers at the very end of
the process by polymerase 1
○ Primers only bond to the target sequence, so by the end you
lose information on the sides because not everything can be
replicated (unpaired ends)
● Extension: DNA polymerase extends the primers and replicates the DNA
■ Can’t use this for good whole genes, can use it for fragments only
● Analyzing Genes: everybody is the same except identical twins
○ Gel Electrophoresis: used to separate fragments of DNA based upon their size
○ STR (Short Tandem Repeats): region that is highly polymorphic (many differences) so
varied person to person that no two people have the same sequence, but is very
repetitive (ATGATGATG…). No-one has the same number of repeats.
■ Most of everyone’s genes are the same, we all code for the same proteins, so
we need to find another way to identify people → this is how
■ When the STR is cut with a restriction enzyme, the fragments created have very
unique sizes (very big or very small) called restriction fragment length
polymorphisms (RFLPs)
○ DNA has a negative charge because of phosphate groups (PO4, negative oxygens)
○ RFLPs are put into the wells in a gel, starting from a negative side
○ The current pushes the fragments of DNA through the gel. Repelled by the negative and
attracted by the positive.
■ Shorter RFLPs travel farther because they are quick and small
■ Longer RFLPs travel less from the negative side because they are large and
immovable
○ DNA Fingerprint: the unique banding patterns created during gel electrophoresis for a
certain individual, created by migrating RFLPs across the gel
■ Only 100% conclusive evidence
 56

○ STR Markers: cut the STR at three different sites (there are multiple regions of STRs with
different repeats) There’s a pair of numbers bec. Of DNA from mom and dad
○ Paternity Testing with Gel Electrophoresis:
■ You get half of your DNA from mom, dad
■ All bands need to shared with your mom and dad, so they need to match either
mom or dad

INSERTING GENES
● Human Gene Therapy: insert a gene into a human using a retrovirus as a vector to fix diseases
○ Can only be used if a disease is caused by a single defective gene, just give the cell a
properly functioning gene → doesn’t replace the problematic gene, but the fixed gene is
enough
○ Uses retroviruses, because it incorporates that information into the host cell’s DNA
○ Must put it into a cell that will continue to divide to propagate through the organism
otherwise the fixed gene will die off → must treat cells in the bone marrow bec. of stem
cells that divide throughout your life, works with diseases of the blood.
● If you want to genetically modify an organism, you cannot insert it into an adult, must start with
female eggs or a zygote the gene will be found in every single cell of that organism
● Electroporation: blasts female egg with electricity pulse, opens holes to put genes in
● Or you can use a little needle to put a gene in a female egg (largest cell in the human body)
● Transgenic Animal: an animal that contains genes from other sources
○ Inserting a cloned (amplified) gene into an egg cell
● Plant Engineering:
○ Agrobacterium: naturally grows in soil, that has a Ti plasmid which is what makes
genetic modification of crops possible
○ Insert the gene of interest into the Ti plasmid (same as DNA cloning w/ sticky ends) →
recombinant Ti plasmid
○ The Ti plasmid can be introduced into plant cells → works like a provirus or a lysogenic
cycle, it takes the gene and incorporates it into the plant’s genome
■ Plants can’t otherwise use plasmids
○ GMO Crops:
■ Main types of genes that are inserted:
● Pest Resistance (Bt): make their own pesticide/insecticide proteins
● Herbicide Resistance (glycophosphate, major herbicide to kill weeds):
so you can mass spray the farm, kill weeds but not the crops
■ Pros:
● Mass production of crops, decrease loss due to herbicides and decrease
loss due to pesticides, more crops, less problems
● Increase the health content (vitamins) of food
■ Cons:
 57

● Unknown long-term health effects: don’t really know yet

○ RNAs from GMOs could be interfering, or could just be digested
the same
○ Herbicide is a known carcinogen, GMOs allow for more
herbicide use
● Environment:
○ Resistant (superweeds) weeds and (superbugs) insects will
evolve
○ When GMO plants reproduce, their pollen travels, you cannot
stop the spread of those genes throughout the environment,
genes go off the GMO farm
● Traceability: very difficult to understand which foods in your diet are
GMO or organic, only label it organic when they apply, they don’t label
all of the ingredients if they are GMOs or not
● CRISPR-Cas9: (new genome editing tool) takes out bad genes and puts in a good gene, removing
a gene (knockout) to determine what it doesn’t do anymore
○ Uses an enzyme Cas9 and uses guide RNA (gRNA) begins with a target sequence of DNA,
the guide RNA is complementary to the sequence we are going to target, you need to
find a naturally occurring restriction enzyme to cut out the gene, but with CRISPR, you
have the sequence you want to cut and you have the gRNA
○ gRNA is what tells Cas9 to go to that region and binds to it, once it’s bound, it cuts
through both strands of DNA just like a restriction enzyme would
○ Once the DNA is cut, you rely on the cell’s natural repair system to try to fix the cut
using nucleotide excision repair, can be used to introduce the mutation that we want
● Stem cells: unspecialized cell that can reproduce itself indefinitely and differentiate into
specialized cells of one or more types “blank slate”
○ Can turn into any different type of cell
○ Embryonic Stem Cells (pluripotent): pluri means many, it can become any type of cell in
the body → the best type of stem cell because they can become any cell type,
contained in the blastocyst (early embryo in embryonic development)
○ Adult Stem Cells: mainly found/produced in the bone marrow, but are not pluripotent,
they are multipotent can become multiple types, but not all types
■ Can become blood cells, but not every type of cell in the body
○ Research can be used to grow new organs/tissues for cell-based therapy
■ Stem cells can be directed to differentiate into certain types can become a
source to treat diseases like diabetes, stroke, macular degeneration, → all
diseases caused by cell death
○ Embryonic stem cells are harvested from unneeded embryos during IVF
○ iPSC (induced pluripotent stem cells): take an adult stem cell and undifferentiate it into
a pluripotent cell answer to ethical debate on stem cell research, but cannot completely
unprogram a cell, not true embryonic stem cells
 58

EXTRACELLULAR COMPONENTS
● Extracellular components and connections between cells help coordinate cellular activities
○ Most cells synthesize and secrete materials that are external to the plasma membrane
○ These extracellular (outside plasma membrane) structures include
■ Cell walls of plants- major structural component of plant cells made of cellulose,
also found in prokaryotes, protists and fungi (peptidoglycan)
● Cell wall protects the plant cell, maintains its shape and prevents
excessive uptake of water
● Plant cell walls are made of cellulose fibers embedded in other
polysaccharides and proteins
● Layers
○ Thin Flexible Primary Cell Wall
○ Thick Secondary Cell Wall
■ In between plasma membrane and primary wall gives
structural integrity
○ Middle lamella - material between cell walls
● Plasmodesmata gaps in cell wall allowing for communication and
movement of things between plant cells, rigid cell walls are restrictive
unlike permeable membranes
■ Extracellular matrix (ECM) of animal cells instead of cell walls
● Series of glycoproteins such as collagen (major), proteoglycans, and
fibronectin make up ECM
○ Fibronectin connects collagen to integrin
○ Proteoglycans perform adhesion (glue)
○ Proteins bind to receptor proteins in the plasma membrane
called integrins
● Functions
○ Support
○ Adhesion
○ Movement
○ Regulation
■ Intercellular junctions physically connect cells, adhere interact or communicate
through direct contact
● Types
○ Plasmodesmata gap-like channels that perforate cell walls
○ Tight Junctions membranes of neighboring cells are pressed
together preventing leakage of extracellular fluid in between
cells (in stomach)
○ Desmosomes (anchoring junctions) fasten cells together into
strong sheets--strongest function (muscle cells)
 59

○ Gap junctions (communicating junctions) provide cytoplasmic

channels between adjacent cells (heart cells), enable multiple
cells to act as one

CELL MEMBRANE
● The Cell membrane is selectively permeable - only certain things move through the membrane
○ Amphipathic Molecule: (polar and nonpolar) Made up of phospholipid has a head
(phosphate group PO4, POLAR attracts to water) and two fatty acid nonpolar tails
(hydrocarbons)
■ One straight (saturated) and one bent (unsaturated, removed hydrogens) fatty
acid
■ One half hydrophilic and one half hydrophobic
○ Phospholipid bilayer self assemble into
membrane polar heads face water and lipids face
each other on the inside
● Fluid Mosaic patchwork of proteins that are embedded in
cell membrane
○ “Fluid” refers to phospholipids, the phospholipids
float around in membrane, not rigid structure
proteins are also mobile
■ Phospholipids can move laterally along
membrane but can infrequently flip flop
sides
○ Different membranes have different amounts of
saturated vs unsaturated fatty acids, and determine viscosity. saturated fats are solid,
unsaturated fats are more liquid (because of kinks, can’t stack)
■ In arctic, use more unsaturated fats for liquid membrane, avoid freezing
■ In desert, to combat too much liquidness, have more saturated fats
○ Membranes change over time depending on environment
● Cholesterol (solid four ring carbon structure) - stops membrane from becoming too fluid,
restrains movement of phospholipid
○ Excessive cholesterol (solid) can form plaques
● Membrane Proteins
○ Peripheral Proteins - “outside’ proteins, does not span the membrane, found on one
side of the membrane (in or out of the cell) or the other
■ Polar because outside membrane
○ Integral Proteins - (transmembrane protein) span the entire membrane (embedded)
■ Parts of the protein in bilayer are nonpolar, outside has polar regions
(amphipathic)
○ Functions
■ Signal transduction (receptors)
 60

■ Transport
● To transport quickly thru bilayer, must be very small or nonpolar (e.g.
fats, steroid hormones, H2O, CO2, O2)
● Large and polar things need Transport proteins (integral) to get thru
membrane (glucose, amino acids)
● Transport proteins extreme specific, like enzymes, only transport certain
types of substances, allow hydrophilic substances across the membrane
→ shape determined by sequence amino acids
○ Channel proteins have a hydrophilic channel that certain
molecules or ions can use as a tunnel
■ Polar channel but outside of channel is nonpolar
○ Aquaporins - facilitate the passage of water, make water move
faster but still can fit thru membrane cuz small
○ Carrier Proteins bind to molecules and change shape to shuttle
them across the membrane
■ Changes shape, opens on one side to let it go thru and
then reopen inside the membrane
■ Enzymatic activity
■ Cell-cell recognition
● Glycoprotein MHC - major histocompatibility (work with tissues)
complex (integral in cell membrane)- with carbohydrate (glucose)
attached to it are like billboards on outside of cells (every person has a
unique glycoprotein, that identifies self)
○ CELL TO CELL RECOGNITION
● Recognize by binding to surface molecules often with carbs
● If a foreign cell enters the body, if it doesn’t have the unique
glycoprotein (unless they are twins), immune system attacks it
● Membranes carbs are covalently bonded to proteins forming MHC
■ Intercellular joining
■ Attachment of the cell to the extracellular matrix (ECM) : integrins
● Passive Transport - no energy required, material moves from high concentration from low
concentration == going down the concentration gradient,
○ Own kinetic energy drives reaction
○ Diffusion: movement of molecules from high cons. to low cons. (O2, CO2)
■ Once equilibrium is met, the net concentrations remain equal but are still
moving
■ E.g. chemiosmosis: diffusion of protons
■ Osmosis: diffusion of water
● Look at water vs solute, if you have the same amount of solution on
either side, but more solute on one side, that means there is more
water on the other side, so water will move
● Defies gravity
 61

○ Tonicity: ability of a surrounding solution to cause a cell to gain or lose water i.e.
amount of solute, hypertonic and hypotonic refer to the solution
■ Hypertonic: more solute=less water: dehydrates
● Cells in hypertonic solution: Water leaves the cell, and shrivels
■ Hypotonic: less solute=more water: hydrates
● Cells in hypotonic solution: Water enters the cell and swells (could lyse
cells or when the cell bursts) or when the because these a higher
concentration of water on the outside,
■ Isotonic: solution with equal concentrations
○ Osmolarity of blood: natural concentration of all solutes in your blood (salt
[electrolytes], and sugar, etc.)
○ Osmoregulation: kidneys (excretory system) perform or regulate blood volume, if you
have excess water, you pee out the rest to stop you from exploding
○ Plant cells have cell walls and stop lysing
■ Hypo: Instead become turgid (swollen) cells, better for photosynthesis
● Cells can’t lyse because of cell walls, just flex outward and become
RIGID and hard
■ Iso: cells become flaccid
■ Hyper: Plasmolyzed, cell membrane pulls off oc cell wall and kills plant cell
○ Facilitated Diffusion - passive transport of large polar things by a transport protein down
a concentration gradient (amino acids, sugar, etc.)
● Active Transport - pump against gradient, in the opposite direct, must invest energy (ATP),
usually to build a concentration gradient
○ Sodium-Potassium Pump - ion pump
■ part of nervous system, pumps sodium out of neuron and potassium in the
neuron → pumps ions (atoms with charge)
○ Ion Pumps (aka a proton pump (proton pumps are a type of electrogenic pump) or
electrogenic pump) type of active transport protein that uses ATP to pump ions in one
direction,
■ Establish Membrane Potential: difference in charge outside and inside a
membrane
● Voltage: The difference in charge, generated by ion pumps, can
generate electricity
■ Electrochemical gradient - chemical gradient, the actual amount of ions on
either side, and the electrical gradient which is the difference in charge
■ Simultaneously create two gradients, physical concentration and voltage
difference
■ All types of organisms use proton pumps → protons are used to get work done
(respiration and photosynthesis)
■ Plants use proton pumps for cotransport in plant cells
● Phloem tubes transport sugar, but high concentration of sugar in
phloem, so sugar wants to diffuse into cells, but cells need to load the
 62

phloem with more sugar, so active cotransport pumps sugar into

phloem
● Proton pumps pump protons out of the phloem, and protons want to
diffuse back into the phloem, then second cotransporter that transports
sucrose and protons, sucrose cannot go through without protons,
protons pull sucrose into phloem, uses diffusion of protons in order to
load sugar up its gradient into the phloem, used in roots
■ Plants need to live in slightly acidic soil for more protons in a proton gradient to
absorb nutrients (nitrate) from the soil
● Bulk Transport - movement of extremely large things in and out of the cell, cannot fit through
protein channels
○ Endocytosis - takes big things in, phospholipids in membrane create a vesicle around the
object, membrane caves in
■ Phagocytosis: cell eating
● How WBCs (macrophages) engulf bacteria and viruses make food
vesicles
● And cells are sent to lysosome for destruction (hydrolysis)
■ Pinocytosis: same thing as phagocytosis with liquids
■ Receptor-Mediated Endocytosis when substance is binded to a receptor and
substance and receptor are brought in
○ Exocytosis - sends big things out (like proteins, using transport vesicles from Golgi UPS)
Golgi made out of phospholipid bilayer, can form vesicles easily fuses with membrane
and releases contents
○ Most organelles are membrane bound for vesicle formation and transportation

DNA
● Deoxyribonucleic Acid (DNA):
○ A polymer made up of many monomers
○ Nucleotide: (monomer)
■ Sugar (pentose, deoxyribose C5H10O5): 5 carbon
sugar, in a pentagon shape
● A ribose minus an oxygen
■ Phosphate Group (PO3)
■ Nitrogenous Base: what changes between
nucleotides
● Cing Tut == pyrimidines
● Adenine (purine == double ring structure)
● Thymine (pyrimidine == single ring structure)
● Guanine (purine)
● Cytosine (pyrimidine)
 63

● A always bonded to T and G always bonded C

○ DNA has two strands of nucleotides, and nitrogenous bases
are held together by hydrogen bonds
■ Antiparallel: DNA strands runs in opposite
directions, one strand runs 5 to 3 and the other
runs 3 to 5 (important for DNA replication)
● 5 Prime Side: there are five carbons (where
the point of the pentose sugar points)
● 3 Prime Side: where three carbons at end of
the pentos (fat side of the pentose points to
the end)
● DNA Backbone: sides of the nitrogenous base ladder rung structure, made up of sugar
and phosphate, keep the DNA together
● Double Helix: DNA twists around, made up of two strands of DNA
● Proteins were considered genetic information for a while before discovering DNA, bec.
There were 20 amino acids, which makes more sense for complex combinations than 4
bases
● Frederick Griffith’s Experiment: mixed a rough strain of a disease (harmless) with a
heat-killed smooth (virulent) strain and the mouse died
○ There was a transforming factor, from the heat-killed bacteria to the rough
strain → DNA
● Avery McCarty Macleod Experiments: wanted to discover Griffith’s transforming factor
○ Isolated the bacterial RNA, proteins, and DNA
○ Used enzymes that broke down each of those things until they could find out
what caused the bacteria strain to transform
■ When they broke down DNA, they found that the bacteria could no
longer transform → found life was based off DNA (not definitively)
● Alfred Hershey and Martha Chase Blender Experiment: is it DNA or is it proteins that
actually drive life (definitively)?
○ Dyed sulfur and phosphorus in a virus that invades a bacterial cell
■ Sulfur is found in proteins but not DNA
■ Phosphorus found in DNA and not proteins
■ Showed that the only one that was transforming the cell was the
phosphorus → therefore DNA was hereditary material
● Watson and Crick: credited for discovering DNA’s structure combining Chargaff’s ATGC
levels and Wilkins and Franklin’s helical structure
 64

● Maurice Wilkins and Rosalind Franklin: discovered the crystallographic helical

structure of DNA (basically had the data that Watson and Crick would use)
● Erwin Chargaff: looked at the amounts of bases: ATGC
○ Found that A and T amounts correlated; G and C amounts correlated
■ Must be pairs: Chargaff’s Rule

DNA REPLICATION
● during the S phase of interphase
○ Semiconservative Model (of replication): original/parental strands of DNA
separate, and two new strands fill in with each parental strand. Each new copy of
DNA is composed of one old parental strand and one newly made strand
■ DNA only dies if you don’t pass it down, “the immortal thread”
■ Every new DNA molecule is made up partly of old DNA
■ MESELSON AND STAHL Experiment: discovered semiconservative model
● At the time, there were two other models of DNA that were
proposed:
○ Dispersive Model: DNA was broken up, and each little
DNA model was made up of old and new
○ Conservative Model: original parental molecule was
conserved, and a two new strands were formed
● Grew bacteria in heavy nitrogen, all DNA made in bacteria
contained heavy nitrogen-15
○ Original bacteria has two strands of DNA both with
nitrogen-15
■ Would have low band on centrifuge because of
high density
● Grew bacteria in nitrogen-14, all new DNA would be made using
nitrogen-14 (lighter)
○ Two new daughter strands made using nitrogen-14 but the
old strands are all originally nitrogen-15
○ After first round of replication, each DNA strand was half
15 and half 14
○ Got a medium band on the centrifuge
● Third Round of Replication
○ Centrifuge results:
■ Light Band: daughter strand of second round,
paired with a new strand
 65

■ Medium Band: old 15 band from original paired

again with another new daughter strand
● Never goes away because original nitrogen-
15 DNA strand stays
○ Origin of Replication “bubbles”: different in prokaryotes vs eukaryotes
■ Where replication begins in each cell
■ Bacterial DNA is unicircular has only one origin of
replication and extends outward in both directions
around the circle until completely replicated
■ Eukaryotic DNA: multiple origins of replication with
linear strands of DNA
● “Bubbles” at origins get bigger and bigger until
they converge → multiple origins of replication
make the process go faster and proves
semiconservativeness
○ Contains two replication forks: extends outward at each fork

● Creation of the Replication Bubble (made up of two replication forks)

○ DNA Helicase: responsible for opening DNA up and making the replication
bubble → breaks hydrogen bonds of helix
○ Topoisomerase keeps the DNA unwound and stop hydrogen bonds from
reconnecting “little clamps” DNA doesn’t want to stay apart
○ Single-strand Binding Proteins: keep the bubble open, and binds to the unpaired
bases of DNA to stop them from rematching up
● Making new DNA strands: (S phase of interphase)
○ Primase: not made up of DNA, made up of RNA, lays down a primer to begin
DNA creation
○ 5 to 3 == leading strand
■ Replication happens easily in the leading strand
○ 3 to 5 == lagging strand
○ DNA Polymerase 3: the enzyme that actually makes the new DNA, can’t start
from nothing, it can only extend preexisting nucleotides, needs to go off the
primase’s primer
 66

■ ***can only operate in one direction ONLY operates to make 5 prime to

3 prime so it starts at the 3’ side of the leading strand to make a
complementary 5’ to 3’, builds a complementary strand that’s opposite
prime to opposite prime, by reading the template
■ Starts at the 3 prime side of the template original/parental strand to
make DNA 5 prime to three prime
■ Then how do you make DNA for the other parental 5 to 3 strand but
polymerase 3 can only go the opposite way
● See DNA Replication Sheet on Drive
● In the lagging strand, multiple not just one like leading strand, primers are going to be
laid down, and polymerase 3 operates in between the primers
● Okazaki Fragments: only found in the lagging strand, a segment where DNA is replicated
in the opposite direction, but stops at each primer, and then moves to the left, then
replicates to the right, and moves to the left…
○ P→ P→ P→
○ Overall direction: ←
○ All fragments are polymerased simultaneously, so it is quicker than just two
primers on the end
● Polymerase 1: removes the RNA primers and replaces with DNA
● Ligase: connects fragments of DNA together, connects Okazaki Fragments to make a
continuous strand of DNA
● New daughter strands are IDENTICAL
● If there is a mutation: Polymerase 3 screwed up
● You get all of your materials from your food
● Where do Polymerases get their nucleotides?
○ Nucleoside Triphosphate: an adenine nucleotide with two extra phosphates to
which is ATP
■ Polymerase cuts off the phosphoruses and you get Adenine
■ Releases energy required to build DNA
■ There are also CTP, GTP, TTP, other energy sources that when
phosphorylated become all of the other nucleotides in the body.
● BUT, if at the very end of each DNA fragment, there’s nothing for Polymerase 1/3 to
latch on to; end DNA is never replicated
○ With every single replication of DNA, your DNA gets shorter
○ Telomeres: contain non-coding DNA, long sequences of repetitive DNA at the
end of each chromosome, it can be burned up through the process of DNA
replication as to not affect your coding DNA
 67

■ When telomeres run up, you die because you start eating into your genes
when you replicate
○ Telomerase: enzyme found in germline cells (sperm/egg) that extend telomeres
so you pass on full DNA

DNA REPAIR
● If a mistake/mutation occurs, Polymerase 1 or 3 is at fault, by laying down the wrong
nucleotides
● We have enzymes that proofread our DNA and fix problems
● “Mismatch Repair”/ Nucleotide Excision Repair: if nucleotides are mismatched, don’t
line up properly, then a protein cuts out the bad nucleotides and fixes it
○ If this process were perfect there would never be any variation or mutations for
evolution
○ Nuclease: DNA cutting enzymes, and it cuts out the mutation
○ Polymerase just reinserts the DNA
○ Ligase reconnects the DNA
○ ***bacteria and viruses lack proofreading proteins, they want and need to
mutate in order to evolve and create new strains

GENES AND PROTEINS

● A gene is the instruction manual that creates a certain protein, each gene codes for 1
protein polypeptide

● Beadle and Tatum Experiment:

○ Studied metabolic defects in a fungus
○ Mutated each specific gene that coded for a specific enzyme in a metabolic
pathway and discovered that when a certain gene mutated a certain protein
screwed up in the pathway causing a buildup of that product
○ Discovered the 1 gene 1 enzyme (now protein and now polypeptide)
hypothesis
● Every protein is different because it has a different sequence of amino acids

PROTEIN SYNTHESIS
 68

● Different in eukaryotes vs prokaryotes

DNA (deoxyribonucleic acid) RNA (ribonucleic acid)

Nucleic acid Nucleic acid

Double stranded Single stranded

Deoxyribose (missing an oxygen) Ribose

A, T, G, C A, U (uracil), G, C

mRNA: messenger RNA

tRNA: transfer RNA
rRNA: ribosomal RNA, etc.

● TRANSCRIPTION: takes place inside the nucleus

○ DNA in chromosomes is too long and condensed, must use mRNA to leave
through nuclear pores
○ Genes tell the ribosome what order to put amino acids in
○ One specific gene is read and used to make a sequential copy called mRNA
(messenger RNA)
 69

○ mRNA is a transcript/copy of a gene and goes to the ribosome

○ Gene DNA is read in triplets of bases called the reading frame TEMPLATE
STRAND IS ALWAYS 3’ to 5’, the COPIED RNA CODING STRAND IS 5’ to 3’
○ RNA Polymerase 2: reads the template strand of DNA makes an RNA coding
strand, which is complementary but where there’s an A in the DNA, polymerase
puts a U (uracil) in place of a T
○ The result is mRNA which in triplets has codons each codon corresponds to a
specific amino acid
○ Determination of Structure/Function: ultimately the DNA determines protein
structure
■ Sequence of DNA → mRNA (codons) → amino acids → protein structure
→ protein function
■ Proteins in different shapes perform different functions
○ AUG (start codon): codes for amino acid methionine, ALWAYS the first codon,
and methionine is always the starting amino acid in every protein
■ Therefore, in DNA, the beginning of every gene is TAC
■ There are also stop codons, each gene always starts with a start codon
and ends with a stop codon
○ Noncoding DNA: DNA that does not correspond to coding for a protein, it acts as
a buffer, only 1% of DNA actually codes for proteins, the majority is noncoding
■ Most noncoding DNA is used to regulate our genes,
■ Promoter: region right before the gene of noncoding DNA where RNA
polymerase binds to after transcription factor binds to TATA. Never
transcribed as part of mRNA, only part of DNA. TURNING ON A GENE:
● TATA Box: first four nucleotides of promoter (TATA)
● When a transcription factor binds to the TATA Box, begins the
process of transcription. The transcription factors (steroid
hormones) are what turn genes on. Steroid hormones control
the process of protein synthesis
○ Terminator Sequence (AUAAA): a sequence that causes the RNA polymerase to
stop transcription and send off the mRNA
○ mRNA transcription starts at the promoter and ends at the terminator sequence
○ Before mRNA can leave the nucleus, the Pre-mRNA must go under RNA
Processing: stuff added to the Pre-mRNA before leaving the nucleus
■ 5 Prime Cap: made out of GTP, how the ribosome knows what part of the
mRNA is the front
■ Poly A tail: long string of adenine, that protects against degradation
(back of mRNA)
 70

■ RNA Splicing:
● Exon: parts of the RNA are coding, each exon corresponds to a
location in a polypeptide called a domain
● Intron: part of RNA, that is noncoding
○ Alternative Splicing: why have introns when you could just
have exons?
■ 23,000 genes can actually code for more than
23,000 proteins
■ One piece of mRNA can code for multiple proteins
in the body by switching the exon and intron parts
● Spliceosome: cuts out the introns and splices together the exons
so only coding mRNA is left
● TRANSLATION: comes after transcription in ribosome
○ Ribosome receives and reads the mRNA and reads it, puts together a sequence
of amino acids
○ Redundancy of codons: if a mutation takes place you may not put down the
wrong amino acid, protection against mutations
■ Multiple codons can code for the same amino acid
○ Silent Mutation: mutation that doesn’t do anything, doesn’t change the amino
acid it codes for, because of redundancy
○ tRNA: (transfer RNA) bottom part of the tRNA is a complementary, anticodon
that is complementary to the codon (STILL USES URACIL) and carries an amino
acid on the top. tRNAs can be recycled, just attach new amino acids to build a
protein
■ Each has a specific anticodon and amino acid
○ Aminoacyl-tRNA-synthetase: enzyme that attaches tRNA to new amino acids,
using ATP (get amino acids from food)
○ Ribosome Structure: (GTP powers everything) CONVEYOR BELT
■ Binding sites:
● Small Subunit: scans mRNA for the start codon, the mRNA lays on
top of the subunit and tRNA attaches
● Large Subunit: (Left to Right: Environmental Protection Agency)
attaches on top of small subunit
○ E Site: exit site, where the used tRNA leaves
○ P site: first tRNA enters
○ A Site: next tRNA enters
○ Works like a conveyor belt, tRNA attaches to the codon
○ SEE THE ANIMATION ON GOOGLE CLASSROOM
 71

■ Release Factor: carries water and performs hydrolysis, enters the A site
instead of another tRNA and stops the building of a protein
■ GTP used to dehydration synthesize the amino acids, creating peptide
bonds and GDP
■ Polyribosomes: Since it’s a conveyor belt, you have multiple ribosomes
working on the same strand of mRNA, speeds up the rate of protein
production
○ Bound Ribosomes:
○ Protein Structure:
■ Primary Structure: linear sequence of amino acids peptide bonded
together
■ Protein folding takes place in the endoplasmic reticulum
■ Secondary Protein Structure: hydrogen bonding creates beta pleated
sheets and alpha helices
■ Tertiary Protein Structure: Hydrophobic bonds, ionic bonding, disulfide
bridges, etc. creates one polypeptide subunit
■ Quaternary Protein Structure: multiple polypeptides come together to
form a complex protein
○ Wobble: for each amino acid, there is only ONE tRNA that carries it, even though
there are multiple codons that code for a single amino acid (redundancy), only
the first two nucleotides of codon and anticodon fit together, the last one
doesn’t usually matter, so the tRNA and mRNA fit wobbles, not perfectly
together to save energy
■ Relaxation in the base pairing rules for the third nucleotide
● Eukaryotes vs. Prokaryotes:
○ RNA processing only takes place in Eukaryotic cells (prokaryotes don’t have
spliceosomes)
○ Prokaryotes don’t have a nucleus

MUTATIONS
● Mutations take place during the process of DNA replication (polymerases screw up)
● Point Mutation: single base modification causes a nucleotide base change, insertion,
deletions, substitutions, etc.
● Substitution: one nucleotide is substituted for another (Sickle Cell Anemia)
○ Changes only one amino acid in a protein, can radically change the shape of a
protein (change takes place in the primary structure, and all other structures,
etc.)
 72

○ Tay Sachs: lipase in the brain (breaks down lipids) mutates so lipids in the brain
build up and kill the baby
○ Missense: when you have the wrong nucleotide and it changes the amino acid
○ Nonsense: when the mutation creates a premature stop codon (bigger effect on
the protein than missense)
○ Silent Mutation: change at a point that doesn’t change the amino acid because
of redundancy (third nucleotide usually doesn’t matter)
● Insertion & Deletion:
○ If a nucleotide is put in where it shouldn’t or if a nucleotide is removed.
■ Causes a shift in the reading frame, causes all triplets to be screwed up
○ Frameshift: all reading frames moves
■ Affect every amino acid after that mutation

CONTROL OF GENE EXPRESSION

● Not all genes are turned on all of the time, else you would be making all of your proteins
constantly which would waste resources and energy.
● Cells regulate genes to control the production of proteins in the body using hormones (mainly
steroids)
● Turning on genes causes:
○ Create different proteins
○ Create different cells
○ Development (changes that take place during your lifetime, puberty especially)
● If a gene is being expressed it means its being transcribed or turned on
● Cell Differentiation: Different types of cells (heart cells, skin cells, etc.) are created by turning on
and off certain genes even tho every cell has the same code
○ Happens in the womb
○ Stem Cell: a cell that has not yet differentiated
○ Differential Gene Expression: having certain genes on or off
● Internal and External Factors can affect gene expression
● Operons and other structures herein are only found in prokaryotes, not eukaryotes, a simplified
model
● Operon: a region consisting of the operator, genes, and promoter
○ Operator: only in prokaryotes, sits in front of RNA polymerase before gene and after
promoter, controls whether or not genes are turned on or off
● Regulatory Gene (way before operon): codes for the repressor protein which can bind to the
operator, if the repressor binds to the operator, RNA polymerase cannot get to the genes →
turns off the genes/inhibits gene expression or transcription
● Repressible Operon: normally turned on but can be turned off
○ Trp (tryptophan) Operon
 73

○ EXAMPLE: Leads to the production of tryptophan proteins

○ The bacterium will turn off the tryptophan if it consumes enough of it
○ The repressor is normally the wrong shape so it cannot bind to the operator to shut off
the gene, so tryptophan acts as a corepressor, binds to the repressor changing its shape.
The new structure can now bind to the operator and shut off production of that gene →
don’t waste energy making more of the protein when you have enough
○ Turned back on when you run out of tryptophan because the repressor turns back into
its inactive shape
● Inducible Operon: normally turned off but can be turned on
○ The lac operon (stands for lactose sugar found in milk)
■ Produces lactase enzymes needed to break down lactose
■ Only want to produce these enzymes when you ingest lots of lactose/milk
○ The repressor is normally bound to the operator, RNA polymerase normally does not
have access to the genes → turned off most of the time
○ Lactose is an inducer changes the shape of the repressor to release it from the operator,
and makes it inactive
■ If there’s no more lactose it would shut off the gene

EUKARYOTIC GENE CONTROL

● Eukaryotic Genome:
○ 70% of the genome occurs only once 1% is actually coding the other 69% is used to
regulate your genes
○ 30% is repetitive
● Control Elements: regions where transcription factors (steroids or growth hormones NOT just
roids, etc.) bind, noncoding regions
○ Promoter
○ Proximal Control Elements: close to promoter
○ Distal Control Elements (enhancers): far from promoter
● Transcription Factors:
○ Activators: turn genes on
■ Usually bind to the enhancer/distal region
○ Repressors: turn genes off
● *Can delay/stop the process of protein production is to not process the Pre-mRNA
● Noncoding RNAs: used to slow or stop the production of proteins by blocking or destroying
mRNA before they get to the ribosome, instead of turning off the gene → regulate protein
synthesis
○ Coding RNAs are rRNA tRNA and mRNA used to make proteins
○ MicroRNA (miRNAs)
○ Small interfering RNAs (siRNAs)
■ Interference: prevents mRNA from hitting the ribosome put in a holding pattern
 74

■ Degradation: destroy mRNA

● Proteases break down extra proteins in a proteasome to purely destroy unneeded proteins
● Modifications to Chromatin Structure
○ Control whether genes are on or off by changing chromatin structure
○ Either loosen or contract DNA to expose or hide genes for replication, if hidden,
polymerase cannot get to the DNA
○ Histone modifications
■ Acetylate histones: expands chromatin by attaching acetyl groups to the
histones
■ Creates euchromatin (active)
○ Methylate DNA:
■ Add a methyl group (CH4) to the DNA, to condense the chromatin making DNA
inaccessible
■ Creates heterochromatin (silent)
○ Regions like centromere or telomeres are made up of heterochromatin cuz they are
noncoding and you don’t need them unwound
○ During mitosis no genes are turned on because chromatin is condensed
○ Epigenetic Inheritance:
■ Traits are much more than just DNA
● It’s about what genes are on or off
■ Studying inheritance abt what genes are on or off
● Outside factors, like lifestyle

MICROBIAL GENETICS
Mainly viruses
● Bacteria is considered alive but viruses aren because they aren’t cells
● Size: animal cell > bacterium > virus
● VIRUSES: aggregate of nucleic acids and proteins
● All viruses have
○ Capsid: Outer coat of proteins called capsomeres
■ Give virus it’s shape
■ Some viruses use DNA, RNA and single/double stranded variations
● Viral Envelope made up of cell membrane and glycoproteins
○ Only SOME viruses have this because cells steal it from the host cell
● Tobacco Mosaic Virus: infects tobacco plants most common viral model
● Adenovirus: causes meningitis, common cold, stomach bug, etc. (incl. Rhino viruses)
● Influenza Virus: has a viral envelop, flu
● Bacteriophage (phage): viruses that only infect bacteria, look like a space moon lander
● Virus goal: Replication
 75

○ Like a parasite, hurts specific host cells and hurts us for benefit → can’t reproduce on
their own
○ Does not contain enzymes or ribosomes → cannot make own DNA or proteins → uses a
host cell
○ ***all viruses have some mechanism to get information into the host cell, takes over
organelles + enzymes to make virus components
■ Have existed since the very first cells, viruses evolved to exploit them
○ Viruses self assemble in host cells, lyse the cell when there’s enough
○ Viruses don’t intend to kill you, they want to get you sick enough to spread the viruses
around
● Vaccines: you receive a component of the virus (viral proteins, genes, heat-killed virus, live virus)
to trigger an immune response and antibodies to defend against a real attack
● Lytic Cycle: used by virulent viruses → KILLS HOST CELL
○ Hydrolyzes host cells DNA
○ Injects viral DNA and builds new viral parts
○ Used by phages, bust out of the cell and lyse it
● Lysogenic Cycle: used by temperate viruses DOES NOT KILL HOST CELL
○ Prophage: viral genes inserted into a bacteria
○ Provirus: viral genes inserted into an animal cell
○ Viral DNA incorporates into the cell’s genome
○ When cell reproduces, builds viral proteins and replicates the bad DNA
○ If the cell is stressed, it causes the phage to be released from cell → NO LONGER
DORMANT, will enter the lytic cycle (e.g. shingles)
○ Stays dormant until there are optimal conditions, then releases to create an infection in
the lytic cycle
● HIV:
○ Viral envelope surrounds capsid containing RNA (used by retroviruses)
○ Retrovirus: has RNA for its genetic information
○ Reverse Transcriptase: undoes transcription, takes RNA and makes DNA for host cell
○ Enters Helper-T cells thru endocytosis, that's why envelop so important
○ Then capsid appears and makes DNA to incorporate in the cell → provirus that’s
dormant in lysogenic cycle
■ Why HIV appears years after infection
○ Drugs keep the provirus a provirus, keep it dormant
○ HIV LEAVES THRU EXOCYTOSIS → makes a viral envelope
○ Over time the the cell’s membrane would be destroyed because it's eaten up
○ ***cell no longer functional wipes out the core of the immune system
■ Why the virus is bad → virus badness depends on which type of host cell is
affected
● Even simpler infectious agents:
 76

○ Viroids: infect plants, just floaty RNA

○ Prion: infectious misfolded proteins (mad cow disease in humans)

BACTERIA
● Unicellular organisms
● Binary Fission (mitosis for bacteria): asexual reproduction (w/o a partner)
○ Doesn’t produce any genetic variation → asexual
○ W/o genetic variation you can’t have evolution not able to evolve so you need another
way to produce genetic variation
○ High rate of mutation → lack proofreading enzymes, the primary method of creating
variation
● Bacteria have a single circular chromosome and no nucleus (just nucleoid region), one origin of
replication
● Plasmid: extra small circular pieces of DNA, that has a relatively small number of genes on it (3-7
genes)
○ Can be exchanged with other bacteria
○ Can cause increased genetic variation
○ R(resistance)-plasmid: contain genes for resistance, in particular, antibiotic resistance,
used in labs, not usually in natural bacteria
● Genetic Recombination: mixing up all of the genes to increase the amount of variation
○ Transformation: (most common) when a bacteria takes in plasmids from their
environment (Griffith experiment), new genes make new proteins, increases genetic
variation
■ In order to make the bacteria accept the plasmids, you must induce
competency, using a process known as heat-shocking (expose to cold-hot-cold
to open bacteria to take in plasmid)
○ Transduction: transfer of DNA through phages
■ When a virus accidentally transfers DNA from one bacteria to another
■ When a host cell assembles viruses, sometimes bacterial DNA will be packaged
into one of the virus capsids
■ This virus infects another cell, and inserts the host cell’s bacteria
○ Conjugation (‘bacterial mating’): direct transfer of genetic material between bacteria
pairs
■ F-plasmid: allows bacteria to form a cytoplasmic bridge (mating bridge/sex pili)
outside the cell can only make this if the bacteria has the F-plasmid
● “Male bacteria”
■ The sex pili can be attached to a “female bacteria” and transfer plasmids,
(including the F-plasmid, change the bacterial sex of the female)
● Can copy the plasmid over, cannot lose a plasmid, so once it’s male it
stays male
 77

● LOOK AT IMMUNE PATHWAYS CHART ON DRIVE

● Nonspecific Defense (innate immunity) GENERAL
○ Your body targets everything the same, it doesn’t adapt to things, everyone has the
same nonspecific defense
○ 1st line of defense: prevents stuff from entering the body
■ Skin: protects body from external world
● Skin is pH acidic, creates bad, antibiotic environment for bacteria
■ Mucous: lines the holes/orifices in your body
● Acidic to repel bacteria and contains lysozymes: which break down and
destroy bacteria
● This is why licking a wound helps because of the pH of the mouth and
the enzymes of the saliva
○ 2nd line of defense: if stuff enters the body
■ Phagocytic White Blood Cells: large cells that perform phagocytosis
(endocytosis) and destroy invaders, all target slightly different things,
 78

encapsulates the invader in a vesicle and the vesicle travels to the lysosome and
performs hydrolysis. Doesn’t matter if the invaders are viruses or bacteria, eat
em anyway
● Neutrophils
● Natural Killers (NKs): target tumors (cancer) and virus-infected body
cells (only highly specific WBC)
● Eosinophils: specialized for worms
● Macrophage (most important, but still nonspecific): eats everything
■ Antimicrobial Proteins: float around in the bloodstream and destroy or lyse
microbial invader cells
● Part of the Complement System
■ Interferons: (chemical messenger) secreted by virus-infected cells and cause all
nearby cells to change their cell membrane, to prevent them from being
infected. Prevent virus spread from cell-to-cell.
○ Lymphatic System: has a bunch of macrophages and transports using vessels usually for
bacterial infections
■ Pathogens enter the lymphatic system through the intestinal fluids bathing the
cells
■ Has a bunch of vessels (in green) that are around your veins, interconnected
with your bloodstream, has a whole lot of macrophages
● Everything in blood except blood cells enter the lymphatic system in
lymph fluid
■ Spleen: also where macrophages are produced (not as much)
■ Lymph Nodes: where macrophages get activated, if you have an infection,
lymph nodes swell because they are filled with macrophage WBCs.
■ Lymph: fluid in lymphatic vessels, also goes thru veins collected from veins
○ Inflammation: redness, swelling, and warmth → caused by #1. Increased blood flow
makes it warm and red and #2. Swelling caused by blood vessels leaking fluid into that
area
■ Caused by:
● Physical tissue damage
● Infection: entry of a microorganism
■ Histamine: released when a tissue damage or infection occurs (chem. msger)
CAUSED INFLAMMATION
■ Increased blood flow increased/speedy transport of things you need
● More macrophages get to that area
● Blood vessels get much more permeable so things can leave the blood
vessels (large phagocytes) easily
■ Hypersensitivity: things that cause inflammation when they shouldn’t e.g.
allergies
 79

● Allergies: swollen sinuses cause a runny nose, by fluid draining out of

nose
○ Can be assuaged by antihistamines
● Specific Defense/Immunity (ADAPTIVE):
○ Adapts to each specific antigen that enters your body, your actual “immune system”
○ Antigen: ANY MOLECULE THAT TRIGGERS THE RELEASE OF ANTIBODIES AND AN
IMMUNE RESPONSE
■ T-dependent: originally goes through the helper T cell to produce antibodies
■ T-independent: antigen originally went to the B-cell to produce antibodies
○ Passive Immunity: antibodies provided the mother guard against pathogens that have
never infected the newborn
■ Breastfeeding passes her antibodies to the baby so the baby is immune to
everything the mom was, so the vulnerable newborn is protected. Antibodies go
away after the mother stops breastfeeding.
○ Active Immunity:
■ Primary Immune Response: when your body first encounters the antigen
■ Secondary Immune Response: when your body is exposed to the antigen in the
future (ANTIBODIES PART OF SECONDARY IMMUNE RESPONSE)
○ Epitope: part of the antigen that a B or T cell goes into the cell’s receptors for the T and
B cells to recognize the antigen
○ Lymphocytes: major WBCs, made in the bone marrow just like rest of blood
■ ***both made in bone but mature in different places
■ ***respond to specific antigens, every single B/T cell has unique receptors for
any type of antigen and gets more thru genetic recombination
● You have receptors for antigens that may not even have evolved yet, so
anything that enters your body can be countered
■ If an antigen is received by a lymphocyte’s specific receptor, that WBC clones
itself a lot in order to combat the antigen
● Clonal Selection: create a lot more of that lymphocyte to combat the
antigen
○ Half of the cells produced become:
○ Effector Cells: short lived cells, immediate response and take
care of the problem initially
○ Memory Cells: stick around for weeks, years, etc. in case there
is a recent second exposure, so you can’t catch the same cold
again, but don’t stay with you forever
■ T-cells: mature in the Thymus
● Effector T’s:
○ Cytotoxic T’s (w/ memory T’s part of the CELL-MEDIATED
RESPONSE) : “soldiers of the immune system” attacks infected
 80

cells in the body, does not kill the antigen directly, do not
produce antibodies
■ Perforin: a protein that forms pores in the target cell’s
membrane → causes cell to lyse and die
■ Respond to tumor antigens that are involved in cancer
formation
○ ***Helper T’s: "the core of the immune system”
■ Responds to Class II MHC from WBCs
■ Activates both B-cells and T-cells using cytokinins
● Memory T’s:
■ B-cells: mature in the Bone HUMORAL RESPONSE
● Effector B’s (Plasma Cells): produces ANTIBODIES which remain in your
bloodstream for the rest of your life so you can’t get it again
○ Immunoglobulin (Igs/antibody formal name):

quaternary protein made

of multiple polypeptides, in a “Y” shape
■ 2 purple subunits: heavy chains
■ 2 blue subunits: light chains
■ Used in the SECONDARY immune response
■ The two top tips of the “Y”are where antigens would
attach to the antigen
○ Neutralization: can’t kill a virus but antibody covers entire
surface of virus, to prevent it from infecting any other body cells
○ MAC (Membrane Attack Complex): only happens to bacteria,
when antibody punctures holes in bacteria, and lyses the
bacteria
● Memory B’s
● Self vs. Nonself:
○ Glycoprotein (MHC, Major Histocompatibility Complex): every person and every cell
has a glycoprotein unique to the body for cell-to-cell recognition
■ Class I: found on all normal body cells with nuclei
■ Class II: found on white blood cells
○ Also used for antigen presentation: holding out a piece of the antigen for T-cells from
infected cells so they can come kill that cell
 81

■ Cytotoxic T’s respond to Class I MHC

■ Helper T’s respond to Class II MHC on WBCs
● Vaccinations: try to trigger a primary immune response
○ Inactivated bacterial toxins, heat-killed pathogens, parts of pathogens, genes coding for
microbial proteins → injected with antigen material
■ If you trigger a primary immune response you build antibodies to prevent an
actual attack from a disease
● Disorders:
○ Autoimmune Diseases: loss of self tolerance, body attacks part of self because it doesn’t
recognize it
■ Lupus: attacks histones and DNA
■ Rheumatoid Arthritis: cartilage and bones in joints are attacked
■ Multiple Sclerosis: CNS and schwann cells are targeted
■ Diabetes Mellitus (Type I): pancreatic cells are targeted
○ Immunodeficiency Diseases: defective or absent immune system
■ SCID (Severe Combined Immunodeficiency): treated with gene therapy, born
without an immune system
■ Hodgkin’s: (lymphoma, and cancers): lymphocytes in the body are cancerous →
cancers form in the lymph nodes
■ AIDS: (Acquired Immunodeficiency Syndrome) targets Helper T-cells using HIV,
will destroy the immune system
● HIV+ just means you have the HIV virus
● AIDS is when a certain percent of the immune system has been wiped
out → shuts down cell-mediated and humoral responses
● Can’t die of AIDS, because you die of simple infections because you
don’t have normal defenses

WATER POTENTIAL
H20 Potential is used to predict the direction in which water will diffuse through plant tissues.
Plant cells placed in a hypotonic solution cannot lyse due to their cell wall. As a result, pressure
builds up in the plant cell. When press is high, no additional water can enter causing the cell to
reach equilibrium.

H2O Potential = Pressure Potential (+++) + Solute Potential

(Concentration ---)

Y(solution) = -iCRT where C is molarity, R is 0.0831, I is 1, and T is temperature in Kelvin

· Pressure increases
· Solute potential decreases as we add more solute.
Pure water (O) is the highest H2O potential

Equilibrium is met when the Pressure Potential = Solute Potential

 82

Enough water can’t come in to reach equilibrium, as water enters plant cell, pressure builds up
against cell walls and this resists the water coming in, and when pressure builds up add positive
numbers to cell h2O potential, when solution and cell ==0, dat quilibrium is reached

LIFE CYCLES
● Sexual Life Cycle: alteration of halving and doubling chromosome count in each generation
○ Meiosis: halving chromosome count in testes and ovaries to make sperm and egg,
makes germline cells (all about halving chromosomes and creating variation)
○ Fertilization: doubling chromosome count, sperm meets egg, creates a zygote
○ Every single life cycle contains both of these events
● but only applies to organisms that reproduce sexually with male and female, not asexuals who
require only mitosis (no variation, with redwoods or hydras) without a mate, so without
mutation there is no evolution. Asexual reproduction keeps species going without available
mates
● Haploid (n): cells with half of the number of chromosomes (sperm and egg/ova)
○ Gametes: sperm and egg created thru meiosis
● Diploid (2n): cells with two sets of chromosomes
● Number of chromosomes varies per species
● Somatic Cells: (normal) body cells, that have 46 chromosomes, half from mom half from dad,
really 23 pairs of chromosomes
 83

○ Each pair is a homologous pair, NOT sister chromatids, each chromosome is duplicated,
two sister chromatids on either side of the X held together by a centromere.
Homologous means they have the same genes located in the same regions not
necessarily the same versions of the genes
● Allele: different versions of the same gene
● Locus (loci): exact location of a gene on a chromosome
● Karyotype: picture showing 23 pairs of chromosomes (only visible in mitosis because of
condensing)
○ Autosomal pairs (22): all of the genes for normal traits
○ Sex chromosomes (23rd): XY male and XX female
● What changes for organisms to organism, one or the other, either diploid or haploid stage is
dominant
○ Animals are mainly diploid because their body cells are somatic and not germline
○ Fungi usually haploid with only one set of chromosomes, can’t cut one set of
chromosomes in half so they do not have meiosis use mitosis is reproduce asexually to
make haploid spores (like a gamete but do not fertilize each other) spores find a good
environment and grow into a new fungus (everything is haploid and no variation)
■ However, if two fungi come into contact, they will fertilize each other to
produce a zygote, and then goes thru meiosis to produce more haploids for
variation (evolution)
● Plant Life Cycle: both haploid and diploid split equally there is no dominant stage, for every
species of plant there is a haploid and diploid form of that plant
○ Alternation of generations: one gen is haploid and the next may be diploid, it flips every
gen
○ Sporophyte: diploid (2n) generation of a plant, (e.g. ferns that we usually see), goes
through meiosis next → produces haploid (n) spores
 84

○ Gametophyte: spores grow into a haploid (n) generation, produces GAMETES BUT THRU
MITOSIS (sperm + egg) that create a zygote to reenter the sporophyte stage: haploid

egg + haploid sperm = diploid plant

MEIOSIS
● Meiosis I: chromosome number is cut in half
● Two types of meiosis: I and II
 85

● Only germline cells go thru mitosis (ovum and sperm) but ova are already produced at birth,
whereas sperm is produced all thru a male’s lifetime
● Prophase I: mitotic chromosomes form, nuclear envelope disappears, spindle fibers reach out
(e.g. four total chromosomes and 2 homologous pairs)
 86

○ Homologous pairs have the same gene in the same place (locus) one from dad and one
from mom
● Tetrads: homologous pairs come together (4 sister chromatids) during PROPHASE I
● Chiasma: where the homologous pairs overlap, the pairs exchange pieces of chromosomes,
through crossing over important to create genetic variation
○ The areas that cross over are completely random
● Metaphase I: tetrads line up on the equator of the cell using spindle fibers, not like mitosis, they
line up in their homologous pairs, but in mitosis has the chromosomes lined up single file not in
pairs
● Anaphase: cell splits in half
● Meiosis I: 2n diploid parent splits to two n haploid daughters
● Meiosis II: anaphase II the sister chromatids are pulled apart
● End with four haploid variable gametes

VARIATION
● Genetic recombination: put back together after mixing the genes “genetic lottery”
○ Crossing Over: in meiosis
○ Independent Assortment of Chromosomes:
■ Pairs that line up in metaphase determines the combination of chromosomes
that end up in the gametes, completely random order of lining up
● Aa
● Bb
● aA
● bB
¿ of homologous pairs
■ 2 =number of possible combinations(typically 8M combos)
○ Random Fertilization: random chance decides which sperm gets to each egg
■ Each sperm is 1/8M combos and each egg 1/8M combos, each person is 1/64
trillion combos, not even considering crossing over events
● All new variation came about/created from mutation at some point, but a limited role in genetic
variation, variation is about mixing up preexisting genes

MENDELIAN GENETICS
● Gregor Mendel: Austrian monk who is the father of modern day genetics
○ Worked with Pisum satium plant
○ Came up with laws of inheritance based off pea plant experiments
○ Characters: big overarching things (color, height, shape, etc.)
■ Trait: different form of a character (tall, short, blue, yellow)
○ Controlled which pea plants breed with other pea plants, or he self-pollinated and bred
the pea plant with itself
 87

■ Self-bred pea plants became purebred/true breeding, 100% the same organism
without any variation
○ Mendel’s First Cross:
■ P generation: Parental generation, crossed a purebred purple with a purebred
white plant
■ People used to believe in blending inheritance: traits are mixed so tall person
mates with short person would equal a medium height baby
■ F1 generation: created only purple plants, traits didn’t blend, so it proves
blending inheritance wrong
● Hybrids: combination of two organisms, half-purple and half-white
■ F2 generation: bred purple hybrids and created 75% purple and 25% white
flowers
● Traits do not blend together
● Traits can be hidden and come out in a later generation
● Genotype: genetic makeup of an organism containing all of the alleles
○ Homozygous Dominant
○ Heterozygous (shows Dominance)
○ Homozygous Recessive
● Phenotype: the physical appearance
○ If someone has a dominant phenotype, you cannot figure out the genotype, either AA or
Aa
○ Dominant (heterozygous, homozygous dominant)
○ Recessive (homozygous recessive)
○ One allele cannot suppress another allele, every allele is always expressed
■ AA making correct proteins → dominant trait
■ Aa making enough correct proteins → dominant trait
■ aa making defective proteins → recessive trait
■ Don’t need two functioning alleles, only one is necessary
● Mendel’s LAWS OF INHERITANCE:
○ Laws of Segregation: for every character there are two different forms/versions called
alleles (two different versions of a gene, but Mendel didn’t know that)
■ During formation of gametes, the two alleles for each character separate.
(During anaphase)
■ Each gamete gets one of the alleles randomly
■ Homozygous: (same) two of the same allele are inherited
■ Heterozygous: (different) two different alleles are inherited
● One allele will be expressed → dominant
● One allele will not be expressed → recessive
■ Punnett square demonstrates that two alleles from one character (for example
Aa) segregate and can match up with the other parent’s segregated alleles to
make percentages of possible combinations
 88

● Genotypic Ratio: 1:2:1 if (AA, Aa, Aa, aa) homozygous

dominant:heterozygous:homozygous recessive of the possible
combinations
● Phenotypic Ratio: 3:1 dominant(D):recessive(R) expressing of the
possible combinations
○ For dihybrids, the ratio is D/D : D/R : R/D : R/R
■ Double Heterozygous (AaBb) x Double heterozygous =
9:3:3:1
■ Double Heterozygous x Double homozygous (aabb) =
4:4:4:4
■ Double Homozygous x Double homozygous = 0:0:0:16
○ Law of Independent Assortment: inheritance of one character doesn’t affect the
inheritance of another character, each is inherited independently
■ Each pair of alleles segregates into gametes independently
■ ASSUMES EVERY GENE IS FOUND ON A DIFFERENT CHROMOSOME
■ E.g. brown hair doesn’t mean you’ll get brown eyes
■ Dihybrid Cross: a cross involving two characters to find all of the possible allele
results (16 squares, there are also trihybrid crosses with 64 square and quadra
hybrid crosses) (SEE PHOTO ON GOOGLE DRIVE)
■ Testcross: find out the unknown dominant allele that corresponds with the
dominant phenotype of an organism
● Cross the dominant organism with a homozygous recessive organism, if
any of their offspring are recessive, then the dominant organism is
heterozygous (Bb) because you need a recessive copy from this parent
in order to have recessive (bb) offspring.
■ Rule of Multiplication: likelihood of multiple genetic events happening
consecutively which depends on the individual likelihoods of each individual
event.
● E.g. have four male children in a row = 6.25% chance, because each
child is a 50/50 chance, so ½ * ½ * ½ * ½ = 1/16
● Complete Dominance: simple dominance, one allele is expressed over
another allele BUT not all characters are completely dominant
● Incomplete Dominance: one allele is not dominant over the other, you
cannot use capital and lowercase letters (GREY OR PINK)
○ The heterozygote is an intermediate phenotype (sort of like
blending == pink) half way between the two alleles
● Codominance: both alleles are equally expressed (both red and white) it
creates spots on organisms only thing that really exists at the level of
the protein
● BLOOD TYPES: use multiple alleles to decide type, but only inherit two
alleles like normal
 89

○ A allele (I^A)
○ B allele (I^B)
○ O allele (ii)
○ O is recessive to both A and B, but A and B are codominant
○ Phenotypes:
■ Type O: OO
■ Type A: AA, AO
■ Type B: BB, BO
■ Type AB: AB (codominance)
○ If you’re blood type A you have A antigens (glycoprotein MHCs) on blood cells, if you’re
blood type B you have B antigens, if you are blood type AB you have both A and B
antigens, and if you are type O then you have no antigens
○ You have antibodies that fight off foreign blood, if type A, you have B antibodies, if type
B you have A antibodies, if you are type AB, you have no antibodies, bec. You would
target your own cells with A or B antigens, and if you are blood type O you have A and B
antigens
○ O is the universal donor because it has no antigens, cannot read blood type O as being
foreign, AB is the universal receiver because it has no antibodies to detect and fight off
foreign blood
○ RH Factor: important antigen another way to detect foreign blood, either positive (+) if
you have it or negative (-) if you don’t
■ O negative is the real universal donor because it’s an extra antigen on cells
■ AB positive is the true universal receiver because it has no RH factor
■ RH factor is controlled by complete dominance you can only be RH negative if
you’re are (nn, but if you’re Nn or NN) you’re positive
○ Do not need to have the same blood type as your parents
● In reality the only type of dominance that exists at the molecular level is codominant (two
different alleles, half of one protein and half of another)
● Two characters control blood type, A/B/O and RH
● Pleiotropy: when one gene has multiple phenotypic effects (most human genes are pleiotropic)
○ E.g. PKU, caused by a single gene, causes severe mental impairment and reduced skin
pigmentation (gene involved in skin and in brain, does multiple things in the body) Most
genetic diseases have multiple effects
● Epistasis: when one gene directly affects another gene
○ E.g. one gene B/b in mice determines if fur coat is brown or black, another gene
determines if B/b pigment is deposited in skin if homozygous recessive (cc) for second
gene, B/b dominant or recessiveness doesn’t matter → creates albinism
● Polygenic Inheritance: multiple genes work together to create a character
○ Quantitative Characters: characters that vary along a continuum, not caused by one
gene, but caused by multiple genes that add up
 90

■ E.g. three genes produce melanin, if you get two dominant alleles and one
recessive, two genes are producing melanin, and one is producing nothing →
determines skin color
○ Any human character that is polygenic, cannot be predicted (like eye color)
● Norm of reactions: Environment plays a large role in converting genotype to phenotype, norm is
the normal phenotype that goes with a genotype
○ But sometimes your environment can change your phenotype away from the original
norm prescribed by the genotype
○ Some genes are not affected by the norm of reactions (environment plays no role)
○ E.g. affects height if you work out too much early on you stunt growth
● Multifactorial Character:
○ E.g. hydrangeas color depends on pH of soil even though they have the same genotype,
so color is considered multifactorial
○ Trait determined by the effects of multiple genes
● Pedigree Analysis: information about the presence/absence of a particular phenotypic trait is
collected from as many individuals in a family as possible and across generations.
● Square is male, circle is female, painted in means they have that trait
● Sex-linked trait: genes inherited only on the X-chromosome (males have one X and females
have two Xs) only get one allele, males can’t be carriers
○ Hemophilia: not able to form blood clots
○ Sex-linked diseases are more common for males because there are less combinations,
females get two alleles which one could be dominant good
○ Male pattern baldness
○ Muscular dystrophy
○ Color blindness

DISORDERS
● Recessively inherited: must be homozygous recessive
● Heterozygotes are disease carriers, you yourself are normal, but carrying a recessive allele that
causes the disease and can pass it to the offspring.
● Cystic Fibrosis: recessively inherited, caused by a mutated Chloride channel gene
○ Dominant allele codes for functional protein
○ Recessive allele codes for a misfolded protein
○ Heterozygote: dominant allele will make enough correct channels and ignore the bad
ones
○ Homozygous Recessive: no chloride channels work, you have CF
○ Homozygous Dominant: All chloride channels work
○ Mucus builds up in your lungs and get choked over time.
● Sickle Cell Anemia: mutated hemoglobin gene also recessively inherited
 91

○ Heterozygotes have the Sickle Cell Trait, can have problems at high altitudes, where
there is less oxygen, since you’re making half normal and half defective hemoglobin, so
they can have anemia symptoms
● Tay Sachs Disease: mutated gene codes for a mutated lipid breakdown protein in the brain, also
recessively inherited, but at the molecular level, is incomplete dominance, only digest half the
amount of enzymes
● Consanguineous Mating: inbreeding, creates diseases because it brings out recessive and bad
traits, because you’re more likely to mate two carriers to create recessive expressing bad
offspring
● Achondroplasia: dwarfism, dominantly inherited
● Lethal Dominant (Huntington’s Disease): only need one dominant allele to kill you/make you
diseased
● Genetic Testing:
○ Probability: just look if the parents are carriers and find the percentage/likelihood of
what the kids might get
■ Pedigree: use for members of a family to determine who is a carrier of a genetic
disease
○ Genetic Tests: available for over 2000 genes, before having children to find out if you
are a carrier
■ Use gel electrophoresis, run your alleles next to dominant or recessive alleles, if
dominant, your fingerprint would match the dominant banding patterns, but if
you’re a carrier it would be different that both the dominant and recessive
allele.
○ Fetal Testing: if something in the ultrasound indicates something is wrong, so they test
within the uterus, both invasive can cause harm to mom and child
■ Amniocentesis: (safer) 4-16 weeks into pregnancy, 2nd trimester,
● Big needle to go through stomach and into the amniotic fluid in uterus,
look at fetal cells in the fluid
○ Test karyotype → down syndrome?
○ Genetic tests/ Gele electrophoresis
■ Chorionic villus sampling (CVS): much more invasive, more potential harm, can
be done earlier between 8-10 weeks in pregnancy
● Take a piece of the chorionic villus through the cervix
○ Newborn Screen:
■ Heel prick: test for PKU (can’t break down amino acid phenylalanine) can cure
this if they just put them on a special diet

CHROMOSOME THEORY OF INHERITANCE

● Females have two copies of sex-linked genes, and males only have one sex-linked copy
● T. H. Morgan: discovered sex-linkage of genes
 92

○ Flies display white eyes instead of normal dominant red eyes are more common in
males
■ Must be sex-linked, on the X chromosome
● Y chromosome is much smaller than the X chromosome
○ SRY Gene: makes males male, directs development of male anatomical features
● LINKED GENES: two genes found on the same autosomal chromosome
○ ***goes against Mendel’s Law of Independent Assortment (every character inherited on
its own, but ASSUMES EVERY GENE IS FOUND ON A DIFFERENT CHROMOSOME)
○ If two genes are found on the same chromosome, the
characters are inherited together
○ If you have GG, you might also have RR.
○ The only thing that can separate two genes is when
crossing over occurs, only way to separate two genes.
○ When OBSERVED amounts do not match the EXPECTED
offspring phenotypes, → genes must be linked
○ AaBb x aabb = 4:4:4:4 (1:1:1:1) expected amount
○ Parental Type: offspring same as the parents
○ Recombinant Type: offspring different from the parents
(nonparental type)
■ Result of
crossing over
○ Determine the
percent
recombination: add
up the recombinants
2016+185m = 391,
divide by total
number of results
(2300) = 17% were
created through
crossing over
■ Divide
percent
 93

recombination by 2 to get map unit distance btwn. genes (high map units = high
percent recombination)
■ 4:4 arrangement of spores no recom, 2:2:2:2 means recombination
■ The percent recombination (aka rate of crossing over) is directly proportional
to the distance between the two linked genes
● If genes are farther apart (either end of the chromosome), there’s more
of a chance they will cross over
● If closer together, more unlikely to inherit them separately through
crossing over
■ Chromosome/Linkage Map: Percent recombination can be used to create this,
provides the locus (location) of each linked gene on a chromosome

CHROMOSOMAL DISORDERS
● Nondisjunction: occurs when
chromosomes fail to separate
during anaphase I or anaphase
II
○ Both pairs (of sister
chromatids or
homologous pairs) can
go to one side, and the
other cell doesn’t have
another chromosome
○ One gamete will have
one more
chromosome, one will have one less chromosome
● Aneuploid: abnormal number of chromosomes
○ Trisomy 21 (Down Syndrome): 21st pair went thru nondisjunction, would have three
chromosomes for the 21st pair (47 chromosomes instead of 46)
○ Klinefelter’s Syndrome: nondisjunction of the sex chromosomes (XXY - still male, as long
as you have the Y chromosome still have SRY gene), have some female attributes →
makes them sterile
■ Wider hips, minor breast development *****lack of (facial/leg) hair*****
○ When your chromosomes are screwed up you’re always sterile
○ Turner’s Syndrome: XO (normal female that’s sterile) 45 chromosomes
■ Cannot reproduce because they don’t have the right number of chromosomes
■ Barr body: Second X chromosome is inactivated (still have two x chromosomes)
turned off through DNA methylation
■ Sometimes, the one X chromosome can be active, but sometimes the other x
chromosome can be active
 94

■ Males cannot exhibit these features because they don’t have mutually exclusive
inactivated chromosomes
● Alterations to Chromosome Number:
○ Crossing over errors:
■ Duplications and Deletions: caused by the same event, at cross over, one
chromosome takes (deletions more harmful) the WHOLE part of the other that
crossed over and the other one is left shorter
● Cri du chat: cry of the cat, caused by deletion in chromosome 5, have a
cat-like cry, severely mentally impaired, microcephaly, die in infancy
■ Inversion: piece of chromosome that is crossed over goes on backwards, order
of the genes matters (not as harmful as a deletion)
■ Translocation: when two nonhomologous chromosomes cross over which
shouldn’t
● Chronic Myelogenous Leukemia: caused by unusual crossover of
chromosome 9 and chromosome 22; chromosome 22 is translocated a
piece of 9 becoming a Philadelphia chromosome
■ Genomic Imprinting: GOES AGAINST EVERYTHING, sometimes you only use the
allele inherited from the mom or from the dad, doesn’t deal with dominance
● For IGF (growth factor) gene ONLY the paternal allele is the only one
that matters, maternal allele is shut off completely through methylation
throughout the body
○ If you get a bad allele from dad for IGF, you get dwarfism
● Same genotype doesn’t even matter

CHI SQUARE ANALYSIS

● Tells you if your results are valid or not, determines if genes are linked or not, must do a
statistical test; analyzes difference between actual (observed) to expected outcomes, tell you if
they are different or the same
○ EQUATION RETURNS THE VALUE NOT THE PROBABILITY
○ MUST ADD UP VALUES THEN COMPARE TO THE CHART
○ You almost never get a perfect ratio (9:3:3:1, e.g.)
● Null Hypothesis = H0
○ NO difference between observed and expected, 27;23 is no different from 25:25 when
flipping a coin
 95

● Alternate Hypothesis: There is a difference, more likely to flip heads than tails
● x^2: just symbol for chi square, not actually squared
x 2=Σ¿¿
● 0.05: ALWAYS the cutoff
○ If value is greater than number that corresponds with 0.05 value, then there IS a
difference (alterative hyp.)
○ If the value is smaller than the number that corresponds with 0.05, then there’s NO
DIFFERENCE (null hyp.)
○ Probability that chance alone creates your results
https://www.youtube.com/watch?v=WXPBoFDqNVk

● Degrees of Freedom: number of groups minus 1 (heads, tails - 1 = 1)

ANIMAL BEHAVIOR
● Ethology: the study of animal behavior
● Behavior: an animal’s response to sensory input (stimulus)
● Stimulus: any factor that causes a response in an organism
 96

● BEHAVIORS:
○ Learned Behavior: organisms learn over lifetime
■ Associative Learning: a link or association is made between a stimulus
and a particular behavior, association between a stimulus and behavior is
learned
● Classical Conditioning: (Pavlov’s Dogs): one stimulus is associated
with another stimulus in terms of a particular response (rang a
bell and sprayed a meat spray in a dog’s mouth, many times →
salivation, eventually when he rang the bell, the dog would begin
salivating)
● Operant Conditioning: trial and error learning, behavior is
modified by consequences (B. F. Skinner)
● Habituation: loss of behavior to a recurring stimulus (organism
gets used to it
■ Observational (social) learning: learn from the actions of others
■ Spatial Learning: memory that reflects environment’s spatial structure
(squirrels/bees remember where their nuts/hive are by remembering
parts of the environment)
■ Insight (cognition): only in chimps, humans, really think about a problem
and past experience to come up with a solution
○ Innate Behavior: genetically pre programmed, instinct
■ Instinct: genetically inherited behavior
■ Fixed Action Pattern: behavior complete when the first time the
organism sees the stimulus→ automatically performed (studied by Niko
Tinbergen on stickleback fish)
■ Imprinting: (Konrad Lorenz) organisms have a critical period in which a
particular behavior is learned (learn who mother is, if time passes or
isolated, will not learn the behavior)
○ Orientation Behaviors: place an organism in its most favorable environment
■ Taxis: movement directly towards or away from a stimulus
● Phototaxis: movement towards/away a light (plants grow to sun)
● Thermotaxis: movement towards or away from heat
● Chemotaxis: towards or away from chemicals in environment
■ Kinesis: random movements in response to a stimulus
● Slow movements indicate like, fast movements indicate dislike
● Usually occurs when a organism first encounters a stimulus and
doesn’t know how to respond
■ Migration: long distance, seasonal movement
 97

● Environment change, availability of food etc.

○ Agonistic Behaviors: animals respond to each other to aggressive or submissive
responses
■ Usually for animal competition (food, mates, territory) or make the
animal look bigger, saves energy, determine who’s top dog without
actually fighting
○ Altruistic Behaviors: reduce organism’s fitness (in harm’s way) to help other
organisms, unselfish (prairie dogs watch the night and warn others of danger)
○ Foraging Behaviors: search for, recognize, or capture of food

INTRO TO EVOLUTION AND NATURAL SELECTION

● Evolution: changes over time
○ Populations and species can change
● Population: group of members of the same species living in the same place at the same
time (first level of evolution, micro), change over time to adapt to environment
● Species: group of individuals that can mate and make fertile offspring → biological
species concept (second level of evolution, macro) change over time makes new species,
speciation
● Individuals cannot evolve only populations can
● Evolution is a change in proportions of genes
● Early Evolution Views
○ Curvier and Fossils: Catastrophism
■ Curvier was one of the first paleontologists
■ Species used to exist that don’t anymore and species that exist now may
have not existed in the past
■ Catastrophism: the reason you saw different fossils in different strata of
rock because all of the species in certain times went extinct
○ Hutton and Lyell:
■ Gradualism (Hutton): earth is gradually changing over time
■ Uniformitarianism (Lyell): earth changing at a uniform rate
■ Darwin thought that if earth is changing, then species must be too
○ Lamarck: early theories on evolution
■ Use and disuse: only correct idea
 98

● Use it or lose it, parts of the body that are used heavily will be
accentuated, but parts that are reduced will not be maintained
(won’t waste energy)
■ Inheritance of acquired characteristics:
● Characteristics created over an
individual’s lifetime would be
passed on
○ Bonzai trees would not
reproduce as small trees
■ Natural Transformation of Species: each
species naturally goes from simple to
complex, no speciation and no extinction
● CHARLES DARWIN: traveled to Galapagos Islands and
other places
○ Came up with the idea of Natural Selection NOT
the idea of evolution → On the Origin of Species
on the Basis of Natural Selection
○ “Descent with modification”
■ Generation to generation change for a
particular trait that takes place in a
population, constantly changing to
become better adapted to the
environment → Natural Selection
○ Environment is the driving force of natural selection
■ Selection Pressures: control which traits are the most beneficial
● E.g. food source, temperature, avoid predation
○ Theory of Natural Selection: differential reproductive success, different ability to
pass on genes
■ I. Organisms overproduce offspring
● Based on Charles Malthus’ idea that human pop will exceed
resources
■ II. Offspring are variation in appearance and function and some of those
variations are heritable → variation is the fuel for selection
● Variation is created through genetic recombination (random
fertilization, independent assortment, crossing over) originally
from mutation
■ III. Environmental resources are limited and those varied offspring must
compete for their share → struggle for existence
 99

■ IV. Individuals best able to survive in the environment will survive and
reproduce → differential inheritance of genes
○ Focus on Adaptation:
■ Adaptation to an environment causes changes within a population and
the forming of new species, if changes build up and can no longer mate
must be two new species
■ Observations:
● Unity of Life: all organisms are similar (common ancestor)
● Diversity of Life: better adapted to unique environments
● Match between organisms and environment
● History of Life: phylogenetic tree tree with branches showing life’s diversity, and where
the come from
● Alfred Russel Wallace: sent his ideas of natural selection to Darwin, Darwin’s ideas were
more developed so only Darwin published
● Natural Selection in Action:
○ Beak depth in a finch changes as an environment changes
■ Drier years mean nuts they eat are harder → thick deep beaks survive
■ Wetter years means nuts are easy to eat → beak depth decreases
○ Drug and antibiotic resistance from bacteria and viruses
○ Peppered moths got polluted, trees became darker as covered by soot and other
material, peppered moths became darker for camouflage
● Artificial Selection: nature does not determine selected traits, but humans select them
○ Wild mustard creates brussel sprouts, cabbage and broccoli, by selecting for
various traits
■ E.g. select for leaves, breed those to make kale
● Evidence of Evolution:
○ Biogeography: geographical distribution of species
■ Modern species are found where they are because they come from
ancestors in the hose regions
○ Fossil Record (palaeontology): deeper the rock fossil, older it is, can look
progression of species over time
○ Comparative Embryology: different stages in embryonic dev.
■ Most animals look extreme similar in the womb, closer species are more
similar embryonic development
○ Comparative Anatomy: anatomical similarities between species, to determine
common ancestry → evidences evolution
■ Focuses on homology (w/ bones often), similarity from common ancestry
 100

● Homologous structures: same structure but different function in

different species, only different because of adaptation
● Analogous structures: structures that look similar, adapted to the
same environment, but do not share a common ancestor, or
similar structures
● Vestigial Structures: leftover pieces of from ancestors that used
to serve a function when it was necessary
○ Coccyx (tailbone) when humans had tails
○ Molecular Biology: study molecules amino acids and DNA that are shared in
common between species, distant species have less DNA base pairs in common

MICROEVOLUTION
● Change in ratios (in phenotypes/genotypes, change in proportion of alleles, one of
those alleles is being selected for) in a population over time
● Individuals cannot evolve, only populations can, generation after generation, it adapts
better to the environment
● Population Genetics: combines evo with genetics to measure change taking place in a
population
○ Gene Pool: all alleles in a populations
● Genetic Variation: crucial for natural selection and evolution
○ Measured by average heterozygosity, contains both alleles for a particular gene
● Natural Selection: selects for advantageous alleles within a population
● Evolution: when a population’s gene structure changes
○ Gene structure: ratio of dominant alleles to ratio of recessive alleles AA:Aa:aa
● Hardy-Weinberg Theorem: measure the ratio of alleles and genotypes in a population
○ Genetic structure of a non evolving population remains constant, in Hardy-
Weinberg equilibrium
■ p^2+2pq+q^2=1(100% of alleles, p + q =1) equation can measure ratio of
genes in equilibrium
● p^2: frequency of AA
● 2pq: frequency of Aa
● q^2: frequency of aa
● P: frequency of A allele
● Q: frequency of a allele
■ If frequencies change over time then evolution has occurred, always
begin by finding q^2, easy because only recessive expressing people have
aa
 101

■ Measure frequency at time A and then at time B, if you find a difference

in the ratios, then quantified evolution must be occurring
○ Equilibrium Requirements: pop will not evolve in equilibrium can only use the
equation in this theoretical state
■ Very large pop.
● Genetic Drift: when a small random change has a large effect on a
small population frequencies, doesn’t affect large pops
○ Bottlenecking: when an event drastically reduces
population size (disaster, disease event), will not reflect
same frequencies of same population → microevolution,
chance creates new frequencies
○ Founder Effect: small subgroup moves away from large
pop. will have a different ratio of genotypes of alleles than
original → also microevolution, random events will change
this pop. drastically
○ NOT adaptive (doesn’t make population better)
■ Isolation from other populations
● Gene Flow: when two different populations begin mating, reduce
the differences between the populations (become similar) →
microevolution, still evolving, movement of alleles betwee pops
■ No net mutations
● Mutations are the raw source where new variation is created (not
the major source of variation though, that would be
recombination)
■ Random mating
● Nonrandom mating/Sexual Selection: just as important to drive
evolution as natural selection, not adaptive, just about mating
○ Intrasexual Selection: happens within a sex (male
competition for the right to mate with females, males with
better genes get to pass them on) males get big and strong
○ Intersexual Selection: between sexes (female choice,
choose which male they allow to mate with them) males
usually look fabulous to please the female (best genes
correspond with best colors sometimes, color of mane
corresponds with testosterone levels in lions, so lionesses
pick the best color)
○ Both create sexual dimorphism or differences between
the sexes of a species
 102

■ NO natural selection
● Major force that causes evolution (better adaptation to the
environment) ONLY ADAPTIVE MECHANISM (helps organisms to
be better at environment, all the others are just ways the change)
● Darwinian Fitness: indicator of how strong an individual’s genes are, based on children's
production, more children == more fitness
○ Measured 0-1, others’ fitness is compared to that of the most fit individual
● Modes of Selection:
○ Stabilizing Selection: average individual is favored (e.g. average birth weight 7
lbs)
○ Directional Selection: one extreme is favored over the other, giraffes with the
longest necks survived and reproduced
○ Disruptive Selection: both extremes are favored could lead to two new species
being formed
● Genetic Variation: natural selection would get rid of all variation (high rate of extinction
because of this) but the environment keeps changing so variation is preserved
○ Without different forms, one cannot be selected for over the other
○ Quantitative Characters; vary along a continuum (not discrete in an either or
basis tall or short, black or blue etc.), has many different possible phenotypes
○ Mutation: important source of variation, raw source, but only mutations that
take place in germlines pass on (only really effective for bacteria and viruses)
○ Sexual Recombination: during meiosis, crossing over, independent assortment
and random fertilization
● What prevents natural selection from extinguishing the bad allele?
○ Diploidy: hides genetic variation in the form of carrier recessive alleles through
heterozygotes, two alleles for every gene, contain two alleles except only
express one
○ Balanced Polymorphism: ability of nature to maintain diversity/variation/shape
■ Heterozygote Advantage: selected as the best option (like sickle cell
anemia, and malaria trait, if you heterozygous, Sickle Cell Trait, doesn’t
have SCA but resistant to malaria), keeps both alleles in the population
■ Hybrid Vigor: breed homozygous dom and homozygous rec to have
better quality
■ Frequency-dependent selection: what trait is successful depends on how
many organisms have that trait, more of the trait == bad
● Fish either latch onto prey on right side or left side. If left side
more successful, then prey will being defending that side, so right
side now becomes more successful.
 103

● Natural Selection cannot fashion perfect organisms

○ A population can only modify preexisting traits, locked into ancestry
○ Not all evolution is adaptive, things can change because of outside events

MACROEVOLUTION
● The formation of new species
● Anagenesis (phyletic evolution): where one species transforms into a new species, old
species no longer exists
● Cladogenesis (branching evolution): new species buds off another species, increases
biodiversity (number of species in an environment)
● Biological Species Concept: group of individuals that can produce fertile offspring,
reproductive isolation
● Speciation: formation of new species
○ Allopatric: MAJOR way to make species when a physical barrier (e.g. grand
canyon, newly formed river, etc. each new environment has different selection
pressures) prevents two populations from being able to mate, two populations
become different that they cannot mate anymore → breakup of Pangaea
■ Prevents gene flow
■ Adaptive Radiation: spreading out of new species from a common
ancestor
○ Sympatric: anything other than a geographic barrier separates new populations
■ Chromosomal Changes: nondisjunction in meiosis
● Polyploidy (in plants only because animal gametes with different
numbers cannot fertilize): whole extra sets of homologous
chromosomes in gametes (do not separate), diploid plants can
become tetraploid → can no longer mate, but can self-fertilize
and propagate a new species
● Nonrandom Mating: sexual selection, subgroup of a population
decides to only mate with one type of individual
■ Habitat Differentiation: two groups within a population begin to exploit
different resources within the environment, What obtain different food
sources, e.g. females prefer certain males at certain level, and in deep
water like certain males, create new species (a set of different groups
with sexual selection in a population)
● Reproductive Barriers: prevent different species from mating
○ Prezygotic barriers: prevent mating (stops zygote from mating, if two species hit
the horny bing bong) between species or hinder fertilization of ova if members
of different species attempt to mate
 104

■ Habitat Isolation: two species live in different habitats, can’t meet up to

mate
■ Temporal Isolation: mating seasons of two different species differs
■ Behavioral Isolation: (mainly birds) have unique mating rituals, if ritual
not performed by male, female will not receive the mating
■ Mechanical Isolation: when physical reproductive parts of organisms do
not line up
■ Gametic Isolation: when sperm of one species is physically unable to
fertilize the egg of another (need same number of chromosomes, which
is unique to the species)
○ Postzygotic barriers: occurs if two species do mate and make a hybrid offspring
→ prevent species from mating which maintains biodiversity
■ Reduced Hybrid Fertility: (MOST IMPT.) most hybrids are sterile, mules
■ Reduced Hybrid Viability: fail to complete development or have birth
defects prevent them from mating
■ Hybrid Breakdowns: first gen of hybrids might be fertile, but next
generation will NOT be viable or fertile (more important with plants)
● Hybrid Zones: region where members of different species meet and mate to make
hybrids (closely related species of course), would normally be separated
○ Can lead to:
■ Reinforcement: strengthening reproductive barriers, species become
more and more distinct (don’t mate successfully)
■ Fusion: weakening reproductive barriers. Hybrid zone increases in size,
two species are fusing together (to become one)
■ Stability: continued formation of hybrids, constant unchanging size
○ Take biological species concept into question → fusing species?
● Patterns of Evolution: pull species in different directions
○ Divergent Evolution: one parent or ancestral species diverges into two new
species, since new species evolve from common ancestor, will have homologous
structures
○ Convergent Evolution: two unrelated species evolve to share similar traits, NO
COMMON ANCESTRY, because they are separately adapted to the common
environment → have analogous structures different structure but looks the
same, natural selection favors a similar shape
○ Parallel Evolution: when two unrelated species share similar trends in evolution,
do NOT live in the same environment, look similar but do NOT live together
○ Coevolution: one species evolves due to the evolution of another species
(adapting predator to prey, host to parasite)
 105

● Speciation Speed:
○ Punctuated Equilibrium: can also be very abrupt, drastic change in environment
changes one species very fast
○ Gradual Evolution: evolution occurs in slow changes accumulating over time,
creates intermediate species in transition

SYSTEMATICS/PHYLOGENY
● Systematics: classify organisms and determine evolutionary relationships
● Phylogeny: Evolutionary history of a species and related species
○ Determined through fossils and homologous structures
● Phylogenetic Tree: visualizes inheritance and relationship between species (divergent
evolution)
● Dating Fossils:
○ Relative Dating: look at fossils and determine age relative to another tells the
order in which different species exist → not exact date
■ Index Fossils: organisms that we know when existed, refer to this for a
new fossil (e.g. trilobyte) to determine when it existed
○ Lower the rock strata, older the fossil is in it
○ Absolute Dating: radiometric dating, use radioactive isotopes (carbon
dating=C14), C14 decays over time at a specific rate, less C14 = older
● Taxonomy: classification of organisms
○ Carl Linnaeus: creates binomial nomenclature, two word naming system (genus
species)
■ Homo sapies, Canis lupus, etc.
○ Taxonomic Categories: (taxons)
■ Species Genus Family Order Class Phylum Kingdom Domain, each taxon
more comprehensive than the previous one
○ Cladistic Analysis: used to make phylogenetic tree
■ Cladogram: look at number of structures shared in common
(homologous), more in common → closely related
● Cladogram doesn’t give TIME like phylogenetic tree
● 1. Tells order when characters evolved and 2. order in which
species evolved
● Shared Primitive Character: a trait that is preexisting (you inherit
from common ancestor)
● Shared Derived Character: new trait you get that makes you
unique from other descendants
 106

● Outgroup (O) comparison: species that existed before any

members of the ingroup, less closely related but still a starting
point, not real member of the cladogram Only has that one
starting character in the cladogram
○ First character will be the one that is shared by all
organisms
● Look for:
○ Synapomorphies: characters shared by groups
(homologies)
○ Parsimony: simplest explanation is usually the correct one
(Occam’s Razor)
■ Construct tree on the basis of simplest shared (inherited traits) and

simplest derived (new similar traits different from preexisting) characters

■ Cladogram shows the inheritance of specific characters, whereas a
phylogenetic tree has taxa (branches) that show time
■ Monophyletic Taxon: have ancestor and all species that evolved from it
(complete evolutionary history branch, best option
 107

■ Polyphyletic Taxon: are closely related by don’t yet know the common
ancestor (humans)
■ Paraphyletic Taxon: incomplete branch has common ancestor but some
descendents aren’t known
■ Which taxon you have depends on many fossils you discover

ECOLOGY
● Ecology: the study of how organisms interact with their environment (intertwined with
evolution, environment creates selection pressures, ecology studies the results between
environment and organisms)
● Biotic Interactions: between living organisms predator-prey relationships, symbiotic
relationships,
● Abiotic Interactions (Abiotic factors CONTROL biotic factors): between nonliving things
and living organisms, things like weather, climate, water, geography, etc., control where
the living organisms can actually survive
● Levels of study:
○ Organismal Ecology: interactions that happen within an organism
○ Population Ecology: group of organisms of the same species living in the same
place at the same time, study interactions within a population
■ Size (total number of individuals is always shown by the letter N)
■ Density (total number of individuals per square unit area)
■ Clumped: found in specific regions
■ Uniform: spread out with an even rate
■ Random: spread out randomly
○ Community Ecology: study groups of populations in the same area together and
study the interactions of different species populations (predator prey
relationships)
○ Ecosystem Ecology: biological community + abiotic factors in an ecosystem,
study interactions therein
○ Landscape Ecology (biomes): major ecosystems of the planet
○ Global Ecology: interactions on the planetary scale
● Demography: study of vital statistics in a population over time
○ Life Table: age-specific summary of a survival pattern of a specific population
○ Survivorship Curves: different populations follow different curves
■ Type I: (humans) most individuals die old
■ Type II: (squirrel roadkill) length of survivorship is random
■ Type III: most individuals die young (most animals and bacteria)
○ Life-history Strategies: lifestyle affected by survivorship curve
 108

■ K selected (type I, K for care):

● Produce less offspring, because they live old
● Invest more parental care → live long life
● Pros: you’ll probably live a long life
● Cons: population size is slow to recuperate if the population is
decreased, elephants are k selected so when poached, population
will recover too slowly
■ R selected (type III, R for risky):
● Produce many young: very little parental care
○ Short life expectancy
● Pros: can recover very fast from population decrease
● Cons: risky lives
● Mice, insects, bacteria
○ Size increases as gestation time increases
● Population Growth: how fast is a population growing?
○ Biotic Potential: max growth rate of population under ideal conditions
■ Factors:
● Age of reproductive maturity
● Clutch size: how many babies to have at one
● Frequency of Reproduction (gestation period)
● Reproductive lifetime (how long are they reproductively active?)
● Survivorship of offspring
○ Carrying Capacity (shown by the letter K): max amount of individuals in a
population
■ Limiting Factors: limit population growth
● Density-dependent limiting factors (more important): increase as
the population size increases, have more and more of an effect on
the population, more competition and predation takes place,
more disease/parasites, more stress, etc. stops population from
going past the carrying capacity
● Density-independent limiting factors: isn’t changed as population
increases, just decreases numbers in total → e.g. natural disasters
■ Mass death would occur if you reach and pass the carrying capacity
○ Calculating population growth rate (SLOPE OF THE LINE), change in y/change in
x= (y2-y1)/(x2-x1), time is x and change is y
■ N/t pop size over time = B - D (briths - deaths)
■ ZPG (zero population growth): when a population hits carrying capacity
when slope is 0 so when N = K then rate = 0
 109

■ If slope is positive then population is growing, if negative then it is

decreasing
○ Logistic Population Growth (S shaped curve): pop size increases and levels off by
the carrying capacity, the rate turns to 0, and stays around carrying capacity for
NORMAL populations
○ Exponential Population Growth (bad): occurs when a limiting factor is removed
(predators become extinct, competition is eliminated, etc.) J shaped curve, WILL
EXCEED carrying capacity → mass death (run out of resources, or disease
happens) without predators, they are going to overproduce
■ Why humans are growing exponentially:
● Increase in food supply
● Reduction of disease
● Expansion of habitat
● Reduction in human waste (septic system)
● Community Ecology: study of multiple populations put together
○ Competition: takes place due to limited resources
■ Intraspecific Competition: competition WITHIN a population (for mates)
■ Interspecific Competition: competition BETWEEN populations (all
competing for the same sources of food)
■ Niche: your job and role in community (if you obtain food, shelter, etc.)
● Fundamental Niche: optimal niche without any other competition
(if population existed in isolation), where/what you would like to
do
● Realized Niche: what the populations actually end up doing
because of competition
■ Interference Competition: physically fighting each other for the right to
mate in a population
■ Exploitative Competition: better getting resource than other individuals,
they remove the competition’s resource
● Competitive Exclusion Principle: two species cannot occupy the
same niche at the same time, one species would be outcompeted
to extinction (no one can have the exact same source of water,
shelter, food, etc.)
● Resource Partitioning: instead of competing until one species dies
for a niche, the populations split up their resources, one
population will begin doing something different to get some
resources while the other takes the niche (peaceful coexistence)
 110

○ Character Displacement: traits of a population change in

order to adapt to a new niche from resource partitioning
because of a niche shift
○ Predation: eating of live or freshly killed organisms
■ Parasite: only type of predators that don’t kill prey/host, just feed off
them
■ Predator-prey populations keep each other in check, the prey is not
controlled without the predator and the predator cannot exist without
the prey (prey goes up, predator goes up, prey then goes down, predator
goes down → fluctuating/cyclic pattern)
■ Lag time: time it takes between populations for each to affect each other,
measure distance between peaks/valleys in the wave
■ Defenses: example of coevolution, evolution of one species due to
another
● Cryptic Coloration (camouflage): camo
● Aposematic Coloration: bright colors indicate poison
● Mimicry: look like another organism as a defense mechanism
○ Batesian Mimicry: a harmless species mimics a harmful
species to scare away predators
○ Mullerian Mimicry: when two bad species mimic each
other (all bees look the same so all animals know to stay
away from bees)
○ Symbiosis: close and permanent relationships between organisms of two
species, two species that are totally dependent on each other
■ Mutualism: when both organisms benefit from the relationship
● E.g. clownfish and sea anemone, live together permanently,
clownfish cleans the sea anemone, and clownfish gets protection
● E.g. Remora cleans the inside of the mouth of a moray eel/shark,
but also eats up all the parasites and bad stuff in the eel’s/shark’s
mouth
● ***Lichen: TWO different species that live together it’s a fungus +
algae, algae make food using photosynthesis, but fungus lets
algae attach to trees and rocks to live on land, so fungus gets food
in return.
● *** Mycorrhizae: plant root and mycorrhiza, the plant takes in
more water and nutrients because of the fungus because it
increases surface area, the fungus also gets food from plant
 111

(oldest mutualistic relationship, since plants first evolved from

algae)
■ Commensalism: least common type of symbiosis, one species benefits
and nothing happens to the other (neutral)
● E.g. egrets live on top of rhinos, elephants, get protection, but the
rhino/elephant gets nothing in return
● E.g. Plants that grow on the branches of large trees, gets more
sunlight, and the large tree gains nothing
■ Parasitism: one species benefits and the other is harmed (ticks)
● E.g. Cuckoo/Brown headed Cowbird, parasitic bird that flies
around and kills the babies in a found nest, then lays its own eggs
for the returning mom to feed them and raise the cowbird’s
young
○ Community Composition and Stability: no biological community remains the
same for a period of time, always changing, constant state of change
■ Ecological Succession: the natural change in the composition of species
over time, this is initiated through some type of disturbance (a storm,
drought, humans, overgrazing, etc.)
● Primary Succession: begins when a community is totally wiped
out, starting from nothing but bare rock (catastrophes, forest
fires, clear cutting, construction, volcanoes, etc.)
○ Pioneer Species: (usually lichen, bacteria, moss, protists,
etc.) first species to move into the area ***break down
rock and turn it into soil (broken down rock + decaying
organic material)
○ Small R-selected plants (weeds/annuals) move in with
short life of one year
○ K-selected plants move in (perennials, comes back year
after year) shrubs, bushes, etc.
○ R-selected trees move in, pine, poplar trees
○ K-selected trees maples, birches, oaks, etc., live for long
times
○ Climax Community: mature, unchanging community →
reduces biodiversity, more different stages of succession
== more different types of species
● Secondary Succession: starting from a middle stage (crop land
that got abandoned for ex.)
○ Species Diversity:
 112

■ Species Richness: number of different species that you have (but you can
have a lot of different species but with one dominant one)
■ Relative Abundance: how many of each species do you have
○ Human Activities and Biodiversity:
■ Threats:
● Habitat Destruction:
○ Deforestation: high extinction rate of plants and animals,
forests are clear-cut, tree roots maintain the structural
integrity of the land so if you cut down the trees, it can
cause erosion, flooding, etc.
● Introducing species: invasive species can be introduced into new
areas where they don’t belong (boats, airplanes, cars, etc.),
invasive species lack predators, competition, LACK density-
dependent limiting factors and outcompete native species to
extinction → grow exponentially
● Overharvesting/Overhunting/Overfishing/Poaching: can hunt
species to extinction, or damage/imbalance ecosystems
● Toxins in the Environment: humans release damaging toxins in
the environment
○ Biomagnification: tuna consumed human mercury wastes
(carcinogen) through the food chain, phytoplankton eat
the mercury, zooplankton each phytoplankton, fish eat the
zooplankton, tuna eat the fish → mercury content isn’t lost
organism to organism, but with less population, there is
higher mercury concentration
○ E.g. PCB released into the Great Lakes ppm just keeps
going up as you go up the food chain (herrings get lots of
birth defects), DDT was so biomagnified that every
organism has the carcinogen
● Climate Change/Greenhouse Effect: when solar radiation hits the
earth, some is absorbed and warms up the planet, some is
reflected back into outer space.
○ Greenhouse Gases: (CO2 and CH4/Methane) They cause
the greenhouse effect, work as a blanket over the
atmosphere. Take the solar radiation that should be
reflected and trap it in our atmosphere, cannot return to
space → heat up planet
○ More CO2 and CH4 in our atmosphere than ever before
 113

○ But CAUSES (increased global population, deforestation,

burning fossil fuels, livestock (methane cow farts), natural
causes), and effects of climate change are unknown → debate
○ EFFECTS: global warming also causes other things
■ Shifting weather patterns: air currents moving south,
more severe storms, etc.
■ Increased glacial/arctic melting
■ Ocean acidification: CO2 + H2O → Carbonic acid
■ Changes in biological communities
■ Increased water levels
■ Increased ocean temperatures
■ Not all effects are known

PLANTS
● All plants evolved from a type of green algae called carophycenes, but modern plants
are different (derived character) they can live on land
● Evolutionary History: chronologically
○ Bryophytes: mosses, first group to evolve
○ Pteridophyta: ferns
■ Vascular Tissue: next derived character (xylem= water transport,
phloem=sugar transport)
○ Evolution of Seed Plants: (MAJOR) adaptation that allows plants to no longer
rely on water to reproduce → reproduce on land more
■ Gymnosperms: use cones as a reproductive structure, rely on wind to
carry pollen from cone to cone
■ Angiosperms (flowering plants): produce flowers (reproductive
structure)
● Alternation of Generations:
○ Every generation plants flip between haploid to diploid and then back
○ Sporophyte: (2n) goes through meiosis to make haploid spores
○ Gametophyte: (n) goes through mitosis to make gametes, create a diploid
zygote
○ In ANGIOSPERMS, the sporophyte version is dominant whereas the gametophyte
is extremely reduced
● The Flower: used to reproduce in angiosperms, help from animals, wind, and insects to
transport pollen, brightly colored to attract other animals/bugs to it
○ Nectar: sugary substance produced by flowers to attract birds and bees to
consume, the pollen will stick to the animals so pollen can go from plant to plant
 114

○ Contains both male and female reproductive parts (lilies) but most flowers are
either male or female
■ Stamen: male reproductive part
● Anther: structure that produces pollen, flower is the sporophyte,
whereas pollen produced has two male gametophytes (sperm)
● Filament: long stalk that comes out of the anther
■ Carpel (pistil): female reproductive part
● Stigma: sticky part where pollens gets stuck (top)
● Style: long tube that connects to the ovary
● Ovary: contains the ovule (inner structure) which
produces/contains the female gametophyte (egg)
○ Contains a lot of a small eggs, but one big giant egg with
polar nuclei (two nuclei)
○ Sepals: leaves beneath the flower
○ Petals: colored part to attract organisms with pollen
● Cross-Pollination: gives genetic variation, pollen of one flower goes to the carpel of
another flower
● Self-Pollination: staying within the same flower anther sperm goes directly into the
stigma, no genetic variation → can survive on its own without other individuals in the
population (e.g. polyploidy)
● Double-Fertilization: (used in angiosperms) pollen goes from male anther to female
stigma, it grows a pollen tube down the style into the ovary into the ovule
○ Essentially, two sperm from pollen enter the ovary and fertilize two eggs
○ One egg in ovule (big one) contains two nuclei (polar nuclei), two sperm (from
pollen) go down the tube and into the ovule, one sperm will fertilize one egg to
make a zygote. The other will fertilize the big egg, to have three nuclei (triploid
→ endosperm, functions as a food source for the developing embryo. The Ovule
becomes a seed with the endosperm and embryo. The ovary around the seed
becomes a fruit
○ Fruit: mature ovary used to disperse seeds (sporophyte embryos)
■ Fruit is made to taste good so herbivores eat fruit, they cannot digest
seed, so they poop out seeds everywhere, seed gets fertilizer to grow
into a new plant
■ You eat the endosperm which is the nutritious part of the nut/seed
■ Any type of flowering plant produces some sort of fruit
● Embryo Development:
○ Germination occurs when mitosis of the seed occurs (begins to grow)
○ Cotyledons: first seed leaves upon germination
 115

■ Monocot: one leaf (smaller angiosperms, orchids, grasses, lilies) VEINS

RUN PARALLEL, with fibrous root systems, cannot grow that big without a
lot of support
■ Dicots: two leaves, bigger angiosperms, has central tap roots to grow big,
branching veins in leaves (maple trees, sunflowers, beans, etc.)
BRANCHING VEINS
■ These are the two distinct and different types of angiosperms
● Nitrogen: needed to make nucleic acids and proteins
○ Atmospheric N2 is the greatest nitrogen reservoir, but can’t do anything with
that, you need to convert it
○ Nitrogen-fixing Bacteria: take in N2 and convert it into ammonium (NH4)
○ Ammonifying Bacteria (detritivores): break down dead organisms (humus) and
convert it into ammonium
○ Nitrifying Bacteria: convert ammonium into nitrates (NO3)
○ The plants can accept the nitrates and use those to build macromolecules
○ Nitrates are the key ingredient in fertilizer to nourish plants
○ Roots have lots of hair things to increase surface area for rate of exchange
● Transport: movement of materials in a plant
○ Cell Level: nutrients from soil -> roots
■ Depends on water potential (ONLY USED TO MOVE WATER IN PLANTS,
everywhere else it only depends on osmosis/diffusion) (pressure
potential + solute potential)
■ The lowest the pressure can be is 0, the highest the solute potential can
be is 0 (pressure is nonnegative, the solute is nonpositive)
■ Solute potential = -iCRT, C= concentration of solutes/molarity, more
solute you have the more negative the potential becomes
■ Plant roots have lots and lots of sugar → really low water potential (0
pressure and high positive amount of solute), TAKES IN WATER
■ Since plant roots have low potential, roots will absorb water from the
environment, soil has no pressure, and some low solute content, higher
water potential in the soil (water moves high → low potential) so the
water will move into the roots
■ Roots will gain pressure from the water, until the water potential on the
outside EQUALs the pressure on the inside, (not when the pressure is 0
necessarily) so you add a specific amount of pressure to the roots to get
the same water potential
■ Turgor Pressure: BEGINS movement of water up the plant that builds up
in the roots forces the water up from this initial transaction
 116

■ Xylem: system of tubes water moves up

■ Transpirational Pull (evaporation): FINISHES movement of water up the
plant; pulls water through and up the plant, also works through cohesion
(water stuck to water) and adhesion (water stuck to other things) as the
top water molecules are pulled out the stomata, and pull up the rest
through hydrogen bonding
■ Stomata: holes in leaves where water leaves that can open and close
■ Guard Cells: can open and/or close stomata
■ What causes an increase in transpiration rate (bad too much water loss):
● Higher temperatures
● Arid/dryer conditions
● ***Wind
● → causes guard cells to close stomata to preserve water
● If O2 enters the calvin cycle instead of carbon dioxide will cause
photorespiration (but C4 and CAM plants can store carbon
dioxide)
○ Short distance: water from roots into xylem tubes (turgor pressure), or sugar
from leaves into phloem (active transport)
○ Long distance: movement of water in xylem or sugar in phloem (sugar goes
down to the roots to decrease water potential, but is built in the leaves through
photosynthesis), phloem and xylem run side by side
■ Bulk Flow/Pressure flow/Translocation: water diffuses into phloem
pushes sugar down using pressure into the roots
● Xerophytes: desert plants that have adaptations for arid conditions (extreme CAM
plants)
○ Only open stomata at night
○ Store water inside of them
○ Cacti needles are leaves without surface area, prevents water from evaporating
as much (and protection from eaters)
○ Thick cuticle: feels waxy because the wax prevents water loss (wax =
hydrophobic)
○ Stomata are always on the bottom of the leaves to prevent water loss
● Plant Defenses/Immune Systems against Herbivores: physical and chemical defenses to
prevent eating
○ Physical: thorns, trichomes (irritating hair things), prevent them from being
eaten
○ Chemical: (poison ivy) release toxins
 117

■ Chemicals in the saliva of an eating caterpillar causes a signal

transduction pathway in the plant, plant releases volatile attractants to
attract parasitoid wasps to kill the caterpillars and reproduce in them
● Plant Defenses/Immune Systems against Pathogens: against organisms that can infect
the plant
○ Virulent Pathogen: (viral lytic cycle) would kill the plant entirely
○ Avirulent Pathogen: the plant has a chance to defend itself and live (THIS
defense system only works for this type of pathogen)
○ Gene-for-gene recognition:
■ R-genes: code for R-proteins that can activate plant immune system
■ Hypersensitive Response: causes cell and tissue death near the infection
site → LOCALIZED, not across the entire plant, kill everything that is
infected to save the rest of the plant, create changes in the cell wall of
plant cells to confine the pathogen
● Produced chemicals that can kill the specific pathogen
■ Systemic Acquired Resistance: spreads across the ENTIRE plant, causing
the plant to become resistant to the virus (long term).
● Salicylic Acid: chemical ligand that initiates SAR, (aspirin), spreads
throughout the entire plant to make plant immune to that specific
pathogen