AP Bio, Unit 1

Structure of Water and Hydrogen Bonding

• The subcomponents of biological molecules determine the properties of that molecule. “You are what you eat”

• Linked with covalent bonds (shares electrons)

O •
•
Water is composed of 2 main elements, oxygen and hydrogen (1:2 ratio)
Oxygen attracts more electrons than hydrogen, creating polarity (a

H H
difference in charges)

• Hydrogen bonds are an interaction between the negative and positive regions of two molecules. It’s
more of an “attraction” than a real bond where there is a sharing of electrons. It is very weak.

• Water can form hydrogen bonds with other water molecules/charged molecules

Cohesion Adhesion

When two of the same molecules form When two different molecules form a
a hydrogen bond it’s called cohesion hydrogen bond it’s called adhesion
Hydrogen bond Hydrogen bond
H
H

H
C
O
O

O
O
H
H

H
C H

• Living systems depend on water’s properties

• The combination of cohesion, adhesion and surface tension are called emergent properties
• Surface tension is the effect caused by increased hydrogen bonds at the surface of water. (Ex.
A leaf floating)
• Water’s adhesive property makes it a nearly universal solvent
• Water’s cohesive property allows for solid water (ice) less dense, so it floats
• Water’s cohesive property allows for high heat capacity
• Cohesive + adhesive = capillary action
 Elements of Life
• Living systems require a constant input of energy, and follow the laws of conservation. Living systems mainly use
energy stored in chemical

• Atoms and molecules from the environment are necessary to build new molecules

Carbon is the element of life, it can:

• bond to other bond to other carbon atoms, forming “carbon skeletons”, allowing for very large
complex molecules
• be used as energy storage
• be used to form basic cell structures, (cell membranes)

Intro to Biological molecules

covalent bond Monomers: chemical subunits used to form
polymers
Polymers: macromolecule made of many
monomers
monomer

polymer

• monomers have specific chemical properties that allow them to interact with one
another
• polymers are specific to the monomers they are made of

Monosaccharides-> Carbohydrates Amino acids -> proteins

Fatty acids -> Lipids Nucleotides -> Nucleic acids

Properties of biological molecules
• Function is related to structure, in living systems the properties of bio. molecule

Nucleic acids:
• Nucleic acids are made of nucleotides
• Nucleotide’s structure is: a 5 carbon sugar, a phosphate group and a nitrogen base
• All Nucleic acids store biological information in the sequence of nucleotide monomers
• General structure:

phosphate nitrogen base

group

5 carbon sugar

Proteins:
• Proteins are made of amino acids
• Amino acids have directionality with an amino (NH2) terminus and carboxyl (COOH)
terminus
• A polypeptide is a chain of amino acids linked together by peptide bonds (covalent bond)
• General structure:

H
H O
amino
N C C carboxyl

H OH

R group

Group of atoms, can be

hydrophobic, hydrophilic
or ionic

Carbohydrates:
• Carbohydrates are made of monosaccharides
• Complex carbohydrates can have monomers whose structures determine
the properties and functions of the carbohydrate
• general structure:

H H H
H carbon chain/ring with
C C C C CH2OH multiple hydrogen atoms
or hydroxyl (-OH) groups
O attached
OH OH OH

Lipids:
• Lipids don’t have true monomers, but their main subunit are fatty acids
• Saturation (the amount of hydrogen bonds) determine structure and function
• Specialized lipids, phospholipids, have hydrophobic and hydrophilic regions

C C C C C C C
saturated fatty acid unsaturated fatty acid C

polar head (hydrophilic)

phospholipid

non polar tail (hydrophobic)

Fluid mosaic model

*molecules both
hydrophobic and
hydrophilic are called
amphipatic
Structure & function of bio. macromolecules

Nucleic Acids:

• The linear sequence of all Nucleic acids is characterized by a 3’ hydroxyl and 5’

phosphate of the sugar in the nucleotide

• In DNA each strand is in an antiparallel 5’-3’ direction

• Hydrogen bonds in a DNA molecule stabilize the molecule’s structure

• The linear sequence of nucleotides encodes biological information

• Any change in the sequence of nucleotides may lead to a change in the encoded
information

• Adenine and thymine have 2 hydrogen bonds, cytosine and guanine have three

Proteins:

• Proteins comprise linear chains of amino acids that have directionality with an
amino terminus and a carboxyl terminus.

• Amino acids are connected by covalent bonds between the amino group
and carboxyl group. (New acids are added to the carboxyl group)
Carbohydrates:

• Carbohydrates comprise linear chains of sugar monomers connected by covalent bonds

• Small direction change in the components of a molecule can result in functional differences

• Carbohydrates can be linear or branched

• Starch and glycogen both function in energy storage

• Cellulose is structural

Independent pH Review
pH is the measure of how acidic or basic a solution is. It is measured on a scale of 0-14
with 7 being neutral.

0 •
acidic
High H+ ion concentration 7 •
basic
High OH- ion concentration
14
• Sour • Bitter
• React with metals • Dissolve grease and oils
• Corrosive • Neutralize acids
• Electrolytic conductivity • Electrolytic conductivity

• Cells have a way to regulate pH and maintain homeostasis

• pH alteration can denature enzymes
• pH can affect ion transportation

Hydrolysis and dehydration

Hydrolysis is a chemical reaction in which a compound reacts with water, resulting in the breaking
of chemical bonds within the compound and the formation of two or more substances.

Dehydration is a chemical reaction in which water is removed from a compound reacts and new
bonds are formed
AP Bio, Unit 2

Cell Structure, Subcellular Components

genome
nucleus
ribosomes
genome

ribosomes

• All living cells contain a genome and ribosomes

• Ribosomes synthesize proteins according to mRNA sequences that come from the cell’s genome

Ribosomes
Polypeptide chain • Ribosomes consist of two subunits
that are not membrane bound
ribosome large unit
• Ribosomes are made of ribosomal
RNA and proteins
• Ribosomes synthesize proteins

mRNA

ribosome small unit

Endoplastic Reticulum

rough ER
• Rough ER:
- Has ribosomes attached
- Associated with packaging the newly synthesized
proteins made by the attached ribosomes smooth ER

• Smooth ER:
- Doesn’t have ribosomes attached
- Detoxification and lipid synthesis
Golgi Apparatus
• Involved in the correct folding
and chemical modification of
proteins + protein trafficking
Vesicle

• Vesicles transport materials

around the cell

Mitochondria
Inner membrane
• Has a double membrane Cristae
• Powerhouse of the cells
• Generates ATP energy via cellular respiration
Matrix

Outer membrane

Lysosomes
Vacuoles

• Membrane enclosed
sacs found in • Water/
eukaryotic cells that macromolecules storage
contain hydrolytic • Cell stability
enzymes • Release of waste
• Used to digest
different materials
such as damaged cell
parts or
macromolecules

Chloroplasts
• Double membrane
• Found in plant cells
• Capturing energy from the sun and produces sugar
Cell Size

Why aren’t cells huge?

• The surface area of the plasma membrane must be large enough to adequately exchange
materials.

• Smaller cells typically have a higher surface area-to-volume ratio and more efficient
exchange of materials with the environment

• As cells increase in volume, the relative surface area decreases and the demand for
internal resources increases

• More complex structures are necessary to adequately exchange materials with the
environment.

• As organism increase in size their surface area to volume ratio decreases, affecting
properties like heat exchange

Membrane folding

Membrane folding increases surface area without compromising resource

demand
Ex:

Root hairs on the surface Small intestine villis

area of plant roots increase increase surface area for
surface area for water and nutrient transport
nutrients
Plasma membranes

Fluid mosaic model

*molecules both
hydrophobic and
hydrophilic are called
amphipatic

Fluid mosaic model includes:

• Steroids (ex. Cholesterol, regulates bilayer fluidity)
• Carbohydrates (ex. Glycoproteins, glycolipids, function as markers)
integral proteins transmembrane
proteins peripheral
proteins

Peripheral Proteins: Integral Proteins:

• Loosely bound to the surface of the • Span the membrane
membrane • Hydrophilic with charged and polar side
• Hydrophilic with charged and polar groups
side groups • Hydrophobic with non polar side groups
penetrate hydrophobic interior bilayer

Proteins functions
• Transport
• Cell-cell recognition
• Enzymatic activity
• Signal transduction
• Intercellular joining
• Attachment for extracellular matrix or cytoskeleton
Membrane permeability
The ability of molecules to move across the cell membrane depends on two things: (1) the
semipermeability of the plasma membrane and (2) the size and charge of particles that want to get
through.
Selective permeability is a direct consequence of membrane structure
Membranes become polarized by movement of ions
Osmoregulation is
• Small non polar molecules pass freely through the membrane the movement of
- N2 water and solute
- O2 across membranes to
- CO2 maintain homeostasis.

• Hydrophilic substances move through transport proteins

- Channel Proteins: a hyd

The ability of molecules to move across the cell membrane depends on two things: (1) the
semipermeability of the plasma membrane and (2) the size and charge of particles that want to get
through.

Facilitated transport occurs when hydrophilic substances pass through the phospholipid bilayer
with assistance. Facilitated transport depends upon a number of proteins that act as tunnels through
the membrane. Channels are very specialized types of tunnels that let only certain things through.
Passive transport:

Diffusion: If there is a high concentration of something in one area, it will move to spread
out and diffuse into an area with a lower concentration
When substance is hydrophobic it’s called simple diffusion
When requiring proteins it’s called facilitated diffusion

*Passive transport DOES NOT require energy input

 Osmosis: Water diffuses. Often times, water will move from high concentration to low
concentration. Water is not always pure, instead it is a solution, so it will diffuse from
“watery solution” to “concentrated solution.”

watery concentrated
Tonicity is used to describe osmotic gradients
Hypertonic Isotonic Hypotonic
inside
outside
outside inside
inside outside

Outside environment has lower Outside environment has the same Outside environment has higher
concentration than inside concentration as inside environment concentration than inside
environment environment

Water potential is the measure of potential energy in water and describes the eagerness of
water to flow from one area of high waste concentration to low water concentration.

Endocytosis: When the particles that want to enter a cell are just too large, the cell uses a portion of
the cell membrane to engulf the substance.

Pinocytosis cell drinks, phagocytosis cell eats, receptor mediated Endocytosis cell
membrane folds.

Exocytosis exit

Bulk flow: movement through pressure

Dialysis is the diffusion of solutes across a selectively permeable membrane.
AP Bio, Unit 3

Enzyme Structure and function

Enzymes are biological catalysts that speed up biochemical reactions
• Most enzymes are proteins
- Tertiary shape must be maintained for functionality
- Have a region called an active site
• Enzymes have an active site that specifically active site
substrate enzyme
interacts with substrates
- Has unique shape and size
- Can have chemical charges or not
- Physical and chemical properties of the substrate
must be compatible
- Slight changes can occur to align with substrate
• Enzyme names often indicate the substrate/chemical reaction
• Enzymes are reusable/not chemically changed by the reaction
- Cells typically maintain a specific enzyme concentration
• Enzymes can facilitate synthesis or digestion reactions

All biochemical reactions require initial starting energy called activation energy
- Some reactions result in a net release of energy and some in a net absorption of energy
- Typically reactions resulting in a net release of energy require less activation energy

Enzymes lower the activation energy requirement, accelerating the rate of reactions.
Enzyme Denaturing

Enzymes have unique functional 3D shapes; known as the conformational shape or tertiary structure
• Changes in the tertiary of the enzyme = denaturation
- Changes in temperature
Enzymes do not make reactions occur that
- Changes in pH would otherwise not occur at all
• Enzyme denaturation is typically irreversible
• In some cases enzyme denaturation can be reversible

Optimum temperature: range in which enzyme mediated reactions occur the fastest

• If temperature increases
- Initially increases reaction rate
reaction - Increases frequency of enzyme
rate substrate collisions
- Too much temperature: denatures
• If temperature decreases
- Typically decreases reaction rate
- Decreases frequency of enzyme
temperature substrate collisions
- Does not denature enzyme

Optimum pH: range in which enzyme mediated reactions occur the fastest

Increases and decreases in pH may

denature enzymes
reaction
rate

pH
Concentration of substrates and products affect reaction rate

• Increase in substrate concentration:

reaction - Increase in reaction rates (more
rate substrates means more opportunities to collide
with enzyme)

- Substrate saturation will eventually occur

- Increase in product takes up space, less
substrate concentration collisions
Enzyme concentration impacts reaction rate

• Less enzyme = slower reaction rate

• More enzyme = faster reaction rate
• Too much enzymes, not enough substrates
reaction
rate

enzyme concentration

Competitive inhibitors can bind to the active site.

substrate
competitive substrate
inhibitor

competitive
inhibitor

enzyme
enzyme

Higher concentration of competitive inhibitors slows reaction rates

Noncompetitive inhibitors change enzyme shape

Higher concentration of substrates does not prevent effects of non competitive inhibitor binding (slow
reaction rates)
Cellular Energetics
All living systems require a constant input of energy

• Sunlight is the main energy input for living systems

• Autotrophs capture energy from physical sources like

sunlight, or chemical sources and transform that energy
into usable energy.

• During every energy transformation,ration forces some

energy is unusable, often lost as heat

photosynthesis

CO2 + H2O

C6H12O6 + O2
cellular
respiration

Life requires a highly ordered system

• Living cells are not at equilibrium; there is a constant flow of materials in and out of the cell.
• Cells manage energy resources by coupling processes. Energy-releasing reactions (exergonic)
drive energy storing reactions (endergonic).

Pathways in biological systems are sequential

• The product of one reaction can be the reactant of another
• This allows for a controlled and efficient transfer of energy.

ATP is full of energy

The breaking of ATP bonds produces energy. Through ATP hydrolysis, ATP becomes ADP + Pi
(inorganic phosphate) and releases usable energy.

Energy
Phosphate Diphosphate

Adenine Adenine

ATP ADP + P
hydrolysis
Photosynthesis
Organisms capture and store energy for use in biological processes

Photosynthesis is the biological process that captures energy from the sun and produces sugars
• Light dependent reactions capture light energy by using light absorbing molecules called
pigments
• Pigments help transform light energy into chemical energy
• Chemical energy is temporarily stored in chemical bonds of carrier molecules called NADPH
• Light dependent reactions help facilitate ATP synthesis
• ATP and NADPH transfer stored chemical energy to power the production of the Calvin
Cycle
• Oxygen is the result of water hydrolysis

Evidence supports the claim that

prokaryotic photosynthesis by
organisms was responsible for
the production of oxygen in the
atmosphere
Photosynthesis
Organisms capture and store energy for use in biological processes

Light Reactions Location: Thylakoids

PSII Cytochrome
Complex PSI
Photosystem II
• Chlorophyll absorbs energy from photons of light,
which excites (energizes) electrons.
• Mobile electron carriers transport the excited
electrons through the ETC (electron transport chain)
• Photolysis is the process where water is split into
Hydrogen, Oxygen, and Electrons to replenish the
ones lost to the ETC

Cytochrome Complex

• Energy from the electrons in the ETC is used to pump

out protons to the thylakoids, which charges it like a
battery
• The protons create a concentration gradient
• The protons are pumped through the membrane via ATP
Synthase which uses the energy to pack an inorganic
phosphate onto ADP, forming ATP

PSII
• Photons reenergize the electrons from
the ETC, which then are carried
through another transport chain
• Energy is used to make NADPH
• NADP+ Reductase uses 2 electrons, 1
hydrogen ion and NADP+ to make
NADPH
Light Independent Reactions: The Calvin Cycle Location: Stroma

from air very unstable

CO2 + RuBP = 6 carbon chain

5 Carbon chain

The enzyme RuBisCo welds CO2 and RuBP together to form a 6 carbon chain, this carbon chain
is split into two becoming 3-Phosphoglycerate. This process occurs 3 times simultaneously.

“Processing Line” 1

C-C-C C-C-C
“Processing Line” 2

C-C-C C-C-C
“Processing Line” 3

C-C-C C-C-C
ATP adds to the phosphoglycerate a phosphate
group, NADPH adds electrons. The 3-
Phosphoglycerate become G3P, a high energy
carbon compound that can be converted to almost
any carbohydrate.

Most plants close their stomata on hot, dry days to prevent water loss by transpiration (the
evaporative loss of water from leaves. Plants that live in hot climates have evolved two different
ways around this

CAM Plants: Separate carbon C4 Plants: Have carbon fixation

fixation from the Calvin cycle occur in a different part of the leaf,
separated from the Calvin cycle

Open their stomata at night and incorporate CO2 into

C4 plants produce a four-carbon molecule as the first
organic acids. During the day, they close their stomata
product of carbon fixation and perform cyclic electron
and release CO2 from the organic acids while the light
flow in the light reaction
reactions run.
Cellular Respiration
How we transform sugars into energy

Is oxygen present?
Yes No
Aerobic respiration Anaerobic respiration

Aerobic respiration
Aerobic respiration mainly consists of 4 stages containing a series of coupled
reactions that establish an electrochemical gradient across membranes:

1. Glycolysis
2. Formation of Acetyl-CoA
3. Krebs Cycle
4. Oxidative phosphorylation (the electron transport chain +
chemiosmosis)

Glycolysis
The breaking of glucose into 2 3-carbon molecules called pyruvic acids/pyruvate.
Glycolysis uses 2 ATP and produces 4 ATP, net 2 ATP, 2 Pyruvates, and 2 NADH.
• Glycolysis is an anaerobic process
• Occurs in the cytoplasm

*NAD+ —> NADH through transfer of

electrons

*Pi (inorganic phosphate) is gained as a

material from the cytoplasm
Acetyl CoA Formation
Pyruvate is oxidized (added oxygen) and forms Acetyl CoA and CO2. Meanwhile an NAD+
molecule gains a hydrogen and becomes NADH. Process catalyzed by enzyme PDC
• Aerobic process
• Occurs in mitochondria
• Catalyzed by: pyruvate dehydrogenase complex (PDC)
CO2

NAD+ NADH
Acetyl CoA

Krebs Cycle
Takes the products of glycolysis (pyruvates) and transforms them into 2 ATPS per glucose molecule +
energy.
• Glycolysis is an aerobic process
• Occurs in the mitochondria matrix

oxaloacetate

citric acid/citrate

Acetyl CoA

NAD+
Acetyl CoA
NAD+ NADH

NADH
oxaloacetate Citric Acid

NAD+
FAD
NADH
NAD+
FADH2
NADH

Electron carriers NADH and FADH2 are the main products from the Krebs Cycle. These will be used in
the ETC.

Electron Transport Chain

Electron carriers NADH and FADH2 “shuttle” the electrons they carry (reverting back to NAD+
and FAD) through an electron transport chain (with carrier molecules such as NADH
dehydrogenase and cytochrome C)l. As the electrons are moved, they lose energy, which is
used to pump H+ ions (protons) across the inner mitochondrial membrane, creating a proton
gradient. Through ATP synthase the protons are “released” and ATP is produced. This is called
chemiosmosis.
Anaerobic Respiration
If oxygen is not present, only glycolysis will take place generating 2 ATP, while pyruvates and NADHs are
recycled through fermentation and producing either lactic acid or ethanol instead.
AP Bio, Unit 4

Cell Communication

• Cells of multicellular organisms often maintain physical contact with other cells or make physical
contact with other cells during certain activities.

• Some unicellular organisms live in colonies and are in physical contact with other organisms in that
colony.

• Cells can send chemical signals directly into adjacent cells.

• Cell membrane and cell wall modifications allow for communication to occur between adjacent
cells.

The cell receiving the signal is referred to as the target cell

Short distance communication
• cell sends out local regulators (signals) Local regulators: biological
mechanism or structure that
• Target cell is within a short distance of the signal regulates a specific process or
• Often used to communicate with the cells of the same type function within a localized area
of an organism

Long distance communication

• Target cell is not in the same area as the cell emitting the signal
• Signal travels long distance to reach the target cell
• Often used to signal cells of another type

Signal Transduction Pathways

Signal transduction: the process by which an external signal is transmitted to the inside of a cell

Reception Transduction Response

• Reception: detection of a signal molecule coming from outside the cell
• Transduction : convert signal to a form that can bring about a cellular response
• Response : specific cellular response to the signal molecule

Hydrophobic signaling molecules can diffuse across the plasma membrane. Other molecules that
cannot pass through the membrane need a plasma membrane receptor; a high specific integral
membrane proteins that transmit signals from the extracellular space into the cytoplasm.

*A ligand is a signaling molecule, a receptor receives it.

There are 3 types of plasma membrane receptors:

G-Protein Receptors Ligand-Gated Ion Catalytic Receptors

“on” Channels “off”

• Ligand gated ion channels: open or close an ion channel upon binding a particular ligand.

• Catalytic receptors: have an enzymatic active site on the cytoplasmic side of the membrane.
Enzyme activity is initiated by ligand binding at the extra cellular surface.

• G-Protein linked receptor: binds a different version of a G-Protein (often GDP or GTP) on the
intracellular side when the ligand is bound extracellularly. This causes the activation of secondary
messengers (amplify the intracellular signal) within the cell.

Signal construction pathways, often include protein modifications (turning on/off genes in nucleus,
regulate protein activities in cytoplasm) and phosphorylation cascades (cascades of molecular
interactions relay signals from receptors to target molecules, enhance/amplify signals)

Signaling begins with the recognition of a chemical messenger (ligand) by a receptor protein in a
target cell.
• Signaling cascades relay signals from receptors to cell targets
Signal transduction may result in changes in gene expression and cell function
• Signaling Pathways can target gene expression and alter the amount and/or type of a particular
protein produced in a cell
- Changes in protein type and/or amount can result in phenotype change

• Apoptosis can be the response of signal transduction

Changes in signal transduction pathways can alter cellular response

• Mutations can affect the downstream components by altering the subsequent transduction of the
signal
- Change in protein structure can result in change in function

Chemicals that interfere with any component of the signaling pathway may activate or inhibit the
pathway

Feedback Mechanisms
The set of conditions under which living things can successfully survive is called homeostasis. The
body is constantly working to maintain this state by taking measurements and then responding
appropriately.

Feedback mechanisms are processes used to maintain homeostasis by increasing or decreasing a

cellular response to an event

Negative Feedback: If a system is disrupted, negative feedback mechanisms return the system
back to its target set point.
Target Set Point
disruption

Positive Feedback: If a system is disrupted, positive feedback mechanisms amplify responses

and processes in biological organisms

disruption
positive feedback
Mitosis
interphase

Interphase involves three sequential stages:

S • G1: Cell growth
growth and DNA
replication - G0: Some cells will opt out of the cell cycle and
stay for extended periods of time in the G0 phase
G1 growth & final
preparations for
growth division

G2 • S: Growth and DNA replication

M
Cytokinesis P • G2: Cytoplasmic components are doubled in
T A M
preparations for division
• Cytokinesis: Equal distribution of cytoplasm for
both cells

M Phase:
Prophase:
• Nuclear envelope begins to disappear
• DNA coils into visible chromosomes
• Fibers begin to move double chromosomes
toward the center of the cell

Metaphase:
• Fibers align double chromosomes across the
equatorial line (center of the cell)

Anaphase
• Fibers separate double chromosomes into
single chromosomes (chromatids)
• Chromosomes separate at the centromere
• Chromatids migrate to opposite sides of the
cell

Telophase
• Nuclear envelope reappears and establishes
two separate nuclei
• Each nucleus contains a complete genome
• Chromosomes will begin to uncoil

Cytokinesis
• Cytokinesis will divide the cytoplasm
completely.
Checkpoints
G1 Checkpoint
• At the end of the G1 phase
• Cell size check
• Nutrient check
• Growth factor check
• DNA damage check

G2 Checkpoint
• At the end of the G2 phase
• DNA replication check
• DNA damage check

M spindle
• Fiber attachment to chromosome check

Cyclins
A group of related proteins associated with specific phases of the cell cycle
• Different cyclins are involved in different stages of the cell cycle
• Concentrations can fluctuate depending on cell activity
• Produced to promote cell cycle progression
• Degraded to inhibit cell cycle progression

Used to activate cyclin-dependent kinases (CDKs)

• Cyclins are specific to the CDK they activate

Issues in cell checkpoints may cause cancer or apoptosis

AP Bio, Unit 5

Meiosis

Proteins are/can be: enzymes, structural supports, transport, storage, metabolic functions, catalysis, cellular communication, etc.
The are the workers of the cell

Chromosome: Thread like structure composed of

DNA and proteins that carries genetic information.

Chromatin: The genetic “threads” chromosomes

are made of.

Chromatid: One of the two identical duplicates of

a chromosome during replication.

Gene: Section of the DNA

Allele: Variation of a gene

Haploid: One set of chromosomes

Diploid: Two sets of chromosomes

Tetrad: Group of 4 sister chromatids

• Humans have 23 pairs of chromosomes in their gametes, 46 in total. These are diploid cells.
- Somatic cells are diploid, sex cells are haploid

• In synapsis homologous chromosomes get together, while crossing over they exchange alleles
• Random assortment: random organization
• Crossing over: random switching

Random assortment, crossing over and fertilization all contribute to genetic diversity
Mendelian Genetics
genetics is the study of heredity

• Traits—or expressed characteristics—are influenced by one or more of your genes

• When an organism has two identical alleles for a given trait, the organism is homozygous. If an
organism has two different alleles for a given trait, the organism is heterozygous

• Phenotype: physical, genotype: genetic

Mendel’s Laws:
• Law of dominance: when an organism inherits two different forms of a gene (alleles) for a
particular trait, one allele will be dominant over the other, and determine the expression of
the gene.

• Law of segregation: the inheritance of one gene does not affect the inheritance of another

• Law of Ind. assortment: the alleles of two (or more) different genes get sorted into gametes
independently of one another

more info: https://www.youtube.com/watch?v=CBezq1fFUEA

Non- Mendelian Genetics

Exceptions:
• Linked genes: genes placed closely in a chromosome they tend to get inherited together (i.e,
flower color and pollen shape
• Sex-linked traits: traits found in the 23rd chromosome, coding for sex. Ex. hemophilia,
balding.
• Incomplete dominance: blend of both alleles
• Codominance: neither allele is dominant to the other
• Polygenic inheritance: multiple genes code for a single trait (ex. weight)
• Non-nuclear inheritance: mitochondrial DNA inheritance

Pedigrees
 Environmental Effects on Phenotypes
• Phenotypic plasticity occurs if two individuals with the same genotype have different phenotypes
because they are in different environments.

• Epigenetics: environmental changes to gene expression

• Epigenetics marks: chemical modifications to DNA and histone proteins that can influence gene expression without
altering the underlying DNA sequence. Ex: Methylation, histone methylation, histone acetylation/deacetylation.
Can be inherited
Their presence and concentration makes the difference
 DNA and RNA Structure

DNA
deoxyribonucleic acid
•
•
Stores genetic information
Nucleic acid (polynucleotides)
Made up of:
• Adenine
nucleotides -> DNA ->
• Cytosine
chromatid -> chromosomes
• Thymine
• Guanine
To maintain things organized,
DNA is often wrapped
around histones 5 carbon sugars phosphate group 1 of 4 nitrogenous bases

Adenine Thymine
sugar A-T 3’ to 5’
phosphate 2 hydrogen
backbone bonds
5’ to 3’ C-G

T-A Cytosine Guanine

3 hydrogen
bases linked together by hydrogen bonds bonds
pyramidine
5’ can be thought of the end where the
phosphate group is attached, while 3’ the end purine
which is free

RNA
Stores genetic information
Nucleic acid (polynucleotides)
Made up of:
ribonucleic acid
3 main types of RNA
• Messenger RNA
(mRNA)
• Ribosomal RNA
(rRNA)
• Transfer RNA
(tRNA)
Replication
For the information in DNA to be passed on, it must first be copied. This copying of
DNA is known as DNA replication.
topoisomerase
leading strand loosens up each strand

replication
fork helicase

lagging strand

*each strand provides a template for creating a new strand of DNA

leading strand

RNA primase polymerase

adds primer *polymerase can only copy in the 5’ and 3’ direction
primer

Okazaki fragments

RNA primase
*in the lagging polymerase
strand polymerase
works backwards

lagging strand

lagging strand

afterwards, exonuclease removes the primers and another DNA polymerase replaces them. Finally
ligase joins all the fragments together and girase “twists” the DNA back

This replication is semi conservative.

Enzymes used:
• Topoisomerase: loosens up strands, • Polymerase: adds the bases
cuts up and rejoins helix • Exonuclease: removes primers
• Helicase: unzips the DNA • Ligase: joins Okazaki fragments
• Primase: adds primers • Girase: twists it back together
Transcription and RNA Processing
Promoter, defines when the transcription unit will begin

Transcription Unit RNA Polymerase: begins copying down DNA

downstream of the TATA box into mRNA

contains the genetic instructions

polymerase
Termination
Signal

5’ cap Poly-A tail

adenine for introns
guanine exons
protection

mRNA
RNA splicing removes unnecessary info

Poly-A tail
5’ cap adenine for
guanine protection

mRNA
triplet codons
Ribosome
mix of proteins and rRNA
AP Bio, Unit 7

Natural Selection
Natural selection is a major mechanism of evolution
• Evolution: Evolution is the change in the genetic makeup of a population over time
• Natural Selection: the process by which organisms having adaptations suited for a particular
environment, have a greater chance of survival and reproduction, thereby passing the
adaptations to subsequent generations
• Charles Darwin is mainly credited with the development of the theory of natural selection

Evidence for evolution

• Paleontology, shared ancestry, biogeography, embryology, molecular biology

There is a competition for limited resources.

- Not all organisms have the same chance of survival.
- Differences in phenotype will determine how competitive an organism is.

• Variation: genetic differences among organisms within a population (mutations and sexual
reproduction increase variation within populations

• Adaptations: traits that provide an advantage in a particular environment (can increase over
time)

• Fitness: the ability of an organism to survive and produce fertile offspring

- Reproductive success: refers to the production of offspring.
- Reproductive success over several generations is a component of evolutionary fitness

• Heritability: ability to pass on adaptations to successive generations

Ecosystem stability determines the rate and direction of evolution

Biotic and abiotic environments can
remain more or less table

• Populations are less likely to involve

in a stable environment.
Environments change and apply
selective pressures to populations?
• Selective pressures: refers to any
biotic or abiotic factors influencing
survivability.
Artificial Selection
Artificial selection: process by which humans select desirable traits in other species and selectively
breed individuals with the desired traits.

Convergent evolution: process by which similar environmental conditions select for similar traits in
different populations or different species over time.
Analogous structures: similar traits in unrelated species

Population Genetics
Evolution is driven by random occurrences (mutations)
Genetic drift: (non selective) random change in the frequency of a particular allele within a population
Something that causes a change in the genetics of the population, that isn’t natural selection
- Bottleneck events can contribute to genetic drift (big population reduced to small population)
- Founder effect reduces genetic variation of a population due to the separation from a larger one
(migration, geological events)
- Migration/Gene flow movement of individuals between populations causing an exchange of
alleles between populations. (Introduces new genes)

Bottleneck Founder

Hardy Weinberg Equlibrium

Model for describing and predicting allele frequencies in a non-evolving population
• A population in Hardy-Weinberg Equilibrium is not evolving

Five conditions must be met for Hardy-Weinberg equilibrium

• Large population - No Genetic Drift
• Absence of migration - No Gene Flow
Hardy-Weinberg equation
• No net mutation - No genes are modified, deleted or duplicated • p^2 = frequency of
• Random mating - No Sexual Selection homozygous dominant
• 2pq = frequency of
• Absence of selection - No Natural Selection
heterozygous
• q^2= frequency of
homozygous recessive
Used to determine the genotype/and or phenotype Used to determine the frequency of an allele
frequencies of individuals in a population in a population

Example:
Evolution is one of the unifying themes of biology. Evolution involves change in the frequencies of
alleles in a population. For a particular genetic locus in a population, the frequency of the recessive
allele (a) is 0.4 and the frequency of the dominant allele (A) is 0.6.

What is the frequency of each genotype (AA, Aa, aa) in this population? What is the frequency of the
dominant phenotype?

AA = 36% Dominant phenotype: 84%

Aa = 48%
aa = 16%

Speciation
Speciation: creation of a new species
• Reproductive isolation is critical for speciation. Prevents gene flow between populations.
Allopatric (geographically isolated), sympatric (reproductively isolated)

Prezygotic barrier: prevents production of a fertilized egg

• Habitat isolation: Species occupied different and rarely come in contact
• Temporal isolation: species breed during different times of day, seasons or years
• Behavioral isolation: species have different courtship behaviors or mate preferences
• Mechanical isolation: reproductive, structural differences prevent successful mating and
reproduction
• Gamete isolation: sperm of one species may not be able to fertilize the eggs of another

Post-zygotic barrier: prevents a zygote from developing into a viable offspring

• Hybrid inviability: mating results in a zygote , but incompatibility may stop the development of it
• Hybrid sterility: a hybrid offspring is produced that is vigorous, but may be sterile
• Hybrid breakdown: first generation hybrids are viable and fertile but resulting generations are
feeble or sterile
Punctuated equilibrium: Punctuated equilibrium:
• Evolution occurs rapidly after a long • Evolution occurs slowly over millions of years
period of stasis due to ecological
conditions

Divergent evolution: closely related species evolve different traits and characteristics over time
Divergent evolution occurs when adaptation to new habitats results in phenotypic diversification
• Adaptive Radiation: the evolution of new species that allows empty ecological roles or niches
to be filled

Extinction
The disappearance of a species, such that no future generations will naturally
populate the Earth.
• Occurs naturally, a part of the history of life
• Can be ongoing and occur on a small scale over long periods of time
• Can serve as a marker for geologic times

Extinction rates can increase during times of ecological stress. Species diversity greatly decreases.
Human activity can drive changes in ecosystems that cause extinctions
• Habitat Loss • Pollution
• Climate change • Poaching
• Habitat degradation • Invasive species
Extinction provides newly available niches (roles; producer, decomposer, scavenger, consumer, etc) that
can be exploited by different species
• This can lead to rapid speciation rates and adaptive radiation
AP Bio, Unit 8

Ecology, Responses to the Environment

An organisms behavior and/or physiological response is related to environmental changes
• Organisms response to changes in their environment through behavior and physiological mechanisms
• A stimulus is an external or internal signal/signals that causes a response

Organisms exchange information with one another in response to stimuli

• Communication between organisms can change behavior. This is called signaling behavior.
This can result in changes in reproductive success

Communication Mechanisms: Often used to:

• Visual • Indicate dominance
• Audible • Find food
• Tactile • Establish territory
• Electrical • Ensure reproductive success
• Chemical Signals
Natural selection favors, innate, and learned behaviors that increase survival and reproductive
success
• Innate behaviors are genetically controlled and can occur without prior experience or training
• Learned behaviors are developed as a result of experience
- Imprinting is a learned behavior where organisms will accept the first moving object they
see as their mother
• Cooperative behaviors involve teamwork between organisms of the same species. This
increases the fitness of the individual and the survival of the population

Aposematism: evolved warning traits to ward off predators (e.g. coral snake’s pattern indicating
venom)

Social Behaviors:
• Agonistic behavior is aggressive behavior that occurs as a result of competition for food or
other resources. Animals will show aggression toward other members that tend to use the same
resources.

• Dominance hierarchies occur when members in a group have established which members are
the most dominant.

• Territoriality is a common behavior when food and nesting sites are in short supply. Usually, the
male of the species will establish and defend his territory within a group in order to protect
important resources.

• Altruistic behavior is defined as unselfish behavior that benefits another organism in the group
at the individual’s expense because it advances the genes of the group.
Symbiotic relationships:

mutualism commensalism parasitism

Mutualism: both organisms benefit from each other

Commensalism: in which one organism lives off another with no harm to the host organism
Parasitism: in which the organism actually harms its host
Predation: one organism preys on the other
Energy Flow through Ecosystems
Organisms use different strategies to regulate body temperature and metabolism
• Endotherms: use thermal energy generated by metabolism to maintain homeostatic body
temperatures
- Ex: change in heart rate, fat storage, muscle contractions (shivering)
• Ectotherms: lack efficient internal mechanisms to regulate and maintain body temperatures so
they rely on behaviors to regulate temperature
- Ex: moving into or out of the sun

Organisms use energy to grow and reproduce

There is a relationship between metabolic rate per unit, body mass and the size of multicellular
organisms

Metabolic rate: the amount of energy expended by an animal over specific amount of time
• A net gain in energy can result in energy energy storage or growth
• A net loss of energy can result in loss of mass and possibly death
• The smaller the organism, the higher the metabolic rate

Changes in energy availability affect populations and ecosystems

• changes in energy availability can result in changes in population size
• Changes in energy availability can result in disruptions to system
• Changes in an energy resource, such as sunlight can affect the number and size of the trophic
levels

The transfer of energy between trophic levels is inefficient. Roughly, around 10% of the energy passes
through. This inefficiency limits population size. Typically, population size decreases up trophic levels.
The activities of autotroph and heterotrophs enable the flow of energy within an ecosystem

Autotrophs are organisms that capture energy from physical or chemical

sources in the environment. They synthesize their own food.
• photosynthetic organisms capture energy in sunlight
• Chemosynthetic organisms, capture energy from small inorganic
molecules, present in their environment with or without oxygen

autotrophs

Heterotrophs capture energy present in carbon compounds

produced by other organisms
• they metabolize, carbohydrates, lipids, and proteins as
sources of energy by hydrolysis
heterotrophs
Organisms adapt and use various strategies in response to energy availability

Population Ecology
A population is comprised of organisms of the same species in the particular area
• organisms within a population, often interbreed with one another more than interbreeding with
individuals from other populations

The size of populations largely depends upon availability of resources. Different species have
adaptations that Aiden survival when energy availability changes
• Ex:
- Storage of fat during winter months
- Losing leaves are growing leaves when day length changes
- migrating in response to changes in food availability

Several factors can affect population growth :

• age at reproductive maturity
Formula for
• Number of offspring produced population size
• Frequency of reproduction
• Survivorship of offspring during reproductive maturity
 exponential growth logistic growth

Exponential growth: a sharp increase in the growth of a population

• occurs under ideal conditions when resources are abundant
• The number of organisms added each generation increases as the population gets
larger

Logistic growth: a population size becomes restricted due to limited resources

Effects of density of populations

Density dependent factors are abiotic or biotic factors whose effect in population size relies on a
population density
• competition for resources
• Territoriality
• Disease
• Predation

Maximum amount of individuals and environment can sustain is referred to as the carrying capacity
Under certain conditions a population can temporarily exceed the carrying capacity, but limiting
factors will always always bring the population back down.
Community Ecology
A community refers to a group of different species, living together in the same location and
interacting with one another
• species diversity refers to the variety of species and the quantity of individuals included in each
species within a given community
• Species composition refers to the identity of each of the species in the community

The structure of a community is measured in terms of species composition and diversity

Simpson’s Diversity Index: used to measure the biodiversity of an habitat. The higher the value, the
more diverse the community

Biodiversity
Typically, environments with higher biodiversity are more resilient to changes
• Changes in diversity can lead to changes in organization
• The long term structure of an ecosystem can be stabilized with more diversity
• Changes in diversity can lead to long term or short term structural changes

Abiotic factors help maintain ecosystem diversity.

- Climate
- Water and nutrient availability
- Light availability

Biotic factors help maintain ecosystem diversity

- Producers are food sources for organisms
- Reduce erosion
- predators keep prey populations under control

Keystone species: species the entire community structure depends on (often control the size of
populations)
Disruptions to Ecosystems
Adaptations: genetic variation that is favored by selection
Invasive species: species that is not native to a specific area and harms the community it is introduced
to.

The distribution of local and global ecosystems changes overtime

• habitat change can occur because of human activity
• Human impact accelerates change at local and global levels
- Urbanization
- Deforestation
- Erosion
- Extinction
- Pollution
- Climate change
The introduction of new diseases can devastate native species

Geological and meteorological activities lead to changes in ecosystem

• large habitat disruptions
• Chemical disruptions (changes in atmosphere)
• can accelerate evolution
- reproductive isolation
- changes in selective pressures
• Can cause extinction
Control Groups Review
A controlled experiment is a scientific investigation, there are two types of tests set up in a controlled
experiment.

Control test (group) Experimental test (group)

• Generates data under conditions with • Generates data under abnormal/unknown

no treatment/manipulation conditions
• Generates data under normal/ • Generates data under treated/
unchanged conditions manipulated conditions
• Considered baseline data • Results often compared with control test
results to determine possible impacts of a
treatment/manipulation

A control group is used as a standard for comparison

• Negative control: not exposed to the experimental treatment or any treatment known to have
an effect
• Positive control: exposed to a treatment that has a known effect, not exposed to the
experimental treatment

Controlled variables (constants) are aspects of an experiment that could be changed but are
intentionally not changed.
- Important to help isolate/identify the impact of an intentional change/treatment
- Only variables known to have an impact should be considered as possible controlled
variables

Phylogenetic tree
Hypothesis Review
A null hypothesis (Ho): The hypothesis which states experimental variables have no relationship and
experimental observations are the result of chance.

An alternative hypothesis (HA): One of several hypotheses stating experimental variables have a
relationship and the experimental observations are the result of some nonrandom cause.

Phylogeny Charts
Phylogenetic trees and cladograms both show evolutionary relationships among lineages

node (most recent

common ancestor)

root (common
ancestor)

A phylogenetic tree is a branched diagram showing the evolutionary relationships amongst species.
• Phylogenetic trees can show changes over time calibrated by fossils or a molecule clock.
A cladogram is a diagram used to show evolutionary relationships amongst species mostly based on
shared characteristics.
• A clade includes any group on a cladogram sharing a common ancestor.

Error Bars
Error bars show the mean standard error (a range of how accurate the information could be)

• Overlap, difference
isn’t very statistically
relevant (the
difference may not
be very reliable to
draw conclusions)
• No overlap, the
difference may be
statistically different.
Drawing error bars:

+-2 standard
errors of the
mean

Plot point, add x, subtract x