AP Biology
Study Guide
Table of Contents
Table of Contents
2
Biochemistry
4
Water Properties
4
Macromolecules
4
Enzyme Kinetics
6
Thermodynamics
6
Cell Biology
8
Cell Structure
8
Cell Membrane
11
Cell Metabolism
12
Cell Signaling
16
Cell Cycle
17
Genetics
18
Heredity
18
DNA Replication
19
Genetic Expression/Regulation
20
Genomics
22
Viruses
23
Cancer
26
Embryonic Development
26
Biotechnology
27
Evolution
30
Evidence of Evolution
30
Microevolution
30
Speciation
32
Macroevolution
33
Biosystematics
34
Abiogenesis
34
Prokaryotic Diversity
35
Eukaryotic Diversity
39
Ecology
42
Ecosystem Ecology
42
Community Ecology
45
Population Ecology
47
Human Anatomy/Physiology
49
Organ Systems
49
Nervous System
49
Endocrine System
50
Digestive System
51
Excretory System
52
Respiratory System
52
Circulatory System
53
Immune/Lymphatic System
53
Biochemistry
Water is polar & can form hydrogen bonds between its δ+ H and δ- O.
Water Properties
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Co/Adhesion: hydrogen bonding to itself/other substances to hold a substance together
Surface Tension: hydrogen bonded layers of water molecules increase tension on surface
Capillary Action: Water moves up tubules opposing gravity due to cohesion/adhesion
High Specific Heat/Heat of Vaporization: 1 cal/g⋅°C; able to conserve temperature (more
energy used to break hydrogen bonds), stabilized internal temperatures for organisms &
external environments & climate
Evaporative Cooling: As water evaporates, the liquid remaining cools down (net loss of
average kinetic energy); this preserves temperature & prevents organismal overheating
Expansive Freezing: As water freezes, it forms a crystalline structure (hydrogen bonds),
which has a lower density than liquid water; preserves aquatic environments (ice floats)
Universal Solvent: Water’s polarity can dissolve polar substances, forming hydration shells
around charged particles
Neutral pH: 7 ([H+] = 10-7 at 25°C; Neutral); 2H2O → H3O+ + OH- (Dissociation)
Essential elements are elements an organism needs to live and reproduce (20-25% of natural
elements; O, C, H, N – 96%, Ca, P, K, S, etc. – 4%). Trace elements are required by organisms in
smaller quantities (Fe, I [thyroid gland], etc.)
Organic compounds consist of hydrocarbons: most(4)/strongest(electronegativity) covalent bonds.
Macromolecules
Monomer/Functional Groups
Polymer
Carbohydrates: Instant
Energy, Structure (Polar),
C/H/O
[CH2O], Carbonyl (>C=O) &
Hydroxyl (-OH) Groups,
Monosaccharides
(Ketone/Aldehyde if carbonyl
in/at the end of C-skeleton)
● G3P
● (Deoxy)Ribose
● Glucose, Fructose,
Galactose
Bonded by glycosidic linkages
Disaccharides
● Sucrose (G-F)
● Maltose (G-G)
● Lactose (gl-G)
Oligosaccharides
● Glycolipids
● Glycoproteins
Polysaccharides
● Cellulose (plant walls)
● Glycogen (animal
energy)
● Starch (plant energy)
● Chitin (animal/fungi
structure)
Lipids: Stored Energy,
Insulation, Structure
(Nonpolar), C/H/O
Triglycerides: Glycerol, 3
Fatty Acids - Methyl Groups
Phospholipids: Choline,
Phosphate (PO4) Group,
Glycerol, Hydrophobic Tail (2
Fatty Acids - Methyl Groups)
Steroids: 4 Carbon-fused
rings (3 6-C, 1 5-C: 17 total
C atoms) w/ Methyl (-CH3)
Groups
Bonded by ester linkages
Triglycerides (Energy)
● Saturated (Solid)
● Unsaturated (Liquid)
● Trans (Hydrogenated)
Phospholipids (Structure)
● Lipid Bilayer
Steroids (Structure/Ligand)
● Cholesterol
● Estrogen
● Progesterone
● Androgens
(Testosterone)
Proteins: Catalysis, Storage,
Hormonal, Contractile/Motor,
Defensive, Transport,
Receptor, Structural,
C/H/O/N/S
Amino Acids: Amino Group
(NH3), H, R-Group, &
Carboxyl Group (OH>C=O)
bonded to Cα.
● Cysteine (contains
Sulfhydryl (-SH)
Groups)
● Methionine (begins
polypeptides)
Bonded by peptide bonds
Primary: Amino Acid
Sequence (20 amino acids)
Secondary: 2D Structure
(α-helix, β-sheets, h-bonds)
Tertiary: 3D Structure
(Hydrogen, Disulfide, Ionic
Bonds, Hydrophobic/philic,
Van der Waals Interactions)
Quaternary: Multiple protein
subunits (Noncovalent bonds)
Globular (spherical), Fibrous
(long fiber shaped)
● Pancreatic Lipase
● Casein, Ovalbumin
● Insulin/Glucagon
● Actin/Myosin
● Antibodies
● Aquaporins
● Tyrosine Kinase
Receptors
● Collagen/Keratin
Nucleic Acids: Store Genetic
Information, Energy,
Catalysis, C/H/O/N/P
Nucleotide Monomer
(5-Carbon Sugar, Phosphate
(-PO4) Group, Nitrogenous
Base)
Nucleoside is sugar
([Deoxy]ribose) and
Nitrogenous Base
Purines have two N-rings
(Adenine, Guanine)
Pyrimidines have one N-ring
Bonded by phosphodiester
bonds
● DNA (Deoxyribose)
● RNA (Ribose)
● ATP (Adenine)
● GTP (Guanine)
Methyl (-CH3) Groups bonded
to DNA decrease expression,
Acetyl Groups bonded to
histones increase expression
(Thymine, Uracil, Cytosine)
(O=C-CH3)
Enzyme Kinetics
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●
Anabolic pathways build polymers and use energy (condensation/dehydration synthesis)
○ Endergonic: Nonspontaneous; ΔG > 0 (Energy Absorbed)
○ Dehydration Synthesis/Condensation reactions remove H2O, form covalent bond
Catabolic pathways break polymers and release energy (hydrolysis)
○ Exergonic: Spontaneous; ΔG < 0 (Energy Released)
○ Hydrolysis reactions add H2O, cleave (break) covalent bond
Catalysts reduce reaction activation energy (main biological catalysts are ribozymes & enzymes)
of specific reactions (enzyme-substrate complex forms as a transition state (substrate-induced fit)
on the active site) in 4 ways:
1.
2.
3.
4.
Orient substrates
Strain substrate bonds
Create a favorable microenvironment
Covalently bond w/substrate
Local Conditions on Enzyme Activity
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Temperature: Increases reaction (more kinetic energy) until enzyme denatures
○ Denaturation: Tertiary/Secondary structure (noncovalent interactions) is broken
pH: Moderate, optimal pH, variation causes denaturation of the enzyme
Compartmentalization: Enzymes are grouped with other enzymes for reactions in
favorable environments (temperature, pH, etc.)
Cofactors/Coenzymes: Metals (Inorganic)/Vitamins (Organic), assist in the reaction
Enzyme Inhibitors: Covalent is irreversible, Noncovalent Interactions are reversible
○ Competitive Inhibitors: Mimic the substrate, compete for the active site
○ Noncompetitive Inhibitors: Bind to another site, modify active site shape
■ Allosteric Regulation: Allosteric Activators stabilize the active form,
Allosteric Inhibitors stabilize the inactive form
● Positive Feedback: Reaction product stimulates enzyme
● Negative Feedback: Reaction product inhibits enzyme
Substrate Concentration: Affects enzyme activity logarithmically
○ Cooperativity: One substrate activates multiple enzyme subunits’ active sites
Enzyme Concentration: Affects enzyme activity linearly
Phosphorylation reduces molecular stability, promoting reactions.
Thermodynamics
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0th Law: Transitive property of heat
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1st Law: Conservation of energy
2nd Law: Entropy (chaos) increases with spontaneous reactions
3rd Law: Entropy is 0 at 0 K (no movement/uncertainty/chaos)
Cell Biology
Cell Structure
All cells contain plasma membrane, ribosomes, cytosol, & DNA (nucleus/nucleoid).
Prokaryotes (Bacteria/Archaea) are smaller (0.1-5 μm) w/o membrane-bound organelles,
Eukaryotes (Eukarya) are larger (10-100 μm) w/ membrane-bound organelles
Endomembrane, Endosymbionts, Cytoskeleton, Eukaryotes, Plants, Animals, Prokaryotes, All
Organelle
Description/Function
Nucleus
DNA/Nucleolus surrounded by double membrane nuclear envelope
Nucleoid
Region in prokaryotes where DNA is found (no compartmentalization)
Nucleolus
Synthesis site for rRNA and ribosomal subunits
Ribosomes
Protein synthesis sites (on ER (secretion) or in cytosol (for cell use))
Vesicles
Sacs of membranes, transport chemicals through the cell
Endoplasmic
Reticulum (ER)
Smooth (w/o ribosomes) synthesizes lipids, metabolizes carbs, detoxifies
drugs, stores Ca+; Rough synthesizes secretory proteins & membranes
Golgi Apparatus
Modifies proteins, synthesizes glycans/carbs, and sorts/secretes products
Lysosome
Hydrolytic enzymes surrounded by membrane; breaks down ingested
substances (food vacuole) and recycles damaged organelles (apoptosis)
(Central) Vacuole
Large vesicle; digestion, storage, waste disposal, osmoregulation
Peroxisome
Single membrane w/ enzymes that produce hydrogen peroxide and water
Mitochondrion
Double membrane (w/ cristae); aerobic cellular respiration
Chloroplasts
Double membrane around stroma and thylakoids; photosynthesis (plastids)
Amyloplasts
Colorless, Stores starch (amylose) in roots
Chromoplasts
In fruits/flowers, give orange/yellow color
Cell Wall
Polysaccharide outer layer, exerts turgor pressure on the cell, keeps shape;
primary cell walls of adjacent cells connected by middle lamella pectins
(sticky polysaccharide) (w/ cell junctions called plasmodesmata); after
maturation, cells may strengthen or add secondary cell wall behind primary
Cytoplasm
Fluid within the cell (mostly water - cytosol)
Cytoskeleton
Fibers in cytoplasm; support cell structure, tracks for vesicle movement,
manipulates membrane for endocytosis & motility; Microfilaments (actin)
bear tension for cell structure & w/ myosin provide motility; Intermediate
Filaments are more permanent for cell shape & organelle anchorage
Centrosomes
Microtubule organizing complex (2 centrioles, duplicate for cell division)
Flagella/Cilia
Microtubules (2*9+2 pattern connected by motor protein dyneins) for
movement (few, long, undilating/many, short, dynamic); single nonmotile
primary cilium for signaling; anchored by basal body (3*9+0) (in animal
sperm, flagellum’s basal body becomes centriole); Bacterial flagella different
Extracellular
Matrix
Fibrous collagen glycans support cell structure, adhesion, movement, and
regulation (fibronectin connects complex to membrane integrins for control)
Cell Membrane
Lipid bilayer surrounding the cell w/ proteins & glycans for homeostasis
Microvilli
Membrane projections that increase cell surface area
Cell Junctions
Gap Junctions/Plasmodesmata allow macromolecules to pass between cells,
Tight Junctions prevent extracellular fluid leakage, Desmosomes allow for
maintaining structure in stretching tissue (Anchoring Junctions)
Cell Membrane
Cell Membrane is a selectively permeable (small nonpolar molecules pass easiest (N2, O2, CO2,
Hydrocarbons), ionic/large/polar molecules utilize transport proteins) fluid mosaic (dynamic
structure with moving phospholipids/proteins laterally).
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Phospholipids are amphipathic: both hydrophobic/hydrophilic
○ Cholesterol maintains fluidity in animal cells
■ Restrains movement at high temperatures (Lowering Fluidity)
■ Disrupts packing at lower temperatures (Lowering Viscosity)
Integral Proteins span the membrane
Peripheral Proteins are outside the membrane
Protein Functions:
○ Transport (Aquaporins, Na+/K+ Pump)
■ Channel Proteins act as a tunnel, no conformational change
■ Carrier Proteins change conformation for transport
○ Enzymatic Activity (Metabolism, ATP Synthase)
○ Extracellular Matrix/Cytoskeleton Integration (Coordination)
○ Cell-Cell Recognition (Oligosaccharide Recognizers)
○ Intercellular Joining (Gap/Tight Junctions)
○ Signal Transduction (Tyrosine Kinase Receptors)
Passive Transport does not expend energy
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Diffusion is the net movement along a concentration gradient (high to low concentration)
○ Tonicity is a solution’s solute concentration relative to another
■ Hypertonic is greater solute concentration (net diffusion inside)
■ Hypotonic is lower solute concentration (net diffusion outside)
■ Isotonic is similar solute concentration (no net diffusion)
Facilitated Diffusion is diffusion with transport proteins
Osmosis is the diffusion of water (water potential gradient)
○ Water Potential is the potential energy of water (Ψ=Ψp+Ψs+Ψg+Ψm)
■ Ψp is pressure potential (closed systems only, only to cells)
■ Ψs=-iCRT is solute/osmotic potential
● i is Ionization constant (how many resulting molecules)
● C is solution molarity (mol/L)
● R is pressure constant (0.0831 (bar∙L)/(mol∙K))
● T is temperature/kinetic energy (K)
■ Ψg is gravity potential
■ Ψm is matrix potential (adhesive intermolecular forces)
○ Osmoregulation is the control of solute concentrations/water balance
■ Osmoconformers: Isosmotic with environment (marine animals)
■ Osmoregulators: Control internal osmolarity (freshwater/terrestrial)
○
Osmolarity: Total solute concentration (Molarity, Moles per Liter of Water)
■ Isosmotic: Same osmolarity (no net osmosis)
■ Hypoosmotic: Lower osmolarity (net osmosis outside)
■ Hyperosmotic: Higher osmolarity (net osmosis inside)
Net Diffusion
Animal Cell
Plant Cell
Outside the Cell
Crenated (Shriveled)
Plasmolysis
No Net Diffusion
Normal
Flaccid
Inside the Cell
Cytolysis (Lysed)
Turgid (Normal)
Active Transport expends energy, net movement against a concentration gradient (low to high)
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Membrane Potential is potential energy difference across a membrane
○ Electrochemical Gradient is both concentration and membrane potential forces
Electrogenic Pumps generate voltage (membrane potential)
○ Na+/K+ Pump exchanges Na+ for K+ creating an electrochemical gradient
○ H+ Pump actively transports protons creating an electrochemical gradient
○ Cotransport uses the active transport of one molecule to power that of others
■ Sodium/Glucose Transporters (Na/K Pump)
■ Sucrose/H+ Transporters (Proton Pump)
Bulk Transport moves large particles
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Exocytosis is the fusion of vesicles from inside the cell to membrane (bulk transport out)
Endocytosis is the fusion of vesicles from outside the cell to membrane (bulk transport in)
○ Phagocytosis is endocytosis of particles with the use of pseudopodia (food vacuole)
○ Pinocytosis is endocytosis of extracellular fluids resulting in coated vesicles
○ Receptor-Mediated Endocytosis is pinocytosis of specific molecules (bind to
receptors on the membrane triggering vesicle formation)
Cell Metabolism
Primary Catabolism (Glycolysis/Fermentation)
1. Glycolysis: Glucose is split; the products are oxidized/rearranged to result as pyruvates
(net 2 ATP by substrate level phosphorylation, occurs in cytoplasm)
a. Energy Investment Phase: Glucose is phosphorylated twice (2 ATP) to form
Fructose 1,6 Bisphosphate which is split into G3P and DHAP
b. Energy Payoff Phase: G3P is oxidized/dephosphorylated forming 2 Pyruvates, 2
H2O, 4 ATP, & 2 NADH/2 H+
c. Regulation: Phosphofructokinase is stimulated by AMP, inhibited by ATP/Citrate
2. Lactic Acid Fermentation: directly reduces 2 pyruvates into 2 lactates (cytoplasm)
a. Oxidizes 2 NADH/2 H+ into 2 NAD+ (recycled to glycolysis)
b. Lactic Acid is a toxin, bonds with O2 and is transported to the liver
3. Alcoholic Fermentation: directly reduces 2 pyruvates into 2 ethanol (cytoplasm)
a. Releases 2 CO2
b. Oxidizes 2 NADH/2 H+ into 2 NAD+ (recycled to glycolysis)
Secondary Catabolism (Aerobic/Anaerobic Cellular Respiration)
Aerobic Carbohydrate Metabolism: C6H12O6 + 6O2 → 6CO2 + 6H2O + ~33 ATP (686 kcal/mol)
1. Glycolysis: Glucose is split; the products are oxidized/rearranged to result as pyruvates
(net 2 ATP by substrate level phosphorylation, occurs in cytoplasm)
2. Pyruvate Oxidation: Pyruvate is transported into the mitochondrial matrix, oxidized
releasing CO2 and reducing NAD+ into NADH + H+, and bonded to a CoA group forming
Acetyl-CoA (2x)
3. Krebs (Citric Acid) Cycle: Full oxidation of pyruvates releasing 2 CO2 per pyruvate (2
ATP by substrate level phosphorylation, occurs in the mitochondrial matrix, 2x)
a. Primary Oxidation: Acetyl-CoA loses the CoA-SH and is oxidized releasing 2 CO2
and reducing 2NAD+ into 2 NADH + 2 H+
b. ATP Formation: CoA group is readded and removed from α-ketoglutarate
phosphorylating GDP into GTP which can be used to phosphorylate ADP→ATP
c. Regeneration: Succinate is further oxidized to form oxaloacetate, reducing NAD+
into NADH + H+ & FAD into FADH2
4. Oxidative Phosphorylation: Electron transport chain of carrier electrons, chemiosmosis
generates energy (32-34 ATP by oxidative phosphorylation, occurs in inner membrane)
a. Electron Transport Chain: e- from NADH/FADH2 are transferred through the
cytochrome complex pumping H+ (electrochemical gradient) and finally binding to
O­2­, producing H­­2O
b. Chemiosmosis: The flow of H+ through ATP Synthase along their electrochemical
gradient, generating (~32-34) ATP from ADP + Pi
Aerobic Lipid Metabolism:
1. Triglyceride Formation: Bile/Lipase hydrolyze lipids to form triglycerides
2. Glycerol is substituted into glycolysis (~38-40 ATP produced from the entire metabolism
because glycolysis energy input phase missed)
3. Beta oxidation: Converts fatty acids into 2 Acetyl CoA (mitochondrial matrix)
a. Reduces 2 NAD+ into 2 NADH + 2 H+
b. Releases 2 CO2
c. Requires 2 CoA (Recycled from Krebs Cycle)
4. Carbohydrate Metabolism: CTC/ETC, ~28-30 total ATP produced
Aerobic Protein Metabolism:
1. Amino Acid Formation: Polypeptides are hydrolyzed to amino acids (pepsin/peptidases)
a. Breaking the peptide bonds results in products that can be metabolized for ~28-30
total ATP produced (added in the end of glycolysis)
2. Amine Metabolism: Amine groups (hydrolyzed by aminopeptidase) are converted into urea
at the liver and excreted at the kidneys
a. Requires CO2
b. Some molecules enter the CTC and are further metabolized (~22-24 ATP)
3. R-Group Metabolism: R groups directly enter the Krebs Cycle
a. ~22-24 total ATP produced
4. Carboxyl Metabolism: Carboxyl group enters pyruvate oxidation
a. ~28-30 total ATP produced
Anaerobic Cellular Respiration:
1. Glycolysis: Splits glucose into two pyruvates
2. Krebs (Citric Acid) Cycle: Full oxidation of pyruvates releasing CO2
3. Nonoxidative Phosphorylation: Electron transport chain of carrier electrons, chemiosmosis
generates energy (32-34 ATP by oxidative phosphorylation, occurs in inner membrane)
a. Electron Transport Chain: e- from NADH/FADH2 are transferred through the
cytochrome complex pumping H+ (electrochemical gradient) and binding to the
oxidizing agent (final electron acceptor):
i.
Nitrate Reduction: NO3 → NO2
ii.
Nitrite Reduction: NO2 → N2
iii.
Sulfate Reduction: SO4 → H2S
iv.
Sulfur Reduction: S → H2S
b. Chemiosmosis: The flow of H+ through ATP Synthase along their electrochemical
gradient, generating (~32-34) ATP from ADP + Pi
Cellular Respiration Regulation: Phosphofructokinase (enzyme in Glycolysis) is allosterically
stimulated by AMP, inhibited by ATP/Citrate (from Oxidative Phosphorylation/Krebs Cycle).
Primary Anabolism (Chemo/Photosynthesis)
Photosynthesis: 6CO2 + 6H2O + Solar Energy (686 kcal/mol) → C6H12O6 + 6O2
1. Light Reactions: Solar energy excites electrons in pigments which are used in an electron
transport chain to generate chemical energy, splitting water/releasing oxygen (thylakoid)
a. Linear Electron Flow: Electrons are finally transferred to NADP+, forming
NADPH
i.
Photosystem II (PSII): Photons excite pigments in PSII’s light-harvesting
complex, nearby pigments are simulated as others return to their ground
state, P680 chlorophyll a pigments finally lose their electrons to a primary
electron acceptor, triggering photolysis of H2O to compensate for the lack of
electrons, releasing O2 and H+ for the electron transport
chain/chemiosmosis
ii.
Electron Transport Chain: e- from the primary electron acceptor are
transferred through the phytochrome complex pumping H+ (electrochemical
gradient)
iii.
Chemiosmosis: The flow of H+ through ATP Synthase along their
electrochemical gradient, generating ATP from ADP + Pi
iv.
Photosystem I (PSI): Photons excite pigments in PSI’s light-harvesting
complex, nearby pigments are simulated as others return to their ground
state, P700 chlorophyll a pigments finally lose their electrons to a primary
electron acceptor, P700+ accepts the electrons from the electron transport
chain
v.
Second Electron Transport Chain: e- from PSI’s primary electron acceptor
are transferred through the phytochrome complex
vi.
NADP+ Reduction: NADP+ reductase reduces NADP+ into NADPH w/
ETC 2 e-/H+
b. Cyclic Electron Flow: Electrons are recycled in the photosystems/ETC, generating
ATP
i.
Photosystem I (PSI): Photons excite pigments in PSI’s light-harvesting
complex, nearby pigments are simulated as others return to their ground
state, P700 chlorophyll a pigments finally lose their electrons to a primary
electron acceptor, P700+ accepts the electrons from the electron transport
chain
ii.
Electron Transport Chain: e- from the primary electron acceptor are
transferred through the phytochrome complex pumping H+ (electrochemical
gradient)
iii.
Chemiosmosis: The flow of H+ through ATP Synthase along their
electrochemical gradient into the thylakoid lumen, generating ATP from
ADP + Pi
2. Calvin Cycle: Chemical energy from the light reactions reduces 3 CO2 to G3P (stroma)
a. Carbon Fixation: Rubisco bonds 3 CO2 to 3 RuBP forming 6-PGA
i.
C3 Plants: CO2 is fixed into 6-PGA (3 Carbon, Calvin Cycle)
ii.
C4 Plants: CO2 is fixed into oxaloacetate (moved to bundle-sheath cells)
iii.
CAM Plants: CO2 is fixed into malic acid (used during day: Calvin Cycle)
b. Reduction: 6-PGA is reduced to 6-G3P using 6 ATP and 6 NADPH to 1-G3P
c. Regeneration: 5-G3P are rearranged to form 3 RuBP using 3 ATP
3. Photorespiration: Rubisco binds to O2 rather than CO2, releasing CO2 and using ATP
Chemosynthesis: CO2 + 2H2S → [CH2O] + H2O + 2S; sulfur/methanogens
Cell Signaling
Signaling
Summary
Examples
Synaptic (Neuro)
Neurotransmitters at synapses
Nervous system synapses
Paracrine
Neighboring Cells
Growth hormone following injury
Endocrine
Through blood
Pituitary gland hormones
Exocrine
Through ducts
Pancreas
Autocrine
Self-signaling
Apoptosis (programmed cell death)
Pheromones
Outside the organism to another
Fruits promoting maturation
Cell-Cell Recognition Membrane glycans recognition
Immune system recognition
1. Reception: ligand (lipid/protein) is first recognized and triggers pathway
a. Lipids are membrane soluble; bind to intracellular receptors; hormone-receptor
complex binds to nuclear DNA (Transcription Factor) causing gene expression
b. Proteins aren’t membrane-soluble; bind to membrane receptors which trigger
internal response
i.
G-Protein Coupled Receptor: ligand binds, G-protein activates, moves, and
activates membrane enzyme (i.e. adenylyl cyclase): response (i.e. cAMP)
ii.
Tyrosine Kinase Receptor: 2 ligands bind, monomers dimerize, 6 ATP
phosphorylate 6 tyrosines, relay proteins bind and trigger responses
iii.
Gated Ion Channel: ligand binds, channel opens/ions diffuse, relay response
c. Signaling specificity to only cells expressing the receptor gene protein
2. Transduction: relays protein reception to cellular targets (by phosphorylation cascade)
a. Secondary Messengers are relay molecules that trigger transduction
i.
Adenyl Cyclase (ATP → Cyclic AMP [cAMP]) activates Protein Kinase A
ii.
Phospholipase C cleaves PIP2 leaving Diacylglycerol (DAG) [second
messenger] and Inositol Triphosphate (IP3) which bond to an ER Gated
Ca2+ Channel, releasing them into cytosol as secondary messengers
b. Secondary messengers can activate protein kinases (transfer Pi from ATP to other
proteins), creating a phosphorylation cascade (secondary messenger → PK1 →
PK2 → … → Target Response Protein)
i.
Protein Phosphatases dephosphorylate kinases, regulating response
ii.
Signal Amplification: enzymes use many substrates (i.e. 1PK1→10PK2)
iii.
Signaling Efficiency affected by Scaffolding Proteins holding relay proteins
3. Response: transcription factors (gene expression/protein synthesis) & cellular responses
(activation of enzymes, other signaling pathways, cell division, ligand secretion, etc.)
Cell Cycle
Controlled by specific cyclin-dependent kinases bonding to cyclin (CDK-Cyclin complex can
prevent/progress cell cycle by triggering cellular responses such as being transcription factors).
1. Interphase: Cell Growth/Development
a. G1 Phase: First Gap, Growth
i.
G1 Checkpoint: Usually signals whether cell division will occur or not
1. Growth Factors stimulate cell division via signal transduction
2. Density-Dependent Inhibition: Crowded cells stop dividing
3. Anchorage Dependence: Cells need substratum to divide
4. G0 Phase: Non Dividing phase; fails first checkpoint (neurons)
b. S Phase: Synthesis, DNA Replication
c. G2 Phase: Second Gap, Growth/Preparation of Division, Organelle Division
i.
G2 Checkpoint: Checks for DNA damage/repair & other things
2. Mitotic Phase: Cellular/Nuclear Division (promoted by MPF & CDK-Cyclin abundance)
a. Mitosis: Division of Genetic Material (Somatic Cells)
i.
Prophase: Chromosome condensation, spindle formation
1. Condensin II creates a central pillar scaffold for DNA to loop
around and coil; Condensin I binds outside the middle scaffold and
coils those DNA loops further
ii.
Prometaphase: Nuclear envelope disintegrates, kinetochore attachment
iii.
Metaphase: Chromosomes lineup on Spindle Metaphase Plate
1. M Checkpoint: Cells are arrested in metaphase until all
chromosomes attach to the spindle (controlled by anaphase
promoting complex protein, which triggers move to anaphase)
iv.
Anaphase: Cohesins cleaved, microtubules pull chromosomes/elongate cell
v.
Telophase: Endomembrane system reforms, chromosome uncoiling
b. Cytokinesis: Cytoplasmic division; Cleavage Furrow (Animals)/Cell Plate (Plants)
c. Meiosis: Genetic Material Reduction (Germ Cells)
i.
Prophase: Mitosis Prophase/Prometaphase, Synapsis/Crossing Over,
Tetrads (w/ Chiasmata, crossover points hold homologs together)
ii.
Metaphase: Homologs Lineup on Spindle Metaphase Plate Independently
iii.
Anaphase: Cohesins are cleaved (except centromere to keep chromatids
together), Microtubules separate & pull chromosomes/elongate cell
iv.
Telophase/Cytokinesis: Complete duplicated haploid genome (nuclear
envelope & decondensation occur in some organisms), Cytokinesis
v.
Another meiotic division similar to mitosis (4 non-identical gametes)
d. Fertilization: Random fusion of 2 gametes & their nuclei to form a zygote
e. Binary Fission: Chromosome replication, membrane cleavage/division (Bacteria)
Genetics
Heredity
Characters/Genes: heritable features with traits/alleles as variants for the phenotype/genotype
Testcross is between unknown dominant phenotype (homo/heterozygous) and recessive phenotype
Mendel’s Laws of Inheritance:
●
●
●
Dominance: Dominant alleles determine the phenotype if alleles at the gene locus differ
Segregation: Alleles separate during gamete formation (meiosis) into separate gametes
Independent Assortment: Segregation of alleles on different chromosomes is an
independent event; genes aren’t required to inherited together and do so by probability
○ Linked genes are on the same chromosome (AB/ab); lead to more parentals in F1
testcrosses, recombinants arise from crossing over, shuffling the linked alleles.
○ Recombination frequency is recombinants/total offspring; genetic maps (1%/mu)
■ Genetic map frequencies don’t add up because of interference (multiple
crossovers on a chromosome); don’t represent actual distances (relative)
Nonmendelian Inheritance
Degrees of Dominance
1. Complete: Dominant completely masks recessive (mendelian traits like pea color)
a. Dominant alleles code for proteins, recessive alleles are nonfunctional proteins
2. Incomplete: Traits are mixed and expressed (blending hypothesis; snapdragon color)
a. Both dominant alleles code for proteins, phenotype varies in smaller groups
3. Codominance: Traits are expressed distinctly from each other (MN/AB Blood Group)
a. Both dominant alleles code for proteins, phenotype varies in larger groups
Multiple alleles: More than 2 alleles (ABO blood system has alleles IA, IB, & i)
Pleiotropy: A gene has multiple phenotypic effects (Sickle-Cell Disease & Cystic Fibrosis)
Epistasis: One gene affects the expression of another (Black/Brown/Yellow Labradors)
Polygenic Inheritance: Multiple genes affect one phenotype, opposite of pleiotropy (human
height/skin color)
Multifactorial Traits: genes and environment influence phenotype (human nutrition & height)
Genomic Imprinting: Phenotype variation depending on gene parent (gene silencing, methylation)
Organelle (Cytoplasmic/Extranuclear) Genes are found in plastids/mitochondria in egg cytoplasm
only (those from sperm are destroyed in zygote); therefore, show maternal inheritance patterns.
Wild Type is the most common trait in natural populations (mutant first letter (white); w+, w)
Chromosomal Theory of Inheritance: Genes housed on chromosomes, anaphase I in meiosis is
segregation, metaphase I independent assortment, random fertilization in crosses.
Chromosomes consist of DNA coiled around 8 histones (20% of amino acids are positively charged
(lysine/arginine), H2A/B/3/4; H1 on +30nm level) twice to form a nucleosome. Nucleosomes are
separated by linker DNA.
Chromosomal Systems of Sex Determination
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XY System: Mammal Males (XY), Females (XX); sex determined sperm carries X or Y
○ Y Chromosome contains SRY gene which triggers male testicular development;
Female development begins with gene WNT4 (Chromosome 1) which triggers
female ovary development
○ In somatic cells, 1 X chromosome is randomly inactivated to form a Barr Body
(DNA methylation, XIST becomes active on the future Barr Body, lncRNA coded
from that gene attach/cover the chromosome, preventing expression)
X0 System: Insect Males (X0), Females (XX); sex determined by sperm carries X or not
ZW System: Bird Males (ZZ), Females (ZW); sex determined by egg carries Z or W
Haplo-Diploid System: Bees/Ants Males (Haploid), Females (Diploid); sex determined by
fertilization (females) or not (males)
Other: ratio of sex chromosomes to autosomes or the environment, etc.
X linked traits (on X-chromosome) in males are hemizygous; females: homozygous & heterozygous
Nondisjunction (failure for chromosomal separation in anaphase I/II) results in aneuploidy, an
abnormal number of a chromosome (monosomy for missing 1, trisomy for 1 extra chromosome)
Chromosomal Abnormalities
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Deletions: Chromosomal fragment is lost
Duplication: Chromosomal fragment is repeated in the same orientation
Inversions: Chromosomal fragment is repeated in a different orientation
Translocations: Chromosomal fragment is moved between nonhomologous chromosomes
○ Reciprocal translocation is an exchange & transfers 2 segments
○ Nonreciprocal translocations just transfer one segment w/o another in return
Central Dogma of Molecular Biology: DNA (Replicates) → RNA → Proteins
DNA Replication
1. Topoisomerase unwinds, helicase separates leading/lagging strands at recognized origin(s)
of replication, single-strand binding proteins keep strands separate
2. RNA Primase synthesizes RNA, DNA Polymerase III (ε) continually synthesizes the
leading (5’- 3’) [uses nucleotides (dNTP), releases a Pyrophosphate (2Pi), and hydrolyzes
it to 2Pi for energy]
3. RNA Primase synthesizes RNA, DNA Polymerase 𝛼 synthesizes first stretch, DNA
Polymerase III (𝛿) synthesizes an Okazaki fragment until it reaches the prior RNA primer,
DNA Polymerase I (RNAse/𝛼) replace RNA Primer w/ DNA, DNA Ligase binds Okazaki
fragments lagging strand (3’ - 5’)
4. The DNA replicated “bubbles” are bonded together by DNA Ligase, forming two daughter
DNA molecules; Telomerase extends telomeres (has RNA molecule for DNA synthesis)
DNA Repair
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Direct Reversal: Dimers by UV light, reversed photoreactivation by photolyase, not in
humans, in bacteria, fungi, some animals.
Excision: Nuclease cuts, DNA Polymerase I (𝛼) fill in the missing nucleotides, DNA Ligase
bonds strands, in most organisms
Postreplication (Translesion Synthesis): Gap is left at Okazaki fragment, filled in through
recombinant homology directed repair (sequence from homolog) or error-prone
non-homologous end joining repair (damaged strand as template)
Genetic Expression/Regulation
Bacteria do transcription/translation simultaneously, no RNA processing
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Operons: Genes in bacteria, consist of the promoter region, operator (where repressor,
from regulatory gene, binds), and genes of interest typically all related to a single
metabolic pathway (e.g., tryptophan synthesis).
○ Lac Operon: regulate lac genes (z,y,a), inducible (norm off, repressor binds to
allolactose to inactivate it), positive regulation by cAMP bonded to CAP (more w/
low glucose, CAP/CRP is an activator & binds to an upstream site, used in many
more operons)
○ Trp Operon: regulate trp genes (a-e), repressible (norm on, trp binds to repressor
to activate it)
Eukaryotes do RNA processing compartmentalized by nucleus
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Epigenetic Inheritance: Histone Acetylation (uncharged lysine residues) increases
expression (DNA is more accessible); CpG site (Cytosine-Phosphate-Guanine) Methylation
(5M-Cytosine) decreases expression (DNA less accessible, more tightly coiled, hydrophobic
interactions)
TADs (topologically associated domains: regions of chromatin loops) may extend from
individual chromosome territories into specific sites in the nucleus (transcription factories
inside the middle of nucleus for expressed genes, unexpressed genes on the outside of the
nucleus)
Transcription (RNA Polymerase synthesizes mRNA 5’-3’)
TATA Box: Eu/Archaea Promoter (TATAWAW); W = A/T
Pribnow Box: Bacterial Promoter: -10 (TATAAT); -35 (TTGACA) (σ TF binds)
Specific Transcription Factors are activators or repressors, bind to DNA (homeodomain), general
transcription factors and mediator proteins connect them to the promoter site (DNA Bending)
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RNA Poly I - All Eukaryotes - large r
RNA Poly II - All Eukaryotes - pre-m, some sn/sno/mi
RNA Poly III - All Eukaryotes - t, small r, some sn/mi
RNA Poly IV - Plants - Some si
RNA Poly V - Plants - for heterochromatin formation
Bacteria have only 1 Type RNA Polymerase
Rho Termination: Rho protein binds at RNA rut site, releases; Non-Rho: Rich C-G (3 H-Bonds),
forms hairpin that stalls strand, downstream codes for U-A (weaker, 2 H-Bonds), strand separates
RNA Processing (Post-Transcriptional, pre-mRNA→mRNA, Only Eukaryotes):
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5’ Cap: Modified Guanine, 20-40 nucleotides
3’ Poly-A-Tail: 50-250 Adenine nucleotides
○ Polyadenylation Sequence: AAUAAA, polyadenylation tail in RNA processing
RNA Splicing: spliceosomes (snRNP/snRNA) splice introns, leaving exons (code for
protein domains)
○ Alternative Splicing: exon shuffle, new protein
○ U1 snRNP and BBP bind to the mRNA
○ U2 snRNP displaces Branchpoint Binding Protein (BBP)
○ Branch site (nucleophile) is extruded
○ snRNP complex creates a lariat shape to initiate a cut
RNA Editing: Alters mRNA nucleotide sequence
Small Noncoding RNAs:
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Micro RNA (miRNA): in exons/introns, multiple target mRNAs
Small Interfering (siRNA): argonaute RISC complex, 1 target
Piwi-interacting RNA (piRNA): heterochromatin transposons, reestablish appropriate
DNA methylation in germ cells
Long Noncoding RNAs: Example is XIST Gene, transcripts lead to lncRNAs which bind
back to the X chromosome, causing heterochromatin formation and the chromosome
inactivation
Translation (mRNA to Polypeptide)
1. Initiation (Met, AUG, A site, 1 GTP, Small then large subunit bind)
2. Elongation (rRNA (made w/ snoRNA) 5’-3’, tRNA moves through A-P-E sites adding
AA to chain, 2 GTP, one to recognize AA, other to translocate tRNA)
a. Prokaryotes have 70s (50s/30s), Eukaryotes have 80s (60s/40s) ribosomes
b. Wobble: G-U, I-A/U/C (assuming X-Y, Y-X pairing prior), flexible final pairing
c. Aminoacyl-tRNA Synthetases bond tRNA to Amino Acids (hydrolyzing 1 ATP)
3. Termination (Stop Codon, Release Factor, peptide bond H2O, 2 GTP)
Signal Peptide recognized by SRP, binds ribosome to ER (all translation begins in the cytosol);
also targets polypeptides, to mitochondria, chloroplasts, the interior of the nucleus, and other
organelles that are not part of the endomembrane system.
Polyribosome: Multiple ribosomes translating an mRNA (bacteria couple transcription/translation)
Post-Translational Modifications: carbs, lipids P-groups, fold, cleave/add, edit aa, quaternary
structure, proteins tagged with ubiquitin are targeted by proteasomes and degraded
Mutations: Silent: Same AA; Nonsense: Stop; Missense: Diff AA; Suppressor: fixes AA
(Mutagens are physical/chemical elements that cause mutations like high radiation (X-Ray/UV),
base analogs (like DNA bases but don’t pair properly), chemicals that interfere w/ DNA structure,
etc.; many mutagens are carcinogens (cancer-causing chemicals)); Insertion/Deletions are
frameshift mutations; have greater impact than nucleotide-pair substitution (one switched pair).
Spontaneous Mutations: random errors in DNA replication that aren’t fixed (around 1 in 1010)
Genomics
Bacterial/Archaeal Genomes ~ 1-6 Mb (1,500 to 7,500 genes, high gene density); Eukaryotes
much larger (5,000 genes for unicellular fungi (yeasts) to 40,000+ genes for multicellular; low
gene density because of introns, alternative splicing instead, more DNA control regions, noncoding
RNAs, etc.)
Pseudogenes: genes that gained mutations and became nonfunctional over time (unique noncoding)
Transposable Elements: jumping genes (cut-paste or copy-paste; both w/ transposases coded by
the element), 75% of human repetitive DNA, found in prokaryotes/eukaryotes (Barbara
McClintock: variegations color of the kernels on a corn cob); Transposons: DNA intermediate;
Retrotransposons: RNA intermediate (transcription, reverse transcriptase creates dsDNA copy,
enzyme catalyzes insertion; only copy-paste method, DNA is not cut at original site).
Alu elements (transposable) are transcribed into RNA to maybe help regulate gene expression
L1 retrotransposon may be critical for 1-2 cell embryo development by modifying chromatin
structure
Simple Sequence DNA consists of copies of tandemly repeated short sequences (STRs included)
found in centromeres (structural/cell division) & telomeres (protects ends from joining to other
chromosomes and degradation) (also organizes chromatin in the nucleus when found in other
regions)
Human Chromosome 2 is fusion of Chimpanzee chromosome 12/13 (telomere/unused centromere
in center are evidence for this)
Unequal Crossing Over leads to duplications and deletions for each chromosome (Transposable
elements provide homologous regions for translocations/crossing over to occur)
Template slippage during replication could lead to variable STRs (multiplicated regions)
Multigene families: 2+ identical (tandemly clustered, RNA products such as repeated rRNA
genes) or similar genes (in the same chromosomal region such as embryo/fetus/adult version of
globin genes); arise from duplications, transpositions, & mutations (both enhancing functions for a
new type of gene and inhibiting function resulting in a pseudogene)
Exon duplication (multiple of one exon in one gene)/shuffling (multiple different exons from
different genes) can lead to new enhanced proteins (such as TPA, which controls blood clotting)
(Transposable elements can move genes/exons throughout the genome, resulting in genes
scattered (combinatorial control in Eukaryotes))
Transcription factor genes are evolving the fastest as they control genetic expression
Copy-Number Variants (CNVs): loci where some individuals have one or 3+ copies of a particular
gene; Short Tandem Repeats: repeated units of 2-5 nucleotide sequences in specific regions of the
genome; Single Nucleotide Polymorphism: base pair variation site in a species (genetic marker in
disease alleles); Human genome evolution seen in CNVs, STRs, & SNPs.
Viruses
Viruses: single/double stranded DNA/RNA packaged in a protein coat (capsid, built from
capsomeres); no metabolism/reproduction by itself (borrowed life)
Types of Capsids:
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Helical Virus: Capsomeres arranged in helical shape forming a rod, nucleic acid coiled
inside
Adenovirus/Icosahedral Viruses: Infect respiratory tracts, 252 identical capsomeres in
icosahedron formation, protein spikes at vertices, nucleic acid found inside
Influenza Viruses: have phospholipid membranes with glycoproteins/proteins from host
cell; eight double-helical RNA-protein complexes, each associated with a viral polymerase
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Bacteriophages (phages): infect bacteria, elongated icosahedral heads (w/ DNA) & have
tail sheath/fibers that help with cellular attachment; T-even phages infect bacteria w/ their
DNA with their tail injected
Host range is the limited range of host species viruses can infect (membrane receptor specificity)
DNA/RNA Viral Replicative Cycle
1. Viral Entrance (T-even inject DNA, others enter by receptor-mediated endocytosis or
plasma membrane fusion, receptor proteins bind to virus glycoproteins, digestion of capsid
leaves RNA)
2. Genome Replication (host cell uses DNA Polymerase/Primase/Ligase/etc. to replicate
DNA genomes; RNA viruses use virally encoded RNA polymerases to replicate RNA
genomes)
3. Protein Synthesis (host cell uses enzymes to transcribe/translate host cell DNA/RNA
forming capsid proteins (cytosol)/glycoproteins (ER/Golgi), concurrent with genome
replication)
4. Viral Assembly (viral genomes/capsid proteins (w/ viral RNA Polymerase) self-assemble;
vesicles transport glycoproteins to cell membrane; capsid assemblies bud from studded cell
membrane)
Lytic Cycle: After viral assembly, viruses exit and lyse the cell (break open), virulent only lytic
Lysogenic Cycle: Replication of the
viral genome without cell lysis (both
lysogenic/lytic viruses called
temperate; prophage: viral DNA is
incorporated in bacterial genome;
genes inhibit transcription of each
other (may cause different host
phenotype); may become lytic if
exposed to certain
chemicals/radiation)
Prokaryotic defense: restriction enzymes
hydrolyze foreign DNA (not methylated like
genome)
Prokaryotic CRISPR Immune System: clustered
regularly interspaced short palindromic repeats;
genome consists of DNA from previous infections
spaced by spacer DNA (reads the same
backwards/forwards), Cas (CRISPR-associated)
nucleases use processed RNA from CRISPR
region to detect and cut foreign phage DNA,
leading to degradation (genome adds copy).
Most Plant Viruses are RNA helical/icosahedral
capsid. Horizontal Transmission: external source
to plant (i.e., herbivore, human, etc.); Vertical
Transmission: Parent to progeny
Retroviruses use reverse transcriptase to
generate dsDNA copy from ssRNA genome
(incorporated into host genome as provirus,
similar to lysogenic cycle, then gene expression of
viral RNA, virus form).
Viruses cause cellular damage by releasing
hydrolytic lysosomal enzymes, stimulating the
release of toxins, etc. Symptoms result from body
defense and cellular replication of infected tissue.
Vaccine: a harmless derivative of a pathogen
(killed or weak pathogen, toxin, protein, or specific
DNA/RNA) that stimulates the immune response.
Prions: infectious misfolded versions of brain
proteins that cause neurodegenerative diseases by causing functioning brain proteins to misshapen
and aggregate (Alzheimer’s and Parkinson’s disease).
Pandemic: Global Epidemic: widespread disease outbreak (mutation, easy human transmission)
Emerging viruses may arise because RNA has a high mutation rate (viral RNA polymerases don’t
proofread in replication, new viruses may affect people immune to the previous virus), due to high
human travel throughout the world, or because virus originates from animals (75% viruses).
Cancer
Uncontrolled cell division; caused by loss of dependence on growth factors/abnormal cell cycle
control system (genetic mutations); Benign Tumors don’t spread, Malignant Tumors metastasize
Proto-oncogenes: regular growth
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Tumor-suppressor genes proteins prevent uncontrolled growth
Ras Gene G-Protein sends signal from growth factor to transduction
p53 Gene tumor suppressor (ATM protein kinase activates), halts cycle (activates p21
gene), repair, apoptosis (programmed cell death by autocrine cell signaling)
Oncogenes: cancer mutated, changed by epigenetic changes, translocations, gene amplification,
point mutations, or viral DNA integration (abnormally high activity of normally low expressed
genes or knockout of tumor-suppressor genes)
Small molecules can combat cancer by suppressing activity of oncogenes; Cultured cells can mass
produce proteins that can act as steroids lacking in disorders (Insulin/Growth Hormone/TPA)
Embryonic Development
Cell Differentiation: cells are more specialized in structure/function (reversible)”
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Stem Cells are unspecialized, replicate indefinitely, and can differentiate into multiple types
Totipotent: cell can differentiate into all embryonic/extraembryonic cells (new organism,
only Embryonic Stem Cells before blastula/blastocyst and in zygote/morula)
○ Nuclear potential (ability for a cell to develop into a new organism) decreases with
age (embryonic development/cell differentiation) in animals
Pluripotent: cell can differentiate into all somatic/germ cells (Embryonic Stem Cells at
blastula/blastocyst phase)
Multipotent: cell can differentiate into a limited number of cell types (Adult Stem Cells)
Determination: point at which the cell is irreversibly committed to becoming a specific type of cell:
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Cytoplasmic Determinants: Cytoplasmic molecules from the egg of the zygote that
regulate genetic expression (i.e., Transcription Factors, Proteins, RNA, etc.)
○ Maternal Effect Genes: Cytoplasmic determinants involved in axis establishment
coded from the mother’s genome
○ Morphogen Gradient Hypothesis: gradients of substances called morphogens (such
as Bicoid mRNA) establish an embryo’s axes and other features of its form (such as
Anterior end of Drosophila)
Induction: Cell signaling causes changes in genetic expression & phenotype
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Master Regulatory Proteins control cell differentiation as they act as transcription factors
and activate tissue specific genes/TFs while also activating their own gene (Positive
Feedback, MyoD stimulates itself in myoblast determination/differentiation)
Morphogenesis: the development of an organism’s structure/form
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Pattern Formation: spatially organizing the tissues and organs in an organism during
embryonic development, controlled by homeotic (hox in animals) genes contain a
homeobox coding for a homeodomain (which is the DNA binding region of the final
transcription factor) in the final transcription factor (differing hox gene expression and
regions → major anatomical differences)
In animals w/ true tissues, embryo layers into Ectoderm (integumentary & possibly central
nervous system), Endoderm (digestive system and other organs such as liver/lungs), &/or
Mesoderm (muscles and organs between digestive/integumentary system, in bilaterians)
Biotechnology
Genetic Engineering: the direct manipulation of genes for practical purposes
Genetic Therapy: introducing new genes; primarily used to cure tough-to-cure diseases
Nucleic Acid Hybridization: complementary base pairing between similar/different nucleic acids
Polymerase Chain Reaction (PCR):
1. Denaturation: Heat DNA to separate hydrogen bonds
2. Annealing: Cool for DNA primers (40-60% CG, not complementary, 15+ nucleotides)
3. Extension: Taq/Pfu Polymerase; f(n) ~ 2n = 2[f(n-1) + n-2]; f(3) = 2
Sanger Sequencing: smaller DNA splices (<900); expensive/inefficient for large splices; reliable
1. Denature DNA, add primers, polymerase, nucleotides, and fluorescent chain-terminating
dideoxynucleotides (end strand)
2. Primer binds, Polymerase extends until ddNTP is inserted, many diff length strands are
created w/ last colored ddNTP
3. Strands are separated through gel electrophoresis and sequenced based on ddNTP’s
fluorescent color
Next-Generation Sequencing (NGS):
1.
2.
3.
4.
Fragment gDNA (400-1000 base pairs)
Isolate fragments in aqueous solution w/ a bead
Copy fragment (PCR, 106 copies), 5’ ends captured by bead
Bead placed in well w/ DNA Polymerase/Primers (primer 3’)
5. 2 million wells on a multiwell plate, A/C/G/T solution added/washed
6. If light flashed (dNTP → dNMP + PPi), nucleotide is recorded
Third Generation Sequencing: one DNA moved through a nanopore in a membrane, identifying
the bases one by one electrical current interruptions (distinct per base)
Gene/DNA Cloning: Identical copying of DNA/genes by adding the target gene to a cloning
vector (e.g., plasmids (which yeasts have), including an expression vector, which has an active
bacterial promoter, then restriction site to eukaryotic cDNA gene (R Transcriptase recoded w/o
introns) is in correct reading frame; protein may also need to be modified in eukaryotes or
mammalian culture cells (vector can be virus)) and allowing organisms with the vector to replicate
it, producing multiple copies of the gene.
Electroporation: Cells are electrocuted creating cell membrane pores for DNA to enter
Restriction Enzymes cut DNA at specific, typically symmetric restriction sites (used by bacterial
immune system, their genome is appropriately methylated at adenines/cytosines), gene of interest
with same cut side can be added to a cloning vector and ligated to form recombinant DNA
DNA Profiling/Fingerprinting uses gel electrophoresis (runs current through polymer (agarose)
gel w/ DNA (-); smaller molecules move away from the cathode wall; DNA is organized by size
(nicked, linear, covalent, supercoiled, circular), Ethidium bromide to stain).
Transforming Bacteria:
1. Extract plasmid DNA from bacteria
a. Lysis, Phase separation, clear proteins, precipitate DNA
2. Cut plasmid DNA using restriction enzymes
3. Hydrogen bond plasmid DNA to foreign DNA
4. Use DNA ligase to seal the DNA fragments
5. Transform bacteria with recombinant DNA
Nucleic Acid Probe: short ssD/RNA fluorescent complementary to mRNA of interest
RT-PCR Analysis:
1. cDNA Synthesis from each mRNA using reverse transcriptase/RNA polymerase/nucleases
2. PCR Amplification using primers from gene of interest on cDNAs (if gene is present)
3. Gel Electrophoresis reveals more DNA from mRNAs that originally had the gene
qRT-PCR: dye lights/fluoresces when bound to dsDNA, no gel electrophoresis, quantitative data
RNA Sequencing:
1.
2.
3.
4.
mRNAs isolated/cut using nucleases
Reverse transcribed into cDNAs
cDNAs are sequenced (using another method, Sanger/NGS/TGS)
Data mapped into genome by computer, frequency of certain sequences determines
expression
DNA Microarrays: ssDNA on a glass slide, represent the genome, need mRNA sequences prior,
mRNA to fluorescently labeled cDNA by reverse transcriptase, hybridization and color intensity
reveals expression
Gene Drive: new engineered allele is more favorable for inheritance than the wild type
Genes can be knocked out with RNA interference, complementary RNAs to inhibit translation
Genetic markers: DNA sequences that vary in the population (genome-wide association studies)
Blotting: Southern: DNA from film, Northern: RNA from film, Western: Proteins from film,
Eastern: Post-transcript changes in proteins
FISH: Finding specific DNA complementary sequences
CRISPR-Cas9 Gene Editing: Clustered Regularly Interspaced Short Palindromic Repeats: E.coli
defense, Cas genes followed by interspaced repeating DNA (spaced by viral DNA samples), viral
DNA is recognized and added to the genome, transcribed into crRNA, crRNA + tracrRNA →
gRNA (guide); Cas9 enzyme (nuclease) uses gDNA to recognize target DNA (PAM; NGC), target
is cut, replaced with either a mutation of random sequence (non-homologous end joining
translesion synthesis, knocks out gene) or homologous gene used as a template (homologous
recombination/homology directed repair, translesion synthesis); use inserted gene for gene editing.
Nuclear Transplantation: replace the nucleus in a cell with another (most likely a differentiated)
Variations in cloned animals can arise from random events such as X-inactivation, environmental
exposure, and epigenetic variations (differentiated cells are more methylated than zygotes,
improper genetic expression can lead to defects and abnormalities halting development).
Induced Pluripotent Cells: differentiated cells were introduced (retrovirus used) with 4 ES genes
(Oct3/4, Sox2, Klf4, & c-Myc), causing dedifferentiation, restoring pluripotency
Evolution
Evolution: change in the genetic composition of populations over time (perfect species not formed
due to mutation limitations, adaptation compromises, and dynamic environment).
Aristotle: species are unchanging; Linnaeus: grouped species from patterns of their creation;
binomial nomenclature; Lamarck: Individuals evolve through their life, use and disuse (more used
anatomy evolves, less used deteriorates), inheritance of acquired characteristics (used/disused
transferred to offspring); Darwin/Wallace: Populations evolve over time (descent w/
modification/natural selection), variations exist, more offspring than can carry are produced,
favorable variations provide a survival/reproductive advantage, causing the accumulation of those
traits in the gene pool over time (only occur w/ non fixed genes, fixed genes have only one possible
allele and therefore can’t be selected for/against).
Evidence of Evolution
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Paleontology: Shows differing species from the past compared to current life (sedimentary
rock/strata, relatively dated by depth, radiometrically dated with radioactive
isotopes/half-life)
Anatomy: Comparing anatomical structures to determine ancestry/convergent evolution
○ Homologous Structures: Similar anatomy (different physiology), showing
divergent evolution (vertebrate forelimbs)
○ Analogous Structures: Similar physiology (different anatomy), showing
convergent evolution (wings in birds/bats/insects)
○ Vestigial Structures: Anatomy present in ancestor but serves no current purpose
(ostrich wings, human tail bone, whale/snake pelvis/leg bones)
Biochemistry: Comparison of DNA/RNA/Proteins and similarities implies common
descent (universal genetic code, t/rRNA, pseudogenes, etc.)
Embryology: Most animal embryos contain pharyngeal arches, tails, etc.
Biogeography: Ancestor species range compared to similar species range & analyzing
geographic isolation/similar environments (convergent/parallel evolution)
○ Endemic Species: Species only found in one geographic region
Direct Observation: Directly observing evolution occurring (bacteria antibiotic resistance)
Microevolution
Change in the allelic frequencies of a population; can be due to 5 factors:
1. Mutations, introduce new alleles/change current alleles in the gene pool
a. New beneficial mutations in alleles (DNA mutations) or differing number/position
of alleles (chromosomal abnormalities) can enhance survival/reproduction &
2.
3.
4.
5.
expand genomes (mammal olfactory genes); mutations happen more frequently
with rapid asexual reproduction (prokaryotes/viruses)
i.
Mutations in developmental homeotic genes or their expression can cause
massive anatomical/physiological changes (pattern
formation/morphogenesis) and heterochrony (change in developmental
event timings in an organism)
b. Sexual reproduction also produces genetic variation/possible mutations through
crossing over (recombination of paternal/maternal genes), independent assortment
(random segregation of maternal/paternal chromosomes), and random fertilization
(new allelic combinations from each sperm/egg).
c. Genetic Recombination can also enhance prokaryotic variation: transformation
(Geno/phenotype altered by integrated foreign DNA), transduction (viruses
exchange DNA between prokaryotes), & conjugation (DNA transfer by plasmids
through pili)
Natural Selection, differential reproductive success results in some alleles manifesting in a
population over time (relative fitness compared to others, higher contribution to future gene
pool, they pass on their genes and respective traits, called adaptations, which can be in
anatomy (changes in shape), physiology (changes in function), camouflage (blend into
surroundings), or mimicry (Batesian: safe mimics harmful, Mullerian: harmful mimic each
other))
a. Stabilizing Selection: Favors intermediate phenotype
b. Directional Selection: Favors one extreme phenotype
c. Disruptive/Diversifying Selection: Favors both extreme phenotypes
d. Sexual Selection: females’ mate for traits, differential mating/reproduction success
(intersexual competition: one sex choosing mating; intrasexual competition:
members of a sex competing)
i.
Sexual Dimorphism: differences in secondary characteristics to fit traits
e. Balancing Selection: Favors all phenotypes to an extent
i.
Frequency-Dependent Selection: Phenotype favor depends on frequency
(sided-eating fish, less left frequent gives them an advantage)
ii.
Heterozygote Advantage/Balanced Polymorphism: Heterozygous
phenotype is advantageous, maintaining both alleles in the gene pool
(sickle-cell/malaria)
f. Artificial Selection: Humans choosing favorable phenotypes (larger, sweeter crops)
Nonrandom Mating, interbreeding/specific breeding patterns doesn’t shuffle the gene pool
Gene Flow, Migrations into and out of the population introduce and take out alleles
(reduces genetic differences between populations and may cause populations to merge)
Small Population (Gene Drift), smaller populations are subject to significant random
changes in the gene pool due to chance events (e.g., natural disasters or mass extinctions)
i.
ii.
Founders Effect, few individuals of a population colonize a new habitat,
new population gene pool consists only of those individuals, not the original
population
Bottleneck Effect, few individuals of a population survive a natural disaster
event, new population gene pool consists only of those individuals, not the
original population
Hardy Weinberg Equilibrium models this; if a population is not evolving/fits the 5 factors:
𝑝 + 𝑞 = 1(Allelic frequencies p & q consist of the entire gene pool, only 2 alleles)
2
2
𝑝 + 𝑞 + 2𝑝𝑞 = 1(Entire population consists of the 3 possible genotypes)
Species are separate populations that can’t interbreed to yield viable, fertile offspring. Factors that
prevent interbreeding between different species include:
Prezygotic
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Habitat: Differing habitats/biogeography
Temporal: Differing mating seasons/timings
Behavior: Differing mating rituals/preferences (Sexual Selection)
Mechanical: Differing reproductive anatomy
Gametic: Fertilization doesn’t occur (sperm die in reproductive tract or penetrate egg)
Postzygotic
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Inviability: Hybrid organism may be lacking essential genes for development
Infertility: Hybrid organism may have odd diploid number/abnormal chromosomes: sterile
Breakdown: Hybrid inviability/infertility not seen in first gen, seen in future generations
Speciation
Development of multiple new species from an original species; occurs through either gradualism
(slow, steady rate of adaptations) or punctuated equilibrium (rapid burst of evolution followed by
long static periods); 4 main methods:
●
●
Allopatric: geographic isolation, independent mutations, and evolution
Sympatric/Parapatric: no geographic isolation, other factors prevent interbreeding:
○ Intense competition leads to resource partitioning, individuals evolve for their
resource
○ Sexual Selection: females’ mate for certain traits, variants don’t
interbreed/speciate
○ Hybridization: Species interbreed after speciation in hybrid zones
■
■
■
■
●
Reinforcement: Hybrids produced less; reproductive barriers strengthen
Fusion: Hybrids produced more; reproductive barriers weaken
Stability: Hybrids continually produced; reproductive barriers maintained
New Species: Hybrids produced more but evolve viability/fertility
● Balanced Polymorphism: Hybrids advantaged over parent species
● Polyploidy: Extra sets of chromosomes prevent parent species
breeding (as long as there is one functional gene, other copies can
mutate/evolve over time to serve a novel purpose)
○ Autoploidy: Polyploid from one species (asexual
reproduction preserves polyploidy)
○ Alloploidy: Polyploid from 2 species (asexual reproduction
preserves aneuploidy until fertilization creates fertile
polyploid)
Adaptive Radiation: species evolve to fit new niches (new habitat/extinction)
Evolution can be classified depending on the resulting species as:
●
●
●
●
Divergent Evolution: One species evolved into many distinct species
Convergent Evolution: Unrelated species evolve similar traits due to similar pressures
Parallel Evolution: Related species evolved similar characteristics from similar pressures
Coevolution: Species affect each other’s evolution (such as predator-prey relationships)
Macroevolution
Evolution above species level (domain, kingdom, phylum, class, family, order, genus)
Biosystematics
Hadean Eon: 4.6 - 3.85 Billion years ago: Origin of Earth, Rock Formations, Water/Oceans Form
Abiogenesis
1. Abiotic synthesis of organic monomers
a. Hydrothermal vents release alkaline (basic) fluids, causing the formation of lipids
which escape the vent as a blob w/ a basic fluid in an acidic environment (gradient)
b. Celestial objects contain organic molecules (due to high UV radiation/low temps)
c. Oparin/Haldane theorized early reducing atmospheric molecules (NH3, CO2, H2O,
H2, & CH4) and lightning/UV radiation could form organic compounds (Primordial
Oceanic Soup/Electric Spark Theory, tested by Miller/Urey and succeeded,
neutral environment could also produce organic compounds or in reducing
volcanoes/hydrothermal vents)
2. Polymerization of these monomers to form polymers
a. Dripping monomers onto hot clay/sand results in spontaneous polymerization (Iron
Sulfides may have been catalysts through energy from coupled redox reactions)
3. Polymers surrounded by protocells (lipid membrane to restrict internal chemistry)
a. Phospholipid vesicles/bilayers originate from hydrothermal vents/self-assembly
i.
Reproduce (bubble off other smaller vesicles)
ii.
Grow (absorb other smaller vesicles or phospholipids)
iii.
Absorb clay particles (containing polymers like RNA/Proteins)
iv.
Perform chemical/metabolic reactions with external reagents
4. Polymers develop self-replicating abilities (life’s inheritance capabilities)
a. RNA molecules can catalyze reactions (ribozymes, including RNA replication) due
to 3D structure, functional groups, & hydrogen bonding (reaction specificity), RNA
World
i.
Genotype: sequence; Phenotype: shape; competition for NMP, natural
selection
b. RNP World: RNA replication to proteins as proteins were more efficient catalysts
c. Central Dogma: DNA replication to RNA to proteins as DNA is more chemically
stable & accurately replicated compared to RNA for expanding genome
d. Origin of horizontal gene transfer: genes transferred between genomes by
plasmids, transposons, viruses, & endosymbiosis.
e. Viruses may have begun evolving here as catalytic nucleic acids (mobile genetic
elements such as transposons/plasmids) that move between hosts (protocells),
eventually evolved to DNA/Proteins for increased cell infiltration (coevolution)
i.
Viruses have scavenged host genes such as DNA repair, translation, protein
folding, & polysaccharide synthesis, supporting this hypothesis.
5. Primary heterotrophic prokaryotes develop (vesicle w/ nucleic acids)
a. Heterotrophic hypothesis predicts life began as anaerobic (glycolysis) heterotrophs
6. Primary autotrophic prokaryotes develop (cells w/ primitive photosystems in membrane)
a. Produce O2/Sugars (Photosynthesis), ancestors of cyanobacteria
b. Atmospheric oxygen increased (selection against obligate anaerobes towards
facultative/obligate aerobes, including developments in cellular respiration), ozone
layer formed (blocked UV light ending abiogenesis of organic molecules)
Prokaryotic Diversity
Bacteria:
●
●
●
●
Structure: Peptidoglycan cell walls (large layer is gram-positive, small layer w/ outer
glycolipid membrane is gram-negative) covered by a sticky capsule, fimbriae, and/or pili (F
factor genes)
Motility: Flagella enable movement (proton gradient turns curved fibers for motion)
Genome: circular/histone-less in nucleoid w/ extra plasmids & replicative/expressive
machinery
Metabolism: Photo (certain prokaryotes)/Chemoheterotrophs (many prokaryotes, obligate
& facilitative (an)aerobes perform fermentation or anaerobic respiration/aerobic
respiration); Photo (photosynthesis)/Chemoautotrophs (chemosynthesis) perform organic
carbon fixation; some cyanobacteria/methanogens have nitrogen fixation (N2 to NH3) for
amino acids/n-bases
Gram-Negative:
●
●
●
●
Proteobacteria (alpha – eukaryotic symbiosis (mitochondria), beta – nitrogen recycling,
gamma – sulfur/pathogenic, delta – slime-secreting myxobacteria, epsilon – pathogenic)
Chlamydia (lack peptidoglycan in cell walls, rely on animal hosts (for ATP), pathogenic)
Spirochetes (helical heterotrophs (move through rotation like large flagella), pathogenic)
Cyanobacteria (photoautotrophs (chloroplast), oxygen release, make up phytoplankton)
Gram-Positive: Diverse, can be pathogenic, free-living/solitary, Mycoplasmas only w/o cell walls
Archaea: Extreme halophiles (salt) or crenarchaeota (mostly thermophiles), euryarchaeota
(mostly methanogens, H2 + CO2 to CH4, obligate anaerobes), korarchaeota (Koron - young man,
aren’t in previous two clades), & nanoarchaeota (smaller, symbiotic archaea, in other archaea in
hot springs or hydrothermal vents)
7. Primary eukaryotes (protists) develop (cells w/ compartmentalization)
a. Endosymbiotic Theory:
i.
Infoldings of the plasma membrane (endomembrane system engulfing DNA)
ii.
Engulfing of aerobic bacterium (mitochondria performs aerobic respiration)
iii.
Engulfing of photosynthetic bacterium (plastid performs photosynthesis)
b. Evidence for Endosymbiotic Theory (similarities to bacteria):
i.
Independent reproductive process similar to binary fission
ii.
Circular, histone-less, intron-less DNA (simultaneous protein synthesis)
iii.
Smaller ribosomes than Eukaryotes found in Prokaryotes (30S/50S/70S)
iv.
Membranes include structures homologous to those in prokaryotes
v.
Double membrane structure (bacterial membrane & vacuole membrane)
c. Secondary Endosymbiosis:
i.
Autotrophic eukaryotic diversified into green/red algae, which underwent
endosymbiosis again. Red algae endosymbionts diversified into
dinoflagellates and stramenopiles; depending on the heterotroph, green
algae endosymbionts were euglenids or chlorarachniophytes.
d. Evidence for Secondary Endosymbiosis
i.
Plastids surrounded by 4 membranes: 2 inner membranes from original
gram-negative cyanobacterium, 1 from algae plasma membrane, & 1 from
eukaryote food vacuole where endosymbiosis occurred
ii.
Vestigial nucleus/DNA/expressive machinery from primary eukaryote
exists
8. Complex multicellularity develops (colonies of differentiated cells)
a. Originally colonies of cells which cell walls/membranes held together
b. Complex multicellularity arose by reordering genes (protein domains) & a few novel
genes involved in cell junctions/connections & signaling (which led to cell
differentiation by cytoplasmic determinants/induction)
i.
Animals are sister taxa with choanoflagellates, which have genes for protein
domains found in only animals such as for cadherins (cell attachment) and
signaling
c. Mostly marine life
9. Diversification/Colonization of Land by Plants, Animals, & Fungi
a. Land provided unfiltered sunlight, CO2, and soil nutrients but had scarce water/lack
of support against gravity
b. Plants (from Charophytes, a green algae) derived many novel traits for land:
i.
Altering Generations: Diploid (sporophyte) & haploid gens (gametophyte)
arise from zygote (2n, from gamete fertilization) and spores (n) mitotically
dividing
ii.
Walled Spores: Spores from sporophytes (made in sporangia organs)
coated with sporopollenin to survive adverse conditions
1. Charophytes living near edge of water developed a layer of
sporopollenin to prevent drying out, enabling 1st land movement
iii.
Apical Meristems: Regions on roots/shoots for cell division to elongate
iv.
Cuticle Layer: Epidermis covered with layer of wax/polymers, prevents
excessive transpiration/protects from microbial attacks
v.
Stomata: Pores which allow gas exchange for photosynthesis, can be closed
to minimize water losses in hot/dry conditions
vi.
Transport Systems: moved nutrients and water up and carbohydrates down
c. Fungi (from unicellular nucleariids) derived many novel traits to move to land:
i.
Absorptive Nutrition: Fungi bodies are unicellular or multicellular filaments
(hyphae, together form mycelium, which increase SA/V for absorption)
with chitin walls (strong/flexible, more nutrients/water can be absorbed
w/o lysis)
ii.
Plant Mutualism: Specialized hypha (haustoria) exchange absorbed
nutrients with plant roots for carbohydrates (sym genes for mycorrhizal
formation in plants). Ectomycorrhizal don’t penetrate cells, penetrate
extracellular space & form layer outside roots; Arbuscular mycorrhizal
penetrate root cell walls (not plasma membrane) for molecular exchanges;
endophytes live in plants and benefit them by giving them pathogen
resistance, deterring predators, etc.
iii.
Sexual/Asexual Reproduction: Sexual reproduction/fertilization of spores
when cytoplasm (plasmogamy) then nucleus fuse (karyogamy), meiosis then
mitosis for building haploid filaments, yeasts can also asexually reproduce
as single cells
d. Plants began as nonvascular bryophytes and developed:
i.
Vascular tissue to grow taller (outcompete for sunlight, disperse spores
farther, directional selection for taller plants)
ii.
Roots to absorb soil nutrients/anchor plants
iii.
leaves to increase photosynthetic output with a greater SA/V ratio
iv.
Seeds (multicellular w/ protected embryo supplied w/ food for longer
lifetime, seeds can transfer sperm w/o water by pollination and pollen tube
which is better for dry land environments)
v.
Flowers (sexual organs specifically for reproduction)
vi.
Fruit (more viable medium for spreading seed through heterotrophic
nutrition and excretion)
e. Animals began as sponges, mollusks, & cnidarians (grazers/scavengers/filter
feeders, marine); Cambrian Explosion led to rapid diversification of predators/prey
(coevolution), bilaterians, & hard-bodied, large animals (could be due to natural
selection of predator traits, oxygenation selected for larger, metabolically stronger
organisms, or Hox genes regulating body structure develop/mutate)
f. Animals colonized land in many events:
i.
Arthropods first: cuticle prevented dehydration; Insects are most diverse
clade (radiated in response to new plant foods, resource partitioning),
developed flight (extensions of the cuticle, still have walking legs,
evolutionary advantage for land)
ii.
Tetrapods developed limbs from lobe-fins, Amphibians lived on both
land/water, Amniotes developed amniotic egg (reduced aquatic dependence
for reproduction, slowed dehydration, similar to plant seeds)
Summary
Eukaryotic Diversity
Nucleus/membrane-bound organelles, cytoskeleton for shapeshifting/motility, cilia, complex
multicellularity (cell differentiation), sexual life cycles, photosynthesis, large body.
4 Supergroups
●
●
●
●
Excavata: Parabasalids/Diplomonads: modified mitochondria
(mitosomes/hydrogenosomes); Euglenozoans: modified flagella (rod w/ spiral/crystalline
structure)
“SAR” Clade: Stramenopiles/Alveolates (sacs under plasma membrane), (both
photosynthetic from secondary endosymbiosis), Rhizaria (amoeba w/ pseudopodia)
Archaeplastida: Red/Green Algae & Land Plants (Photosynthetic,
one/colony/multicellular)
Unikonta: Amoeba w/ lobe/tube pseudopodia, animals, fungi, choanoflagellates, & other
animal or fungi like protists (may have diverged first based on DHFR-TS gene
divergence/fusion)
Protists refer to all but plants/animals/fungi.
Fungi Diversity
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●
●
●
●
Chytrids: Multicellular branched hyphae body, flagellated spores, lakes/soil
Zygomycetes: Rapid hyphae growth in certain mediums, can be decomposers/parasites
Glomeromycetes: Form arbuscular mycorrhizae with plants roots for commensalism
Ascomycetes: Marine/freshwater/terrestrial habitats, sac fungi
Basidiomycetes: Decomposers/Ectomycorrhizal fungi, long heterokaryotic stage
Plant Diversity
●
●
●
Bryophytes (liverworts, mosses, hornworts): Lacked vascular tissue (height constraint),
moist habitats, flagellated sperm, gametophytes are dominant generation (sporophytes
depend on gametophyte for nutrition)
Seedless Vascular Plants (lycophytes: mosses/monilophytes: ferns): Dominant
sporophyte generations (gametophytes are independent/free-living), well-developed roots
(for water and mineral absorption and anchoring)/leaves (for photosynthesis & SA/V
increase; lycophytes have microphylls with one vascular tissue, others have megaphylls
with branched vascular system), taller growth, flagellated sperm, vascular tissue (xylem
moves water/minerals by tracheid cells (tube shaped with lignin-strengthened walls),
phloem moves organic products)
Seeded Vascular Plants (Gymnosperm/Angiosperm): Dominant sporophyte generations
(gametophytes are reduced/dependent on sporophyte for nutrition), seeds (embryo & food
protected w/ coat)
○
○
megasporangium (2n) covered by integument tissue (2n) contain megaspore (n,
egg) making up ovule, megaspore develops into gametophyte w/ egg; microspores
(n, sperm) develop into pollen grain (gametophyte with sporopollenin wall),
gametophyte germinates in ovule, develops pollen tube to discharge sperm into egg
(water not needed for fertilization, dry environmental advantage), zygote develops
into embryo enclosed with food supply (female gametophyte remnants) by seed coat
derived from the integument tissue
Angiosperms developed flowers (specialized reproductive organs) with four leaf
layers:
■ Sepal (green, sterile, enclose flower before blooming)
■ Petals (colored, sterile, attract pollinators)
■ Stamens (fertile, produce sperm/pollen)
■ Carpels (fertile, produce eggs, pollen enters through stigma into ovary
where multiple ovules can be fertilized into a seed, ovary becomes fruit)
Animal Diversity
●
●
●
Radial Symmetry - no left/right sides; have ectoderm & endoderm
Bilateral Symmetry - dorsal/ventral (top/bottom), left/right, anterior/posterior
(front/back); have ectoderm, mesoderm, & endoderm w/ body cavities
All animals are part of the monophyletic clade Metazoa
○ Sponges Porifera are basal taxon, Eumetazoa have true tissues (germ layers); basal
Eumetazoa (Ctenophora/Cnidaria) are radians/have 2 germ layers, rest are
Bilateria (Deuterostomia (Chordates - only vertebrates, most animals are
invertebrates), Ecdysozoa (Nematodes/Arthropods), & Lophotrochozoa (Molluscs,
Brachiopoda).
○ Chordates have a notochord (flexible rod for skeletal support), dorsal/hollow nerve
cord (brain-spine), pharyngeal slits/clefts (filter feeding, gills, or part of the head),
& post-anal tail (ends after anus)
■ Jawed vertebrates proliferated (Gnathostomes) into Chondrichthyans
(Cartilage Skeleton, sharks/rays), Ray-Finned Fish (Bony Skeleton,
Lungs), & Lobe Fins (rod bones/muscles around pelvic/pectoral bones,
coelacanths, tetrapods)
● Tetrapods consist of Amphibians (Salamanders, Frogs, &
Caecilians) and Amniotes (Reptiles/Mammals, have amniotic egg - 4
membranes, Embryo protected w/ yolk food source, excretion
collection (Allantois), & Chorion gas exchange)
○ Amniotes diversified into Reptiles (Crocodilians, Dinosaurs,
& Birds; keratin scales, shelled eggs, mostly ectotherms external heat is main body heat source) & Mammals
(Monotremes (egg-laying), Marsupials (pouch), &
Eutherians (placenta); mammary glands produce milk for
○
offspring, hair, fat layers, endotherms - high metabolic rate
to maintain body heat, varying teeth)
Arthropods are segmented w/ a hard exoskeleton (cuticle, made from
protein/chitin) & jointed appendages
Ecology
Ecology: study of interactions between organisms/environment
Ecosystem Ecology
Biosphere (Global)/Connected Ecosystems (Landscape)/Ecosystem (Abiotic & Biotic Factors)
Climate: long term abiotic weather conditions (temperature, precipitation, sunlight, wind; from sun
which hits tropics more directly than poles; Earth’s tilted axis causes seasons (December: north
tilts away; June: north tilts towards), water bodies moderate temperature (high specific heat,
currents transport moisture, as air rises over mountain ranges, it cools, mountain backside w/o
moisture)).
Biomes – major life zones characterized by vegetation/physical environment (Ecotone is overlap
area; in water, Benthic is seafloor, Pelagic consists of Photic (surface for photosynthesis) &
Aphotic; warm upper water separated by thermocline from colder deeper water):
●
●
●
●
●
●
●
●
●
●
●
●
Savannah: Equatorial/subequatorial, seasonal rainfall (common fires), grasses are most
common, large herbivores/insects & predators make up animal biodiversity
Dessert: 30° N/S latitudes/in-between, seasonal/daily temperature (low rain), few, widely
scattered plants (C4/CAM photosynthesis), animals: insects, reptiles/birds, mammals
Tropical Forests: Equatorial/subequatorial, little seasonal changes, plants compete for
light, high animal biodiversity
Temperate Broadleaf Forests: North/South midlatitudes, seasonal temperatures,
deciduous forests, hibernating/migrating mammals/birds
Northern Coniferous Forests: North America/Eurasia (taiga), seasonal temperatures,
mostly conifers, moose/bears/birds/Siberian tigers
Chaparral: Midlatitude coastal regions, seasonal temp/precipitation, fire-adapted
trees/shrubs, insects, amphibians, small mammals, birds, large grazing herbivores
Temperate Grassland: Midlatitude interior regions, seasonal temp/precipitation, grasses,
grazing large mammals/burrowing animals
Tundra: Arctic/high mountains, low seasonal temp, mostly mosses/grasses, large grazing
animals & predators (bears/wolves/foxes/owls)
Wetlands/Estuaries: River/Sea zone & flooded areas, cattail/sedges/saltmarsh grasses,
aquatic insects/crustaceans, & other insects/frogs/birds/fish/crabs/oysters
Lakes: Standing bodies of water, oligotrophic are oxygen/nutrient rich/poor, eutrophic is
opposite, rooted aquatic plants/phytoplankton, zooplankton/invertebrates/fish
Streams/Rivers: As salt/nutrients increase oxygen decreases, rocky/silty bottom,
phytoplankton & aquatic rooted plants, fishes/invertebrates
Intertidal Zones: rock/sand periodically submerged by tides (high nutrient/oxygen),
seagrass & algae, invertebrates/small fishes/clams/crustaceans
●
●
●
Coral Reefs: photic zone of oceans (border land), fringing to barrier to atoll, algae,
corals/fish & other invertebrates (high diversity)
Ocean Pelagic Zones: open ocean, phytoplankton, zooplankton/squid/fish/turtle/mammals
Marine Benthic Zones: sandy/rocky seafloor, cold/high water pressure, some seaweed,
algae & chemoautotrophs near deep-sea hydrothermal vents, some invertebrates
(Solar) Energy flows through ecosystems; matter cycles through it (law of conservation of mass);
laws of thermodynamics state energy is transformed inefficiently (entropy); trophic levels:
●
●
●
Primary Producers: Autotrophs, light/chemical energy to synthesize organic compounds
○ Gross/Net Primary Production: represent solar energy converted to chemical
energy (net, includes subtraction of autotrophic metabolism/respiration, ~GPP/2)
○ Primary Production is limited by light for photosynthesis & nutrients (i.e.: N & P)
■ Nutrients can promote cyanobacteria/algae proliferation, death, &
decomposition using O (anoxia, called eutrophication (well-nourished))
■ Land plants adapted symbiosis with nitrogen-fixing bacteria and
mycorrhizal fungi for obtaining nitrogen/phosphates from the soil
Primary/Secondary/Tertiary/etc. Consumers: Heterotrophs of Producers/Consumers
○ Net Ecosystem Production: biomass gain (GPP – respiration of all organisms)
○ Secondary Production: Chemical energy converted to biomass (not excreted or
respired)
■ Production Efficiency: Net Secondary Product (used for growth, not
cellular respiration)/Assimilated Primary Product (food - feces);
Birds/Mammals are low because of endothermy, insects/microorganisms
are higher
■ Trophic Efficiency: energy passed on levels, approximately 10% per level
● Typically, biomass pyramids represent a sharp spike up; aquatic
habitats may be inverted be as phytoplankton have high turnover
Decomposers/Detritivores: Heterotrophs of detritus (dead organic compounds), convert it
into inorganic compounds for producers for energy by chemically recycling;
Biogeochemical Cycles for Water (All), Carbon Dioxide (All), Phosphorous (NA/L),
Nitrogen (NA/P), & Sulfur (P) [NA - Nucleic Acids; P - Proteins; L - Lipids; C - Carbs]:
Disturbances – Storm, fire, drought, or human activity that removes organisms/reduces resources
Nonequilibrium model states communities as changing after disturbances; Intermediate
disturbance hypothesis states most biodiverse communities arise from moderate disturbance
frequency/intensity.
Ecological succession: after disturbance, an ecosystem is rebuilt, and species replace each other
Primary succession: lifeless area w/o soil: Pioneer species are first to colonize (alter soil
properties for future species: prokaryotes, protists, etc.), plants colonize (lichens/mosses first, then
come grass/trees), more species enter the ecosystem and replace/add to the niches of others.
Secondary succession: previous life, left w/ soil, similar to primary succession in ecosystem
rebuilding.
Latitudinal Gradients: more diversity in tropics than poles because less disturbance events and
higher evapotranspiration (total water evaporated, represents precipitation/temperature/sunlight,
richness)
Island equilibrium model states dynamic equilibrium in island habitats when migration =
extinction; species diversity then is correlated to island area & distance from mainland (resource
availability)
Biogeography of a species can be limited by dispersion (migrations away from dense areas), biotic
factors (negative symbiosis, disease, lack of pollinators/food), & abiotic factors (salinity,
water/oxygen availability, pH, temperature (protein denaturing), light availability, rocks/soil, etc.)
Community Ecology
All biotic factors in an ecosystem (many populations of all species)
Interspecific Interactions: Species interactions in a community
●
●
●
Competition: -/-, compete for niche – ecological role (i.e., habitat, food), limits both species
Intraspecific (same species), Interspecific (different species)
○ Competitive Exclusion Principle states best fit for niche outcompetes other
■ Resource Partitioning can result in coexistence of similar species
● Scramble (universally available resource), Contest (specific access)
■ Fundamental (potential) differs realized (actual) niche proves competition
Predation/Herbivory: +/-, predator/herbivore kills/eats prey/producer
○ Adaptations such as predator fitness for hunting and prey colors/toxins/etc.
Symbiosis: Species are in direct permanent contact and interact with each other
○ Parasitism: +/-, parasites (endo/ecto – inside/outside host) use host nutrients
○ Mutualism: +/+, Ex. Flowering plants nectar/fruit attract pollinators (food)
●
○ Commensalism: +/0, Ex. hitchhiker organisms, eating food exposed by another
○ Amensalism: -/0, Antibiosis: anything -, Allelopathy: secreted chemicals influence
○ Altruism: benefits another at its own expense, sacrificing warning organisms
Facilitation: +/+(0), Positive effects without direct/intimate contact (Black Rush makes
New England marshes more habitable for other plants by preventing salt buildup and
storing oxygen)
○ Antagonism: opposite, interference without direct contact
Species Diversity: Species richness: species #; Relative Abundance: individuals per species
Shannon Diversity Index: − (𝑝𝐴𝑙𝑛(𝑝𝐴) + 𝑝𝐵𝑙𝑛(𝑝𝐵)...)where pN is individuals of species N
𝑛
2
Simpson’s Diversity Index: 1 − Σ( 𝑁 ) ; where n is # relative abundance and N is total
individuals.
More diversity increases community stability from disturbances (more genetic variation for
changing conditions, can also prevent invasive species from outside their native range from
manifesting) and increases consistency in biomass (total mass of all individuals in a population).
Diversity threatened by:
●
●
●
●
Habitat loss, resulting in less resources/space for growth/proliferation
Introduced/Invasive Species, which alter communities drastically mostly negatively
Overharvesting, which results in net loss of species if the rate is higher than the birth rate
Global Change, altered climate/chem affects biogeochemical cycles, rupturing ecosystems
○ Humans altering global dynamics by:
■ Nutrient Movement (moved from farms to cities, centralized in new areas,
more fertilizer use, leads to enrichment past critical load resulting in killed
organisms, blooms, eutrophication, etc.)
■ Toxins (arise from pharmaceuticals, manufacturing wastes, & synthetic
compounds, which persist in ecosystems, are recycled, and harm species)
■ Climate Change (more CO2 emissions from fossil fuel burning increases
temperature by absorbing more light and reflecting it back to Earth
(greenhouse effect); changing temperatures reduce habitat, extinction)
○ Human population is no longer exponentially growing, ecological footprint is
resources needed per unit of people to live (can be used to estimate carrying
capacity); sustainable development meets current needs and future needs
Feeding relationships in a community are trophic structure: connected food chains in webs
Bottom-Up model suggests lower trophic levels influence higher levels (changing predators doesn’t
affect producers); Top-down model suggests higher trophic levels influence lower levels (limit
individuals, which increases next species, etc.; trophic cascade model).
Dominant species are the most abundant/biomass (best fit, best resource exploitation, best avoid
predators/disease); Keystone species aren’t abundant but important due to their niche;
Foundation species dramatically alter the environment (ecosystem engineers, beavers: forests into
flooded plains).
Pathogens cause diseases (zoonotic are animal to human, may be by vector – intermediate
species); can kill off species in an ecosystem causing unbalance
Species classification on the path to extinction: Threatened, Endangered, Extinct
Minimum Viable Population is smallest size population can be before entering extinction vortex
(fewer fit individuals, less traits passed on, even fewer fit, continued till extinction)
Effective population size is breeding potential (for proliferation): 𝑁𝑒 =
4𝑁𝑓𝑁𝑚
𝑁𝑓+𝑁𝑚
where Ns is number
of breeding individuals of sex s.
Population Ecology
Population (Species living in same area/time)
Demographics: Population density affected by birth (affected by reproductive rates & age
structure – proportion of males/females in a population; life history is age beginning reproduction,
cycles, and offspring per cycle), immigration, emigration, & mortality (natural selection, more
reproduction decreases survival rate; time/resource investment per offspring).
Dispersion:
●
●
●
Clumped: may grow near areas w/ food/resources
Uniform: evenly spaced for
developmentally inhibiting
pheromones/territoriality
Random: adequate resources
everywhere, location doesn’t
affect life as significantly
Type I/II are K-selected species
(iteroparity (periodic reproduction), few
large offspring/late maturity,
population density dependent traits
selected for; high densities approaching
K due to resource/territory competition,
more predation, disease spread,
secreted toxins, and intrinsic
adaptations to maximize survival); Type III are r-selected species (semelparity (single
reproduction), more small offspring/early maturity, population density independent traits selected
for; low densities with high r)
𝑑𝑁
𝑑𝑡
= 𝑟𝑁 = (𝑏 − 𝑚)𝑁
Where N is population size, t is time, r/b/m are rates of increase/birth/death per capita.
J-curves arise from exponential growth (unlimited resources/no competition/maximum
reproduction)
Carrying Capacity (K) is the max N an environment can sustain, modeled by sigmoidal S-curves:
𝑑𝑁
𝑑𝑡
= 𝑟𝑁(𝐾 − 𝑁)/𝐾 = (𝑏 − 𝑚)𝑁(𝐾 − 𝑁)/𝐾
Metapopulation is linked local populations by migrations (promoted by high N densities)
Human Anatomy/Physiology
Organ Systems
Organs (Anatomy)
Function (Physiology)
Skeletal
Bones, Tendons, Ligaments, Cartilage
Support/Structure (Protect Organs)
Muscular
Skeletal Muscles
Locomotion
Integumentary
Skin, Hair, Claws
Stop Injury/Infection, Homeostasis
Nervous
Brain, Spine, Sense Organs
Coordination, Stimulus Response
Endocrine
Glands (Pituitary, Thyroid, Pancreas)
Coordination
Digestive
Mouth, Stomach, Intestine, Liver, etc.
Food Processing
Excretory
Kidney, Uterus, Bladder, Urethra
Waste Removal, Osmoregulation
Respiratory
Mouth/Nose, Lungs, Trachea
Gas Exchange
Circulatory
Heart, Capillaries, Veins, Arteries
Nutrient/Waste Transport
Immune &
Lymphatic
Bone Marrow, Lymph Nodes, Spleen,
Thymus, White Blood Cells
Body Defense
[Text]
Nervous System
Neurons: Dendrites for input information, cell body, & axon for output information (synapses)
Action Potential: Axon begins negative w/ more Na+/K+ outside/inside, stimulus opens Na+
channels and Na+ diffuses in (axon more positive, triggers more Na+ voltage-gated channels), at
peak Na+ channels close & K+ channels open (K+ diffuses out, axon more negative), original
negative membrane potential established, Na+/K+ pump resets gradients, potential spreads along
the axon as Na+ in the cell move down it and K+ stay outside the back side (stopping double flow).
Synapse: As an action potential moves down the axon, Ca+ voltage-gated channels open, Ca+
influx causes exocytosis of neurotransmitters (i.e.: acetylcholine, amino acids, norepinephrine,
serotonin, dopamine, neuropeptides/endorphins, & nitric oxide), they bind to ligand-gated ion
channels (for Na+ in, K+ out, etc.) in the receiving neuron’s dendrite, allowing action potential to
propagate (memory and learning is changed in chemical synapses rather than electrical axons).
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Sensory Neurons: Input senses (Light (sight), Chemical (smell/taste), Mechanical
(hearing/touch), Thermal), output many axon ends (by Peripheral Nervous System).
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Mechanoreceptors (ion channels connected to cilla/cytoskeleton) detect mechanical
energy (pressure, touch, stretch, motion, sound)
■ Audition (sound) - ear, air pressure waves cause tympanic membrane
(eardrum) & 3 inner ear bones to vibrate oval window causing waves in
cochlea fluid (perilymph), which move basilar hairs on fixed tectorial
membrane, detected by mechanoreceptors.
■ Vestibulation (balance) - ear, utricle/saccule have otoliths in gel to sense
gravity & linear acceleration, angular acceleration in 3 planes sensed by
bent hairs in semicircular canals w/ perilymph pushing cupula.
○ Electromagnetic Receptors detect light, electricity, & magnetism
■ Vision
○ Thermoreceptors detect heat/cold
○ Chemoreceptors detect chemicals (ligand-gated ion channels, etc.)
■ Olfaction (smell) - nose, 1000+ genes for different receptors of new smells
■ Gustation (taste) - taste buds on tongue papilla, taste cells have one
receptor for either sweet, salty, sour, bitter, or umami (delicious, glutamate)
○ Nociceptors detect pain (extreme pressure, temperature, chemicals, etc.)
Interneurons: Input from many sensory neurons, integrate information, output many axon
ends signaling response (Central Nervous System consists of the brain (brainstem:
information to/from the brain, diencephalon: sorts senses, endocrine system, cerebellum:
movement/balance/learning/memory/coordination, cerebrum: occipital lobe is vision,
parietal lobe is touch & integration, temporal lobe is hearing, frontal lobe is skeletal muscle
control, decision-making, speech, etc.) & spine).
Motor Neurons: Input from interneurons (transmitted from CNS through PNS), output to
muscles for contraction (Autonomic (smooth/cardiac muscles & glands) Sympathetic
(fight-or-flight), Parasympathetic (rest and digest), Enteric (digestive system), &
Nonautonomic Motor (skeletal muscles) Systems)
Endocrine System
Glands across the body secrete hormones into the circulatory system to regulate body processes.
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Pineal Gland (Mid-Back Brain)
○ Melatonin: Regulates biological rhythms (i.e. circadian rhythm, sleep)
Hypothalamus (Lower Brain)
○ Releases hormones regulating anterior pituitary secretion
Anterior Pituitary Gland (Under Hypothalamus, Front)
○ Follicle-Stimulating/Luteinizing Hormone (FS/LH): Reproductive gland secretion
○ Thyroid-Stimulating Hormone (TSH): Thyroid gland secretion
○ Adrenocorticotropic Hormone (ACTH): Adrenal cortex glands secretion
○ Prolactin: Mammary gland secretion
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○ Melanocyte-Stimulating Hormone (MSH): Melanocytes (skin epidermis, melanin)
○ Human Growth Hormone (HGH): Cell cycle progression/division in many tissues
Posterior Pituitary Gland (Under Hypothalamus, Back)
○ Oxytocin: Uterus contractions, stimulates mammary glands
○ Vasopressin (Antidiuretic Hormone - ADH): Kidney water retention, sociality
■ Activates more aquaporins in nephron distal tubules & collecting ducts
Thyroid Gland (Neck, Butterfly Shape)
○ Thyroid Hormone (T3/T4): Stimulates/Maintains metabolic processes
○ Calcitonin: Lowers blood Ca+ level
Parathyroid Gland (Circles Within Thyroid)
○ Parathyroid Hormone (PTH): Raise blood Ca+ level
Adrenal Cortex Glands (Atop Kidneys, Outside Surface)
○ Glucocorticoids: Raise blood glucose by liver gluconeogenesis (non-carbs → carbs)
○ Mineralocorticoids: Na+ reabsorption, K+ excretion
Adrenal Medulla Glands (Atop Kidneys, Inside Core)
○ Epinephrine/Norepinephrine: Raise blood glucose level, increase metabolism,
vasoconstriction/vasodilation of certain blood vessels (fight-or-flight response)
Pancreas (Behind Stomach)
○ Insulin/Glucagon: Lower/Raise blood glucose level
Reproductive Glands (Ovaries - Females, Testes - Males)
○ Estrogens/Progestins: Uterine lining/growth, female sexual traits (estrogens only)
○ Androgens (i.e. Testosterone): Sperm formation, male sexual traits
■ Note: all hormones found in both sexes, only play a major role in one
Digestive System
Alimentary Canal: complete mouth-anus extracellular digestive tract (peristalsis - muscles lining
canal push food; sphincters - muscle layers regulating food passage through the canal)
1. Ingestion: Mechanical digestion
a. Oral Cavity (Mouth): Teeth/saliva (salivary gland) break & hydrolyze food
b. Food in ball shape (bolus) transported into throat (pharynx) & esophagus
2. Digestion: Chemical digestion
a. Stomach: Gastric gland secretes HCl, pepsin, & mucus for polypeptide hydrolysis
b. Small Intestine: HCO3- (secretin to pancreas) buffer for stomach acid in duodenum
i.
Pancreatic trypsin/chymotrypsin/carboxypeptidase (proteins), amylases
(carbohydrates), nucleases (nucleic acids), lipase (lipids) with bile (lipid
detergent from liver), (CCK to pancreas/gallbladder, lipids slow peristalsis)
3. Absorption: Nutrients enter body
a. Small Intestine (Jejunum/Ileum): digested monomers transported through
epithelial tissue villi/microvilli and to blood vessels (lipids coated into water soluble
chylomicrons and transported through the lacteal of the lymphatic system)
i.
Blood vessels lead to liver next (can modify/store/detoxify blood nutrients)
b. Large Intestine: Cecum (fermenting undigested material), Colon (Na+ pumped in
body/osmosis for water retention), & Rectum (undigested food/bacteria stored)
4. Excretion: Undigested material/bacteria (feces) excreted
a. Anus: 2 sphincters (voluntary/involuntary) control feces excretion, bacterial colon
metabolism releases gases (CH4, H2S, etc.) through anus
Excretory System
Nitrogenous Wastes: Ammonia (High Toxic, Dilute Urine, Low Energy), Urea (Low Toxicity,
Moderate Water-Urine & Energy), & Uric Acid (Nontoxic, Concentrated Urine, High Energy)
Nephron: Functional unit of the kidney - processes urine from renal artery/vein (Cortical: short
extension into renal medulla, most; Juxtamedullary: deep extension into renal medulla)
1. Afferent Arteriole (Renal Artery) brings blood to Glomerulus (ball of capillaries) where
filtrate diffuses into the Bowman’s Capsule due to blood pressure, blood leaves through
Efferent Arteriole (Filtration)
2. Filtrate moves through Proximal Convoluted Tubule; water, salt, nutrients, potassium, &
HCO3- are reabsorbed by Peritubular Capillaries; protons (H+) and ammonia are secreted
3. Filtrate moves through the Descending Loop of Henle; water is reabsorbed by Vasa Recta;
osmolarity increases in Renal Medulla
4. Filtrate moves through the Ascending Loop of Henle; salt is reabsorbed by active
transport (restoring renal osmolarity; Countercurrent Multiplier System forms salt
chemical gradient)
5. Filtrate moves through the Distal Convoluted Tubule; water, salt, & bicarbonate are
reabsorbed; potassium/ammonia are secreted
6. Filtrate moves through the Collecting Duct; some salt/water is reabsorbed, filtrate is
transported to Renal Pelvis, Urinary Bladder (by the Ureter Tubule), Urethra (Excretion)
Renin-Angiotensin-Aldosterone System (RAAS) regulates blood pressure/volume; when low,
Juxtaglomerular Apparatus secretes Renin which ultimately secretes Angiotensin II (triggers
vasoconstriction (increasing blood pressure) & stimulates the Adrenal Glands releasing
Aldosterone which causes more salt & water reabsorption in the distal tubules/collecting ducts).
Respiratory System
Inhaling: O2 in air (160 mm Hg) moves
down pressure gradient to the nasal/oral
cavity down to the alveoli (circular tips of
bronchioles in lungs, where increased
pressure because expanding rib cage and
lower diaphragm, contracting muscles); O2
diffuses into oxygen-poor blood, CO2
diffuses out of it (CO2 rich); CO2 and oxygen-poor air expelled as diaphragm moves up and rib cage
contracts (relaxing muscles, less V, more pressure, exhaling).
Regulation: More blood pH (7.4 normally, CO2 → H2CO3 + H+ increases it) detected in
cerebrospinal fluid by Medulla oblongata → faster/deep breathing, restoring pH w/ less CO2.
Hemoglobin (4 protein subunits/heme iron group) can bond to and transport O2 (releases it in
acidic, CO2 rich blood)/CO2 (bonds to it after releasing O2 in acidic blood) in the blood.
Circulatory System
Immune/Lymphatic System