AP Biology

UNIT 1: Chemistry of Life

1.1 Structure of Water and Hydrogen Bonding

Properties of Water

• Adhesion 

  • Water molecules are attacted to other polar/charged molecules

  • Contributes to capillary action

• Cohesion

  • Water molecules are attracted to each other → surface tension

  • Contributed to capillary action

• Neutral pH (7)

• Universal Solvent

  • Can dissolve other polar molecules and charged substances

• High Specific Heat (4.18 J/g℃)

  • Specific Heat → amount of energy required to change 1g of substance by 1℃

  • Temperature regulator (acts as a buffer to temperature changes)

    • Due to H-bonds (help it absorb and release heat energy slowly)

• High Heat of Vaporization (2260 J/g)

  • Heat of Vaporization → amount of energy required to change 1g of substance from a liquid to a gas

  • Due to H-bonds (must overcome IMFs to change from liquid to gas)

• Polar Molecule

  • Due to H-bonds

    • Large END (EN of O → 3.4, EN of H → 2.2)

    • Higher e^- density at O (due to stronger pull from nucleus)

  • Attracted to other polar/charged molecules

  • Repelled by nonpolar molecules

Intramolecular Bonds and Intermolcular Forces

• Intramolecular Bonds → ionic and covalent

  • Within a molcule

  • Stronger than intermolecular forces

  • Covalent Bonds → when atoms bond by sharing electrons

  • Ionic Bonds → when atoms bond by transferring electrons (stay bonding due to electronegative forces)

• Intermolecular Forces → H-bonds, London Dispersion Forces

  • Between atoms of different molecules

  • Weaker than intramolecular bonds

  • Hydrogen Bonds → IMF between H and F,O, or N

    • Strongest IMF due to high E.N.D.

  • London Dispersion Forces (Van der Waals Forces) → IMF due to temporary dipoles that are formed

1.2 Elements of Life

• Atoms → Building blocks of matter

  • Made up of protons, electrons and neutrons

• Ions → Atoms with a charge (postive or negative)

• Carbon is the foundation element for molecules in living things

  • Due to bonding properties

    • 4 electrons in outer shell → can form 4 covalent bonds with other atoms/molecules

  • Can form long and branching chains of carbon atoms

  • Can form rings which bonds to other rings

• Organic → contains Carbon

• Inorganic → does not contain Carbon

1.3 Properties of Biological Macromolecules

Polar Molcules (hydrophilic)

• Several highly EN elements (ex: O, N)

• High END → asymmetry

• pH → logarithmic scale used to measure of acidity/basicity 

• Acidic, Neutral or Basic

  • Acidic: pH < 7, H⁺ donor, procduced H₃O⁺ ions in solution

  • Neutral: pH = 7

  • Basic: pH > 7 H⁺ acceptor, produced OH^- ions in solution

Nonpolar Molecules (hydrophobic)

• Many C + H

• Low END → symmetry

• Acidic or Neutral

Symmetrical

Nonpolar

Asymmetrical

Polar

1.4 Strucutre and Function of Biological Macromolecules

Water is esential for building and breaking macromolecules

• Dehydration Synthesis/ Condensation Reaction → water is removed from two monomers when they bond together

• Hydrolysis Reaction → water is added back to separate two monomers

Carbohydrates

• Store energy and provide structure to organisms

• Ring or chain structures

  • Monosaccharide (single ring)

  • Disaccharide (double ring)

  • Polysaccharide (larger molecule)

• Starch (plant energy storage), cellulose, glycogen (animal energy storage)

• 1:2:1 ratio (C:H:O)

• Monomers connected by glycosidic linkage

Lipids

• Made up of C,H,O (sometimes P)

• Many hydrocarbons → hydrophobic

• Fats, phoshpolipids, steroids, waxes, pigments

  • Steroids → mutliple rings connected

  • Fatty Acid → long hydrocarbon chains with a carboxyl group at the end

  • Fats (triglyceride) → 3 fatty acids attatched to a glycerol

    • Saturated (single bonds only) and unsaturated chains (at least one double bond)

    • Glycerol → alcohol that is the backbone of lipids

  • Phospholipid → two fatty cahins and a phosphate attached to a glycerol

    • Amphipathic → has a hydrophilic and hydrophobic side

  • Waxes → hydrocarbon chain with an alcohol (-OH) group and a fatty acid

Proteins

• Made up of C, H, O, N (sometimes S)

• Facilitate chemical reactions, provide structure, carry information between cells

• Shape determines function (how they interact with other molecules)

• Amine group, carboxyl group and R-group (variable group)

  • R-group (side chain) can be nonpolar, polar, or charged (basic or acidic)

• Central Carbon

• Peptides → short chains of amino acids (building blocks of proteins)

Nucleic Acids

• Made up of C, H, O, N, P

• store, transmit, and help express hereditary information

• Monomer: nucleotides

• Phosphate, sugar, base

  • Can have 1-3 phosphate groups

  • Nitrogenous Bases → single or double ring

    • Pyrimidines (single ring) → cytosine, thymine, uracil

    • Purine (double ring) → adenine, guanine

Functional Groups → atoms or groups of atoms with similar chemical properties

1.5 Nucleic Acids

• DNA and RNA

  • Sugar in DNA → deoxyribose (one of the Oxygens is absent)

    • Phosphodiester Bond → covalent bond between sugar and phosphate (runs along outside of leader and makes uo sugar-phosphate backbone)

  • Sugar in RNA → ribose (extra O present)

• ATP (adenosine triphosphate)

  • Adenine (nitrogenous base) + ribose (sugar) + 3 phosphates

1.6 Protein Synthesis

Primary Structure

• Chain of amino acids (specific sequence is determined by DNA)

  • Connected by peptide bonds → bond between Nitrogen in amine and Carbon in carboxyl group (condensation reaction)

• Amino acids join to form a polypeptide

• Only structure maintained after denaturing a protein

Secondary Strucuture

• 3-D folding 

  • Due to H-bonds (between Oxygen in amine group and Hydrogen in carboxyl group)

  • Alpha helix or beta-pleated sheet

Tertiary Structure

• 3-D folding

  • Due to disulfide bridges, H-bonds, hydrophobic interactions (C and H must be present) and ionic bonds

  • Interactions are between R-groups

Quanternary Structure

• Fooding between multiple polypeptide chains

  • Due to disulfide bridges, H-bonds, hydrophobic interactions (C and H must be present) and ionic bonds

• Many proteins, but not all have the fourth level of structure

Transcription & Translation

• Transcription → DNA is used to synthesize mRNA

  • Takes place in nucleus

    • DNA → double helix, can’t leave nucleus, thymine

    • RNA → single helix, leaves nucleus (responsible for communication with rest of the cell), uracil

      • mRNA (messenger RNA) → codes for proteins

      • tRNA (transfer RNA) → brings amino acids to ribosome

• Translation → mRNA is used to synthesize proteins in the ribosome

  • Takes place in cytoplasm 

    • Ribosome has two subunits that come together for protein synthesis

    • Codons → groups of 3 bases that code for amino acids

      • Multiple cdons code for the same amino acid to protoect aginst errors (becuase it allows for some errors in the DNA without changing the protein)

1.7 Enzymes Structure

• Proteins

  • 1⁰, 2⁰, 3⁰, 4⁰ structure

• Reusable

• End in -ase or -in

• Act on substrates (reactants) which bind to the enzyme’s active site

  • Through weak IMFs (Van der Waals forces)

Lock and Key Model

Induced Fit Model

1.8 Enzyme Catalysis

• Enzymes are biological catalysts

  • Catalysts → Speed up chemical reactions by lowering activation energy (E_a)

    • Activation Energy → amount of energy required for a reaction to occur

    • Chemcial Reaction → Process that changes a set of reactants into products

      • Atoms are rearranged due to an energy change

      • Reactants → what is put into a reaction

      • Products → what results from a reaction

• ΔG → Free Energy

  • Energy released during a chemical reaction

• Exergonic Reactions

  • Reactions that have a negative charge in free energy (release energy)

• Endergonic Reaction

  • Reactions where products have more free energy than reactants

  • Non-spontaneous

1.9 Enviornmental Impacts on Enzyme Function

Factors that Affect Enzymatic Reaction Rate

1. Temperature/pH

• When temperature/pH is too high, protein becomes denatured

  • Denaturation → when a proteins becomes unfolded (loses shape and therefore function

2. Enzyme Concentration (with excess substrate concentration)

3. Substrate concentration (with constant enzyme concentration)

4. Cofactors/Coenzymes → increase reaction rate

• Cofactors → inorganic substances that facilitate substrate binding to active sites

• Coenzymes → organic substances that facilitate substrate binding to active sites

5. Inhibitors → decrease reaction rate

• Competitive → molecules that directly lock active site

• Noncompetitive → molecules that bind to allosteric site resulting in a chage in the active site (stop active site conformation)

  • Allosteric Activation → when an allosteric inhibitor binds to a region on an enzyme adn all active sites on the protein subunits are changed

Enzymatic Pathways (relay race)

• Feedback inhibition

  • Don’t want pathways on all the time → want to conserve resources

1.10 Origins of Life on Earth

Three Hypotheses of Life’s Origins

1. Primordial Soup Hypothesis

• Early Earth’s conditions provided inorganic reactants (NH₃, H₂O, H₂, H₂S) and enough free energy in the absence of O₂ that lead to the spontaneousfromation of roganic compounds → organic compounds assembled to form the first living organisms

  • Miller and Urey Experiment → Miller and Urey recreated the conditions of early Earth and successfully sunthesize organic molecules via high voaltge electricity

2. RNA World Hypothesis

• RNA was the first organic molecules and genetic material

  • RNA is self-replicating and has enzyme-like reactions

  • RNA drives protein synthesis and can reverse transcribe into DNA

3. Celestial Orign Hypothesis

• Organic molecules could’ve been transported to Eath by meteorites or other space materials

• Limitation: Where would those organic molecules come from?

UNIT 2: Cell Structure and Function

2.1 Cell Structure: Subcellular Components

Nucleus → controls cell’s activities and serves as the blueprint for controlling cell function and building more cells (contains chromatin → uncondensed DNA)

Nuclear Envelope → membrane that separates the nucleus and the cytoplasm

Mitochondria → sites of aerobic respiration and the major energy production center in cells (produce ATP)

Chloroplast → photosynthesis, synthesizes amino acids and lipids

Rough ER → series of interconnecting flattened tubular channels that have ribosomes attached (role in protein synthesis and folding)

Smooth ER → series of interconnecting flattened tubular channels involved in lipid synthesis

Ribosome → synthesizes proteins (found free floating or in the RER)

Golgi Apparatus → protein modification, sorting and packaging (stack of membranous flattened sacs)

Lysosome → contain hydrolytic enzymes needed for digestion of macromolecules

Cell Membrane → controls exchange between the cell and environment

Cell Wall → gives plants structure and protection

Cytoplasm → aqueous material that contains the other organelles

Cytosol → aqueous component of cytoplasm

Vacuole → involved in storage

Vesicle → used to ship materials around the cell

Cytoskeleton → gives cell structure and maintains intracellular organization

Actin and intermediate filaments → cytoskeleton components

Centrioles → organizes spindle fibers in cell division

Peroxisome → responsible for protecting the cell as they ride the body of toxic substances and break down fat (lipids)

Nucleolus → synthesizes ribosomal RNA

Flagella → Similar to cilia but longer

Cilia → hair-like organelles involved in movement of mucus out of the lungs and the egg in the fallopian tube

Microtubules → found in cilia

2.2 Cell Structure and Function

Missing or dysfunctional organelles lead to disease

• Cystic Fibrosis → thick mucus in the lungs, frequent lung infections, clogged pancreas and digestive problems

  • Cell membrane is affected

• ALD → build up of fatty acids in the brain and spinal cord

  • Peroxisome is affected

• Pompe → build up of excess glycogen within muscle cells, extreme muscle weakness and floppy appearance

  • Lysosome is affected 

• Kartagener → breathing problems, serious anus, ear and/or lung infections, infertility

  • Cilia is affected

2.3 Compartmentalization and Origins of Cell Compartmentalization

Types of Cells

Eukaryotic Cells → Compartmentalized

• Well-defined sections

• Organelles with internal fluid have a phospholipid bilayer membrane

• More surface area

Membrane-Bound Organelles

• Nucleus, mitochondria, chloro[last, RER, SER, Golgi, lysosome, peroxisome, vacuole, vesicle

Non Membrane-Bound Organelles

• Ribosomes, cell wall, cytoplasm, cytoskeleton, cell membrane

The Endomembrane System

• Group of membrane-bound organelles that work together to synthesize, modify, package and transport lipids and proteins

Specialization

• Cells are specialized → java a specific function

• A cell’s shape, size mount and type of organelles determines its function

  • Cell with many mitochondria utilizes a lot of energy (muscle cells)

  • Cell with many Golgi Apparatuses has a secretory function

  • Cell with flagella move (sperm)

• More compartmentalization → more specialization of cell type

Autogenic Hypothesis → the cell began as a prokaryotic cell and evolve into a eukaryotic cell with membrane bound organelles

Evidence: 

• Prokaryotic cells do not have membrane-bound organelles while eukaryotic cells do

• Eukaryotic cells have the same organelles as prokaryotic cells, and in addition have membrane-bound organelles

Endosymbiotic Hypothesis → prokaryotes engulfed other phagocytic prokaryotes and the ingested organisms survived and continued to live within the predator

Evidence:

• membrane -bound organelles are similar to prokaryotes

• Mutualistic relationship would allow them to benefit each other

2.4 Cell Size

• Cells need enough surface area to maintain homeostasis

  • Surface area needed for the exchange of materials through the cell membrane

  • As cells grow the surface area to volume ratio changes (increases) so there is a limit to cell growth

    • Cell becomes too large → materials not exchanged fast enough and homeostasis is not maintained

  • When cell reaches critical surface area to volume ratio it stops growing

    • Cell is signaled to die to divide

2.5 Plasma Membrane

• Phospholipid Bilayer: double layer of phospholipids that speerates extracellular and intracellular space

  • Amphipathic → phospholipids are polar and nonpolar 

    • Polar head is hydrophilic (attracted to water)

    • Nonpolar tails are hydrophobic (repelled by water)

• Flexible (allows for permeability)

  • Cholesterol (more = less flexible)

• Receives external signals and initiates cellular responses

  • Receptor Proteins

  • Ligands

    • Messenger molecules that connect to a receptor to initiate a signal pathway (hormones, neurotransmitters)

  • Glycolipids and Glycoproteins

    • Carb chains tag for self-recognition (only on surface)

  • Intercellular Junctions → direct contact between cells

    • Plasmodesmata (passage through cell wall in plants)

    • Gap Junctions (animals)

• Adhere to neighboring cells

  • Glycolipids and glycoproteins (anchors adjacent cells)

  • Desmosomes (extensions of cytoskeleton that connect cells together in animals)

• Proteins

  • Integral Proteins → span entire lipid bilayer

    • Ex: transport proteins (channels, gates, carrier proteins)

  • Peripheral Proteins → one edge of lipid bilayer

    • Intracellular or extracellular

• Cytoskeleton → proteins scaffold

• Can spontaneously repair small tears in the lipid bilayer

• Eukaryotic cells have membrane-bound organelles that create specialized compartments within a single cell

• Membrane proteins can drift across the lipid bilayer

• Gap Junctions: allow for the rapid transit of ions and small molecules between adjacent animal cell membranes

• Binary Fission: bacterial cells divide when a thin ring of proteins located at the cells midpoints contracts, effectively cleaving the cell in two

2.6 Membrane Permeability

Selective Permeability:

• Small and Nonpolar: can diffuse through membrane

• Small and Polar: can sometimes diffuse through membrane

  • Repelled by nonpolar tails

• Large and Nonpolar: can sometimes diffuse through membrane

  • Hard to it between tails

• Large and Polar: require transport proteins

• Charged: require transport proteins

• Aquaporins: channels for water to pass through

2.7 Mechanisms Transport

Diffusion

• Passive

• No help

• Molecules move from higher to lower concentrations (with concentration gradient) until they are at equilibrium

Facilitated Diffusion

• Passive

• Membrane Proteins

• Movies monosaccharides, amino acids, and other monomers down the concentration gradient into cells with the use of proteins that change conformation

Osmosis (Facilitated diffusion through aquaporins)

• Passive

• Membrane Proteins

• Moves water molecules across cell membrane down the concentration gradient

Facilitate Diffusion through Channel Proteins

• Passive

• Membrane Proteins MOlecules move down the concentration gradient via protein channel

Na⁺-K⁺ Pump

• Active

• Membrane Proteins

• Electrogenic pump that moves 3 Na⁺ out and 2 K⁺ in

Proton Pump

• Active

• Membrane Proteins

• Electrogenic pump that moves H⁺ across a membrane creating an electrochemical gradient

Cotransport

• Active

• Membrane Proteins

• Moves a molecules in/out of cells by carrying its transport to the movement of another

Phagocytosis

• Active

• Vesicles

• Cells engulf large molecules or whole cells

Pinocytosis

• Active 

• Vesicles

• Cells engulf small solutes or fluids

Receptor Mediated Endocytosis

• Active

• Vesicles

• Specific molecules are taken into cells after building to receptors on the cell

Exocytosis

• Transport vesicles fuse to cell membranes and release contents

2.8 Tonicity and Osmoregulation

Osmosis → diffusion of water

Tonicity → ability of an extracellular solution to cause a cell to gain or lose water

• Depends on the concentration of solutes that cannot pass through the membrane

Osmoregulation → cells must be able to regulate their solute concentrations and maintain water balance

Water Potential → a physical property that predicts the direction water will flow

• Includes the effect of solute concentration and physical pressure

• Water flow:

  • Water Potential: high to low

  • Solute Concentration: low to high

    • Increase in solute causes binding to more free water → reduces solute potential

  • Pressure: high to low

Hypotonic

• Animal Cell: swell and lyse

• Plant Cell: turgid

  • Ideal because it helps plants to stay standing

• Osmotic Pressure (turgor): increase

• Net movement of water: inside

• Water Potential inside the cell is less than the outside

Isotonic

• Animal Cell: stays the same

• Plant Cell: plasmolyzed

  • Plasmolysis → vacuole shrinks and the plasma membrane pulls away from the cell wall

• Osmotic Pressure (turgor): stays the same

• Net movement of water: neither

• Water Potential inside the cell is equal to the outside

Hypertonic

• Animal Cell: shrinks and shrivels

• Plant Cell: flaccid

• Osmotic Pressure (turgor): decrease

• Net movement of water: decrease

• Water Potential inside the cell is greater than the outside

Ψ → water potential

Ψ_S → solute potential (pure, distilled water = 0 mPA)

Ψ_P → pressure potential (physical pressure on a solution, “open air” = 0)

i → ionization constant (how many ions are made in solution)

C → molar concentration

R → pressure constant (0.0831 bars or 0.0083 mPA)

T → temperature (K)

Unit 3: Cellular Energetics

3.1 Cellular Energy

Bioenergetics → concept of energy flow through living systems

ATP → energy currency of cells

Metabolic Pathways

Anabolic → requires energy and build molecules

• Endergonic

  • Nonspontaneous

• Positive Gibbs Free Energy

• Ex: cellular respiration

Catabolic → releases energy and builds molecules

• Exergonic

  • Spontaneous

• Negative Gibbs Free Energy

• Ex: photosynthesis

Free Energy

Gibbs Free Energy → energy that takes place with a chemical reaction

• During energy transfer, some becomes as unusable form (heat)

Enthalpy → total energy in a system

Activation Energy → initial amount of energy required for the reaction to occur

Transition State → molecule is contorted prior to breaking chemical bonds

*Most chemical reactions are reversible

The Laws of Thermodynamics

First Law → the total amount of energy in the universe is constant

Heat Energy → energy that transfers without doing work

Second Law → High entropy results in high disorder and low enthalpy (energy)

Entropy → amount of disorder in a system

3.2 Cellular Respiration

3.3 Photosynthesis

3.4 Fitness

Metabolism → all chemical reactions that transpire inside cells

Evolutionary Fitness

• The ability to survive AND reproduce in a given environment

• Variation in traits (ADAPTATIONS) allow for some organisms to be more fit than others

  • Number and types of molecules within cells (ex: pigments)

• Chemical Pathway

  • C3, C4, CAM photosynthesis (differ in where and how carbon fixation occurs)

Plant Adaptations: Leaf Structure

• Spongy Mesophyll → airspaces help with gas exchange

• Palisade Mesophyll → cells have high chloroplast density (where majority of photosynthetic activity occurs)

• Stomata → pore through which gases can enter and exit

  • Open Stomata → hot/dry conditions (prevents water loss and leads to buildup of O₂ gas)

  • Closed Stomata → optimal conditions

• Cuticle → waxy covering (hydrophobic)

• Epidermis

• Lower Epidermis

• Vein → transports substances

  • Xylem → H₂O from roots

  • Phloem → sugars from leaves to roots

Photorespiration

• Occurs when O₂ concentration is high in the spongy mesophyll (Rubisco fixes O₂ instead of CO₂ during the Calvin Cycle)

• Produces CO₂, wasting RuBP, NADPH, and ATP

Transpiration

• Occurs when water exits the stomata at a faster rate than it is entering the lead

• Net water loss, flaccid plant cells (low structural support), possibility of drying out

Unit 4: Cell Communication and Cell Cycle

4.1 Cell Communication

Signaling Pathway → pathway used to send chemical message from cell to cell

Ligand → signaling molecule that fits into the active site of the receptor

Types of Signaling

1. Autocrine (auto=self)

Ex: cancer cells release their own growth hormone (signal themselves to reproduce)

2. Juxtacrine (juxta=bsides, next to, touching)

Ex: Plasmodesmata → channels between plant cells (allow ligand to move directly from one cell to another)

3. Paracrine (para=nearby)

Ex: Quorum Sensing → used by bacteria to determine the population density of their species in a local area (each bacterium produces a ligand and the ligand reaches a critical concentration to indicate a sufficient population)

Ex: Neurotransmitters → ligands released for communication between nerve cells

4. Endocrine (endo=within)

Ex: Pancreas cells release insulin when blood sugar levels are elevated, signaling to liver cells to being absorbing the glucose

Ex: hormones (pheromones released by egg provide pathway for sperm to travel)

Release of a Ligand due to Stimuli

• Over/Underproduction of molecules

• Environmental Factors (light, temperature, sensory triggers)

• Age of cells

• Stress

• Signals from other cells (feedback)

4.2 Signal Transduction

Signal Transduction Pathway: signaling Cell releases ligand → message received → response produced by target cell

1. Signaling → ligand released

2. Reception → ligand binds to receptor protein

3. Transduction → signal is transmitted throughout the cell (amplification)

4. Response → response is produced

*Once response is achieved in a cell, relay protein must be deactivated to stop response

Ligand-Receptor Specificity needed → ligands and receptors have a specific shape so they can only activate certain ligands/receptors (shape determines function)

Phosphorylation Cascade → phosphate groups added to proteins by kinases to activate them (changed shape so protein can function properly), allowing them to activate other relay proteins

*Set off by ligand binding to receptor protein

Amplification is advantageous because increases the chances of transmitting the signal successful (one signal reception lad to a response occurs in several locations in the cell)

Once response is reached, Protein Phosphatases (PP) remove the phosphate groups to deactivate the proteins (otherwise response will happen forever)

Secondary Messengers (ligand → primary messenger)

• Amplify a signal with phosphorylation

Types of Receptors:

• Intracellular Internal (for hydrophobic ligands)

• Cell Surface

• Ion Liked Channels (normally closed, but when ligand binds channel opens to let ions in)

• G-Protein Linked (when receptor binds to ligand, a G-protein activates and interacts with another integral protein (channel or enzyme))

Types of Ligands

• Small Hydrophobic (ex: steroids)

  • Small and hydrophobic so do not need to bind to a surface receptor

• Medium Hydrophilic (ex: protein signal molecules (epinephrine))

  • Can’t go through membrane → must bind to surface receptor

• Small Hydrophilic (ex: nitric oxide (laughing gas) → anesthetic)

Types of Response

• Gene Expression (initiate transcription)

• Increase Metabolism

• Growth (cell division → mitosis)

• Cell Death (apoptosis)

4.3 Changes in Signal Transduction Pathways

• Mutation in DNA coding for ligand or receptor protein structure

• Toxins

  • Ex: anthrax releases a toxin that changes the shape of adenylyl cyclase so it can no longer convert ATP to cAMP

• Diseases

  • Ex: type 1 Diabetes causes the lack of insulin production (autoimmune)

  • Type 2 Diabetes causes the lack of target cells “listening” to ligand binding

4.4 Feedback

Feedback Mechanism → regulatory process that adjusts a system to meet a desired result when stimulated

• Positive Feedback

  • Stimulus is INCREASED → used for amplification

  • Ex: Baby pushes against cervix → hypothalamus releases oxytocin → uterine wall contacts → baby pushes against cervix 

• Negative Feedback

  • Stimulus is DECREASED → used to limit something

  • Ex: Hypothalamus sense temp too low → signal to heat the body sent → blood vessels constrict (limit heat loss), muscles shiver (generate heat) -> body temp increases

4.5 Cell Cycle

Phases:

G0: not dividing/preparing to divide

G1: cell grows by producing more proteins and organelles

S: DNA replication, shootings in sister chromatids

G2: cell prepares for cell division with the appearance of centrosomes, replenishes energy stores, synthesis proteins necessary for chromosome manipulation and mitotic phase

M: mitosis and cytokinesis

Prophase: 

• Nuclear envelope breaks down 

• Membrane organelles fragment and disperse 

• Centrosomes begin to move to opposite poles of cell

• Microtubules that form mitotic spindle extend between centrosomes

• Sister chromatids begin to coil more tightly

Prometaphase:

• Protein structure called the kinetochore forms at each centromeric region

• Proteins bind to the mitotic spindle microtubules

Metaphase:

• All chromosomes line up in the metaphase plate

Anaphase:

• Cohesion proteins that held sister chromatids together degrade

• Each chromatid is pulled toward centrosome

Metaphase:

• Chromosomes reach opposite poles and begin to condense

• Mitotic spindles depolymerize into tubulin monomers (used to build cytoskeletal components of daughter cells

Cytokinesis

• Cells physically separated into daughter cells

• Animal Cells: contractile ring forms

• Plant Cells: vesicles fuse to form phragmoplast vesicular structure that will become the new cell wall

4.6 Regulation of Cell Cycle

• Cell cycle tightly regulated → keeps the multicellular organism healthy

  • Conserving materials

  • Ensures that new cells receive accurate genetic information

  • Prevents uncontrolled growth

Checkpoints: 

G1: ample supply of energy and raw materials available; adequate environment for cells (density dependent inhibition → rate of division regulated by how crowded it is); regulates weather the cell is in G0 or not

Cell not grown sufficiently → daughter cells would be small and not have enough organelles to store nutrients/complete metabolism

G2: ample supply of energy and raw materials available; DNA has been completely replicated and checked for errors

M: all chromosomes are attached to spindles

Chromosomes not prepared for division → uneven amount of chromosomes in each cell

Growth Factors → released by specialized cells and trigger cell division

Kinases → provide the energy (through phosphorylation) for processes needed for mitosis

Cyclin Dependent Kinase (CDK)

Molecule Concentration Throughout Cell Cycle

Ligand → lowest at start of mitosis, highest at end of interphase

Kinase → constant

Complex (kinase+ligand+phosphate) → based on ligand concentration

Positive Regulators → molecules that promote progress of the cell cycle

Ex: Cdk/cyclin complex → works by phosphorylating other proteins, allowing cells to pass through the next phase

Negative Regulators → molecules that halt progress of the cell

Ex: RB, p53, p21

Cancer

• Cancer covers many different diseases involving UNCONTROLLED CELL GROWTH

• Begins with a gene mutation → results in a faulty protein that regulates cell division (snowball effect)

• Tumors results when division of mutated cells surpasses growth of normal cell

  • Benign tumor → cell are NOT cancerous (won’t spread)

  • Malignant Tumor → cells are cancerous (spread to other tissues and organs)

    • Metastasize

    • Rapid Angiogenesis (growth of new blood vessels)

Environmental Cues to permit Cell Growth

• Cells will cease cell division due to external signals from the environment/other cells

  • Density Dependent Inhibition → if cells are crowded, cell division stops

  • Anchorage Dependent → cells must be attached to something else (like another cell) to divide

Proto-oncogenes

• Normal genes (non-mutated version) that code for POSITIVE cell cycle regulators

  • When these genes MUTATE in certain ways, they become oncogenes (dominant)

  • Ex: genes for

    • Cyclins → cell cycle receptors

    • EGFR →receptor for epidermal growth factor

    • KDR → receptor for vascular endothelial growth factor (angiogenesis)

Tumor Suppressor Genes (recessive)

• Genes that code for NEGATIVE regulator proteins

  • Activated → PREVENT uncontrolled division

  • Ex: genes for

    • (t)p53 → protein checks for and repairs DNA damage (active during G1 & G2 checkpoints)

    • RB protein → retinoblastoma, checks for proper DNA replication (G2 checkpoint)

Unit 5: Gene Expression and Regulation

5.1 DNA and RNA Structure

Genetic Information

• Able to store information

• Can be consistently replicated through generations

• Able to allow for changes and thus evolution to occur

• Purine → 2 rings (adenine, guanine) binds to pyrimidine → 1 ring (thymine, cytosine)

  • Bind through H-bonds

  • Uniform diameter

• Found in nucleoid region of prokaryotes, nucleus of eukaryotes

  • In eukaryotes, DNA is wrapped around histones (proteins) to form structures called nucleosomes

• Antiparallel (3’ end and 5’ end)

  • 3’ end has an OH (hydroxyl group)

  • 5’ end had a phosphate

James Watson & Francis Crick

• Bases are complementary (revealed how genes are replicated, stored and mutated)

• Double helix with strands running in opposite directions (antiparallel)

Oswald Avery

• Transforming Factor (allows bacteria to transfer genetic material)

Maurice Wilkins & Rosalind Franklin

• Photo 51 showed DNA is symmetrical and bases are on the inside

Erwin Chargaff

• Amount of A bases and T bases are always the same, amount of G bases and C bases are always the same

  • Base pairing rule (A-T; G-C)

Frederick Griffith

• Bacteria are able to transfer genetic material to one another → transformation

• Experiment used virulent S cells, heat-killed (nonvirulent) S cells, and nonvirulent R cells

• Mixed dead S cells and living R cells and the R cells became virulent

  • Suggests that heat-killed S cells provided a transforming factor to the R cells that in turn made them virulent

Alfred Hershey and Martha Chase (Alfred-Chase Experiments)

• Used phages (a type of virus made of proteins and DNA that infect and reproduce in bacterial hosts) to determine if genetic material was made of proteins or DNA

• Tagged sulfur (proteins) and phosphorus (DNA) → bacterial host cells were infected with radioactively tagged phages → samples were blended and centrifuged → wavy bacterial contents in a pellet were separated from phage contents in liquid

  • Pellet showed phosphorus → genetic material contains phosphorus → DNA is genetic material

DNA vs RNA

5.2 Replication

• DNA must always be protected inside the nucleus except during cell division (mitosis)

  • Gets destroyed by enzymes (nucleases) in cytoplasm

• Enzymes and free nucleotides are available for replication in the nucleus

• DNA is synthesized from 5’→3’ (DNA Polymerase adds nucleotides to the 3’ end)

Part 1: Initiation

• Helicase attaches to DNA and breaks the H-bonds to unwind and separate the complementary strands, creating a replication fork

  • Attaches at multiple sites fo the strands to speed up the process, creating the appearance of bubbles along the strand (replication bubbles)

• Topoisomerase prevents over-twisting of DNA as it is unwound

• Single Stranded Binding Proteins (SSBP) stabilize the single strands of DNA so enzymes can access the bases

Part 2: Elongation

• DNA Primase places an rNA primer which acts as a bookmark/placeholder for DNA Polymerase

• DNA Polymerase III reads the DNA template strand from 3’→5’ an attaches complementary free nucleotides in a 5’→3’ direction

  • Attaches at multiple sites fo the strands to speed up the process, creating the appearance of bubbles along the strand (replication bubbles)

• DNA Polymerase I removes RNA primers and fills in with more free nucleotides and proofreads for mistakes

  • Attaches at multiple sites fo the strands to speed up the process, creating the appearance of bubbles along the strand (replication bubbles)

• Leading and Lagging Strands

  • DNA Polymerase can only attach new nucleotides to the 3’ end of the new DNA strand

  • Must backtrack to copy parts of the newly exposed end of the new DNA strand (process takes longer) → lagging strand

  • Strands hat does not need to back track (process is quicker) → leading stand

• Okazaki Fragments → fragments that are created on the lagging strand

• Ligase fuses the sugar-phosphate backbone of the Okazaki fragments together

Part 3: Termination

• When complete, the result should be 2 perfect copies of the original

• Mistakes (mutations) occur

• Semiconservative → each new molecules had one original strand and one new strand

  • Efficient and lowers risk of errors

5.3 Transcription and RNA Processing

• Process by which cell makes an mRNA copy of the DNA

• RNA Polymerase binds to template strand of DNA (antisense/non-coding strand)

  • Read from 3’→5’

• RNA Polymerase adds nucleotides across from the template strand in the 5’→3’ direction

  • Uses base pairing rules

  • Nontemplate DNA → replace T with U

Prokaryotes

• Occurs in cytoplasm (don’t have a nucleus)

• No exonucleases → mRNA considered mature and ready for translation at end of transcription

Eukaryotes

• Occurs in nucleus

• Produces pre-mRNA at end of transcription (because it contains introns) → mRNA not mature

• RNA Polymerase joins with transcription factor proteins (helpers) at the promoter/TATA box (special sequence of base pairs that singlas beginning of gene)

• Transcription factor proteins and RNA Polymerase → Transcription Initiation Complex

  • Moves along DNA template strand  producing pre-mRNA

• RNA Polymerase reaches terminator sequence of base pairs → complete production of pre-mRNA and releases it into the nucleoplasm

• Must go through post-transcriptional processing before mRNA can leave nucleus (for translation)

  • Introns (non-coding regions) are removed

  • Methyl Cap is added to 5’ end (helps mRNA molecule move through the nuclear pore and attach to ribosome)

  • Poly-A tail is added to 3’ end (helps protect from degradation by exonucleases in the cytoplasm)

• mRNA leaves nucleus through nuclear pores

5.4 Translation

• mRNA read in sets of three nucleotides (codons) by ribosomes

  • Found in either cytoplasm or rough endoplasmic reticulum

• Proteins produced through dehydration synthesis reactions between amino acids

• tRNA carries amino acids to the ribosome

  • tRNA has an amino acid on one end and an anticodon on the other (anticodon pairs with codon on mRNA so ribosome can makes sure that correct amino acid is being incorporated into the protein)

• Translation proceeds until a STOP codon is reached

• Chain of amino acids is released from ribosome and H₂O is bonded to the end

Exception to Central Dogma: Viruses

• Much smaller than bacteria

• No membrane-bound organelles (anaerobic respiration)

• Requires a host to reproduce

  • Raises debate of if they are living or not

• Structure: protein (capsid, enzyme) and nucleic acid (DNA, RNA)

• Classifications based on shape/composition

  • Bacteriophage

  • Retroviruses

Retroviruses

• Class of RNA viruses that use reverse transcription (synthesis of DNA based on RNA template)

• HIV → retrovirus  that causes AIDS by using helper T cells (white blood cell that helps with immune response) as a host

• Reverse Transcriptase allows viruses to convert their RNA genome (7,000-12,000 base pairs long) into DNA so that it can be inserted into hos’s genome in order to replicate genetic material and reproduce

• Converts viral RNA to single stranded cDNA (complementary DNA)

• Creates transposons (“jumping genes”) that allow for variation in the genome

Steps of Reverse Transcription

• Virus infects a host cell by releasing viral RNA into cytoplasm

• Viral RNA is transcribed into single stranded cDNA (SSDNA) by reverse transcriptase (reads 3’ → 5’; synthesizes 5’ → 3’)

• cDNA migrates to the nucleus where it is inserted into the host’s genome by integrase

• Transcription and translation are carried out by the host’s enzymes as normal, synthesizing viral proteins (process is repeatable)

Eukaryotic

• DNA is constantly shortening

• Telomeres are non-coding protective DNA sequences at the end of chromosomes

• Telomerase uses mRNA to add cDNA to elongate telomeres to prevent aging

5.5 Mutations

• Occur due to errors in DNA replication, exposure to mutagens (ex: UV rays, x-rays), or viral infection (ex: HPV)

Point Mutations

• Base Substitution

• Base Insertion (frameshift)

  • Upstream → more impactful

• Base Deletion (frameshift)

  • Upstream → more impactful

Chromosomal Mutations

*All chromosomal mutations occur during cell division

• Deletion → part of a chromosome is missing/removed

• Duplication → part of the chromosome is copied

• Inversion → Parts of chromosome are swapped

• Translocation → part of chromosome is move to another chromosome

Impact on Protein

• Missense Mutation → codes for the wrong amino acid

• Silent Mutation → no change in amino acid (uses different codon for that amino acid)

• Nonsense Mutation → premature STOP resulting in incomplete protein

Effects

• Positive → change in a protein leading to a beneficial trait (passed down to offspring)

  • Drives genetic variation

• Neutral → silent mutations (no change)

• Negative → could lead to major changes in protein structure (shortening, misfolding)

  • Missense and nonsense mutations 

5.6 Regulation of Gene Expression

• Control of gene expression

• Each somatic (body) cell contains the identical genome

• Differential gene expression → cell specialization

• All genes do not need to be expressed simultaneously in each cell

  • Saves energy, space and time

Prokaryotes

• Regulation occurs at the transcriptional level only (inducible and repressible)

• Genes turned on and off based on environmental factors

• Operon → group of genes along with sections of DNA that regulate them

  • Contain promoter operator, repressor and terminator

• Positive Control → when actuator protein binds, transcription begins

• Negative Control → when repressor protein binds, transcription is inhibited

Inducible Operon

• Switched from OFF to ON

  • OFF: Repressor binds to operator → RNA Polymerase inhibited -> no gene expression → no proteins

  • ON: Inducer will bind to repressor → changes repressor shape → repressor no longer binds to operator → gene expression → proteins made

Repressible Operon

• Switched from ON to OFF

  • ON: corepressor molecule not present → repressor protein can’t bind to operator → protein synthesis

  • OFF: corepressor molecule present → binds to repressor → allows repressor to bind to operator → no protein synthesis

Eukaryotes

• Regulated at different stages of the central dogma and DNA packaging

Genomic Regulation (“within” genes)

Positive Regulators

• Promoter sequences occur upstream of the gene (transcription factor binds here)

  • Helps RNA Polymerase bind (initiates transcription)

• Enhancer Sequences can occur upstream or downstream of a gene

  • Activator proteins bind to them and interact with transcription factor to promote RNA Polymerase binding

  • Increases amount of mRNA being made

Negative Regulators

• Silencer Sequences can occur upstream or downstream of a gene (repressor proteins bind to the, blocking RNA Polymerase)

  • Repressor proteins that bind to the promoter sequence prevent transcription

RNA Processing: Alternative Splicing of mRNA

• Alternative splicing of pre-mRNA done by spliceosome (RNA and exonuclease)

• Different combinations of introns and exons leads to variation in the ame protein (different gene expression eben in the same types of cells)

Translation Activation/Repression

• Translation can be activated or repressed by initiation factors (proteins0)

• MicroRNA (MiRNA) and small interfering RNAs (RNAi) can bind/degrade to mRNA, stopping translation

Epigenomic Regulation (“on top of” genes)

Epigenome

• “Above” the genome

• Chemical markers on the genome that affect how it is expressed

Chromatin Structure and Modifications

• If DNA is tightly wound, it is less accessible for transcription

• Chromatin Modifications

  • Histone Acetylation ads acetyl groups to histones, which loosens DNA (gene activating)

  • DNA Methylation adds methyl groups to DNA which causes the chromatin to condense (gene silencing)

Epigenetic Inheritance

• Chromatin modifications do not alter the nucleotide sequence of the DNA but they can be heritable to future generations

  • modification s can be reversed unlike mutations

  • Explains why a identical twin may inherit a disease while the other does not

5.7 Biotechnology

• Process of manipulating organisms or their components for the purpose of making useful products

• Genetic Engineering techniques can be used to analyze and manipulate DNA and RNA

Gel Electrophoresis (DNA Fingerprinting)

• Separates molecules according to size and charge (used for comparison)

• DNA is process with restriction enzymes (molecular scissors) and cut into fragments of differing sizes

  • Smaller fragments travel faster through gel and larger fragments travel slower

  • DNA has a negative charge (migrates towards positive end)

Application

• DNA Paternity Testing

• Analysis of DNA profiles

• DNA Profile/DNA “Fingerprint”

Polymerase Chain Reaction (PCR)

• DNA fragments are amplified (manipulates DNA replication)

• Automated process of denaturation, annealing, and extension in a series of repeated thermal cycles

• Requires template DNA, Taq Polymerase (heat-stable DNA Polymerase), DNA primers and free nucleotides

Application

• Consumer Genomics

• Food and Agriculture

• Medicine

• Forensic Science

• Environmental Microbiology

• Genetic Research

• Phylogenetics

Bacterial Transformation (Recombinant DNA)

• Introducing DNA into bacterial cells

• Bacteria can naturally conduct horizontal gene transfer (HGT)

  • Introduction of new genes from one organism to another

• A driver of bacterial evolution and development of antibiotic resistance

• Bacteria can naturally uptake foreign DNA from a dead bacterium via plasmid

Use as a Biotechnology (Insulin Production for Type 1 Diabetes)

Step 1: Cutting

• Geen of interest is cut out by restriction enzymes

  • Restriction enzymes act like scissors cutting genes at restriction site (specific sequence)

• Same restriction enzyme cuts the same sequence in plasmid

Step 2: Splicing

• Gene of interest is inserted into bacterial plasmid

• DNA Ligase forms bonds between gene of interest and plasmid, making recombinant DNA

Step 3: Integration and Reproduction

• Recombinant DNA is put into bacteria (transgenic)

• Bacteria rapidly reproduce with the new ability to express gene of interest

Application

• Genetic modification of bacteria

  • Human insulin production

  • Human growth hormone production

DNA Sequencing

• Determine the order of nucleotides in a DNA molecule

Application

• Medical Diagnosis → genetic diseases, drug targets

• Evolutionary Biology → relationship between different organisms and how they evolve

• Forensics → DNA Profiling

• Virology → identify and study viruses

CRISPR/Cas9

• Gene editing system

• CRISPR → “clustered regularly interspaced short palindromic repeats”

  • Short Prokaryotic DNA used to detect and destroy viral DNA

• Cas9 → endonuclease enzyme that cuts at specific DNA sequences determined by CRISPR

• Guide RNA (a short RNA sequence) to target a specific location on a DNA strand

• Cas 9 then cuts the DNA which allows gene editing by inserting, deleting or modifying the DNA

Unit 6: Heredity

6.1 Meiosis

Meiosis: process by which haploid gametes are produced

• Haploid → one set of chromosomes (n)

• Gametes → sex cells (sperm and egg)

Sperm and egg will eventually combine to make a diploid zygote

• Diploid → two sets of chromosomes (2n)

• Zygote → diploid cell resulting from fusion of sperm and egg

Ploidity: number of sets of chromosomes in an organism

Haploid (n) or Diploid (2n)

Diploid zygote goes through cell division and differentiation

Chromosomes: 

• Human females have two X chromosomes in each cell

• Human males have one X and one Y chromosome in each cell

Chromosomes are sorted in karyotypes in homologous pairs

• Karyotype → picture of all chromosomes in a cell

• Autosomes → chromosomes that are ot X or Y (humans have 22 pairs)

• Homologous Pairs

  • Same size

  • Same centromere position

  • Contains the same genes at the same loci position on chromosome

  • Each chromosome can have different alleles

    • Alleles → alternative forms of the same gene

  • Come together to form a tetrad

How Sex Cells are Created: Meiosis

• Cell division is 3D (duplicate, divide, divide)

• 1 diploid parent cell → 4 haploid daughter cells (all genetically different)

How is sex determined in humans?

SRY (Sex-Determining Region of the Y Chromosome) ← gene

• Males: Early in development, the SRY gene on the Y chromosome activates and the gonads develop as testes

• Females: With no SRY gene, the gonads develop as ovaries

Meiosis I

• Cell growth takes place before meiosis 1 can begin

• Homologous chromosomes separated

• At the end of telophase I, cells have two copies of half the genetic information of the cell

Meiosis II

• Sister chromatids separated

• At the end of telophase II, cells have one copy of half the genetic information of the cell

Gametogenesis and Fertilization

6.2 Meiosis and Genetic Diversity

• Meiosis creates genetic variation

  • Independent assortment → homologous chromosomes are randomly distributed to the four daughter cells

    • Possible combinations = 2ⁿ

  • Crossing-over increases variability, also known as recombination (mix and match)

Errors in Chromosome Distribution: Nondisjunction

• Chromatids (or homologs) do NOT separate during the process resulting in daughter cells with either too many or too few

6.3 Mendelian Genetics

Mendel worked with pea plants to show genetics

• P Cross (parental cross) → homozygous dominant bred with homozygous recessive

  • Results in F1 generation

• F1 Cross → 2 hybrids

  • Results in F2 generation

Mendel’s Laws

• Law of Segregation → random separation of two alleles (random chance)

• Independent Assortment → traits on different chromosomes don’t affect each other (may travel together if on same chromosome)

Genotypic Ratio: ratio of the genotypes of offspring

• For F1 cross

  • 1:2:1 (AA, Aa, aa)

Phenotypic Ratio: ratio of phenotypes of offspring

• For F1 cross

  • 3:1 (tall:short)

6.4 Non-Mendelian Genetics

Many traits do not follow ratios predicted by Mendel's laws

• Varying degrees of dominance (blend of traits)

• Many traits are produced through multiple genes acting together

• Some traits are produced by big genes on sex chromosomes

• Some traits are the results of non-nuclear inheritance (ex: chloroplast and mitochondrial DNA)

Linked Genes

• Genes located near each other on the same chromosome that tend to be inherited together

• Violates Law of Independent Assortment

• Genes for two or more traits are linked when they are expressed both by parents and offspring

• Genes are very close on chromosomes and are often not separated when crossing over 

• Crossing Over/ Recombination Frequency

  • Frequency of which crossing over occurs between two genes on homologous chromosomes during meiosis

  • The closer two genes are on the same chromosome, the lower the probability that a crossing over event will occur and the lower the recombination frequency (close to 0 %)

  • The further apart two genes are on the same chromosome, the higher the probability that a crossing over event will occur and the higher the recombination frequency

Mapping Distance

• Linkage map: genetic map that is based on crossover frequencies

  • The distance between the genes are MAP UNITS

    • One amp unit is equivalent to 1% recombination frequency

      • Express the relative distances among chromosomes

      • 50% recombination frequency means that the genes re far apart on the same chromosomes or on two different chromosomes (unlinked genes)

Incomplete Dominance

• Compromise (both traits blend to make final object)

Codominance

• Both genes expressed equally and separately

Heterozygote Advantage

• Heterozygote has an advantage over homozygous dominant and recessive

  • Ex: sickle cell anemia and malaria (AS is resistant to malaria and no sickle cell)

Multiple Alleles

• Multiple alleles code for one trait, resulting in many possible phenotypes

  • Ex: eye color

Sex-Linked Genes

• Genes on sex chromosomes

• On Y chromosome

  • Only males can get it

• On X chromosome

  • Recessive → less chance for females to get because they need 2 copies while males only need one copy

    • Ex: Red-green colorblindness

  • Dominant → if dad has disease, daughter will always have it

Polygenic Traits

• Bell curve

  • Ex: flower color

    • AABB (4 dom) → dark red

    • AaBB, AABb (3 dom, 1 rec) → red

    • AaBb, AAbb, aaBB (2 dom, 2 rec) → pink

    • Aabb, aaBb (1 dom, 3 rec) → light pink

    • Aabb (4 rec) → white

Pleiotropic Traits

• Single gene can influence multiple seemingly unrelated traits

  • Ex: Marfan’s syndrome

Episatsis

• One gene overrides another/modifies another gene

  • Ex: yellow lab could have genetic potential to be black but this is overrode by another gene)

  • Ex: summer squash has two genes that code for shape but spherical shape gene overrides the long/round shape gene

6.5 Environmental Effects on Phenotype

• Phenotypic plasticity occurs in individuals

  • Ability to change phenotype to adapt

  • Ex: Arctic foxes’ fur color

    • White in winter to camouflage with snow

    • Brown in summer to camouflage with woods and dirt

  • Ex: aquatic invertebrates helmets and tail spines

    • Grow longer when predators are nearby

    • No predators will result in adults with less armor

  • Boosts evolutionary fitness

• Evolution occurs in populations over multiple generations

Unit 7: Natural Selection

7.1 Microevolution & Population Genetics

Variation → individuals in a population or group differ in some trait of interest

Inheritance → the variation in the trait of interest is at least partially inherited (passed down from parents to offspring). The variation stems from random mutations and the recombination that companies sexual reproduction. The genetic variation may have arisen many generations in the past

Differential survival and Reproduction → more offspring are born than can survive, resulting in competition among individuals within a population. Some individuals with a particular trait are more likely to survive and/or have relatively more offspring compared to individuals that do not have that trait. Selection depends on the specific context of a species. Traits that are beneficial in one environment may cause problems in another environment

Adaptation → the frequency of the trait that helps individuals survive or leave more offspring will increase in the population over time, as will the alleles that affect the trait. This process can take many generations and extend over a very long period of time.

Evolution in the change in the allele frequency of gene pool in a population over time

Microevolution

• Small changes in allele frequency in a SINGLE POPULATION over time

• 5 mechanics of evolution

Macroevolution

• Larger changes in multiple populations an explores COMMON ANCESTRY of different species

Ingredients for Evolution

1. Variation in heritable traits 

2. Overproduction

3. Competition for limited resources

*Organisms with the greatest fitness will survive and reproduce → shift in allele frequency

Mechanisms of Evolution (the HOW)

Genetic Drift

• Random chance event that equally affects all member of the population

• Lowers genetic diversity and makes survivability more difficult

• Founder Effect → a small group of an existing population leaves to colonize a new area

  • Consequences → if the alleles for rare, recessive traits are presented in high frequency in the new population, there can be a higher incidence of rare, recessive disease

• Bottleneck Effect → sharp reduction in the population due to natural disaster

  • Ex: lancaster Amish Community and microcephaly

    • All families in an area are descended from one couple approximately 10 years ago that carried the genetic predisposition for microcephaly

Sexual Selection (Non-Random Mating)

• Allele frequency shifts due to selection of mates based on physical characteristics/behaviors

Mutations

• Random changes in allele frequency caused by changes in DNA sequence

Gene Flow (migration)

Natural Selection

• Alleles that boost evolutionary fitness are selected for by an environmental factor

• These processes change allele frequency non-selectively (random) or selectively for an allele

Population Genetics

• Darin and Wallace developed natural selection

• Endel helped improve understanding of genetic inheritance

• Modern synthesis blends genetic and evolution

• Connects to microevolution (population changing over time)

• Macroevolution (new species and taxonomic groups)

Population Genetics

• Polymorphisms are differences in phenotypes displayed, this distribution is known as population variation

• Natural Selection, genetic drift, gene flow, mutation, nonrandom mating all leads to evolution of populations

• Studied microevolution

• Measures changes in how selective forces change population through changes in allele and genotype frequencies

Mutation → introduces new alleles/traits through random errors/changes in a DNA sequence

Non Random Mating occurs when embers of a population select their mating partner based on the presence of specific desirable traits

Genetic Drift → is the movement of alleles in or out of a population through migration

Gene flow describes how the fittest members of a population pass on their inheritable advantageous traits to their offspring

Natural Selection occurs when a random chance event (like a natural disaster)affects the allele frequency of small populations)

7.2 Natural Selection

Natural Selection → the improved fitness of certain individuals in the population that allows for survival and reproduction (primary mechanism by which populations change over time)

*The world “selects” (although not as a conscious decision) when environmental conditions allow organisms with a particular genetic trait to live healthier lives than other organisms. Populations of most living organisms exhibit genetic diversity among individuals. Certain traits in a  population give some organisms a greater cache of survival than individuals that lack these traits. Because these traits tend to increase the chance of survival, these individuals within the population possessing the favorable trait increases while the number of offspring with the favorable trait decreases.

Adaptive Evolution

• Natural selection is adaptive evolution, selects stabilizing phenotypes

• Frequency-dependent selection selects for common or rare traits

• Secual selection mans one sex has more variability in reproductive success

• Stabilizing selection, directional selection and disruptive selection

Patterns of Evolution

1. Divergent evolution → same ancestor, becoming more different

2. Convergent Evolution → different ancestor, becoming more similar

3. Parallel Evolution → same ancestor

4. Coevolution → different ancestor

7.3 Artificial Selection

Artificial Selection → the effect of humans purposefully breeding animals to select fo desirable traits

Ex: breeding domestic animals (choose more tame traits)

7.4 Hardy-Weinberg Equilibrium

A population is in EQUILIBRIUM (and therefore not evolving) when all of the following are assumed

1. The population is large and diverse

2. There is no migration

3. There are no mutations

4. Mating is random

5. There is no natural selection

To determine whether a population’s gene pool is changing, allele frequencies must be calculated.

Two equations are used to calculate the frequency of alleles (presented as decimals) in a population:

p represents the frequency of the dominant allele

q represents the frequency of the excessive allele

Allele Frequencies (gene pool): p + q = 1

Says that if there are only two alleles for a gene, one dominant and one recessive, then 100% of the alleles are either dominant (p) or recessive (q)

Genotype Frequencies (population/individuals): p² + 2pq + q² = 1

Says that 100% of the individuals in the population will have one of these genotypes: AA, Aa, aa

7.5 Evidence of Evolution

How do we evaluate if a population is evolving?

The genetic definition of evolution is a change to a population’s gene pool

Gene pool is defined as “the total number of alleles present in populations at any given time

Homologous and Analogous Structures

Homologous Structures → occur in organisms that have the same shared ancestor and the structures are similar but have different functions

Analogous Structures → serve similar functions but arise in organisms that are not closely related and don’t share the same ancestor

Theory of Evolution

• Analogous Homologies

  • Morphology (physical structures)

  • Vestigial Structures → no longer have a purpose in current-day organisms but did in the past

• Fossil Record

  • Relative Dating → older at the bottom, younger at the top

  • Radioactive Dating → Carbon dating, half-lives

• Embryological Homologies

  • Sonic Hedgehog Protein → found in vertebrate and invertebrates involved in a signal transduction pathway for embryological development

• Molecular Homologies

  • Cytochrome C → a protein involved in the electron transport chain

7.6 Continuing Evolution

1. Changes in fossil record

2. Changes in Genome (mutation, jumping genes, transposons, alternative splicing,. “Extinction” of deleterious genes)

3. Development of genetic resistances

7.7 Phylogeny & Common Ancestry

Cladograms

Evolutionary tree that depicts relationships between species based on physical and biochemical similarities (shows macroevolution)

• Macroevolution → overtime, evolution can lead to SPECIATION

  • Formation of a new species from a common ancestor

  • Occurs when 2 populations become REPRODUCTIVELY ISOLATED from each other (can’t reproduce and make viable offspring)

• Macroevolution observed speciation/extinction events and common ancestry

What is a common ancestor?

• A species of organism, from which one or more new species evolves

• ALL living organisms share a distant common ancestor as they all share the same fundamental molecular and cellular features (ex: central dogma, anaerobic respiration, fermentation, DNA, glycolysis)

• All living EUKARYOTES share distant common  ancestor as evidence by the fact that they all

  • Have membrane-bound organelles

  • Contain linear chromosomes

  • Have genes that contain introns

How closely 2 species are related depends on how recently they shared a common ancestor

• More recent common ancestor → more related to each other

• Less recent common ancestor → less related to each other

Common ancestry is illustrated in diagrams called CLADOGRAMS

Phylogeny

• Study of history of evolution in a group of organisms

Cladograms

• Illustrated common ancestry

• DOES NOT take into account time

Phylogenetic Tree

• Illustrated common ancestry

• DOES take into account time

• Shows the traits that separate one group of organisms from another

Constructing Cladograms

• Each line represents a lineage

• Each branch point is a node

  • Nodes represent common ancestors

• Nodes and all branches from it are called CLADES

• Species in a clade have derived features

  • The ROOT is the common ancestor of ALL the species

Parsimony

• Can be SEVERAL arrangements in a  cladogram that are all supported by the data 

• Use the SIMPLEST cladogram with the least amount of evolutionary changes/forks in the road

Outgroup vs Ingroup

• Ingroup → set of organisms under study

• Outgroup →  more distantly related group of organisms that serves as a companion group when determining the evolutionary relationship of the ingroup

*RELATIVE

7.8 Speciation

Species → individual organisms can interbreed AND produce fertile offspring

Speciation → formation of two species from one original species due to REPRODUCTIVE ORGANIZATION

• Allopatric

  • “Other homeland”

  • Occurs when a geographic barrier forms, splitting 2 populations

• Sympatric

  • “Same homeland”

  • Individuals of a single population develop a genetic polymorphism (difference) WITHOUT geographic isolation

• Adaptive Radiation

  • One ancestral species branches into many, each occupying a different NICHE (ecological role or habitat)

Reproductive Isolation (What prevents species from interbreeding?)

• Prezygotic Barriers (blocks reproduction from taking place at all)

  • Temporal Isolation → breeding at different times

  • Mechanical & Gamete Barriers → anatomy and sperm/egg problems

  • Habitat Isolation → living in different place

  • Behavioral Isolation → mating and courtship behavior

• Post Zygotic Barriers

  • Egg and sperm produce offspring that don’t survive or are sterile

Hybrid → cross between two species (often results in infertile offspring → result of post-zygotic barrier)

Rates of Speciation

Gradual speciation → slow change, small steps, relatively stable environment

Punctuated Equilibrium → rapid change, due to major environmental disruption

7.9 Extinction

Extinction → permanent loss of species

Causes

Habitat Loss/Destruction → Deforestation, urbanization, pollution
Invasive Species → Non-native species outcompete or prey on native ones

Overexploitation → Overhunting, overfishing, poaching

Climate Change → Alters ecosystems; species can’t adapt quickly
Natural Disasters → Volcanoes, asteroid impacts, etc.

Genetic Bottlenecks → Loss of genetic variation casuing reduced adaptability

Ecology

8.1 Responses to the Environment

• Ecology → the study of the relationship between living organisms and their environment

• Biotic Factor → any LIVING factor in an organism’s environment (ex: producers, consumers, decomposers) 

• Abiotic Factor → any NON LIVING factor in an organism's environment (ex: temperature, water, sunlight, soil oxygen, pH levels, CO₂ levels)

Levels of Organization

1. Organism → individual living and responding to their environment

2. Population → group of interbreeding individuals living in the same location

3. Community → different species interacting with abiotic factors

4. Ecosystem → biotic factors interacting with abiotic factors

5. Biome → a group of ecosystems that share the same climate and have similar types of communities

6. Biosphere → global sums of all ecosystems and living things

Habitat vs Niche

Habitat = address, Niche = occupation

*Niche reflects an organism’s ROLE in the ecosystem (how the organism uses or interacts with different biotic and abiotic factors in its environment)

Ethology → study of animal behavior

Behavior → actions performed in response to a stimulus

• Both genetic and environmental factors

• Essential for survival and reproduction

• Subject to natural selection over time

How do organisms sense changes in the environment?

Cues that are visual (sight), auditory (hearing), physical (movement/touch), chemical (pheromones), phototrophic (circadian rhythm)

Overlap of Niches

• Results in competition over resources

• Competitive Exclusion Principle → suggests that species with identical niches cannot coexist indefinitely an  competition will result in natural selection

  • Results in a displacement of one species (NICHE PARTITIONING) → species occupy different niches to avoid competition (usually RESOURCE PARTITIONING → To not compete over one resource)

How do organisms respond to their environment?

• Organisms are in constant interaction with their environment and each other

• They can respond behaviorally or physiologically (via internal mechanisms)

 Responses to Environment

Responses to One Another

Types of Communication

Animal-Specific Communication

Innate, Learned and Cooperative Behaviors

Innate → developmental fices and closely controlled by genes (littke to no environmental influence)

• All members of the species perform the behavior in the same way

• Usually involve basic life functions (finding food, caring for offspring)

Learned Behaviors → result of experience

• Learned behaviors are adaptive because they are flexible and can change if environment changes

• Specific behavior may not be passed onto the next generation but ability to learn is passed down

• Many complex ways that animals can learn (spatial learning, associative learning (conditioning), observation, insight learning)

Cooperative Behaviors → increase fitness of the individual and increase survival of the population

• Pack behvior in animals

• Herd, flock and schooling behaviors in animals

• Colony and swarming behavior in insects

Kin Selection → Favors altruistic behavior (that reduces the individual organism’ fitness) by enhancing the reproductive success of relatives

• Lowers fitness of individual but increases fitness of another individual

• Kin selection allows for the fitness of a family member to increase

8.2 Population Ecology — Population Dynamics

• Populations are composed of individual organisms of the same species

Population Growth

Depends on

1. Birth rate (B)

2. Death rate (D)

3. Population Size (n)

Birth rate greater than death rate → population increases

Birth rate less than death rate → population decreases

Birth rate equal to death rate → population stays stable

8.3 Population Ecology — Effect of Density of Populations

Exponential growth

• No constraints on the population

• Creates huge populations

• Only possible when infinite natural resources are available

• Biotic Potential → highest rate of natural increase for a population when resources are unlimited

Logistic Growth

• Shows that there is something that limits the populations size

• Seen in real life

• Limiting Factor → biotic or abiotic factor that restricts the  number, distribution or reproduction of a population within a community

  • Density-dependent Factors → impact of the factors depends on how dense the population is (ex: space, resources, disease predation, competition)

  • Density-independent factors → affect populations in the same way, regardless of density (ex: natural disasters, extreme temperatures, rainfall, seasonal cycles)

• Tolerance → an organism’s ability to survive biotic and abiotic factors

Carrying Capacity → sustainable abundance of a species that can eb supported by the ecosystem’s total available resources

• Determined by limiting factors

• Prevents true exponential growth

• Population growth generally overshoots carrying capacity and then settle around carrying

8.4 Community Ecology and Biodiversity

Biodiversity

• Genetic diversity within a population

• Species diversity within a community

• Ecosystem diversity (number of different habitats and ecosystems in a given area)

Genetic Diversity in Populations

Population’s ability to respond to changes in the environment is affected by genetic diversity (species and populations with little genetic diversity are at risk of decline or extinction)

Low genetic diversity

• Similar susceptibility to hereditary health problems, potential pathogens or environmental changes (may lead to population collapse) 

• Often genetically similar as sibling or cousins

Genetic diversity allows individuals in a population to respond differently to the same changes in environmental conditions

• More likely to contain individuals that can withstand environmental pressure

Species Diversity

• Variety of different species within a specific area and has two components

  • Species richness → measures the total number of species in the community. High richness leads to high diversity

  • Species evenness → measures the relative abundance of each species. More evenly represented species make up a more diverse ecosystem

Simpson’s Diversity Index

• Gives the probability that two individuals randomly selected from a community will be different

• The higher the value, the more diverse the community

• 1 represents high diversity: all individuals in this community are from different species

• 0 represents no diversity: all individuals in this community are the same species

Community Interactions

• How species and populations interact with each other affect the distributions and abundance of populations

Types of Interactions

Niche Partitioning

• Competing species use the environment differently in a way that helps them coexist

  • When species shift niches, they no longer directly compete

• Competitive Exclusion → no two species can indefinitely occupy the same niche at the same time

  • Over time, either one population replaces the other or the two species evolve to occupy different niches

  • If it appears two species occupy the same niche, there must be slight differences

• Specifically called resource partitioning when they use different resources

Keystone Species

• An organism that plays a unique and crucial role in the way an ecosystem functions

• Without a keystone species, the ecosystem would be dramatically different or cease to exist altogether

  • The effects of keystone species on the ecosystem are disproportionate relative to their abundance in the ecosystem

  • A small number of keystone species can have a large impact on the environment

  • When they are removed from the ecosystem, the ecosystem often collapses

Predator/Prey Population Changes

Reasons for peaks and valleys with the predator population lagging slightly behind the prey:

• The biotic potential of the predator may be great enough to over consume the prey, the prey population declines and the predator population then follows

• The biotic potential of the prey is unable to keep pace and the prey population overshoots the carrying capacity and suffers a crash

• Trophic cascades can also occur, where the impact of a predator on its prey’s ecology trickles down one more feeding level to affect the density and/or behavior of the prey’s food source

8.5 Ecosystem Ecology — Energy Flow and Nutrient Cycling

All organisms require free energy and matter to organize grow, reproduce and maintain homeostasis

*Energy FLOWS, matter CYCLES

Energy

• To offset entropy, energy input has to exceed energy lost from and used by an organism to maintain order (laws of thermodynamics)

• Energy converted from one type to another

• Energy deficiencies are detrimental to individual organisms and cause disruptions to populations and ecosystems

Matter

• Matter cycles between various inorganic and organic forms within the environment but DO NOT leave the ecosystem

• Organisms need matter (nutrients/mass) to build their macromolecules and maintain systems within their cells

• Main elements needed to make organic compounds → Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus, Sulfur

• Organisms lose matter to environment through cellular respiration

• Matter moves between environment and organisms through BIOGEOCHEMICAL CUES

Importance of Energy in Organisms

Growth, reproduction, and the maintenance of homeostasis all require a constant input of energy

\Many reactions inside of the organism and their cells require energy (endergonic processes)

• Protein synthesis

• Active transport

• Muscle contraction (in animals)

• Maintaining concentration gradients

• Cell division

• Cell signaling

• Gene expression

Changes in energy levels over time determine the fate of the organism

Net Gain of Energy → energy is stored (as fat, glycogen o starch) and growth of the organism

Net Loss of Energy → loss of mass and ul;timatly the death of the organisms

Classifying Organisms by Role in Energy Flow

Organisms have different roles in cycling matter and transferring energy

Reproductive Strategies in response to Energy Availability

Different organisms use various reproductive strategies in response to energy availability

• LIFE HISTORY STRATEGY → describes the series of events over and organism's lifetime, such as how resources are allocated for growth, maintenance and reproduction

• A species’ life history is genetically determined and shaped by the environment and natural selection

• The amount of energy available to the organism and the stability of the environment heavily influence its life history and fitness

*Spectrum that differs in how much ENERGY a parent devotes to each offspring

Alternating between Asexual Reproduction and Sexual Reproduction

• Some orgnaisms can rpedice both asexaulyl and sexually

• Sexual reproduction requires a mate and organisms often invest energy in order to acquire a mate

• Ex: jellyfish and sponges

Plant Life Cycles: Annuals, Biennials, Perennials

Flowering plants are generally split into three reproductive categories based on their lifespan and the energy they devote to each part of their life cycle

Annual Plants

• Favored when adult mortality is higher than seed or seedling mortality

  • Plants invest all their energy into the production of offspring

• Dominate environments with disturbances that reduce adult survival (climates with dry summers and regions with high variability year to year)

• Common early species in ecological succession

• Terrestrial ecosystem is disturbed → pioneer species (lichen, fungi) often followed by annual plants

  • Grow and spread quickly in disturbed environment

Regulating Body Temperature and Metabolism

• Animal can be split into two categories based on how they regulate their body temperature

• Regulation directly relates to their energy usage, metabolism and rate of cellular respiration

  • Metabolism → set of life-sustaining chemical reactions that take place inside cells and bigger structures, requires ENERGY to maintain

Representing Energy Flow

• Food Chain → follows a single path of energy flow

• Food Web → follows many paths of energy flow

  • More accurate depiction

    • Shows how all organisms are interdependent on others

    • Shows the multiple means by which organisms obtain energy

    • Shows the dependence on producers

    • Allow for the prediction of the effect of a change to a system

*Depending on the food chain, organisms have multiple trophic levels, making food webs hard to label by trophic level

Trophic Levels

• Indicator of feeding level or position n the food chain

  • (Primary) producer

  • Primary consumerSecondary consumer

  • Tertiary Consumer

  • Quaternary Consumer, etc

Dependency on Primary Productivity

• Food webs and chains dependent on primary productivity

  • Producers (photosynthetic and chemosynthetic organisms) are the base of food chains and webs

  • Without the organisms, no new energy would be captured/new energy won’t enter the system

• Change in producer level affects the number and size of other trophic levels

Ecological Pyramids

• Representations of the flow of energy and matter in an ecosystem

• Represent a single food chain and are organized by trophic level

  • Producers on bottom

  • Primary consumers 2nd level

  • Secondary consumers 3rd level…

• Energy is lost at each trophic level (lower level will have more energy)

  • Some energy lost as HEAT due to metabolic processes

  • Energy also lost due to incomplete digestion of food and excretion of waste products

  • Each level had 10 PERCENT of the energy form the previous level (10% rule)

• Largest population funda the bottom

  • Fewer and fewer individuals at each level (related to the loss of energy)

• Amount of biomass decreases at each trophic level (related to loss of energy and numbers)

  • Biomass → how much matter is made up by living organisms

Biogeochemical Cycles

• Flow of nutrients from lying to non living components p Earth

• Chemicals sometimes sequestered for long periods of time and taken out of circulation

• Reservoirs → locations where elements are stored for long periods of time

• Eac cycle demonstrated the conservation of matter

• Cycles are interdependent and connected to each other

• Each cycle includes matter cycling between abiotic and biotic reservoirs and the processes that cycle matter between reservoirs

  • Bio → organisms

  • Geo → inorganic processes

  • Chem → reactions

Water Cycle

Major Processes

• Precipitation → condensed water vapor falls to earth as rain, now, sleet, hail

• Evaporation → transformation of water from liquid gas from the ground or bodies of water into the atmosphere

• Transpiration → release of water from plants into the air

• Condensation → water from gas to liquid water droplets in air, creating clouds and fog

Major Reservoirs

• Oceans

• Surface Water

• Atmosphere

• Living Organisms

Water is Necessary for…

• Components of the cell (ex: cytosol)

• Photosynthesis

• Hydrolysis

Carbon Cycle

Major Processes

• Photosynthesis → fixes CO₂ into organic carbon compounds (ex: g;ucose and other carbohydrates); removes CO₂ from atmosphere and water reservoirs

• Cellular Respiration → break down organic compounds and releases CO₂ into atmosphere or water reservoirs

• Decomposition → the decay of organism by decomposers releases CO₂ back into the atmosphere, soil, or water

• Combustion → burning of fossil fuels releases stored CO₂ into the atmosphere

Major Reservoirs

• CO₂ in the atmosphere

• CO₂ dissolved in water

• Organic compounds in living organisms (including forests, animals, etc)

• Fossil fuels and sedimentary rock (take many years to form)

Molecules that require carbon:

• All organic molecules, including carbs, lipids, protein, nucleic acids

Nitrogen Cycle

Major Processes

• Nitrogen Fixation → nitrogen gas (N₂) is fixed into ammonia (NH₃) which ionizes into ammonium (NH₄⁺) by acquiring hydrogen ions from the soil solution

• Nitrification → bacteria convert ammonium (NH₄⁺)  via nitrite (NO₂^-) into nitrate (NO₃^-) by acquiring hydrogen ions from the soil solution

• Assimilation → plants absorb nitrate from soil to make organic molecules

• Ammonification → bacteria/fungi convert organic nitrogen from organisms into ammonia

• Denitrification → bacteria convert nitrate (NO₃^-) back into nitrogen gas (N₂)

*Steps performed by microorganisms in the soil

Major Reservoirs

• Atmosphere (largest → 78% nitrogen)

• Soil

• Living Organisms

Molecules that require nitrogen

• Proteins

• Nucleic Acids

Phosphorus Cycle

Major Process

• Rock Weathering → the weathering of rocks release phosphate (PO₄>^3-) into soil and groundwater

• Producers take in phosphate

• Consumers eat producers and/or each other

• Excretion → returns phosphates back to soil ia the release of waste by organisms

• Decomposition → returns phosphates back to soil

*Phosphorus is often the LIMITING NUTRIENT in ecosystems (nutrient in shortest supply due to the slow weathering of rocks)

Major Reservoirs

• Rocks, ocean sediments

• Soil

• Groundwater

• Ocean

• Living Organisms

*Only cycle without an atmospheric reservoir

*Most phosphorus is recycled within a community

Molecules that require phosphorus

• Nucleic acids

• Phospholipids

8.6 Disruptions to Ecosystems

Natural Changes in Ecosystems

Geological and meteorological events affect habitat change and ecosystem distribution (biogeographical studies illustrate these changes)

Humans have also cause environmental changes though logging, urbanization and monocropping (practice of growing a single crop on the ame land year after year → lead to soil degradation, pests, disease) 

Genetic Variation in Changing Environments

Affects how well population respond to changes in their environment

More genetic variation/diversity → more lilly individuals will survive and reproduce in the new environment

• Adaptations that are advantageous in one environment might not be advantageous in another

  • Ex: Polar Bears well adapted to cold weather and living on the ice in the Arctic → not well adapted as global warming melts the ice

• Changes in the environment cannot cause specific mutations, as mutations are not directed b specific environmental pressures

  • Ex: Global warming will not cause mutations in polar bears (if polar bears have variation that help them survive and reproduce in new environment, then it will have higher fitness than other polar bears)

Heterozygote Advantage → when heterozygous genotype has a higher relative fitness than homozygous genotype (dependent on particular environment)

Human Impact on Ecosystems

Human populations increase → impact on habitats for other species magnified → reduced population size of affected species, resulted in habitat destruction and extinction of species

1. Biogeochemical Cycles

Humans affect the biogeochemical cycles of ecosystems (especially carbon, nitrogen and phosphorus cycles)

Fertilizers, animal waste, and sewage are adding more nitrogen and phosphates to the water, result in eutrophication

• Eutrophication → water pollution from nitrogen-rich and phosphorus-rich substances flowing into waterways, causing algal overgrowth

• Algal blooms block sunlight from organisms below and when the algae dies, decomposer suse up O₂ as they break down the algae

When fossil fuels are burned, sulfur dioxide and nitrogen dioxide are released into the atmosphere which reacts with water to form acid precipitation

• Acid Precipitation → su;fur dioxide and nitrogen dioxide react with water to form sulfuric acid and nitric acid which fall to earth in rain, sleet, snow or fog

• Acid Rain weakens tees by dissolving nutrients (like calcium and potassium) in the soil before pants can use them

• Trees more susceptible to infections and damage from insects and cold weather

• pH of lakes and streams decreases → affect the health of aquatic organisms

2. Climate Change

Broad range of changes seen in our planet (caused by greenhouse effect)

• Naturally live in a greenhouse effect or planet would be much colder

• Certain gases block heat from escape (water vapor, carbon dioxide, methane, nitrous oxide, and chlorofluorocarbons)

• Burning of fossil fuels increases concentration of greenhouse gasses (block more what from escaping)

Why does it matter?

• Temperatures will continue to rise

• Frost-free season (and growing season) will legnhten

• Changes in precipitation patterns’mroedroughts and heat waves

• Hurricanes will become stronger and more intense

• Sea level will rise 1-4 feet by 2100

• Arctic likely to become ice-free

3. Pesticides and Chemicals

People use pesticides and chemical everyday

• Runoff (movement of land water) usually carries these pesticides from the fields into watershed

Biomagnification

• Toxic chemicals and heavy metals flow into ocean when industrial;, agricultura; and human wastes run off or are deliberately discharged inot rivers that then empty inot the sea

• Pollutants can cause disease, genetic mutations, birth defect, reproductive difficulties, behavioral changes, and death in many organisms

  • Severity of damage varies between species

• Animals near the top of the food chain usually the most affected due to biomagnification

  • Toxic compound are digested so they accumulate in the animals that injst them

  • Become more and more accumulated as they pass along the food chain as animals eat and in turn are eaten

• High level predators build up greater and more dangerous amounts of toxic materials than animals lower on the food chain

4. Invasive Species

• Organisms that are introduced (by international or unintentional human action) to an area where they do not naturally live and breed

  • Often have no competition or predation to control their population (very few limiting factors) and experience exponential growth

  • Plants and animals in the area have no adaptations to protect themselves from the new species

• Often devastated the ecosystems to which they are introduced

  • No natural predators, parasites, pathogens

  • Little limitation on resources

  • No environmental inhibitors (pollutants)

  • Available nice not occupied by any other species → no successful competitor

  • Prey lack effective defense mechanism against introduced species

  • Appropriate environmental conditions (rainfall, temperature)

5. Human-Caused Extinctions and the Sixth Major Extinction Event

Always background extinction rates (“normal” extinction) but modern extinction raters are exceptionally high and continually increasing

• Current extinction rates are 35 time higher than expected background rates prevailing in the last million years under the absence of human impacts

  • Groups (genera) lost in the last 500 years would have taken some 18,000 years to vanish in the absence of human beings

• We have seen 543 land vertebrate species go extinct between the years 1900 and 2000 ecosystems become more fragile when high numbers of animals go extinct