AP Biology

Big Idea 4 — Systems Interactions: Biological systems interact, and these systems and their interactions exhibit complex properties.

Learning Objective 1.1.A: Explain how the properties of water that result from its polarity and hydrogen bonding affect its biological function.

• 1.1.A.1 Living systems depend on the properties of water to sustain life.
  • 1.1.A.1.i Water has polarity, because of the formation of polar covalent bonds between hydrogen and oxygen within water molecules. This polarity contributes to hydrogen bonding between and within biological molecules.
  • 1.1.A.1.ii Water has a high specific heat capacity, which allows for the maintenance of homeostatic body temperature within living organisms.
  • 1.1.A.1.iii Water has a high heat of vaporization, which allows for the evaporative cooling of the surrounding environment. In living organisms, this property allows for body temperature to be maintained.
• 1.1.A.2 The hydrogen bonds between adjacent polar water molecules result in cohesion, adhesion, and surface tension.

Big Idea 2 — Energetics: Biological systems use energy and molecular building blocks to grow, reproduce, and maintain dynamic homeostasis.

Learning Objective 1.2.A: Describe the composition of macromolecules required by living organisms.

• 1.2.A.1 Atoms and molecules from the environment are necessary to build new molecules. Carbon, hydrogen, and oxygen are the most prevalent elements used to build biological molecules such as carbohydrates, proteins, lipids, and nucleic acids. Additionally:
  • 1.2.A.1.i Sulfur is used in the building of proteins.
  • 1.2.A.1.ii Phosphorus is used in the building of phospholipids (a type of lipid) and nucleic acids.
  • 1.2.A.1.iii Nitrogen is used in the building of nucleic acids.

Big Idea 4 — Systems Interactions: Biological systems interact, and these systems and their interactions exhibit complex properties.

Learning Objective 1.3.A: Describe the chemical reactions that build and break biological macromolecules.

• 1.3.A.1 Hydrolysis is a chemical reaction involving the cleaving of covalent bonds. This type of reaction breaks down molecules into smaller molecules. When water is added to the bond between monomers in a polymer, the bond is broken. The hydrogen ion from a water molecule is added to one monomer and the hydroxyl group of the water molecule is added to the other monomer, completing the reaction.
• 1.3.A.2 Dehydration synthesis occurs when two smaller molecules are joined together through covalent bonding. A hydrogen ion is removed from one monomer and a hydroxyl group is removed from the other. This causes the loss of the equivalent of a water molecule from the reactants and the connection of the two remaining monomers. The connection of many monomers is known as polymerization.

Big Idea 4 — Systems Interactions: Biological systems interact, and these systems and their interactions exhibit complex properties.

Learning Objective 1.4.A: Describe the structure and function of carbohydrates.

• 1.4.A.1 Monosaccharides (simple sugars) are the monomers for polysaccharides (complex carbohydrates). These monomers are connected by covalent bonds to form polymers such as complex carbohydrates, which may be linear or branched.
  • Illustrative examples for 1.4.A.1:
    • Cellulose
    • Starch
    • Glycogen
  • Exclusion statement: The molecular structure of specific carbohydrate polymers is beyond the scope of the AP Exam.

Big Idea 4 — Systems Interactions: Biological systems interact, and these systems and their interactions exhibit complex properties.

Learning Objective 1.5.A: Describe the structure and function of lipids.

• 1.5.A.1 Lipids are typically nonpolar, hydrophobic molecules whose structure and function are derived from the way their subcomponents are assembled. Fatty acids can be described as either saturated or unsaturated.
  • 1.5.A.1.i Saturated fatty acids contain only single bonds between carbon atoms.
  • 1.5.A.1.ii Unsaturated fatty acids contain at least one double bond between carbon atoms, which causes the carbon chain to kink.
  • 1.5.A.1.iii The more double bonds in a fatty acid tail, the more unsaturated the lipid becomes.
  • 1.5.A.1.iv The more unsaturated a lipid is, the more liquid it is at room temperature.
• 1.5.A.2 Lipids provide a variety of functions for living organisms. Some examples of lipids are fats, steroids including cholesterol, and phospholipids.
  • 1.5.A.2.i Fats provide energy storage and support cell function. In some cases, they can also provide insulation to help keep mammals warm.
  • 1.5.A.2.ii Steroids are hormones that support physiological functions including growth and development, energy metabolism, and homeostasis.
  • 1.5.A.2.iii Cholesterol provides essential structural stability to animal cell membranes.
  • 1.5.A.2.iv Phospholipids group together to form the lipid bilayers found in plasma and cell membranes.
  • Exclusion statement: The molecular structure of specific lipids is beyond the scope of the AP Exam.

Big Idea 3 — Information Storage and Transmission: Living systems store, retrieve, transmit, and respond to information essential to life processes.

Learning Objective 1.6.A: Describe the structure and function of DNA and RNA.

• 1.6.A.1 In nucleic acids (DNA and RNA), biological information is encoded in sequences of nucleotide monomers. Each nucleotide has the following structural components: a five-carbon sugar (deoxyribose or ribose), a phosphate, and a nitrogenous base (adenine, thymine, guanine, cytosine, or uracil).
• 1.6.A.2 Nucleic acids have a linear sequence of nucleotides that have ends, defined by the 3' (three prime) hydroxyl and 5' (five prime) phosphates of the sugar in the nucleotide. During nucleic acid synthesis, nucleotides are added to the 3' end of the growing strand, resulting in the formation of covalent bonds between nucleotides.
  • Exclusion statement: The molecular structure of specific nucleotides is beyond the scope of the AP Exam.
• 1.6.A.3 DNA is structured as an antiparallel double helix, with two strands of nucleotides running in opposite 5' to 3' orientation. In DNA, adenine nucleotides pair with thymine nucleotides via hydrogen bonds (A-T), and cytosine nucleotides pair with guanine nucleotides via hydrogen bonds (C-G). In RNA, adenine pairs with uracil (A-U).
• 1.6.A.4 Structural differences between DNA and RNA include:
  • 1.6.A.4.i DNA contains the sugar deoxyribose, and RNA contains the sugar ribose.
  • 1.6.A.4.ii DNA contains the nitrogenous base thymine, and RNA contains the nitrogenous base uracil.
  • 1.6.A.4.iii DNA is typically double stranded, while RNA is typically single stranded.

Big Idea 3 — Information Storage and Transmission: Living systems store, retrieve, transmit, and respond to information essential to life processes.

Learning Objective 1.7.A: Describe the structure and function of proteins.

• 1.7.A.1 Proteins comprise linear chains of amino acids connected by the formation of covalent (peptide) bonds that form between a carboxyl group ($-\text{COOH}$) of one amino acid and an amine group ($-\text{NH}_2$) of the next amino acid, resulting in a growing peptide chain.
• 1.7.A.2 Amino acids are composed of a central carbon atom with a hydrogen atom, a carboxyl group, an amine group, and a variable R group covalently bound to it. The R group of an amino acid can be categorized by three possible chemical properties: hydrophobic/nonpolar, hydrophilic/polar, or ionic. The interactions of these R groups determine the structure and function of that region of the protein.
• 1.7.A.3 The specific sequence of amino acids in proteins determines the primary structure of a polypeptide as well as the overall shape of the protein.
  • Exclusion statement: The molecular structure of amino acids is beyond the scope of the AP Exam.
• 1.7.A.4 Secondary structures of proteins are made through the local folding that forms from interactions between atoms of the polypeptide backbone of the amino acid chain. Hydrogen bonding forms shapes such as alpha-helices and beta-pleated sheets.
• 1.7.A.5 The three-dimensional shape of the tertiary structure of a protein results from the formation of hydrogen bonds, hydrophobic interactions, ionic interactions, or disulfide bridges.
• 1.7.A.6 The quaternary structure arises from interactions between multiple polypeptides. All four levels of a protein structure determine the function of a protein.

Big Idea 4 — Systems Interactions (SYI): Biological systems interact, and these systems and their interactions exhibit complex properties.

Learning Objective 2.1.A: Explain how the structure and function of subcellular components and organelles contribute to the function of cells.

• 2.1.A.1 Ribosomes are comprised of ribosomal RNA (rRNA) and protein. These non-membrane, subcellular structures are found in cells in all forms of life and reflect the common ancestry in all known life. Ribosomes synthesize proteins according to messenger RNA (mRNA) sequences.
• 2.1.A.2 The endomembrane system consists of a group of membrane-bound organelles and subcellular components (endoplasmic reticulum (ER), Golgi complex, lysosomes, vacuoles and transport vesicles, the nuclear envelope, and the plasma membrane) that work together to modify, package, and transport polysaccharides, lipids, and proteins intercellularly.
• 2.1.A.3 Endoplasmic reticulum provides mechanical support by helping cells maintain shape and plays a role in intracellular transport.
  • i. Rough ER is associated with membrane-bound ribosomes, allows for the compartmentalization of cells, and helps carry out protein synthesis.
  • ii. Smooth ER functions include the detoxification of cells and lipid synthesis.
  • Exclusion statement: Knowledge of the specific functions of smooth ER in specialized cells is beyond the scope of the AP Exam.
• 2.1.A.4 The Golgi complex is a membrane-bound structure that consists of a series of flattened membrane sacs. Functions of the Golgi include:
  • i. Correctly folding and chemically modifying newly synthesized cellular products
  • ii. Packaging proteins for trafficking
  • Exclusion statement: Knowledge of the role of Golgi in the synthesis of specific phospholipids and packaging of specific enzymes for lysosomes, peroxisomes, and secretory vesicles is beyond the scope of the AP Exam.
  • Illustrative examples for 2.1.A.4:
    • Glycosylation and other chemical modifications of proteins that take place within the Golgi and determine protein function or targeting
• 2.1.A.5 Mitochondria have a double membrane that provides compartments for different metabolic reactions involved in aerobic cellular respiration. The outer membrane is smooth, while the inner membrane is highly convoluted, forming folds that enable ATP to be synthesized more efficiently.
• 2.1.A.6 Lysosomes are membrane-enclosed sacs that contain hydrolytic enzymes that digest material. Lysosomes also play a role in programmed cell death (apoptosis).
• 2.1.A.7 Vacuoles are membrane-bound sacs that play many different roles.
  • i. In plant cells, a specialized large vacuole maintains turgor pressure through nutrient and water storage.
  • ii. In animal cells, vacuoles are smaller in size, are more plentiful than in plant cells, and store cellular materials.
• 2.1.A.8 Chloroplasts are specialized organelles that are found in plants and photosynthetic algae. Chloroplasts contain a double membrane and serve as the location for photosynthesis.

Big Idea 2 — Energetics (ENE): Biological systems use energy and molecular building blocks to grow, reproduce, and maintain dynamic homeostasis.

Learning Objective 2.2.A: Explain the effect of surface area-to-volume ratios on the exchange of materials between cells or organisms and the environment.

• 2.2.A.1 Surface area-to-volume ratios affect the ability of a biological system to obtain necessary nutrients, eliminate waste products, acquire or dissipate thermal energy, and otherwise exchange chemicals and energy with the environment.
  • Relevant equations:
    • Volume of a Sphere: $V = \dfrac{4}{3}\pi r^3$
    • Volume of a Cube: $V = s^3$
    • Volume of a Rectangular Solid: $V = lwh$
    • Volume of a Cylinder: $V = \pi r^2 h$
    • Surface Area of a Sphere: $SA = 4\pi r^2$
    • Surface Area of a Cube: $SA = 6s^2$
    • Surface Area of a Rectangular Solid: $SA = 2lh + 2lw + 2wh$
    • Surface Area of a Cylinder: $SA = 2\pi rh + 2\pi r^2$
    • $r$ = radius
    • $l$ = length
    • $h$ = height
    • $w$ = width
    • $s$ = length of one side of a cube
  • Illustrative examples for 2.2.A.1:
    • SA/V Ratios and Exchanges
      • Root hairs
      • Guard cells
      • Gut epithelial cells
    • Cilia
    • Stomata
• 2.2.A.2 The surface area of the plasma membrane must be large enough to adequately exchange materials.
  • i. The surface area-to-volume ratio can restrict cell size and shape. Smaller cells typically have a higher surface area-to-volume ratio as well as a more efficient exchange of materials with the environment than do larger cells.
  • ii. As cells increase in volume, the surface area-to-volume ratio decreases and the demand for internal resources increases.
  • iii. More complex cellular structures (e.g., membrane folds) are necessary to adequately exchange materials with the environment.
  • iv. As organisms increase in size, their surface area-to-volume ratio decreases, affecting properties like rate of heat exchange with the environment. Smaller amounts of mass exchange proportionally more heat with the ambient environment than do larger masses. As mass increases, both the surface area-to-volume ratio and the rate of heat exchange decrease.
  • v. There is a relationship between metabolic rate per unit body mass and the size of multicellular organisms; typically, the smaller the organism, the higher the metabolic rate per unit body mass.

Big Idea 2 — Energetics (ENE): Biological systems use energy and molecular building blocks to grow, reproduce, and maintain dynamic homeostasis.

Learning Objective 2.3.A: Describe the roles of each of the components of the cell membrane in maintaining the internal environment of the cell.

• 2.3.A.1 Phospholipids have both hydrophilic and hydrophobic regions. The polar hydrophilic phosphate regions of the phospholipids are oriented toward the aqueous external or internal environment, while the nonpolar hydrophobic fatty acid regions face each other within the interior of the membrane.
• 2.3.A.2 Embedded proteins can be hydrophilic (with charged and polar side groups), hydrophobic (with nonpolar side groups), or both.
  • i. Hydrophilic regions of the proteins are either inside the interior of the protein or exposed to the cytosol (cytoplasm).
  • ii. Hydrophobic regions of proteins make up the protein surface that interacts with the fatty acids in the interior membrane.

Learning Objective 2.3.B: Describe the fluid mosaic model of cell membranes.

• 2.3.B.1 Plasma membranes consist of a structural framework of phospholipid molecules embedded with proteins, steroids (such as cholesterol in vertebrate animals), glycoproteins, and glycolipids. All of these can move around the surface of the cell within the membrane, as illustrated by the fluid mosaic model.

Big Idea 2 — Energetics (ENE): Biological systems use energy and molecular building blocks to grow, reproduce, and maintain dynamic homeostasis.

Learning Objective 2.4.A: Explain how the structure of biological membranes influences selective permeability.

• 2.4.A.1 Plasma membranes separate the internal environment of the cell from the external environment. Selective permeability is the result of the plasma membrane having a hydrophobic interior.
• 2.4.A.2 Small nonpolar molecules, including $\mathrm{N_2}$, $\mathrm{O_2}$, and $\mathrm{CO_2}$, freely pass across the membrane. Hydrophilic substances, such as large polar molecules and ions, move across the membrane through embedded channels and transport proteins.
• 2.4.A.3 The nonpolar hydrocarbon tails of phospholipids prevent the movement of ions and polar molecules across the membrane. Small polar, uncharged molecules, like $\mathrm{H_2O}$ or $\mathrm{NH_3}$ (ammonia), pass through the membrane in small amounts.

Learning Objective 2.4.B: Describe the role of the cell wall in maintaining cell structure and function.

• 2.4.B.1 Cell walls of Bacteria, Archaea, Fungi, and plants provide a structural boundary as well as a permeability barrier for some substances to the internal or external cellular environments and protection from osmotic lysis.

Big Idea 2 — Energetics (ENE): Biological systems use energy and molecular building blocks to grow, reproduce, and maintain dynamic homeostasis.

Learning Objective 2.5.A: Describe the mechanisms that organisms use to maintain solute and water balance.

• 2.5.A.1 The selective permeability of membranes allows for the formation of concentration gradients of solutes across the membrane.
• 2.5.A.2 Passive transport is the net movement of molecules from regions of high concentration to regions of low concentration without the direct input of metabolic energy.
• 2.5.A.3 Active transport requires the direct input of energy to move molecules. In some cases, active transport is utilized to move molecules from regions of low concentration to regions of high concentration.

Learning Objective 2.5.B: Describe the mechanisms that organisms use to transport large molecules across the plasma membrane.

• 2.5.B.1 The processes of endocytosis and exocytosis require energy to move large substances or large amounts of substances into and out of cells.
  • i. In endocytosis, the cell takes in large molecules and particulate matter by folding the plasma membrane in on itself and forming new (small) vesicles that engulf material from the external environment.
  • ii. In exocytosis, internal vesicles release material from cells by fusing with the plasma membrane and secreting large molecules from the cell.

Big Idea 2 — Energetics (ENE): Biological systems use energy and molecular building blocks to grow, reproduce, and maintain dynamic homeostasis.

Learning Objective 2.6.A: Explain how the structure of a molecule affects its ability to pass through the plasma membrane.

• 2.6.A.1 Facilitated diffusion requires transport or channel proteins to enable the movement of charged ions across the membrane.
  • i. Membranes may become polarized by the movement of ions across the membrane.
  • ii. Charged ions, including $\mathrm{Na^+}$ (sodium) and $\mathrm{K^+}$ (potassium), require channel proteins to move through the membrane.
• 2.6.A.2 Facilitated diffusion enables the movement of large polar molecules through membranes with no energy input. In this type of diffusion, substances move down the concentration gradient.
• 2.6.A.3 Aquaporins transport large quantities of water across membranes.

Big Idea 2 — Energetics (ENE): Biological systems use energy and molecular building blocks to grow, reproduce, and maintain dynamic homeostasis.

Learning Objective 2.7.A: Explain how concentration gradients affect the movement of molecules across membranes.

• 2.7.A.1 External environments can be hypotonic, hypertonic, or isotonic to internal environments of cells. Movement of water can also be described as moving from hypotonic to hypertonic regions. Water moves by osmosis from regions of high water potential to regions of low water potential.
  • Equation (Water Potential): $\psi = \psi_p + \psi_s$
    • where:
    • $\psi_p$ = pressure potential
    • $\psi_s$ = solute potential
  • Illustrative examples for 2.7.A.1:
    • Contractile vacuole in protists
    • Central vacuole in plant cells

Learning Objective 2.7.B: Explain how osmoregulatory mechanisms contribute to the health and survival of organisms.

• 2.7.B.1 Growth and homeostasis are maintained by the constant movement of molecules across membranes.
• 2.7.B.2 Osmoregulation maintains water balance and allows organisms to control their internal solute composition and water potential. Water moves from regions of low osmolarity or solute concentration to regions of high osmolarity or solute concentration.
  • Equation (Solute Potential of a Solution): $\psi_s = -iCRT$
    • where:
    • $i$ = ionization constant
    • $C$ = molar concentration
    • $R$ = pressure constant $\left(R = 0.0831 \dfrac{L \cdot bars}{mol \cdot K}\right)$
    • $T$ = temperature in Kelvin (°C + 273)

Big Idea 2 — Energetics (ENE): Biological systems use energy and molecular building blocks to grow, reproduce, and maintain dynamic homeostasis.

Learning Objective 2.8.A: Describe the processes that allow ions and other molecules to move across membranes.

• 2.8.A.1 Metabolic energy (such as that from ATP) is required for active transport of molecules across the membrane and to establish and maintain electrochemical gradients.
  • i. Membrane proteins are necessary for active transport.
  • ii. The $\mathrm{Na^+}/\mathrm{K^+}$ pump and ATPase contribute to the maintenance of the membrane potential.

Big Idea 2 — Energetics (ENE): Biological systems use energy and molecular building blocks to grow, reproduce, and maintain dynamic homeostasis.

Learning Objective 2.9.A: Describe the membrane-bound structures of the eukaryotic cell.

• 2.9.A.1 Membranes and membrane-bound organelles in eukaryotic cells compartmentalize intracellular metabolic processes and specific enzymatic reactions.

Learning Objective 2.9.B: Explain how internal membranes and membrane-bound organelles contribute to compartmentalization of eukaryotic cell functions.

• 2.9.B.1 Internal membranes facilitate cellular processes by minimizing competing interactions and by increasing the surface area where reactions can occur.

Big Idea 1 — Evolution (EVO): The process of evolution drives the diversity and unity of life.

Learning Objective 2.10.A: Describe similarities and/or differences in compartmentalization between prokaryotic and eukaryotic cells.

• 2.10.A.1 Membrane-bound organelles such as mitochondria and chloroplasts evolved from once free-living prokaryotic cells via endosymbiosis.
• 2.10.A.2 Prokaryotes typically lack internal membrane-bound organelles but have internal regions with specialized structures and functions.
• 2.10.A.3 Eukaryotic cells maintain internal membranes that partition the cell into specialized regions.

Big Idea 2 — Energetics: Biological systems use energy and molecular building blocks to grow, reproduce, and maintain dynamic homeostasis.

Learning Objective 3.1.A: Explain how enzymes affect the rate of biological reactions.

• 3.1.A.1 The structure and function of enzymes contribute to the regulation of biological processes. Enzymes are proteins that are biological catalysts that facilitate chemical reactions in cells by lowering the activation energy.
• 3.1.A.2 For an enzyme-mediated chemical reaction to occur, the shape and charge of the substrate must be compatible with the active site of the enzyme. This is illustrated by the enzyme-substrate complex model.

Big Idea 2 — Energetics: Biological systems use energy and molecular building blocks to grow, reproduce, and maintain dynamic homeostasis.

Learning Objective 3.2.A: Explain how changes to the structure of an enzyme may affect its function.

• 3.2.A.1 Change to the molecular structure of a component in an enzymatic system may result in a change to its function or efficiency.
  • i. Denaturation of proteins, such as enzymes, occurs when the protein structure is disrupted by a change in temperature, pH, or chemical environment, eliminating the ability to catalyze reactions.
  • ii. Environmental temperatures and pH outside the optimal range for a given enzyme will cause changes to its structure (by disrupting the hydrogen bonds), altering the efficiency with which it catalyzes reactions.
• 3.2.A.2 In some cases, enzyme denaturation is reversible, allowing the enzyme to regain activity.

Learning Objective 3.2.B: Explain how the cellular environment affects enzyme activity.

• 3.2.B.1 The relative concentrations of substrates and products determine how efficiently an enzymatic reaction proceeds.

Big Idea 2 — Energetics: Biological systems use energy and molecular building blocks to grow, reproduce, and maintain dynamic homeostasis.

Learning Objective 3.3.A: Describe the role of energy in living organisms.

• 3.3.A.1 All living systems require an input of energy.
• 3.3.A.2 Life requires a highly ordered system and does not violate the first and second laws of thermodynamics.
  • i. Energy input must exceed energy loss to maintain order and to power cellular processes.
  • ii. Cellular processes that release energy may be coupled with cellular processes that require energy.
  • iii. Significant loss of order or energy flow results in death.
  • Exclusion statement: Students will need to understand the concept of energy, but the equation for Gibbs free energy is beyond the scope of the AP Exam.
• 3.3.A.3 Energy-related pathways in biological systems are sequential to allow for a more controlled transfer of energy. A product of a reaction in a metabolic pathway is typically the reactant for the subsequent step in the pathway.

Learning Objective 3.3.B: Explain how shared, conserved, and fundamental processes and features support the concept of common ancestry for all organisms.

• 3.3.B.1 Core metabolic pathways (e.g., glycolysis, oxidative phosphorylation) are conserved across all currently recognized domains (Archaea, Bacteria, and Eukarya).

Big Idea 2 — Energetics: Biological systems use energy and molecular building blocks to grow, reproduce, and maintain dynamic homeostasis.

Learning Objective 3.4.A: Describe the photosynthetic processes and structural features of the chloroplast that allow organisms to capture and store energy.

• 3.4.A.1 Photosynthesis is the series of reactions that use carbon dioxide $(\mathrm{CO_2})$, water $(\mathrm{H_2O})$, and light energy to make carbohydrates and oxygen $(\mathrm{O_2})$.
  • i. Photosynthetic organisms capture energy from the sun and produce sugars that can be used in biological processes or stored.
  • ii. Photosynthesis first evolved in prokaryotic organisms.
  • iii. Scientific evidence supports the claim that prokaryotic (cyanobacterial) photosynthesis was responsible for the production of an oxygenated atmosphere.
  • iv. Prokaryotic photosynthetic pathways were the foundation of eukaryotic photosynthesis.
  • Exclusion statement: Memorization of the steps in the Calvin cycle, the structure of the molecules, and the names of the enzymes involved, with the exception of ATP synthase, is beyond the scope of the AP Exam.
• 3.4.A.2 Stroma and thylakoids are found within the chloroplast.
  • i. The stroma is the fluid within the inner chloroplast membrane and outside the thylakoid. The carbon fixation (Calvin cycle) reactions of photosynthesis occur in the stroma.
  • ii. The thylakoid membranes contain chlorophyll pigments organized into two photosystems, as well as electron transport proteins.
  • iii. Thylakoids are organized in stacks called grana. The light reactions of photosynthesis occur in the grana.
• 3.4.A.3 The light reactions of photosynthesis in eukaryotes involve a series of coordinated reaction pathways that capture energy present in light to yield ATP and NADPH, which power the production of organic molecules in the Calvin cycle. This provides energy for metabolic processes.

Learning Objective 3.4.B: Explain how cells capture energy from light and transfer it to biological molecules for storage and use.

• 3.4.B.1 Electron transport chain (ETC) reactions occur in chloroplasts, in mitochondria, and across prokaryotic plasma membranes. In photosynthesis, electrons that pass through the thylakoid membrane are picked up and ultimately transferred to $\mathrm{NADP^+}$ reducing it to NADPH in photosystem I.
  • Exclusion statement: The full names of the specific electron carriers in the electron transport chain are beyond the scope of the AP Exam.
  • Exclusion statement: Specific steps, names of enzymes, and intermediates of the pathways for these processes are beyond the scope of this course and the AP Exam.
• 3.4.B.2 During photosynthesis, chlorophylls absorb energy from light, boosting electrons to a higher energy level in photosystems I and II. Water then splits, supplying electrons to replace those lost from photosystem II.
• 3.4.B.3 Photosystems I and II are embedded in the thylakoid membranes of chloroplasts and are connected by the transfer of electrons through an ETC.
• 3.4.B.4 When electrons are transferred between molecules in a series of oxidation/reduction reactions as they pass through the ETC, an electrochemical gradient of protons (hydrogen ions) is established across the thylakoid membrane. The membrane separates a region of low proton concentration outside the thylakoid membrane from a region of high proton concentration inside the thylakoid membrane.
• 3.4.B.5 The formation of the proton gradient is linked to the synthesis of ATP from ADP and inorganic phosphate via ATP synthase. The flow of protons back through membrane-bound ATP synthase by chemiosmosis drives the formation of ATP from ADP and inorganic phosphate; this is known as photophosphorylation.
• 3.4.B.6 The energy captured in the light reactions and transferred to ATP and NADPH powers the production of carbohydrates from carbon dioxide in the Calvin cycle. This occurs in the stroma of the chloroplast.

Big Idea 2 — Energetics: Biological systems use energy and molecular building blocks to grow, reproduce, and maintain dynamic homeostasis.

Learning Objective 3.5.A: Describe the processes and structural features of mitochondria that allow organisms to use energy stored in biological macromolecules.

• 3.5.A.1 Cellular respiration uses energy from biological macromolecules to synthesize ATP. Respiration and fermentation are characteristic of all forms of life.
• 3.5.A.2 Aerobic cellular respiration in eukaryotes involves a series of coordinated enzyme-catalyzed reactions that capture energy from biological macromolecules.
• 3.5.A.3 The ETC transfers electrons in a series of oxidation-reduction reactions that establish an electrochemical gradient across membranes.
  • i. In cellular respiration, electrons delivered by NADH and $\mathrm{FADH_2}$ are passed to a series of electron acceptors as they move toward the terminal electron acceptor, oxygen. Aerobic prokaryotes use oxygen as a terminal electron acceptor, while anaerobic prokaryotes use other molecules.
  • ii. The transfer of electrons, through the ETC, is accompanied by the formation of a proton gradient across the inner mitochondrial membrane, with the membrane(s) separating a region of high proton concentration outside the membrane from a region of low proton concentration inside the membrane. The folding of the inner membrane increases the surface area, which allows for more ATP to be synthesized. In prokaryotes, the passage of electrons is accompanied by the movement of protons across the plasma membrane.
  • iii. The flow of protons back through membrane-bound ATP synthase by chemiosmosis drives the formation of ATP from ADP and inorganic phosphate. This is known as oxidative phosphorylation in aerobic cellular respiration.
  • iv. In aerobic cellular respiration, decoupling oxidative phosphorylation from electron transport generates heat. This heat can be used by endothermic organisms to regulate body temperature.
  • Exclusion statement: The full names of the specific electron carriers in the electron transport chain are beyond the scope of the AP Exam.
  • Exclusion statement: Specific steps, names of enzymes, and intermediates of the pathways for these processes are beyond the scope of this course and the AP Exam.

Learning Objective 3.5.B: Explain how cells obtain energy from biological macromolecules in order to power cellular functions.

• 3.5.B.1 Glycolysis is a biochemical pathway that releases the energy in glucose molecules to form ATP (from ADP and inorganic phosphate), NADH (from $\mathrm{NAD^+}$), and pyruvate.
• 3.5.B.2 Pyruvate is transported from the cytosol to the mitochondrion where oxidation occurs. This process releases electrons during the Krebs (citric acid) cycle, reducing $\mathrm{NAD^+}$ to NADH and FAD to $\mathrm{FADH_2}$, and releasing $\mathrm{CO_2}$.
• 3.5.B.3 The Krebs cycle takes place in the mitochondrial matrix. During the Krebs cycle, carbon dioxide is released from organic intermediates, ATP is synthesized from ADP and inorganic phosphate, and electrons are transferred by the coenzymes $\mathrm{NAD^+}$ and FAD.
• 3.5.B.4 Electrons extracted in glycolysis and Krebs cycle reactions are transferred by NADH and $\mathrm{FADH_2}$ to the ETC in the inner mitochondrial membrane.
• 3.5.B.5 When electrons are transferred between molecules in a sequence of reactions as they pass through the ETC, an electrochemical gradient of protons (hydrogen ions) across the inner mitochondrial membrane is established. The pH inside the mitochondrial matrix is higher than in the intermembrane space.
• 3.5.B.6 Fermentation allows glycolysis to proceed in the absence of oxygen and produces organic molecules such as alcohol and lactic acid.
  • Exclusion statement: Memorization of the steps in glycolysis and the Krebs cycle, and of the structures of the molecules and the names of the enzymes involved, is beyond the scope of this course and the AP Exam.

Big Idea 3 — Information Storage and Transmission: Living systems store, retrieve, transmit, and respond to information essential to life processes.

Learning Objective 4.1.A: Describe the ways that cells can communicate with one another.

• 4.1.A.1 Cells communicate with one another through direct contact with other cells or from a distance via chemical signaling.
  • Illustrative examples for 4.1.A.1:
    • Immune cells interact through cell-to-cell contact, antigen-presenting cells (APCs), helper T-cells, and killer T-cells.

Learning Objective 4.1.B: Explain how cells communicate with one another over short and long distances.

• 4.1.B.1 Cells communicate over short distances by using local regulators that target cells in the vicinity of the signal-emitting cell.
  • Illustrative examples for 4.1.B.1:
    • Neurotransmitters
    • Plant immune response
    • Quorum sensing in bacteria
    • Morphogens in embryonic development
• 4.1.B.2 Signals released by one cell type can travel long distances to target cells of another type.
  • Illustrative examples for 4.1.B.2:
    • Insulin
    • Human growth hormone
    • Thyroid hormones
    • Testosterone
    • Estrogen

Big Idea 3 — Information Storage and Transmission: Living systems store, retrieve, transmit, and respond to information essential to life processes.

Learning Objective 4.2.A: Describe the components of a signal transduction pathway.

• 4.2.A.1 Signal transduction pathways link signal receptions with cellular responses.
• 4.2.A.2 Many signal transduction pathways include protein modifications and involve phosphorylation cascades.

Learning Objective 4.2.B: Describe the role of components of a signal transduction pathway in producing a cellular response.

• 4.2.B.1 Signaling begins with the recognition of a chemical messenger—a ligand—by a receptor protein in a target cell.
  • i. The ligand-binding domain of a receptor recognizes a specific chemical messenger, which can be a peptide (protein) or a small molecule.
  • ii. G protein-coupled receptors are an example of a receptor protein in eukaryotes.
  • iii. Receptors may be located on the surface of a target cell or in the cytoplasm or nucleus of the target cell.
• 4.2.B.2 Signaling cascades relay signals from receptors to cell targets, often amplifying the incoming signals, resulting in the appropriate responses by the cell. Responses could include cell growth, secretion of molecules, or gene expression.
  • i. After the ligand binds, the intracellular domain of a receptor protein changes shape, initiating transduction of the signal.
  • ii. Enzymes and second messengers such as cyclic AMP (cAMP) relay and amplify the intracellular signal.
  • iii. Hormones are an example of a signaling messenger that can travel long distances in the bloodstream.
  • iv. The binding of ligands to ligand-gated channels can cause the channel to open or close.

Big Idea 3 — Information Storage and Transmission: Living systems store, retrieve, transmit, and respond to information essential to life processes.

Learning Objective 4.3.A: Describe the different types of cellular responses elicited by a signal transduction pathway.

• 4.3.A.1 Signal transduction may result in changes in gene expressions and cell function, which may alter phenotype or result in programmed cell death (apoptosis).
  • Illustrative examples for 4.3.A.1:
    • Use of chemical messengers by microbes to communicate with other nearby cells and to regulate specific pathways in response to population density (quorum sensing)
    • Epinephrine stimulation of glycogen breakdown in mammals

Learning Objective 4.3.B: Explain how a change in the structure of any signaling molecule affects the activity of the signaling pathway.

• 4.3.B.1 Changes in signal transduction pathways can alter cellular responses. Mutations in any domain of the receptor protein or in any component of the signaling pathway may affect the downstream components by altering the subsequent transduction of the signal.
  • Illustrative examples for 4.3.B.1:
    • Cytokines regulate gene expression to allow for cell replication and division.
    • Mating pheromones in yeast trigger mating gene expression.
    • Ethylene levels cause changes in the production of different enzymes allowing fruits to ripen.
    • HOX genes regulate animal body plans during embryonic development.
• 4.3.B.2 Chemicals that interact with any component of the signaling pathway may activate or inhibit the pathway.

Big Idea 2 — Energetics: Biological systems use energy and molecular building blocks to grow, reproduce, and maintain dynamic homeostasis.

Learning Objective 4.4.A: Explain how positive and negative feedback helps maintain homeostasis.

• 4.4.A.1 Organisms use feedback mechanisms to maintain their internal environments in response to internal and external changes.
  • i. Negative feedback mechanisms maintain homeostasis by reducing the initial stimulus to regulate physiological processes. If a system is perturbed or disrupted, negative feedback mechanisms return the system back to its target set point. These processes operate at the molecular, cellular, and organismal levels.
    • Illustrative examples for 4.4.A.1.i:
      • Blood sugar regulation by insulin/glucagon
  • ii. Positive feedback mechanisms amplify responses and processes in biological organisms. The variable initiating the response is moved further away from the initial set point. Amplification occurs when the stimulus is further intensified, which, in turn, initiates an additional response that produces system change.
    • Illustrative examples for 4.4.A.1.ii:
      • Lactation in mammals
      • Onset of labor in childbirth
      • Ripening of fruit

Big Idea 3 — Information Storage and Transmission: Living systems store, retrieve, transmit, and respond to information essential to life processes.

Learning Objective 4.5.A: Describe the events that occur in the cell cycle.

• 4.5.A.1 The cell cycle is a highly regulated series of events that controls the growth and reproduction of eukaryotic cells.
  • i. The cell cycle consists of sequential stages of interphase (G1, S, G2), mitosis, and cytokinesis.
  • ii. G1 phase: The cell is metabolically active, duplicating organelles and cytosolic components.
  • iii. S phase: DNA is in the form of chromatin and replicates to form two sister chromatids connected at a centromere.
  • iv. G2 phase: Protein synthesis occurs, ATP is produced in large quantities, and centrosomes replicate.
  • v. A cell can enter a stage (G0) in which it no longer divides, but it can reenter the cell cycle in response to appropriate cues.
  • vi. Nondividing cells may exit the cell cycle or be held at a particular stage in the cell cycle.

Learning Objective 4.5.B: Explain how mitosis results in the transmission of chromosomes from one generation of cells to the next.

• 4.5.B.1 Mitosis is a process that ensures the transfer of a complete genome from a parent cell to two genetically identical daughter cells in eukaryotes.
  • i. Mitosis plays a role in growth, tissue repair, and asexual reproduction.
  • ii. Mitosis occurs in sequential steps (prophase, metaphase, anaphase, telophase) and alternates with interphase in the cell cycle.
  • iii. Prophase: Sister chromatids condense, mitotic spindle begins to form, and centrosomes move to opposite poles of the cell.
  • iv. Metaphase: Spindle fibers align chromosomes along the equator of the cell.
  • v. Anaphase: Paired sister chromatids separate as spindle fibers pull chromatids toward poles.
  • vi. Telophase: Mitotic spindle breaks down, a new nuclear envelope develops, and then the cytoplasm divides.
  • vii. Cytokinesis: A cleavage furrow forms in animal cells or a cell plate forms in plant cells, resulting in two new daughter cells.

Big Idea 3 — Information Storage and Transmission: Living systems store, retrieve, transmit, and respond to information essential to life processes.

Learning Objective 4.6.A: Describe the role of checkpoints in regulating the cell cycle.

• 4.6.A.1 A number of internal controls or checkpoints regulate progression through the cell cycle.
• 4.6.A.2 Interactions between cyclins and cyclin-dependent kinases control the cell cycle.
  • Exclusion statement: Knowledge of specific cyclin-CdK pairs or growth factors is beyond the scope of the AP Exam.

Learning Objective 4.6.B: Describe the effects of disruptions to the cell cycle on the cell or organism.

• 4.6.B.1 Disruptions to the cell cycle may result in cancer or apoptosis (programmed cell death).

Enduring Understanding (BIG IDEA 3 — Information Storage and Transmission): Living systems store, retrieve, transmit, and respond to information essential to life processes.

Learning Objective 5.2.A: Explain how the process of meiosis generates genetic diversity.

• 5.2.A.1 Correct separation of the homologous chromosomes in meiosis I and sister chromatids in meiosis II ensures that each gamete receives a haploid (1n) set of chromosomes that comprises an assortment of both maternal and paternal chromosomes. When incorrect separation occurs (nondisjunction), gametes are no longer haploid.
• 5.2.A.2 During prophase I of meiosis, non-sister chromatids exchange genetic material via a process called crossing over (recombination), which increases genetic diversity among the resultant gametes.
• 5.2.A.3 Sexual reproduction in eukaryotes increases genetic variation, including crossing over, random assortment of chromosomes during meiosis, and subsequent fertilization of gametes.
  • Exclusion statement: Knowledge of the details of sexual reproduction cycles in various plants and animals is beyond the scope of the AP Exam.

Enduring Understanding (BIG IDEA 1 — Evolution): The process of evolution drives the diversity and unity of life.

Enduring Understanding (BIG IDEA 3 — Information Storage and Transmission): Living systems store, retrieve, transmit, and respond to information essential to life processes.

Learning Objective 5.3.A: Explain the inheritance of genes and traits as described by Mendel's laws.

• 5.3.A.1 Mendel's laws of segregation and independent assortment can be applied to genes that are on different chromosomes.
• 5.3.A.2 In most cases, fertilization involves the fusion of two haploid gametes, restoring the diploid number of chromosomes and increasing genetic variation in populations by creating new combinations of alleles in the zygote.
  • i. Rules of probability can be applied to analyze the passing of single-gene traits from parent to offspring.
  • ii. Monohybrid, dihybrid, and test crosses can be used to determine whether alleles are dominant or recessive.
  • iii. An organism's genotype is the set of alleles inherited for one or more genes by an individual organism. An organism's genotype can be homozygous or heterozygous for each gene.
  • iv. An organism's phenotype is the observable expression of the inherited traits.
  • v. Patterns of inheritance (autosomal, genetically linked, sex-linked) and whether an allele is dominant or recessive can often be predicted from data, including pedigrees. Punnett squares can be used to predict the genotypes and phenotypes of parents and offspring.
  • Equation (Laws of Probability): If $A$ and $B$ are mutually exclusive, then: $P(A \text{ or } B) = P(A) + P(B)$
  • Equation (Laws of Probability): If $A$ and $B$ are independent, then: $P(A \text{ and } B) = P(A) \times P(B)$

Enduring Understanding (BIG IDEA 3 — Information Storage and Transmission): Living systems store, retrieve, transmit, and respond to information essential to life processes.

Learning Objective 5.4.A: Explain deviations from Mendel's model of the inheritance of traits.

• 5.4.A.1 Patterns of inheritance of many traits do not follow the ratios predicted by Mendel's laws and can be identified by quantitative analysis, when the observed phenotypic ratios statistically differ from the predicted ratios.
  • i. Genes located on the same chromosome are referred to as being genetically linked. The probability that these linked genes segregate together during meiosis can be used to calculate the map distance (or map units) between them on a chromosome. This calculation is called gene or genetic mapping.
  • ii. Codominance occurs when the phenotype from both alleles is expressed such that the heterozygote would have a different phenotype than either homozygote.
  • iii. Incomplete dominance occurs when neither allele of a gene can mask the other, so the phenotype of the heterozygote is a blended version of the dominant and recessive phenotypes.
• 5.4.A.2 Some traits, known as sex-linked traits (X- or Y-linked), are determined by genes on sex chromosomes. The pattern of inheritance of sex-linked traits can often be predicted from data, including pedigrees, indicating the genotypes and phenotypes of both parents and offspring.
  • Illustrative examples for EK 5.4.A.2:
    • Sex-linked traits (X- or Y-linked) reside on sex chromosomes.
    • Sex-linked traits (X- or Y-linked) are inherited at higher rates in XY individuals than they are in XX individuals.
    • In certain species, the chromosomal basis of sex determination is not based on X and Y chromosomes (e.g., ZW in birds, haplodiploidy in bees).
• 5.4.A.3 Pleiotropy is a phenomenon in which the expression of a single gene results in multiple traits or effects; these traits therefore do not segregate independently.
• 5.4.A.4 Some traits result from non-nuclear inheritance.
  • i. Chloroplasts and mitochondria are randomly assorted to gametes and daughter cells; thus, traits determined by chloroplast and mitochondrial DNA do not follow simple Mendelian rules.
  • ii. In animals, mitochondria are usually transmitted by the egg and not by sperm; thus, traits determined by the mitochondrial DNA are typically maternally inherited.
  • iii. In plants, mitochondria and chloroplasts are transmitted in the ovule and not in the pollen; as such, mitochondria-determined and chloroplast-determined traits are typically maternally inherited.

Enduring Understanding (BIG IDEA 4 — Systems Interactions): Biological systems interact, and these systems and their interactions exhibit complex properties.

Learning Objective 5.5.A: Explain how the same genotype can result in multiple phenotypes under different environmental conditions.

• 5.5.A.1 Environmental conditions influence gene expression and can lead to phenotypic plasticity (e.g., the ability of individual genotypes to produce different phenotypes).
  • Illustrative examples for EK 5.5.A.1:
    • Height and weight in humans
    • Flower color based on soil pH
    • Seasonal fur color in arctic animals
    • Sex determination in reptiles
    • Effect of increased UV on melanin production in animals
    • Presence of the opposite mating type on pheromone production in yeast and other fungi

Enduring Understanding (BIG IDEA 3 — Information Storage and Transmission): Living systems store, retrieve, transmit, and respond to information essential to life processes.

Learning Objective 6.1.A: Describe the structures involved in passing hereditary information from one generation to the next.

• 6.1.A.1 Genetic information is stored in and passed to subsequent generations through DNA molecules and, in some cases, RNA molecules.
  • 6.1.A.1.i Prokaryotic organisms typically have circular chromosomes.
  • 6.1.A.1.ii Eukaryotic organisms typically have multiple linear chromosomes that are comprised of DNA. These chromosomes are condensed using histones and associated proteins.
• 6.1.A.2 Prokaryotes and eukaryotes can contain plasmids, which are extra-chromosomal circular molecules of DNA.

Learning Objective 6.1.B: Describe the characteristics of DNA that allow it to be used as hereditary material.

• 6.1.B.1 Nucleic acids exhibit specific nucleotide base pairing that is conserved through evolution.
  • 6.1.B.1.i Purines (guanine and adenine) have a double ring structure.
  • 6.1.B.1.ii Pyrimidines (cytosine, thymine, and uracil) have a single ring structure.
  • 6.1.B.1.iii Purines pair with pyrimidines: adenine with thymine (or uracil in RNA) and guanine with cytosine.

Enduring Understanding (BIG IDEA 3 — Information Storage and Transmission): Living systems store, retrieve, transmit, and respond to information essential to life processes.

Learning Objective 6.2.A: Describe the mechanisms by which genetic information is copied for transmission between generations.

• 6.2.A.1 DNA replication ensures continuity of hereditary information.
  • 6.2.A.1.i DNA is synthesized in the 5' to 3' direction.
  • 6.2.A.1.ii Replication is a semiconservative process, meaning one strand of DNA serves as the template for a new strand of complementary DNA.
  • 6.2.A.1.iii Helicase unwinds the DNA strands.
  • 6.2.A.1.iv Topoisomerase relaxes supercoiling in front of the replication fork.
  • 6.2.A.1.v DNA polymerase requires RNA primers to initiate DNA synthesis.
  • 6.2.A.1.vi DNA polymerase synthesizes new strands of DNA continuously on the leading strand and discontinuously on the lagging strand.
  • 6.2.A.1.vii Ligase joins the fragments on the lagging strand.
  • Exclusion statement: The names of the steps and particular enzymes involved, excluding DNA polymerase, ligase, RNA polymerase, helicase, and topoisomerase, are beyond the scope of the AP Exam.

Enduring Understanding (BIG IDEA 3 — Information Storage and Transmission): Living systems store, retrieve, transmit, and respond to information essential to life processes.

Learning Objective 6.3.A: Describe the mechanisms by which genetic information flows from DNA to RNA to protein.

• 6.3.A.1 The sequence of the RNA bases, together with the structure of the RNA molecule, determines RNA function.
  • 6.3.A.1.i Messenger RNA (mRNA) molecules carry information from DNA in the nucleus to the ribosome in the cytoplasm.
  • 6.3.A.1.ii Distinct transfer RNA (tRNA) molecules bind specific amino acids and have anticodon sequences that base pair with the codons of mRNA. tRNA is recruited to the ribosome during translation to generate the primary peptide sequence based on the mRNA sequence.
  • 6.3.A.1.iii Ribosomal RNA (rRNA) molecules are functional building blocks of ribosomes.
• 6.3.A.2 RNA polymerases use a single template strand of DNA to direct the inclusion of bases in the newly formed RNA molecule. This process is known as transcription.
• 6.3.A.3 The enzyme RNA polymerase synthesizes mRNA molecules in the 5' to 3' direction by reading the template DNA strand in the 3' to 5' direction.
• 6.3.A.4 In eukaryotic cells the mRNA transcript undergoes a series of enzyme-mediated modifications.
  • 6.3.A.4.i The addition of a poly-A tail makes mRNA more stable.
  • 6.3.A.4.ii The addition of a GTP cap helps with ribosomal recognition.
  • 6.3.A.4.iii The excision of introns, along with the splicing and retention of exons, generates different versions of the resulting mature mRNA molecule. This process is known as alternative splicing.

Enduring Understanding (BIG IDEA 3 — Information Storage and Transmission): Living systems store, retrieve, transmit, and respond to information essential to life processes.

Learning Objective 6.4.A: Explain how the phenotype of an organism is determined by its genotype.

• 6.4.A.1 Translation of the mRNA to generate a polypeptide occurs on ribosomes that are present in the cytoplasm of both prokaryotic and eukaryotic cells, as well as the cytoplasmic surface of the rough ER of eukaryotic cells.
• 6.4.A.2 In prokaryotic organisms, translation of the mRNA molecule occurs while it is being transcribed.
• 6.4.A.3 Translation involves many sequential steps, including initiation, elongation, and termination. The salient features of translation include:
  • 6.4.A.3.i Translation is initiated when the rRNA in the ribosome interacts with the mRNA at the start codon (AUG, coding for the amino acid methionine).
  • 6.4.A.3.ii The sequence of nucleotides on the mRNA is read in triplets, called codons.
  • 6.4.A.3.iii Each codon encodes a specific amino acid, which can be deduced by using a genetic code chart. Many amino acids are encoded by more than one codon.
  • 6.4.A.3.iv Nearly all living organisms use the same genetic code, which is evidence for the common ancestry of all living organisms.
  • 6.4.A.3.v tRNA brings the correct amino acid to the place specified by the codon on the mRNA.
  • 6.4.A.3.vi The amino acid is transferred to the growing polypeptide chain.
  • 6.4.A.3.vii The process continues along the mRNA until a stop codon is reached.
  • 6.4.A.3.viii Translation terminates with the release of the newly synthesized protein.
  • Exclusion statement: The details and names of the enzymes and factors involved in each of these steps are beyond the scope of the AP Exam.
  • Exclusion statement: Memorization of the genetic code, with the exception of the start codon AUG, is beyond the scope of the AP Exam.
• 6.4.A.4 Genetic information in retroviruses is a special case and has an alternate flow of information: from RNA to DNA, made possible by reverse transcriptase, an enzyme that copies the viral RNA genome into DNA. This DNA integrates into the host genome and is transcribed and translated for the assembly of new viral progeny.

Enduring Understanding (BIG IDEA 3 — Information Storage and Transmission): Living systems store, retrieve, transmit, and respond to information essential to life processes.

Learning Objective 6.5.A: Describe the types of interactions that regulate gene expression.

• 6.5.A.1 Regulatory sequences are stretches of DNA that interact with regulatory proteins to control transcription. Some genes are constitutively expressed, and others are inducible.
• 6.5.A.2 Epigenetic changes can affect gene expression through reversible modifications of DNA or histones.
• 6.5.A.3 The phenotype of a cell or an organism is determined by the combination of genes that are expressed and the levels at which they are expressed.
  • 6.5.A.3.i Observable cell differentiation results from the expression of genes for tissue-specific proteins.
  • 6.5.A.3.ii Induction of transcription factors during development results in sequential gene expression.
  • 6.5.A.3.iii The function and amount of gene products determine the phenotype of organisms.

Learning Objective 6.5.B: Explain how the location of regulatory sequences relates to their function.

• 6.5.B.1 Both prokaryotes and eukaryotes have groups of genes that are coordinately regulated.
  • 6.5.B.1.i Prokaryotes regulate operons in an inducible or repressible system.
  • 6.5.B.1.ii In eukaryotes, groups of genes may be influenced by the same transcription factors to coordinately regulate expression.

Enduring Understanding (BIG IDEA 3 — Information Storage and Transmission): Living systems store, retrieve, transmit, and respond to information essential to life processes.

Learning Objective 6.6.A: Explain how the binding of transcription factors to promoter regions affects gene expression and the phenotype of the organism.

• 6.6.A.1 RNA polymerase and transcription factors bind to promoter or enhancer DNA sequences to initiate transcription. These sequences can be upstream or downstream of the transcription start site.
• 6.6.A.2 Negative regulatory molecules inhibit gene expression by binding to DNA and blocking transcription.

Learning Objective 6.6.B: Explain the connection between the regulation of gene expression and phenotypic differences in cells and organisms.

• 6.6.B.1 Gene regulation results in differential gene expression and influences cell products and functions.
• 6.6.B.2 Certain small RNA molecules have roles in regulating gene expression.

Enduring Understanding (BIG IDEA 3 — Information Storage and Transmission): Living systems store, retrieve, transmit, and respond to information essential to life processes.

Learning Objective 6.7.A: Describe the various types of mutation.

• 6.7.A.1 Alterations in a DNA sequence are mutations that can cause changes in the type or amount of the protein produced and the consequent phenotype. DNA mutations can be beneficial, detrimental, or neutral based on the effect or the lack of effect they have on the resulting nucleic acid or protein and the phenotypes that are conferred by the protein.
  • 6.7.A.1.i Point mutations occur when one nucleotide has been substituted for a different nucleotide.
  • 6.7.A.1.ii Frameshift mutations occur when one or more nucleotides are inserted or deleted, causing the reading frame to be shifted.
  • 6.7.A.1.iii Nonsense mutations occur when there is a point mutation that causes a premature stop.
  • 6.7.A.1.iv Silent mutations occur when the change in the nucleotide sequence has no effect on the amino acid sequence.
  • Illustrative examples for 6.7.A.1:
    • Mutations in the CFTR gene disrupt ion transport and result in cystic fibrosis.
    • Mutations in the MC1R gene give adaptive melanism in pocket mice.
  • Exclusion statement: Knowledge of specific mutations and their effects is beyond the scope of the AP Exam.

Learning Objective 6.7.B: Explain how changes in genotype may result in changes in phenotype.

• 6.7.B.1 Errors in DNA replication or DNA repair mechanisms as well as external factors, including radiation and reactive chemicals, can cause random mutations in the DNA.
  • 6.7.B.1.i Whether a mutation is beneficial, detrimental, or neutral depends on the environmental context.
  • 6.7.B.1.ii Mutations are a source of genetic variation.
• 6.7.B.2 Errors in mitosis or meiosis can result in changes in phenotype.
  • 6.7.B.2.i Changes in chromosome number resulting from nondisjunction often result in new phenotypes caused by triploidy (aneuploidy).
  • 6.7.B.2.ii Changes in chromosome number often result in disorders with developmental limitations.
  • 6.7.B.2.iii Alterations in chromosome structure lead to genetic disorders.
  • Exclusion statement: Knowledge of specific disorders related to changes in chromosome number is beyond the scope of the AP Exam.

Learning Objective 6.7.C: Explain how alterations in DNA sequences contribute to variation that can be subject to natural selection.

• 6.7.C.1 Changes in genotype may affect phenotypes that are subject to natural selection. Genetic changes that enhance survival and reproduction can be selected for by environmental conditions.
  • 6.7.C.1.i The horizontal acquisitions of genetic information in prokaryotes via transformation (uptake of DNA), transduction (viral transmission of genetic information), conjugation (cell-to-cell transfer of DNA), and transposition (movement of DNA segments within and between DNA molecules) increase genetic variation.
  • 6.7.C.1.ii Related viruses can recombine genetic information if they infect the same host cell.
  • 6.7.C.1.iii Reproductive processes that increase genetic variation are evolutionarily conserved and are shared by various organisms.
  • Illustrative examples for 6.7.C.1: Sickle cell anemia

Enduring Understanding (BIG IDEA 3 — Information Storage and Transmission): Living systems store, retrieve, transmit, and respond to information essential to life processes.

Learning Objective 6.8.A: Explain the use of genetic engineering techniques in analyzing or manipulating DNA.

• 6.8.A.1 Genetic engineering techniques can be used to analyze and manipulate DNA and RNA.
  • 6.8.A.1.i Gel electrophoresis is a process that separates DNA fragments by size and charge.
  • 6.8.A.1.ii During polymerase chain reaction (PCR), DNA fragments are amplified by denaturing DNA, annealing primers to the original strand, and extending the new DNA molecule.
  • 6.8.A.1.iii Bacterial transformation introduces foreign DNA into bacterial cells.
  • 6.8.A.1.iv DNA sequencing technology determines the order of nucleotides in a DNA molecule. Typically, these techniques result in a DNA fingerprint that allows for the comparison of DNA sequences from various samples.
  • Illustrative examples for 6.8.A.1:
    • Amplified DNA fragments can be used to identify organisms and perform phylogenetic analysis.
    • Analysis of DNA can be used for forensic identification.
    • Genetically modified organisms include transgenic animals.
    • Gene cloning allows propagation of DNA fragments.
  • Exclusion statement: Knowledge of the details of each of these genetic engineering techniques is beyond the scope of the AP Exam.

Enduring Understanding (BIG IDEA 1 — Evolution): The process of evolution drives the diversity and unity of life.

Learning Objective 7.1.A: Describe the causes of natural selection.

• 7.1.A.1 Natural selection is a major mechanism of evolution.
• 7.1.A.2 According to Darwin's theory of natural selection, competition for limited resources results in differential survival. Individuals with more favorable phenotypes are more likely to survive and produce more offspring, thus passing on those favorable traits to subsequent generations.

Learning Objective 7.1.B: Explain how natural selection affects populations.

• 7.1.B.1 Evolutionary fitness is measured by reproductive success.
• 7.1.B.2 Biotic and abiotic environments can fluctuate, affecting the rate and direction of evolution. Different genetic variations can be selected in each generation.

Enduring Understanding (BIG IDEA 1 — Evolution): The process of evolution drives the diversity and unity of life.

Learning Objective 7.2.A: Describe the importance of phenotypic variation in a population.

• 7.2.A.1 Natural selection acts on phenotypic variations in populations.
• 7.2.A.2 Environments change and apply selective pressures to populations.
  • Illustrative examples for 7.2.A.2: Flowering time in relation to global climate change
• 7.2.A.3 Some phenotypic variations can increase or decrease the fitness of an organism in particular environments.
  • Illustrative examples for 7.2.A.3: Sickle cell anemia; DDT resistance in insects

Learning Objective 7.2.B: Explain how variation in molecules within cells connects to the fitness of an organism.

• 7.2.B.1 Variation in the number and types of molecules within cells can provide populations a greater ability to survive and reproduce in different environments.

Enduring Understanding (BIG IDEA 1 — Evolution): The process of evolution drives the diversity and unity of life.

Learning Objective 7.3.A: Explain how humans can affect diversity within a population.

• 7.3.A.1 Through artificial selection, humans affect variation in other species.

Enduring Understanding (BIG IDEA 1 — Evolution): The process of evolution drives the diversity and unity of life.

Learning Objective 7.4.A: Explain how random occurrences affect the genetic makeup of a population.

• 7.4.A.1 Evolution is also driven by random occurrences.
  • i. Mutation is a random process that adds new genetic variation to a population.
  • ii. Genetic drift is a change in allele frequencies attributable to a nonselective process occurring in small populations.
  • iii. The bottleneck effect is a type of genetic drift that occurs when a population size is reduced to a small number of individuals for at least one generation.
  • iv. The founder effect is a type of genetic drift that occurs when a population is separated from other members of the population. The frequency of genes and traits will shift based on the genes in this new founder population.
  • v. Migration can result in gene flow (the addition or removal of alleles from a population).

Learning Objective 7.4.B: Describe the role of random processes in the evolution of specific populations.

• 7.4.B.1 Random processes can lead to changes in allele frequencies in a population.
  • i. Mutations result in genetic variation, which provides phenotypes on which natural selection acts.
  • ii. Genetic drift can allow a small population to diverge from other populations of the same species.
  • iii. Gene flow between two populations prevents them from diverging into separate species.

Learning Objective 7.4.C: Describe the change in the genetic makeup of a population over time.

• 7.4.C.1 Changes in allele frequencies provide evidence for the occurrence of evolution in a population.

Enduring Understanding (BIG IDEA 1 — Evolution): The process of evolution drives the diversity and unity of life.

Learning Objective 7.5.A: Describe the conditions under which allele and genotype frequencies will change in populations.

• 7.5.A.1 The Hardy–Weinberg Equilibrium is a model for describing and predicting allele frequencies in a non-evolving population. Conditions for a population or an allele to be in Hardy–Weinberg equilibrium are:

  • i. A large population size
  • ii. No migration
  • iii. No new mutations
  • iv. Random mating
  • v. No natural selection

  These conditions are never met, but they provide a valuable null hypothesis.

• 7.5.A.2 Allele frequencies in a nonevolving population can be calculated from genotype frequencies.

  • Equation: Hardy–Weinberg Equation— $p^2 + 2pq + q^2 = 1$; $p + q = 1$, where: $p$ = frequency of allele 1 in the population; $q$ = frequency of allele 2 in the population
  • Illustrative examples for 7.5.A.2: Graphic analysis of allele frequencies in a population

Enduring Understanding (BIG IDEA 1 — Evolution): The process of evolution drives the diversity and unity of life.

Learning Objective 7.6.A: Describe the types of data that provide evidence for evolution.

• 7.6.A.1 Evolution is supported by scientific evidence from many disciplines (geographical, geological, physical, biochemical, and mathematical data).

Learning Objective 7.6.B: Explain how morphological, biochemical, and geological data provide evidence that organisms have changed over time.

• 7.6.B.1 Molecular, morphological, and genetic evidence from extant and extinct organisms adds to our understanding of evolution.
  • i. Fossils can be dated by a variety of methods. These include 1) the age of the rocks where a fossil is found; 2) the rate of decay of isotopes including carbon-14; and 3) geographical data.
  • ii. Morphological homologies, including vestigial structures, provide evidence of common ancestry.
• 7.6.B.2 A comparison of DNA nucleotide sequences and protein amino acid sequences provides evidence for evolution and common ancestry.

Enduring Understanding (BIG IDEA 1 — Evolution): The process of evolution drives the diversity and unity of life.

Learning Objective 7.7.A: Describe structural and functional evidence on cellular and molecular levels that provides evidence for the common ancestry of all eukaryotes.

• 7.7.A.1 Structural and functional evidence indicates common ancestry of all eukaryotes. This evidence includes:
  • i. Membrane-bound organelles
  • ii. Linear chromosomes
  • iii. Genes that contain introns

Enduring Understanding (BIG IDEA 1 — Evolution): The process of evolution drives the diversity and unity of life.

Learning Objective 7.8.A: Explain how evolution is an ongoing process in all living organisms.

• 7.8.A.1 All species have evolved and continue to evolve. Examples include:
  • i. Genomic changes over time
  • ii. Continuous change in the fossil record
  • iii. Evolution of resistance to antibiotics, pesticides, herbicides, or chemotherapy drugs
  • iv. Pathogens evolving and causing emergent diseases

Enduring Understanding (BIG IDEA 1 — Evolution): The process of evolution drives the diversity and unity of life.

Learning Objective 7.9.A: Describe the types of evidence that can be used to infer an evolutionary relationship.

• 7.9.A.1 Phylogenetic trees and cladograms show hypothetical evolutionary relationships among lineages that can be tested.
• 7.9.A.2 Phylogenetic trees show the amount of change over time calibrated by fossils or a molecular clock, whereas cladograms do not show time scale or the evolutionary difference between groups.
• 7.9.A.3 Traits that are either gained or lost during evolution can be used to construct phylogenetic trees and cladograms. The out-group represents the lineage that is least closely related to the remainder of the organisms in the phylogenetic tree or cladogram.
  • i. Shared derived characters can be present in more than one lineage and indicate common ancestry. These are informative for the construction of phylogenetic trees and cladograms.
  • ii. Molecular data typically provide more accurate and reliable evidence than morphological traits in the construction of phylogenetic trees or cladograms.

Learning Objective 7.9.B: Explain how phylogenetic trees and cladograms can be used to infer evolutionary relatedness.

• 7.9.B.1 Phylogenetic trees and cladograms can be used to illustrate speciation that has occurred. The nodes on a tree represent the most recent common ancestor of any two groups or lineages.
• 7.9.B.2 Phylogenetic trees and cladograms can be constructed from morphological similarities of living or fossil species and from DNA and protein sequence similarities.
• 7.9.B.3 Phylogenetic trees and cladograms represent hypotheses that are constantly being revised based on evidence.

Enduring Understanding (BIG IDEA 1 — Evolution): The process of evolution drives the diversity and unity of life.

Learning Objective 7.10.A: Describe the conditions under which new species may arise.

• 7.10.A.1 Speciation occurs when two populations become reproductively isolated from each other.
• 7.10.A.2 The biological species concept provides a commonly used definition of a species for sexually reproducing organisms. It states that species can be defined as a group capable of interbreeding and exchanging genetic information to produce viable, fertile offspring.

Learning Objective 7.10.B: Describe the rate of evolution and speciation under different ecological conditions.

• 7.10.B.1 Punctuated equilibrium is when evolution occurs rapidly after a long period of stasis. Gradualism is when evolution occurs slowly over hundreds of thousands or millions of years.
• 7.10.B.2 Divergent evolution occurs when adaptation to new habitats results in phenotypic diversification. Speciation rates can be especially rapid during times of adaptive radiation as new habitats become available.
• 7.10.B.3 Convergent evolution occurs when similar selective pressures result in similar phenotypic adaptations in different populations or species.

Learning Objective 7.10.C: Explain the processes and mechanisms that drive speciation.

• 7.10.C.1 Sympatric speciation occurs in populations with geographic overlap. Allopatric speciation occurs in populations that are geographically isolated.
• 7.10.C.2 Various pre-zygotic and post-zygotic mechanisms can maintain reproductive isolation and prevent gene flow between populations.
• Illustrative examples for 7.10.C: Hawaiian Drosophila; Caribbean Anolis; Apple maggot Rhagoletis

Enduring Understanding (BIG IDEA 4 — Systems Interactions): Biological systems interact, and these systems and their interactions exhibit complex properties.

Learning Objective 7.11.A: Explain how the genetic diversity of a species or population affects its ability to withstand environmental pressures.

• 7.11.A.1 The level of variation in a population affects population dynamics.
  • i. The ability of a population to respond to changes in the environment is influenced by genetic diversity. Species and populations with little genetic diversity are at risk of decline or extinction.
  • ii. Genetically diverse populations are more resilient to environmental perturbation because they are more likely to contain individuals that can withstand the environmental pressure.
  • iii. Alleles that are adaptive in one environmental condition may be deleterious in another because of different selective pressures.
  • Illustrative examples for 7.11.A.1: California condors; Black-footed ferrets; Prairie chickens; Potato blight; Corn rust; Genetic diversity and selective pressures; Antibiotic resistance in bacteria (not all individuals in a diverse population are susceptible to a disease outbreak)