Cellular Energetics · ⁨استقلاب الخلايا⁩

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.