AP Biology Unit 3: Cellular Energetics Flashcards

Enzymes (Topics 3.1-3.3)

• Enzymes are typically proteins (some RNAs can also act as enzymes).
• They catalyze reactions by lowering activation energy and increasing reaction rate.
• Example:
  • Reaction catalyzed by an enzyme has lower activation energy compared to a non-catalyzed reaction.
• Enzymes are highly specific due to the active site complementing the substrate's shape and charge.
• Active Site: Region on enzyme where the substrate binds.
• Substrate: Substance acted upon by enzyme.
• Enzyme-substrate interaction leads to product formation.
• Optimum conditions: Enzymes function best under specific pH, ionic, and temperature conditions due to their protein structure (secondary, tertiary, quaternary).
• These structures involve hydrogen, ionic, and hydrophobic interactions.
• Changes in pH, temperature, or ion concentration disrupts bonds, altering the active site shape and preventing substrate binding.
• Denaturation: Change in enzyme shape that reduces or negates function.
• pH optimum: Enzymes have a pH at which they operate most efficiently.
  • Activity decreases above or below optimum pH due to disruption of protein bonds and denaturation.
• Temperature effects:
  • Enzyme activity increases with temperature (up to a point) due to increased kinetic energy and molecular motion, enhancing enzyme-substrate binding.
  • Beyond a certain temperature, enzymes denature, reducing catalytic ability.
• Reversible vs. Irreversible Denaturation:
  • Reversible denaturation: Enzyme function is restored when optimal conditions are restored, allowing the enzyme to regain its optimal shape.
  • Irreversible denaturation: Enzyme shape is permanently changed, destroying catalytic ability.
  • Example: Cooking an egg; the egg white solidifies and cannot revert to its original state.
• Substrate Concentration:
  • Low substrate concentration: Low probability of enzyme-substrate interaction, resulting in a low product formation rate.
  • Increased substrate concentration: Collision and reaction rates increase.
  • Saturation point: All enzyme active sites are interacting with substrates, leading to a peak reaction rate.
• Competitive vs. Non-competitive Inhibition:
  • Competitive inhibition: A foreign molecule blocks the enzyme's active site, preventing substrate binding and inhibiting the reaction rate.
  • Non-competitive inhibition: A foreign molecule binds to the allosteric site (away from the active site), causing a conformational change in the enzyme, altering the active site shape and preventing substrate binding, thus diminishing or blocking enzyme activity.

Cell Energy (Topic 3.4)

• Metabolic Pathway: A linked series of enzyme-catalyzed chemical reactions within a cell.
  • Involves initial reactants, intermediates, and final products.
  • Examples: Glycolysis, Krebs cycle, Calvin cycle.
  • Pathways can be linear (glycolysis) or cyclical (Krebs cycle, Calvin cycle).
• Autotrophs: Organisms that produce their own food.
  • Photoautotrophs: Use light energy to create organic compounds via photosynthesis.
    • Examples: Plants, cyanobacteria.
  • Chemoautotrophs: Use energy from oxidizing inorganic substances (chemosynthesis).
    • Examples: Some bacteria and archaea (iron, sulfur, hydrogen sulfide oxidation).
• Heterotrophs: Organisms that obtain energy by consuming organic compounds from other organisms.
  • Includes consumers, decomposers, and parasites.
  • They metabolize organic compounds for energy and matter.
• Exergonic vs. Endergonic Reactions:
  • Exergonic reactions: Release energy and increase entropy (disorder).
    • Examples: Cellular respiration, most hydrolysis reactions.
  • Endergonic reactions: Require energy and decrease entropy (increase organization).
    • Examples: Photosynthesis, dehydration synthesis reactions.
• ATP (Adenosine Triphosphate):
  • Structure: Ribose (5-carbon sugar), adenine (nitrogenous base), and three phosphate groups.
  • Function: Powers work within cells; every cell makes its own ATP and does not share with other cells.
  • ATP stores energy by combining ADP and a phosphate group during cellular respiration or photosynthesis.
  • ATP releases energy by removing a phosphate group, creating ADP and phosphate, which fuels cellular work.
• Energy Coupling: Linking an exergonic reaction to an endergonic reaction to drive the endergonic reaction forward.
  • Example 1: Cellular respiration (exergonic) drives ATP formation from ADP and phosphate (endergonic).
  • Example 2: ATP hydrolysis (ATP to ADP + phosphate) powers muscle contraction (endergonic reaction).

Photosynthesis - The Big Picture

• Photosynthesis: Photoautotrophs combine carbon dioxide and water using light energy to create carbohydrates, releasing oxygen as a waste product.
  • Formula: 6CO2 + 6H2O
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    ull C6H{12}O6 + 6O2
• Endergonic reaction: Converts low-energy inputs (CO2 and H2O) to a high-energy product (glucose) and reduces entropy (increases organization).
• Evolution:
  • Evolved approximately 3.5 billion years ago.
  • Consequences: Created an oxygen-rich atmosphere, enabling aerobic metabolism and forming the ozone layer, facilitating life on land.
• Two Phases of Photosynthesis:
  • Light Reactions: Convert light energy into chemical energy (ATP and NADPH) in the thylakoids.
  • Calvin Cycle: Converts chemical energy (NADPH and ATP) into carbohydrates using carbon dioxide in the stroma.
• Chlorophyll:
  • The pigment absorbs light energy.
  • Structure: Hydrocarbon tail (for fitting into thylakoid phospholipid bilayer) and a nitrogen ring with magnesium (for converting light energy to electrical energy).
  • Absorption Spectrum: Shows light absorption at different wavelengths. Chlorophyll absorbs most energy in blue and red parts of the spectrum, reflecting green light (leaves appear green).
  • Chlorophyll a and b have slightly different absorption spectra due to different functional groups.
• Action Spectrum: Shows how various light wavelengths drive photosynthesis. Blue and red light drive the most photosynthesis.
  • Engelmann Experiment: Aerobic bacteria grew best around algae filaments exposed to blue and red light, indicating high oxygen production in these regions.
• Chloroplast Structure and Function:
  • Outer and Inner Membranes: Vestiges of evolutionary origins.
  • DNA and Ribosomes: Also vestiges of its origin as an independent living cell.
  • Thylakoids: Contain membrane-bound photosystems and chlorophyll for light reactions, organized into grana.
  • Stroma: Cytoplasm of the chloroplast, contains DNA, ribosomes, and is the site of the Calvin cycle.

The Light Reactions of Photosynthesis (Topic 3.5)

• Products: Convert light energy into chemical energy (NADPH and ATP).
  • NADPH: Electron carrier (like NADH in cellular respiration).
  • ATP: Energy currency for cells.
  • Occur in thylakoids; oxygen is a waste product.
  • Inputs: Light and water.
  • Outputs: ATP and NADPH (for the Calvin cycle); NADP+ and ADP + P are inputs.
• Key Structures:
  • Photosystems: Protein complexes with embedded chlorophyll molecules in the thylakoid membrane.
  • Function: Convert light energy into a flow of electrons and split water molecules (in Photosystem II).
  • Photosystem II comes before Photosystem I in the electron pathway.
  • Electron flow through proton pumps (cytochromes) pumps protons from the stroma into the thylakoid space, creating a chemiosmotic gradient.
  • ATP synthase: Enzyme that generates ATP as protons diffuse through it from the thylakoid space back to the stroma.
• ATP Creation:
  • Photoexcitation of chlorophyll in Photosystem II leads to electron flow along the electron transport chain in the thylakoid membrane.
  • The electron transport chain powers a proton pump, pumping protons from the stroma into the thylakoid space (chemiosmotic gradient).
  • Protons diffuse through ATP synthase, generating ATP from ADP and phosphate.
  • Water-splitting complex: Part of Photosystem II splits water, creating oxygen, protons, and electrons (enhances the proton gradient).
• NADPH Creation:
  • Photoexcitation of chlorophylls in Photosystem I creates electron flow through its electron transport chain.
  • Electrons flow to NADP+ reductase, which reduces NADP+ into NADPH (reduction is the gain of electrons).
  • NADPH provides electrons and hydrogens to reduce carbon dioxide into carbohydrates during the Calvin cycle.
• Z Scheme: Graphical representation of the light reactions:
  • Y-axis: Electron energy.
  • Light boosts electrons in Photosystem II to a higher energy level, while water is split into protons and oxygen.
  • Electrons flow through the electron transport chain of Photosystem II, powering proton pumps for ATP synthesis.
  • Electrons arrive at Photosystem I (lower energy), where light boosts them again to a high energy level.
  • Electrons pass through the electron transport chain of Photosystem I to NADP+ reductase, creating NADPH from NADP+ and a proton.

The Calvin Cycle

• Overview: Uses the products of the light reactions (ATP & NADPH) and CO2 to create sugars, taking place in the stroma. Occurs in three phases:
  • Carbon Fixation: Carbon dioxide gas is brought into the biosphere.
  • Energy Investment and Harvest: Matter is pulled out to become a part of the plant.
  • Regeneration: The starting compound is regenerated (RuBP).
• Carbon Fixation Phase:
  • CO2 is combined with RuBP (ribulose-1,5-bisphosphate), catalyzed by RuBisCO (may be the most abundant protein on Earth).
  • A six-carbon product is temporarily created but immediately dissociates into two three-carbon molecules.
• Energy Investment and Harvest Phase:
  • Three-carbon product from carbon fixation is reduced and phosphorylated.
  • ATP donates a phosphate group (phosphorylation).
  • NADPH donates an electron (reduction), creating G3P (glyceraldehyde-3-phosphate), also called PGAL (phosphoglyceraldehyde).
  • G3P has more energy than its precursor and can now be harvested to build plants.
• Calvin Cycle – Carbon Tracking:
  • Three RuBPs (15 carbons total) combine with three CO2s (3 carbons) for a total of 18 carbons.
  • The result is six three-carbon molecules (18 carbons total).
  • During energy investment, G3P (glyceraldehyde 3-phosphate) molecules are produced, but there is no carbon added.
  • One G3P molecule is harvested (3 carbons), leaving 15 carbons.
  • The remaining five G3Ps (15 carbons) are rearranged by enzymes into three five-carbon RuBPs, using energy from ATP.

Cellular Respiration - The Big Picture

• Chemical Equation: C6H{12}O6 + 6O2
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• Exergonic reaction: Releases energy and increases disorder (entropy).
• Location in Eukaryotic Cells:
  • Glycolysis: Cytoplasm.
  • Link Reaction: Mitochondrion (moving pyruvate into the Mitochondria).
  • Krebs Cycle: Mitochondrial matrix.
  • Oxidative Phosphorylation: Mitochondrial membrane and intermembrane space (chemiosmosis).
• Brief Description of Each Phase:
  • Glycolysis: Energy in glucose generates ATP and NADH; end product is pyruvate (pyruvic acid).
    • One glucose (6-carbon) becomes two pyruvates (3-carbon each).
  • Link Reaction: Pyruvate enters the mitochondrial matrix and is converted to acetyl CoA (2-carbon), releasing CO2 and producing NADH.
  • Krebs Cycle: Enzymes oxidize carbons in acetyl CoA, producing NADH, FADH2, ATP, and releasing CO2.
    • For every glucose, the Krebs cycle runs twice.
  • Electron Transport Chain (ETC): Oxidizes NADH and FADH2, creating electron flow that powers ATP production via chemiosmosis.
    • Most ATP is produced during this phase.

Cellular Respiration: Glycolysis, Link Reaction, and Krebs Cycle

• Glycolysis: "Come on sugar for the breakdown!" Occurs in the cytoplasm, is anaerobic.
  • Three Parts:
    • Investment: Enzymes phosphorylate glucose, using ATP to create fructose-1,6-bisphosphate.
    • Cleavage: Enzymes cleave fructose-1,6-bisphosphate into two molecules of G3P (glyceraldehyde-3-phosphate).
    • Energy Harvest: G3P is oxidized and phosphorylated to produce ATP and NADH.
• Net Yield of Glycolysis:
  • 2 ATPs (4 produced, but 2 invested).
  • 2 NADHs
  • 2 Pyruvate molecules (still loaded with energy).
• Link Reaction (Between Glycolysis and Krebs Cycle):
  • Pyruvic acid (from glycolysis) is transported across the inner and outer mitochondrial membranes into the mitochondrial matrix.
  • Enzymes remove CO2 from pyruvic acid (one-third of the CO2 you exhale).
  • The resulting two-carbon molecule (acetyl group) is oxidized, and electrons are transferred to NAD+ to form NADH.
  • The acetyl group is attached to coenzyme A, forming acetyl CoA (starting point for Krebs cycle).
• Krebs Cycle (Citric Acid Cycle / Tricarboxylic Acid Cycle - TCA):
  • Occurs in the mitochondrial matrix.
  • Cyclical series of reactions that generate NADH, FADH2, and ATP.
  • Enzymes transfer the two-carbon acetyl group from acetyl CoA to oxaloacetate (4-carbon) to form citrate (6-carbon).
  • Enzymes oxidize citrate, releasing CO2 and transferring electrons to NAD+ to form NADH and to FAD to form FADH2.
  • One ATP is generated per cycle via substrate-level phosphorylation.
  • For each acetyl CoA entering the cycle: 1 ATP, 3 NADH, and 1 FADH2 are generated.
  • Oxaloacetate is the starting and ending compound (regenerated each cycle).
  • CO2 is released as a byproduct (the other two-thirds of the CO2 you exhale).

Cellular Respiration: Electron Transport Chain and Oxidative Phosphorylation

• Electron Transport Chain (ETC):
  • NADH and FADH2 (mobile electron carriers) from glycolysis, the link reaction, and the Krebs cycle accumulate in the mitochondrial matrix and diffuse to the inner membrane, where they are oxidized.
  • Electrons flow through the ETC, a series of membrane-embedded proteins in the mitochondrial inner membrane.
    • NADH electrons enter earlier, having more energy than FADH2 electrons.
    • Some ETC proteins are proton pumps.
  • Proton Pumps: Pump protons from the matrix to the intermembrane space (active transport, requires energy).
  • Source of Energy: Energy from the flow of electrons creates an electrochemical gradient.
• Oxygen as Final Electron Acceptor:
  • Oxygen pulls electrons down the ETC due to its high electronegativity.
  • Oxygen absorbs electrons and protons, forming water, thereby maintaining the proton gradient.
• ATP Synthase and Chemiosmosis:
  • Protons accumulated in the intermembrane space diffuse back to the matrix through ATP synthase (channel and enzyme).
  • Kinetic energy from proton diffusion is used to generate ATP from ADP and phosphate.
• Heat Generation Instead of ATP:
  • Brown fat cells (in newborns, hibernating mammals) are dense with mitochondria and generate heat.
  • Thermogenin (UCP - uncoupling protein) forms channels in the inner mitochondrial membrane.
  • Protons diffuse back to the matrix without passing through ATP synthase, uncoupling the ETC from ATP production.
  • Electron transport still occurs generating heat but not ATP.
• Similarities Between ATP Generation in Mitochondria and Chloroplasts:
  • Both processes use an electron transport chain to pump protons into an enclosed space, creating a proton gradient.
  • Photosynthesis pumps protons from the stroma to thylakoid space.
  • Cellular respiration pumps protons from the matrix to the intermembrane space.
  • Both use chemiosmosis: diffusion of protons through ATP synthase channel to generate ATP.
  • Evolutionary Significance: Mitochondria and chloroplasts share a common ancestor, indicated by similar mechanisms like ATP synthase.

Cellular Respiration: Anaerobic Respiration and Fermentation

• Aerobic vs. Anaerobic Respiration:
  • Aerobic Respiration: Requires oxygen, involves glycolysis, link reaction, Krebs cycle, and electron transport chain. Generates ~32 ATP per glucose molecule.
  • Anaerobic Respiration: Occurs when oxygen is insufficient or lacking. Involves glycolysis followed by fermentation. Generates 2 ATP. All in Cytoplasm.
• Fermentation:
  • Glycolysis followed by reactions that regenerate NAD+.
• Why Fermentation Occurs:
  • Allows glycolysis to continue when oxygen is limited because glycolysis requires NAD+ (substrate for one of the reactions).
• Alcohol vs. Lactic Acid Fermentation:
  • Alcohol (Ethanol) Fermentation: Yeast removes CO2 from pyruvic acid, producing acetaldehyde, which is reduced to ethanol. NADH is oxidized to NAD+ (allows glycolysis to continue).
  • Lactic Acid Fermentation: Pyruvate is reduced to lactic acid in muscle tissue under anaerobic conditions. NADH is oxidized to NAD+ (allows glycolysis to continue). Occurs more commonly during exercise.