AP Bio Unit 3 Review

Enzyme Structure and Catalysis

• Enzymes are proteins that speed up reactions by lowering activation energy.

• They do not change the energy difference between reactants and products

• Active sites bind substrates; specificity (the fact that enzymes are specific to their substrates) is key.

• Factors affecting enzyme activity: temperature, pH, and substrate concentration.

  • Having sub optimal conditions for these factors can denature the enzyme

  • if the amount of enzymes stays constant, if you add so much substrate that all the enzymes are activated, activity can still plateau

• High temperature - disrupts interactions b/t amino acids which can denature the enzyme which makes it lose secondary and tertiary structure

• Enzymes may require coenzymes or cofactors to help catalyze reactions

Environmental Impacts on Enzyme Function

• Temperature and pH can denature enzymes, altering their shape and function.

• Inhibitors (competitive and non-competitive) can decrease enzyme activity.

• Competitive inhibitors bind to the active site which compete with substrates

• Noncompetitive inhibitors bind to an allosteric site which changes the active site

• Regulatory molecules - Enzyme activity may be turned "up" or "down" by activator and inhibitor molecules that bind specifically to the enzyme.

• Cofactors - Many enzymes are only active when bound to non-protein helper molecules known as cofactors.

• Compartmentalization - Storing enzymes in specific compartments can keep them from doing damage or provide the right conditions for activity.

• Feedback inhibition - Key metabolic enzymes are often inhibited by the end product of the pathway they control (prevents too much product from being made)

• Cooperativity - When a substrate serves as an allosteric activator (binds to one site which increases activity of other sites)

• Compartmentalization - Enzymes are stored in a specific part of the cell to do their job

• Vmax means maximum velocity (rate of reaction)

  

• Proteolytic enzymes - enzymes that break down proteins

Cellular Energy

• ATP (adenosine triphosphate) is the primary energy carrier in cells.

• Energy is released when ATP is hydrolyzed to ADP and inorganic phosphate.

• First Law of Thermodynamics - energy cannot be created nor destroyed, only change form or transferred

• Second Law of Thermodynamics - in every energy conversion some amount of useful energy is converted to unusable energy (commonly heat)

• Transfer of heat increases entropy of the environment

• Entropy - the measure of a system's thermal energy per unit temperature that is unavailable for doing useful work

• Structure of ATP

  

• Phosphate group - A functional group characterized by a phosphorus atom bonded to four oxygen atoms

• ATP Hydrolysis Reaction - ATP + H2O ←→ ADP + Pi + energy (Pi is inorganic phosphate group, and ATP regeneration is the opposite)

• Reaction coupling - Energetically favorable reaction (ATP hydrolysis) is directly linked with an energetically unfavorable reaction (endergonic)

  • Shared intermediate - product of one reaction is “picked up“ and used as a reactant in a second reaction

• Anabolic - building up complex molecule

• Catabolic - breaking down complex molecule

• Entropy: A measure of the disorder or randomness in a system. In thermodynamics, the entropy of the universe tends to increase.

• Exergonic Reaction: A chemical reaction that releases energy, usually in the form of heat or work, and has a negative Gibbs free energy change.

• Endergonic Reaction: A chemical reaction that absorbs energy, typically requiring an input of energy to proceed, with a positive Gibbs free energy change.

🌱 Photosynthesis

• Occurs in chloroplasts; converts light energy into chemical energy (glucose).

• Two Phases: (Light and Dark Reactions)

  1. Light Reactions:

     • Sunlight is absorbed by chlorophyll, electrons are passed down a chain, and the energy molecules ATP and NADPH are produced. Water is also split into hydrogen and oxygen

     • Reactants: Light + Water (H₂O)

     • Products: Oxygen (O₂) + ATP + NADPH

     • Location: Thylakoid membranes

     • Process:

       • Photosystems are complexes of proteins and pigments that capture light energy.

       • Photosystem II (PSII):

         • First photosystem (named second in order of discovery).

         • Located in the thylakoid membrane.

         • Absorbs light energy (P680 chlorophyll a) to split water molecules into oxygen, protons, and electrons.

         • Excited electrons move through a series of proteins, creating a proton (H⁺) gradient that drives ATP synthesis via ATP synthase, similar to cellular respiration.

       • Photosystem I (PSI):

         • Also located in the thylakoid membrane.

         • Absorbs light energy to produce NADPH.

         • Peak absorption wavelength is due to chlorophyll a molecules (P700).

         • Excited electrons transfer to NADP⁺, reducing it to NADPH.

  2. Dark Reactions (Light-Independent Reactions):

     • Sugar is made in the Calvin Cycle by using energy from ATP and NADPH, and the carbon from CO2

     • Location: Stroma of the chloroplasts

     • Process: Uses energy from ATP and NADPH to build sugars from carbon dioxide (CO₂)

     • Calvin Cycle (Light-Independent Reactions):

       • Reactants: ATP + NADPH + Carbon Dioxide (CO₂)

       • Products: Sugars

       • Location: Stroma

     • While the calvin cycle does not need light, it still needs the materials from light-dependent reactions, so photosynthesis still cannot occur at night in cactus plants

     • CO2 Contributes to most of the mass gain in plants, not water nor soil

  Redox Reactions:

  • Oxidation: Loss of electrons

  • Reduction: Gain of electrons

  Electron Transport Chain (ETC):

  • Electrons from Photosystem II (PSII) are transferred through the electron transport chain to Photosystem I (PSI).

  • The energy from these electrons is used to produce ATP and NADPH.

  Calvin Cycle Steps:

  1. Carbon Fixation

  2. Reduction

  3. Regeneration of RuBP

Overall Calvin cycle reaction:

Photorespiration:

• C3 plants experience photorespiration, where the enzyme RuBisCO fixes oxygen instead of CO₂.

• C4 plants and CAM plants have adapted mechanisms to minimize photorespiration.

Cellular Respiration

• Process of breaking down glucose to produce ATP.

• Stages:

  • Glycolysis (cytoplasm)

    • 2 ATP used (investment)

    • 4 ATP gained

    • 2 NADH gained

  • Link reactions

    • Connects glycolysis with Krebs Cycle

    • Pyruvate moves into mitochondria

    • Reactants: 2 pyruvates and 2 NAD⁺

    • Produces:

      • 2 Acetyl-CoA

      • 2 CO₂

      • 2 NADH

  • Krebs cycle (mitochondria)

    • Products: ATP, CO₂, NADH, and FADH₂

    • NADH and FADH₂ carry electrons to the electron transport chain (ETC)

    • Oxaloacetate is the starting and final compound

  • Electron Transport Chain mitochondria)

    • Series of proteins embedded in the inner mitochondrial membrane

    • Main site of ATP production

    • Requires oxygen (which is why you breathe)

    • Energy from electrons pumps H⁺ ions into the intermembrane space

    • ATP synthase controls the flow of H⁺ from high to low concentration (passively)

    • The flow of H⁺ produces ATP from ADP

    • Oxidative Phosphorylation: The production of ATP is coupled with the movement of electrons through the electron transport chain (ETC) via ATP synthase.

• Electron Carriers:

  • NAD+ + H+ + 2 electrons = NADH

  • FAD + 2H+ + 2 electrons = FADH2

  • To carry electrons is to carry energy

Anaerobic respiration

• occurs when cells lack oxygen to act as a final electron acceptor

• pyruvates generated by glycolysis are broken down by fermentation to produce lactic acid or ethanol and NAD+

  • this permits glycolysis to continue and provide the 2 ATP it makes

Fitness

• Relates to how efficiently organisms convert energy for growth, reproduction, and survival.

• Metabolic rates and energy expenditure are key factors in fitness.

Key Terms:

• Bioenergetics: The study of the flow and transformation of energy in living systems.

• Redox Reaction: A chemical reaction involving the transfer of electrons between two substances, where one is oxidized (loses electrons) and the other is reduced (gains electrons).

• First Law of Thermodynamics: Energy cannot be created or destroyed, only transferred or converted from one form to another (law of conservation of energy).

• Second Law of Thermodynamics: The total entropy (disorder) of an isolated system always increases over time, and energy transformations are not 100% efficient.

• Entropy: A measure of the disorder or randomness in a system. In thermodynamics, the entropy of the universe tends to increase.

• Exergonic Reaction: A chemical reaction that releases energy, usually in the form of heat or work, and has a negative Gibbs free energy change.

• Endergonic Reaction: A chemical reaction that absorbs energy, typically requiring an input of energy to proceed, with a positive Gibbs free energy change.

• Energy Diagram: A graphical representation showing the energy changes that occur during a chemical reaction, often depicting the energy of reactants, products, and the activation energy.

• Transition State: A high-energy, unstable state in a chemical reaction where old bonds are breaking, and new bonds are forming.

• Activation Energy: The minimum energy required to start a chemical reaction, usually needed to break bonds in reactants.

• Enzyme Specificity: The property of an enzyme to bind only to specific substrates, determined by the enzyme's active site structure.

• Substrates: The reactants in an enzyme-catalyzed reaction that bind to the enzyme's active site.

• Active Site: The region of an enzyme where the substrate binds and undergoes a chemical reaction.

• Enzyme-Substrate Complex: A temporary complex formed when an enzyme binds to its substrate, facilitating the chemical reaction.

• Induced-Fit: A model of enzyme action where the enzyme's active site undergoes a conformational change upon substrate binding to better fit the substrate.

• Cofactors: Non-protein molecules or ions that are required for enzyme activity, either as a coenzyme or a metal ion.

• Coenzymes: Organic molecules that act as cofactors, often derived from vitamins, and assist enzymes in catalyzing reactions.

• Denatured: A process where an enzyme (or protein) loses its shape and, consequently, its function, usually due to extreme conditions like high temperature or pH.

• Q10: A measure of the temperature sensitivity of a biological or chemical reaction, usually the factor by which the rate of reaction increases with a 10°C rise in temperature.

• Allosteric Sites: Specific sites on an enzyme, other than the active site, where molecules (allosteric regulators) can bind and affect the enzyme’s activity.

• Competitive Inhibition: A form of enzyme inhibition where a molecule competes with the substrate for binding to the active site of the enzyme.

• Allosteric Inhibitor: A molecule that binds to the allosteric site of an enzyme and reduces its activity.

• Noncompetitive Inhibition: A form of enzyme inhibition where an inhibitor binds to a site other than the active site, altering the enzyme's shape and decreasing its activity.

• Light Reactions: The first stage of photosynthesis, where light energy is captured by chlorophyll and used to produce ATP and NADPH.

• Dark Reactions: Also known as the Calvin Cycle, the second stage of photosynthesis, where carbon dioxide is fixed into organic molecules using ATP and NADPH produced in the light reactions.

• Stroma: The fluid-filled space inside chloroplasts surrounding the thylakoid membranes, where the Calvin Cycle occurs.

• Grana: Stacks of thylakoid membranes inside chloroplasts where the light reactions of photosynthesis take place.

• Thylakoids: Membrane-bound structures within chloroplasts that contain chlorophyll and other pigments, and are the site of the light reactions of photosynthesis.

• Chlorophyll a and b: The main pigments in plants that absorb light energy for photosynthesis, with chlorophyll a being the primary pigment and chlorophyll b assisting in light absorption.

• Carotenoids: Accessory pigments in plants that absorb light energy and protect against damage from excess light, contributing to photosynthesis.

• Reaction Center: The region of the photosystem where light energy is converted into chemical energy by exciting electrons.

• Antenna Pigments: Pigments that absorb light and transfer the energy to the reaction center during photosynthesis.

• Photosystem I: A protein-pigment complex involved in the light reactions of photosynthesis, primarily responsible for the production of NADPH.

• Photosystem II: A protein-pigment complex involved in the light reactions, primarily responsible for splitting water molecules and producing ATP.

• P680: The reaction center chlorophyll in Photosystem II, which absorbs light most efficiently at a wavelength of 680 nm.

• P700: The reaction center chlorophyll in Photosystem I, which absorbs light most efficiently at a wavelength of 700 nm.

• Photophosphorylation: The process of using light energy to generate ATP through the electron transport chain during the light reactions of photosynthesis.

• Absorption Spectrum: A graph showing the wavelengths of light absorbed by a pigment or photosystem.

• Emission Spectrum: The spectrum of light emitted by a substance after it absorbs energy.

• Photolysis: The splitting of water molecules using light energy in the light reactions of photosynthesis, producing oxygen, protons, and electrons.

• Carbon Fixation: The process of converting inorganic carbon dioxide into an organic molecule, primarily through the Calvin Cycle in photosynthesis.

• Calvin-Benson Cycle: A cycle of reactions in photosynthesis where carbon dioxide is fixed into glucose and other organic molecules.

• Photorespiration: A process that occurs when oxygen is incorporated into the Calvin Cycle instead of carbon dioxide, leading to a loss of energy and reduced efficiency in photosynthesis.

• CAM Plants: Plants that use crassulacean acid metabolism to minimize water loss, opening their stomata at night to fix carbon dioxide.

• C4 Plants: Plants that use a modified pathway for carbon fixation, where carbon dioxide is initially fixed into a 4-carbon compound, improving efficiency in hot environments.

• Aerobic Respiration: Cellular respiration that occurs in the presence of oxygen, producing ATP by fully oxidizing glucose to carbon dioxide and water.

• Anaerobic Respiration: Cellular respiration that occurs without oxygen, producing ATP by partially oxidizing glucose (e.g., fermentation).

• Pyruvic Acid: A 3-carbon compound produced by the breakdown of glucose during glycolysis, which can be further processed in aerobic or anaerobic respiration.

• Acetyl CoA: A 2-carbon molecule that is produced from pyruvic acid and enters the citric acid cycle in aerobic respiration.

• Pyruvate Dehydrogenase Complex: An enzyme complex that converts pyruvate into acetyl CoA in preparation for the citric acid cycle.

• Oxaloacetate: A 4-carbon molecule that combines with acetyl CoA to form citric acid in the citric acid cycle.

• Citric Acid: A 6-carbon compound formed in the citric acid cycle from acetyl CoA and oxaloacetate.

• Cytochrome C: A protein in the electron transport chain that transfers electrons between complexes and plays a key role in oxidative phosphorylation.

• Proton Gradient: A concentration gradient of protons (H+) across a membrane, used in chemiosmosis to drive ATP synthesis.

• Chemiosmosis: The process of generating ATP using a proton gradient across a membrane, as protons flow through ATP synthase.

• ATP Synthase: An enzyme complex that synthesizes ATP from ADP and inorganic phosphate, using the energy of a proton gradient.

• Oxidative Phosphorylation: The process of ATP production through the electron transport chain and chemiosmosis, occurring in the mitochondria.

• Lactic Acid: A 3-carbon compound produced during anaerobic respiration in muscle cells, causing muscle fatigue.

• Ethanol: A 2-carbon alcohol produced by fermentation in yeast and some bacteria.

• Fermentation: An anaerobic process that allows cells to generate ATP by converting glucose into products like lactic acid or ethanol when oxygen is unavailable.