Unit 3 Cellular Energetics - VOCABULARY Flashcards
Topic 3.1: Enzymes
Overview
Enzymes are proteins that act as biological catalysts to facilitate chemical reactions in cells by lowering the activation energy.
They regulate biological processes through their structure and function.
Enzyme-catalyzed reactions differ from uncatalyzed reactions primarily in rate, not in the Gibbs free energy change of the reaction.
What is an enzyme?
A protein that acts as a catalyst to accelerate a chemical reaction in a cell.
An enzyme is associated with an active site where the substrate binds.
The enzyme–substrate complex model illustrates how the shape and charge of the substrate must be compatible with the enzyme's active site for binding to occur.
Monomer: the building block of enzymes is the amino acid; enzymes are polypeptides composed of amino acids.
Structure and function relationships
The structure of an enzyme (shape, charge, and active site geometry) contributes to regulation of biological processes.
The active site provides a unique microenvironment that stabilizes the transition state and lowers activation energy.
Substrate binding to the active site may involve specific interactions (shape and charge) that drive catalysis.
Enzyme–substrate interactions
Substrate binding to an enzyme forms the enzyme–substrate complex.
The substrate must be compatible in shape and charge with the active site for binding to occur.
Once bound, the enzyme catalyzes the chemical reaction and products are released, leaving the enzyme free to catalyze additional reactions.
The rate of the reaction depends on the enzyme concentration, substrate concentration, temperature, pH, and presence of regulators/inhibitors.
What is an enzyme-catalyzed reaction?
An enzyme-mediated chemical reaction where the enzyme binds the substrate and converts it to products via a lower activation energy pathway.
The reaction’s ΔG (Gibbs free energy change) is the same with or without the enzyme; enzymes do not alter the overall free energy change, but they decrease the activation energy barrier.
Activation energy and Gibbs free energy
Activation energy (often denoted ΔG‡) is the energy barrier that must be overcome for a reaction to proceed.
Enzymes lower ΔG‡, increasing the rate of the reaction.
The change in Gibbs free energy (ΔG) between reactants and products remains unchanged by enzymes:
\Delta G = G{products} - G{reactants}Some reactions are exergonic (ΔG < 0) or endergonic (ΔG > 0) independent of catalysis; the enzyme affects how fast the reaction happens, not whether it proceeds spontaneously.
Enzyme kinetics and regulation (essential concepts)
The rate of an enzyme-catalyzed reaction can be influenced by substrate concentration; at high substrate levels, the enzyme can become saturated and the rate levels off.
Inhibitors can regulate enzyme activity (see 3.2.B for inhibitors):
Competitive inhibitors: bind reversibly to the active site, blocking substrate binding.
Noncompetitive inhibitors (allosteric inhibitors): bind to sites other than the active site, altering enzyme activity.
Reversibility of inhibition and ways to overcome inhibition:
Competitive inhibition can be overcome by increasing substrate concentration.
Common questions to study (from transcript prompts)
What is the enzyme? What is the structure of an enzyme? How does structure contribute to regulation? What is an enzyme? How does an enzyme affect reaction rate?
What is the enzyme–substrate complex? How does substrate geometry/charge affect active site binding?
What is an enzyme-catalyzed reaction? How does activation energy differ between enzyme-catalyzed and uncatalyzed reactions?
What is the monomer that makes up an enzyme? How does an enzyme influence the rate of a reaction?
Topic 3.2: Environmental Impact on Enzyme Function
3.2.A: How changes to enzyme structure affect function
Changes to the molecular structure of an enzymatic component can affect function or efficiency.
Denaturation occurs when protein structure is disrupted by changes in temperature, pH, or chemical environment, eliminating catalytic ability.
Environmental temperatures or pH outside the optimal range disrupt hydrogen bonds, alter structure, and change catalytic efficiency.
3.2.A.2: Denaturation can be reversible in some cases (reversible denaturation).
Key concepts and practice prompts (3.2.A)
Identify two conditions that affect enzyme structure and describe what happens to the enzyme’s structure under these conditions.
Explain how a change in structure affects enzyme function.
Predict outcomes when there is a change in enzyme structure (three possibilities: no effect, partial loss of activity, complete loss).
Describe how pH changes (increase or decrease in hydrogen ion concentration) affect enzyme structure and activity.
Describe how temperature changes affect kinetic energy and enzyme activity; what happens if the optimal temperature is exceeded.
Explain reversible denaturation and give examples of proteins that can refold after denaturation and proteins that cannot.
3.2.B: How the cellular environment affects enzyme activity
3.2.B.1: Substrate and product concentrations influence reaction rate; product buildup can slow the reaction (product inhibition); rate often increases with substrate concentration but may level off when enzymes become saturated.
3.2.B.2: Higher temperatures increase molecular movement and collision frequency, increasing reaction rate up to the enzyme’s optimal temperature; beyond that, activity falls due to denaturation.
3.2.B.3: Inhibitors regulate enzyme activity:
Competitive inhibitors bind to the active site and can be overcome by increasing substrate concentration.
Noncompetitive inhibitors bind to allosteric (regulatory) sites, changing the enzyme's activity.
Practice prompts (3.2.B) summarized
What is a competitive inhibitor? How can a researcher overcome competitive inhibition?
What is a noncompetitive inhibitor? Describe the binding site for competitive vs noncompetitive inhibitors.
How does inhibitor binding affect reaction rate?
Topic 3.3: Cellular Energy
3.3.A: The role of energy in living organisms
All living systems require an input of energy to grow, reproduce, and maintain dynamic homeostasis.
Energy input must exceed energy loss to maintain order and power cellular processes.
Cellular processes that release energy may be coupled to processes that require energy (energy coupling).
Exergonic reactions release energy; endergonic reactions require energy input.
Significant loss of energy flow or order results in death; organisms obey the laws of thermodynamics.
Note: An explicit AP exam constraint excludes memorization of the Gibbs free energy equation for this topic, but understanding the concept of energy input, loss, and coupling remains essential.
3.3.A.3: Energy-related pathways are sequential to enable controlled energy transfer
Metabolic pathways are arranged so that the product of one reaction is the reactant for the next step, enabling regulated and stepwise energy capture and use.
3.3.B: Shared, conserved, fundamental processes support common ancestry
Core metabolic pathways (e.g., glycolysis, oxidative phosphorylation) are conserved across Archaea, Bacteria, and Eukarya.
Implications: glycolysis is present in all domains; evidence suggests glycolysis first occurred in the common ancestor of all life; oxidative phosphorylation mechanisms differ among domains (archaea, bacteria, eukaryotes) but share the same fundamental principle.
Representative statements from prompts:
TRUE or FALSE? All organisms perform glycolysis. (Answer: True; glycolysis is highly conserved.)
Glycolysis has been conserved across all domains; the claim that glycolysis first occurred in the common ancestor is supported by its universality.
How oxidative phosphorylation is performed differs among archaea, bacteria, and eukaryotes but relies on a proton motive force and ATP synthase.
Connections to energy concepts
Metabolic pathways enable energy release from macromolecules (carbohydrates, fats, proteins) to drive ATP synthesis.
Energy coupling via ATP hydrolysis or other high-energy phosphate compounds powers cellular work.
Loss of energy or order leads to collapse of cellular homeostasis; cells must continually harvest energy to sustain life processes.
Topic 3.4: Photosynthesis
3.4.A: Photosynthetic processes and chloroplast structure
Chloroplast structure: stroma (fluid inside chloroplast, outside thylakoids), thylakoid membranes organized in stacks called grana; chlorophyll is embedded in thylakoid membranes.
The stroma houses the Calvin cycle; the thylakoid membranes host the light reactions with two photosystems (I and II) linked by an electron transport chain (ETC).
Exclusion: memorization of Calvin cycle steps, exact enzyme names, and Calvin cycle intermediates (except ATP synthase) is beyond AP scope.
3.4.A.1–3: Photosynthesis overview and light–dark reactions
Photosynthesis uses CO₂ and H₂O with light to produce carbohydrates and O₂.
Photosynthesis evolved first in prokaryotes; cyanobacteria are evidence for the origin of atmospheric O₂.
Prokaryotic photosynthetic pathways laid the foundation for eukaryotic photosynthesis.
The Calvin cycle occurs in the stroma; light reactions occur in the thylakoid membranes/grana.
Light reactions produce ATP and NADPH to power the Calvin cycle.
3.4.B: How cells capture energy from light and transfer it to biological molecules
3.4.B.1: Electron transport chain (ETC) reactions occur in chloroplasts, mitochondria, and prokaryotic membranes. In photosynthesis, electrons from the thylakoid membrane are transferred to NADP+ to form NADPH in photosystem I.
3.4.B.2: Photolysis of water in the light reactions provides electrons to replace those lost by photosystem II, producing O₂ as a byproduct.
3.4.B.3: Photosystems I and II are embedded in the thylakoid membrane and connected by ETCs; thylakoids stack to form grana.
3.4.B.4: Proton gradient is generated across the thylakoid membrane as electrons move through the ETC; this gradient drives ATP synthesis via ATP synthase (photophosphorylation).
3.4.B.5: The proton gradient links the light reactions to ATP synthesis; chemiosmosis powers ATP production.
3.4.B.6: The energy captured in light reactions (ATP and NADPH) powers carbon fixation in the Calvin cycle (stroma).
3.4.B.7–8: Structure–function relations of photosystems and thylakoid organization optimize energy capture and ATP/NADPH production; describe light reactions, dark reactions (Calvin cycle), and energy coupling.
3.4.B.9–10: Practice prompts
Structure and location of photosystems I and II; thylakoid membrane organization; diagram labeling; energy coupling between light reactions and Calvin cycle; photophosphorylation; proton gradient roles.
3.4.B.11–12: Connections and applications
NADPH formation during light reactions; ATP synthesis; movement of electrons to NADP+; the role of photolysis in sustaining electron flow.
Relationship between light reactions and Calvin cycle in producing carbohydrate from CO₂ in the stroma.
Topic 3.5: Cellular Respiration
3.5.A: Mitochondria and energy extraction from macromolecules
Cellular respiration uses energy from biological macromolecules to synthesize ATP; both respiration and fermentation are characteristic of life.
Aerobic cellular respiration (in eukaryotes) involves a series of enzyme-catalyzed steps that harvest energy and transfer it to ATP.
The electron transport chain (ETC) transfers electrons through a chain of carriers to a terminal electron acceptor (O₂ in aerobic respiration), creating a proton gradient across membranes.
The proton gradient drives ATP synthesis via ATP synthase; chemiosmosis links electron transport to ATP production (oxidative phosphorylation).
In prokaryotes, ETC occurs in the plasma membrane; in eukaryotes, it occurs across the inner mitochondrial membrane with cristae increasing surface area to maximize ATP yield.
Decoupling oxidative phosphorylation from the ETC can release heat in endotherms.
3.5.A.1–3: Krebs cycle, ETC, and ATP production
3.5.A.1: Glycolysis, fermentation, and respiration are core energy pathways across life.
3.5.A.2: Aerobic respiration involves a series of enzyme-catalyzed steps that extract energy from macromolecules; three major stages are glycolysis, the Krebs cycle, and the ETC/oxidative phosphorylation.
3.5.A.3: ETC details (summary): NADH and FADH₂ donate electrons to the ETC; protons are pumped across a membrane, creating a proton gradient; electrons are finally transferred to O₂ (aerobic respiration) or alternative terminal acceptors in anaerobic respiration; proton flow back through ATP synthase generates ATP.
3.5.A.4: Proton gradient generation across the inner mitochondrial membrane is central to ATP synthesis via chemiosmosis.
3.5.A.5: Differences between prokaryotic and eukaryotic ETCs include the location of the chain and the organization of membranes; cristae increase surface area in mitochondria, enhancing ATP production.
3.5.B: Obtaining energy from biological macromolecules (Glycolysis, Pyruvate oxidation, Krebs cycle, ETC, and Fermentation)
3.5.B.1: Glycolysis: occurs in the cytosol; breaks down glucose to pyruvate, producing a net gain of 2 ATP (substrate-level phosphorylation) and 2 NADH per glucose; does not require O₂.
3.5.B.2: Pyruvate oxidation: pyruvate is transported into the mitochondrion where it is oxidized to acetyl-CoA; produces NADH and CO₂; requires oxygen indirectly because it feeds into the aerobic pathways.
3.5.B.3: Krebs cycle (citric acid cycle) in the mitochondrial matrix: acetyl-CoA is oxidized, CO₂ is released, ATP (or GTP) is produced, and high-energy electrons are transferred to NADH and FADH₂.
3.5.B.4: The ETC transfers electrons from NADH and FADH₂ to a sequence of carriers toward O₂; proton gradient established across inner mitochondrial membrane.
3.5.B.5: Proton gradient drives ATP synthesis through ATP synthase; chemiosmosis links electron transport to ATP production (oxidative phosphorylation).
3.5.B.6: Fermentation (when O₂ is absent) allows glycolysis to continue by regenerating NAD⁺; produces organic molecules such as ethanol or lactic acid; ATP yield is limited to the glycolytic yield (net 2 ATP per glucose).
3.5.B.7: In aerobic respiration, oxidative phosphorylation yields most ATP; fermentation yields far less ATP but permits continued glycolysis under anaerobic conditions.
Key comparative concepts and practice prompts (from transcript)
Glycolysis: location, reactants/products, ATP yield, and oxygen requirement.
Pyruvate oxidation and Krebs cycle: location, major outputs (CO₂, NADH, FADH₂, ATP).
Electron transport chain: role in establishing a proton gradient, coupling to ATP synthesis via ATP synthase, and differences between aerobic and anaerobic respiration.
Fermentation: purpose (NAD⁺ regeneration), products, and why aerobic respiration is more efficient.
Core equations and concepts to remember
Activation energy and Gibbs free energy
Activation energy lowers in enzyme-catalyzed reactions:
\Delta G^{\ddagger}{\text{uncatalyzed}} > \Delta G^{\ddagger}{\text{catalyzed}}Overall reaction free energy change is unchanged by the enzyme:
\Delta G = G{products} - G{reactants}
Energy coupling and thermodynamics
First law: energy cannot be created or destroyed; energy can be transferred or transformed.
Second law: entropy tends to increase; energy transformations are not perfectly efficient; usable energy decreases over time.
Energy coupling: an exergonic process drives an endergonic process (e.g., ATP hydrolysis powering work).
In cells, to maintain order, energy input must exceed energy loss: energy input > energy loss.
Photophosphorylation and ATP synthesis
In photosynthesis, light reactions generate ATP and NADPH via an ETC and a proton gradient across the thylakoid membrane; ATP synthase uses the proton-motive force to synthesize ATP.
In chloroplasts, the proton gradient drives ATP production and is linked to the Calvin cycle in the stroma.
Cellular respiration and oxidative phosphorylation
NADH and FADH₂ donate electrons to the ETC; proton pumping generates the gradient; ATP synthase uses proton flow to synthesize ATP.
Oxygen is the terminal electron acceptor in aerobic respiration; in anaerobic respiration, other acceptors are used; water is produced in the process.
Metabolic pathways
Pathways are sequential, with products of one step serving as substrates for the next (metabolic flux control).
Glycolysis, Krebs cycle, ETC are core pathways that are conserved across domains of life, supporting the concept of common ancestry.
Quick references and study tips
Know the key locations:
Chloroplast: stroma (Calvin cycle), thylakoid membranes (light reactions in grana)
Mitochondrion: matrix (Krebs cycle), inner membrane (ETC and oxidative phosphorylation), cristae increase surface area for ATP production
Distinguish between energy forms:
Exergonic vs endergonic; activation energy lowered by enzymes but ΔG retained
Substrate-level phosphorylation (glycolysis, Krebs cycle) vs oxidative phosphorylation (ETC-driven ATP synthesis)
Inhibitors:
Competitive inhibitors block active site; overcome by increasing substrate
Noncompetitive inhibitors change enzyme activity through allosteric sites
Note on practice materials from transcript
Several practice questions are provided (Multiple Choice Practice and Free Response prompts).
Core concepts tested by these items include: pH effects on enzymes, light reactions vs Calvin cycle, photosystems and ETC, glycolysis and Krebs cycle outputs, oxygen involvement in respiration, and energy coupling thermodynamics.
When studying, focus on:
How enzyme structure governs function and regulation
How environmental factors alter enzyme activity (temperature, pH, inhibitors)
The flow of energy through cellular processes and how pathways are coupled
The structural features and roles of chloroplasts and mitochondria in energy capture and storage
Connections to broader themes
Foundational principles: enzyme catalysis, energy flow, and thermodynamics are central to all cellular processes.
Evolutionary perspective: core metabolic pathways are conserved across domains, illustrating common ancestry.
Real-world relevance: understanding enzyme regulation informs fields from medicine (enzyme inhibitors) to agriculture (photosynthesis efficiency) and bioenergetics in health and disease.