Understanding Enzyme Structure

Enzyme Structure

• Enzymes are biological catalysts that speed up chemical reactions by lowering the activation energy
• Enzymes are proteins, but some can be RNA-based ribozymes
• Enzymes have an active site, which is where the substrate binds
• An active site's shape determines enzyme specificity (lock-and-key vs. induced fit)
• Enzyme-substrate complex forms when an enzyme binds to the substrate to form an unstable intermediate
• Enzymes convert a substrate into a product, but they are not consumed in the reaction and can be reused
• Cofactors are inorganic molecules (e.g., metal ions like Mg2+, Zn2+)
• Coenzymes are organic molecules (e.g., vitamins like NAD+, FAD)

Enzyme Catalysis

• Activation energy describes the energy required to start a reaction
• Enzymes accelerate reactions via stabilizing the transition state and reducing activation energy
• Proximity and orientation: Enzymes bring substrates together in the correct position
• Microenvironment: The active site provides an optimal environment (pH, polarity)
• Induced fit: Enzyme changes shape slightly to better fit the substrate

Environmental Impacts on Enzyme Function

• As temperature increases, the reaction rate increases up to an optimal temperature
• High temperatures denature enzymes by breaking hydrogen bonds
• Low temperatures slow down reactions but do not denature the enzyme
• Enzymes have an optimal pH (e.g., pepsin in the stomach: pH 2; trypsin in the intestine: pH 8)
• Extreme pH levels can disrupt ionic bonds and denature enzymes
• More substrate increases enzyme activity up to saturation point, where all active sites are occupied
• Competitive inhibitors bind to the active site, blocking the substrate
• Noncompetitive inhibitors bind to an allosteric site, changing the enzyme's shape
• Feedback inhibition describes when the product of a reaction inhibits the enzyme that produces it

Cellular Energy

• Energy transfer describes how energy cannot be created or destroyed, only transferred, as described via the First Law of Thermodynamics
• The Second Law of Thermodynamics describes how energy transfer increases entropy (disorder)
• Exergonic reactions release energy (e.g., cellular respiration, ΔG < 0)
• Endergonic reactions require energy (e.g., photosynthesis, ΔG > 0)
• ATP (Adenosine Triphosphate) is the main energy currency of the cell
• Hydrolysis of ATP (ATP → ADP + Pi) releases energy used for cellular work
• Phosphorylation occurs when transferring a phosphate group to another molecule to activate it

Photosynthesis

• Photosynthesis converts light energy into chemical energy (glucose)
• 6CO_2 + 6H_2O + light → C_6H_{12}O_6 + 6O_2
• Photosynthesis occurs in the chloroplasts of plant cells
• Light-dependent reactions occur in the thylakoid membrane and convert light energy into ATP and NADPH
• Photosystem II (PSII) absorbs light, exciting electrons
• Water is split to replace lost electrons, producing O2
• The Electron Transport Chain (ETC) pumps H⁺ into the thylakoid lumen, creating a proton gradient
• ATP Synthase produces ATP by chemiosmosis
• Photosystem I (PSI) absorbs more light, re-energizing electrons
• Electrons reduce NADP+ to NADPH for the Calvin cycle
• The Calvin Cycle occurs in the stroma
• The Calvin Cycle uses ATP and NADPH from light reactions to fix CO2 into glucose
• Carbon fixation: Rubisco enzyme fixes CO2 to RuBP
• Reduction: ATP and NADPH convert 3-PGA to G3P
• Regeneration: Some G3P is used to regenerate RuBP

Cellular Respiration

• Produces: Glucose (after two cycles)
• Cellular respiration converts glucose into ATP
• C_6H_{12}O_6 + 6O_2 → 6CO_2 + 6H_2O + 36-38 ATP
• Occurs in mitochondria (except glycolysis)
• Glycolysis (cytoplasm): Glucose → 2 Pyruvate + 2 ATP + 2 NADH
• Anaerobic process (does not require O2)
• Pyruvate oxidation (mitochondrial matrix): Pyruvate → Acetyl-CoA + CO2 + NADH
• Krebs Cycle (Citric Acid Cycle) (mitochondrial matrix): Acetyl-CoA → 2 CO2 + 3 NADH + FADH2 + ATP
• Electron Transport Chain (ETC) and Oxidative Phosphorylation (inner mitochondrial membrane)
• NADH and FADH2 donate electrons to ETC
• Electrons travel through protein complexes, pumping H+ into the intermembrane space
• O2 is the final electron acceptor, forming H2O
• ATP Synthase produces ~34 ATP via chemiosmosis

Fitness and Energy Flow

• Efficiency of cellular respiration
• Aerobic respiration = 36-38 ATP per glucose
• Anaerobic respiration (fermentation) = 2 ATP per glucose
• Fermentation (Anaerobic respiration) occurs when O2 is absent
• Lactic acid fermentation (muscles, bacteria): Pyruvate → Lactic acid + NAD+
• Alcohol fermentation (yeast, some bacteria): Pyruvate → Ethanol + CO2 + NAD+
• Energy flow in ecosystems:
• Producers (autotrophs) perform photosynthesis
• Consumers (heterotrophs) perform cellular respiration
• Energy is lost as heat at each trophic level (10% rule)

Key Takeaways

• Enzymes lower activation energy and have specific conditions for optimal function
• Photosynthesis stores energy in glucose, while cellular respiration releases energy as ATP
• Aerobic respiration is much more efficient than fermentation
• ATP is the universal energy molecule used by all cells