Lecture 20: Bioenergetics

Announcements and Midterm 2

• Midterm 2 Feedback:

  • Exams appear to be well-managed; grading is expected to be completed this week. Students can expect detailed feedback on their performance, including common mistakes and areas for improvement.

  • Regrade Policy:

    • Initial closure of regrade requests aimed to allow students to focus on upcoming material without distractions.

    • Regrades will reopen this week with revised policies designed to streamline the process and ensure fairness.

    • Historical data indicates a high volume of regrade requests (up to 350 in past quarters), with a significant portion being invalid.

    • Policy Options for Regrades:

      • Option 1: A strict cap of 150 regrade requests for the entire class. If this limit is exceeded, no requests will be processed. Students are encouraged to collaborate and prioritize genuine errors.

      • Option 2: No limit on the number of regrade requests, but penalties will be applied for submitting invalid requests. Details of these penalties will be provided in a poll to ensure transparency and fairness.

• Examples of unacceptable regrade requests:

  • Requesting partial credit for an incorrect answer (e.g., claiming that X and 1/X are similar).

• A poll regarding the regrade policy will be available for student input for one to two days.

• Clarification: The 150 regrade request limit applies to the entire class to manage workload effectively.

• Historically, legitimate grading errors are rare, typically not exceeding 100 per quarter.

• TCA quiz scheduled for this Friday, with content already accessible. Students should review materials promptly to prepare.

• Homework 6, part 1 is due tonight. Students are advised to submit their work on time to avoid penalties.

Bioenergetics: Metabolism

• Introduction to Metabolism:

  • Anabolic Pathways: Biochemical reactions that synthesize complex molecules from simpler ones, requiring energy input.

  • Catabolic Pathways: Biochemical reactions that break down complex molecules into simpler ones, releasing energy.

  • Basic understanding of these pathways is intuitive, as they represent building and breaking down processes inherent in biological systems.

• Catabolism:

  • Involves the breakdown of complex molecules to release energy.

  • Characterized by exergonic reactions, which release energy.

• Anabolism:

  • Involves the synthesis of larger molecules from smaller precursors.

  • Characterized by endergonic reactions, which require energy input, often coupled with exergonic reactions to proceed spontaneously.

• Relationship Between Catabolism and Anabolism:

  • Catabolism harvests energy from the breakdown of molecules and stores it in the form of ATP and NADPH.

  • Anabolism utilizes the energy stored in ATP and NADPH to power the synthesis of complex molecules.

• Catabolic Pathways:

  • Convergent: Diverse molecules are broken down into a limited set of end products, streamlining energy extraction.

• Anabolic Pathways:

  • Divergent: A small number of precursor molecules are used to synthesize a wide array of complex molecules, enabling biological diversity.

• Visual Representation:

  • Catabolism (convergent): Phospholipids, triacylglycerol, starch, glycogen, sucrose, and amino acids are catabolized into Acetyl CoA, a central metabolite.

  • Anabolism (divergent): Acetyl CoA serves as a precursor for the synthesis of fatty acids, sterols, and isoprenes (including rubber), showcasing its versatility.

Free Energy and Metabolic Reactions

• Free Energy:

  • Inherent free energy change (\Delta G^\circ): The change in free energy under standard conditions (298 K, 1 atm, 1 M concentrations).

  • Actual free energy change (\Delta G): The change in free energy under actual cellular conditions, considering temperature, pressure, and concentrations of reactants and products.

• Standard Free Energy Change (\Delta G^\circ):

  • Defined as \Delta G^\circ = -RT\ln K{eq}, where K{eq} is the equilibrium constant, reflecting the ratio of products to reactants at equilibrium.

  • Indicates the natural bias of a reaction towards product formation or reactant regeneration under standard conditions.

  • R is the ideal gas constant (8.314 J/(mol·K)), and T is the temperature in Kelvin.

• Altering \Delta G:

  • Increasing reactant concentrations or decreasing product concentrations can shift the reaction towards product formation, even if \Delta G^\circ is positive.

  • Substrate availability governs metabolic reactions by modulating the balance between products and reactants, influencing reaction spontaneity.

• Driving Unfavorable Reactions:

  • Thermodynamically unfavorable reactions can proceed through:

    • Maintenance of favorable product-reactant ratios, ensuring a negative \Delta G.

    • Coupling with energy carriers like ATP, which provide the necessary energy input.

• Glycolysis Example:

  • Inherent \Delta G^\circ values can be positive for certain reactions in glycolysis, indicating non-spontaneity under standard conditions.

  • Actual \Delta G values in cells are negative due to specific metabolite concentrations that favor product formation.

  • Enzymes like phosphoglucose isomerase drive reactions forward by rapidly converting glucose-6-phosphate into fructose-6-phosphate.

  • Reactions catalyzed by hexokinase and phosphofructokinase are coupled with ATP hydrolysis, making them highly exergonic.

• Regulation and Direction of Metabolic Pathways:

  • Metabolic pathways are regulated via enzyme modulation and substrate availability, ensuring metabolic flux control.

  • Glycolysis and gluconeogenesis are reciprocally regulated to maintain glucose homeostasis.

Coupling Reactions

• General Idea:

  • Coupling an unfavorable reaction with a favorable reaction yields a net favorable reaction, enabling otherwise impossible biochemical transformations.

• Example: Formation of a glycosidic bond between glucose and fructose:

  • Unfavorable reaction: Formation of the glycosidic bond requires energy input.

  • Favorable reaction: ATP hydrolysis releases energy, driving the overall process.

  • Process: Phosphate transfer from ATP to glucose forms glucose-1-phosphate, which then reacts with fructose to form the glycosidic bond, releasing phosphate.

ATP: The Central Energy Currency

• ATP Structure:

  • Adenosine triphosphate (ATP) consists of adenine, ribose, and three phosphate groups.

  • ATP can also be used as a building block for RNA synthesis.

  • ATP contains all three phosphates, ADP contains two, and AMP contains one.

• ATP Hydrolysis:

  • ATP hydrolysis involves breaking the phosphoanhydride bonds between phosphate groups, releasing energy.

  • Reaction: \text{ATP} + H2O \rightarrow \text{ADP} + Pi

  • ATP hydrolysis is favorable due to:

    • Charge Repulsion: Relief of negative charge repulsion among the three phosphate groups.

    • Resonance Stabilization: Increased resonance stabilization of phosphate after cleavage.

    • Solvation: Enhanced solvation of products (ADP and P_i), promoting stability.

    • Entropy: Increase in entropy due to the formation of more molecules.

ATP and Coupling Reactions (Continued)

• ATP is consistently employed in coupling reactions to drive thermodynamically unfavorable processes.

• Examples in Glycolysis:

  • Step 1: Glucose to glucose-6-phosphate, with phosphate derived from ATP hydrolysis.

  • Step 3: Fructose-6-phosphate to fructose-1,6-bisphosphate, also utilizing phosphate from ATP hydrolysis.

  • Glucose to glucose-6-phosphate conversion alone is endergonic (+10 kJ/mol).

  • ATP hydrolysis is exergonic (-30 kJ/mol).

  • The net reaction is exergonic (-20 kJ/mol), making the coupled process favorable.

ATP, ADP, and AMP as Regulators

• Adenylates: Collectively refer to ATP, ADP, and AMP, which serve as indicators of cellular energy status.

• Cellular Energy State:

  • High levels of ADP and AMP indicate a low energy state within the cell.

  • High levels of ATP indicate a high energy state.

• Regulation of Metabolic Pathways:

  • Cells utilize ADP, AMP, and ATP levels to assess energy availability and regulate metabolic pathways accordingly.

• Regulation of Enzymes:

  • Anabolic Enzymes: ATP binding typically activates, whereas ADP/AMP binding inhibits.

  • Catabolic Enzymes: ATP binding usually inhibits, while ADP/AMP binding activates to stimulate energy production.

• Example: Phosphofructokinase-1 (PFK-1) in Glycolysis:

  • PFK-1 is a key regulatory enzyme in glycolysis (a catabolic pathway).

  • ATP inhibits PFK-1 to reduce glycolysis when energy is abundant.

  • AMP activates PFK-1 to increase glycolysis during energy scarcity.

Other Phosphate Compounds

• Compounds with favorable phosphate releases, releasing more energy upon hydrolysis than ATP:

  • Phosphoenolpyruvate (PEP) and 1,3-bisphosphoglycerate.

  • \Delta G for ATP hydrolysis is approximately -30 kJ/mol.

  • \Delta G for PEP and 1,3-bisphosphoglycerate hydrolysis ranges from -50 to -60 kJ/mol.

• Substrate-Level Phosphorylation:

  • Direct transfer of phosphate from a substrate to ADP, forming ATP without involving oxygen.

  • Example: Phosphoenolpyruvate + ADP → Pyruvate + ATP results in a net \Delta G of approximately -30 kJ/mol.

  • Occurs twice in glycolysis, leading to the production of four ATP molecules.

• Relationship Reiterates:

  • Phosphoenolpyruvate’s high-energy phosphate bond is similar to ATP's role in phosphorylating glucose to form glucose-6-phosphate.

• Other ATP Production:

  • Oxidative phosphorylation in mitochondria.

  • Adenylate kinase (myokinase) shuffles phosphates between adenine nucleotides.

Acetyl CoA

• Central Molecule:

  • Acetyl CoA is a central metabolite involved in both catabolism and anabolism.

  • Many molecules are broken down to form acetyl CoA, and many are built from acetyl CoA.

• Two Main Parts:

  • CoA part: Consists of adenosine, pantothenic acid (vitamin B5), and a mercaptoethylamine residue.

  • Acetyl group: A two-carbon unit derived from carbohydrates, fats, and proteins.

• Bond in Question:

  • Thioester bond between sulfur and carbonyl groups is critical for Acetyl CoA's function.

  • Breaking this bond releases energy, making it favorable for driving metabolic reactions.

• Catabolism and Anabolism:

  • Catabolism utilizes energy to synthesize the thioester bond, storing energy for later use.

  • Anabolism cleaves the thioester bond to release energy for building new molecules, such as sterols and fatty acids.

  • Pyruvate to Acetyl CoA: Pyruvate undergoes oxidation to form acetyl CoA, with energy channeled into forming the thioester bond.