Metabolism and Bioenergetics Study Notes

Overview of Metabolism

• Metabolism is defined as the sum of all chemical reactions carried out by living cells. These coordinated enzyme systems convert nutrients into chemical energy, which in turn enables the synthesis of biomolecules.

• Organisms are classified based on their carbon source:

  • Autotrophs: These organisms do not require an external carbon source as they can convert inorganic $CO_2$ into complex biomolecules. Most autotrophs derive their energy from the sun.

  • Heterotrophs: These organisms obtain carbon from organic molecules, such as glucose. They obtain their energy by oxidizing organic molecules that were originally produced by autotrophs.

• The biosphere facilitates a massive cycling of mass. The cycle involving Carbon, Oxygen, Nitrogen, and Water allows for the movement of materials between autotrophs and heterotrophs.

• Scale of the Carbon Cycle: Approximately $4 \times 10^{11}$ metric tons of carbon are turned over in the biosphere every year.

Catabolism versus Anabolism

• Metabolism consists of two main opposing arms:

  • Anabolism: This involves energy-storing processes where sunlight or chemical energy is used to convert simple precursors (like $CO_2$ (represented as X, Y, Z in the hierarchy)) into complex products such as glucose.

  • Catabolism: This involves energy-releasing processes where complex precursors (like glucose) are broken down into simple products (like $CO_2$) through intermediates called metabolites (X, Y, Z).

• Metabolic Pathways:

  • Catabolic pathways: Synthesize ATP by breaking down nutrients.

  • Anabolic pathways: Require the input of energy to synthesize complex biomolecules.

• Regulation Mechanisms: Metabolic pathways are tightly controlled through:

  • Availability of substrate.

  • Allosteric control of enzymes.

  • Influence of growth factors and hormones.

Pathway Dynamics and Convergence

• Acetate (Acetyl-CoA): This is a key metabolic intermediate. It serves as the breakdown product for various fuels and is the essential precursor for a variety of products. These enzymatic steps are highly regulated.

• Fatty Acid Dynamics:

  • After a high-carbohydrate meal, high levels of Acetyl-CoA lead to the synthesis of fatty acids for energy storage.

  • After not eating for an extended period, fatty acids are broken down back into Acetyl-CoA.

• Regulation of Antagonistic Pathways:

  1. Enzyme Modification: Enzymes can be "turned off" through specific modifications.

  2. Enzyme Concentration: The number of enzyme molecules can decrease if they are no longer being produced.

  3. Compartmentalization: Fatty acid synthesis occurs in the cytosol, while fatty acid breakdown and the TCA cycle occur in the mitochondria. Transportation between these compartments serves as a regulated checkpoint.

• Pathway Structures:

  • Converging Catabolism: Various molecules like fatty acids, amino acids (Alanine, Phenylalanine, Leucine, Isoleucine, Serine), and carbohydrates (Starch, Glycogen, Glucose, Sucrose) converge into Pyruvate and ultimately Acetate (acetyl-CoA).

  • Diverging Anabolism: Acetate acts as a starting point for the synthesis of diverse products including Cholesterol, Bile acids, Vitamin K, Eicosanoids, and Phospholipids via intermediates like Mevalonate and Isopentenyl-pyrophosphate.

  • Cyclic Pathways: Illustrated by the TCA cycle, where intermediates like Citrate and Oxaloacetate are regenerated while releasing $CO_2$.

Principles of Bioenergetics (Chapter 13)

• Bioenergetics applies thermodynamic laws to biochemistry while maintaining the validity of organic chemistry principles.

• High-Energy Compounds: Certain biomolecules are considered "high energy" because of the significant energy released during their hydrolysis or group transfers.

• Electron Carriers: Energy stored in reduced organic compounds is used to reduce universal electron carriers like $NAD^+$ and $FAD$.

• Spontaneity in Cells: Spontaneity is determined by the current free-energy change ($\Delta G_{rxn}$) rather than the standard state change ($\Delta G^{\circ}$).

• The Mass-Action Ratio ($Q$): The most important factor in cellular spontaneity is the concentration of substrates and products ($Q = \frac{[P1][P2]}{[S1][S2]}$), which indicates how far a system is from equilibrium.

• The Governing Equation: $\Delta G' = \Delta G'^{\circ} + RT \ln(Q)$ and at equilibrium $\Delta G'^{\circ} = -RT \ln(K'_{eq})$.

Metabolic Reactions and Additivity

• Reaction Classes:

  1. Near-equilibrium reactions: $Q$ is close to $K_{eq}$. These are easily reversed.

  2. Metabolically irreversible reactions: $Q$ is far from $K_{eq}$ (often a difference of >100 \times). These have a $\Delta G \ll 0$ and serve as Control Points in Metabolism. These enzymes are very tightly regulated.

• Additivity of Free Energy: Free energy changes for sequential reactions are additive ($\Delta G'_{3} = \Delta G'_{1} + \Delta G'_{2}$). This allows a thermodynamically unfavorable reaction to proceed by coupling it to a highly favorable one.

• Example of Coupling:

  • Glucose + $P_i$ $\rightleftharpoons$ Glucose 6-phosphate + $H_2O$; $\Delta G'^{\circ} = 13.8\,kJ/mol$

  • $ATP$ + $H_2O$ $\rightleftharpoons$ $ADP$ + $P_i$; $\Delta G'^{\circ} = -30.5\,kJ/mol$

  • Coupled Net Reaction: Glucose + $ATP$ $\rightleftharpoons$ Glucose 6-phosphate + $ADP$; \Delta G'^{\circ} < 0

Standard Free-Energy Changes of Chemical Reactions

Adenosine Triphosphate (ATP) and Thioesters

• Structure: ATP contains three phosphate groups (labeled $\alpha$, $\beta$, and $\gamma$ from the ribose outward) attached to adenosine. It typically exists in complex with $Mg^{2+}$.

• Exergonic Nature of ATP Hydrolysis: Reasons include:

  1. Minimizing electrostatic repulsion between negative charges on the phosphate groups.

  2. Better charge separation in the products.

  3. More favorable resonance stabilization of products ($P_i$).

  4. Energy released by solvation (water molecules forming hydrogen bonds with the phosphate group).

• ATP Usage: ATP is a store of chemical energy used to "activate" molecules for transformation. Transfer can be:

  1. Phosphoryl transfer: Attack on the $\gamma$ phosphate, releasing $ADP$.

  2. Pyrophosphoryl transfer: Attack on the $\beta$ phosphate, releasing $AMP$.

  3. Adenylyl transfer: Attack on the $\alpha$ phosphate, releasing $PP_i$.

• Thioesters: Molecules like Acetyl-CoA are parallel to oxygen esters but use sulfur. Thioester hydrolysis is highly exergonic ($\Delta G'^{\circ} = -31\,kJ/mol$ for Acetyl-CoA).

Enzyme Mechanisms and Group Transfers

• Kinases: Enzymes that catalyze the transfer of phosphate groups, often using ATP as the donor.

• Nucleoside Diphosphate Kinase: Uses a Ping Pong mechanism where a phosphate is transiently attached to a Histidine residue on the enzyme via covalent catalysis.

• Covalent Modification: Phosphorylation/dephosphorylation of proteins on Serine, Threonine, or Tyrosine residues is a major regulatory mechanism. This is mediated by protein kinases (add phosphate) and phosphoprotein phosphatases (remove phosphate).

• Carbanion and Carbocation Intermediates:

  • Carbonyl groups can stabilize carbanions through resonance, lowering the $pKa$ of the adjacent $C-H$ group.

  • Citrate Synthase Example: Oxaloacetate and Acetyl-CoA react via a carbanion mechanism involving Histidine (His 274, His 320) and Aspartate (Asp 375) residues.

• Isomerization: Example: Phosphohexose isomerase converts Glucose 6-phosphate to Fructose 6-phosphate via an enediol intermediate.

• Elimination: Often involves the creation of a carbocation after a good leaving group departs, or through the removal of a proton from a carbon with a low $pKa$.

Oxidation-Reduction (Redox) Reactions

• Redox reactions involve the transfer of energy through the flow of electrons (electromotive force or emf).

• Biological Oxidizing Reagents: $NAD^+/NADP^+$, $FAD/FMN$, and Quinones ($Q$).

• Methods of Electron Transfer:

  1. Directly: e.g., $Fe^{2+} + Cu^{2+} \rightarrow Fe^{3+} + Cu^{+}$.

  2. As Hydrogen: $AH_2 \rightarrow A + 2e^- + 2H^+$.

  3. As Hydride ($H^-$): Transfer of two electrons together (common for $NAD^+$).

  4. From Oxygen: Direct incorporation of oxygen into a substrate.

• Standard Reduction Potential ($E'^{\circ}$): A measure of the affinity for electrons. Electrons flow spontaneously from a carrier with lower $E'^{\circ}$ to one with higher $E'^{\circ}$. In animals, all electrons ultimately flow to $O_2$ ($E'^{\circ} = 0.816\,V$) to form water.

• Redox Math:

  • $\Delta G'^{\circ} = -nF\Delta E'^{\circ}$

  • $1 = n$(number of electrons);$F$= Faraday's constant ($96.48\,kJ/V \cdot mol).\n * \Delta E'^{\circ} = E'^{\circ}{acceptor} - E'^{\circ}{donor}.\n * A positive \Delta E indicates the reaction is proceeding.\n\n# Universal Electron Carriers: NAD and FAD\n\n* **NAD+/NADH:**\n * Acts as a hydride carrier.\n * NADH (reduced form) has a characteristic absorbance peak at 340\,nm$;$NAD^+ (oxidized) does not.\n * Example: Ethanol + NAD^+ \rightarrow$Acetaldehyde +$NADH + H^+ (catalyzed by alcohol dehydrogenase).\n* **FAD/FADH2:**\n * Derived from riboflavin.\n * Contains an isoalloxazine ring.\n * Can accept one electron (forming the semiquinone FADH^{\bullet}$) or two (forming the fully reduced$FADH_2).\n\n# Free Energy of Transport\n\n* The energy required to move a solute against a concentration gradient:\n * \Delta G_t = RT \ln(\frac{C_2}{C_1})$(where$C_2$is destination,$C_1 is origin).\n* For moving an ion across a membrane, the transmembrane potential (DY) must be considered:\n * \Delta G_t = RT \ln(\frac{C_2}{C_1}) + ZFDY\n * Z$= charge on ion;$F$= Faraday constant;$DY = transmembrane potential.\n\n# Important Concepts and Physical Constants\n\n* **Thermodynamic Relationship:** \Delta G = \Delta H - T\Delta S.\n* **Additivity:** Reactions are often coupled through a **Common Activated Intermediate**.\n* **Kinetics vs. Thermodynamics:** A reaction being thermodynamically favorable does not mean it is kinetically rapid.\n* **Physical Constants:**\n * Gas constant R = 8.315\,J/mol \cdot K$($1.987\,cal/mol \cdot K).\n * Faraday constant F = 96,480\,J/V \cdot mol.\n * At 25^{\circ}C$($298\,K$),$RT = 2.478\,kJ/mol.\n * 1\,cal = 4.184\,J.\n * Avogadro's number N = 6.022 \times 10^{23}\,mol^{-1}.\n\n# Questions & Discussion\n\n* **True/False:**\n * Catabolic pathways can provide the cell with ATP: **True**.\n * Catabolic pathways are used to synthesize complex biomolecules: **False** (Anabolic pathways do this).\n * Anabolic pathways do not require the input of energy: **False**.\n * Energy-rich molecules such as CO_2$provide the chemical energy for catabolism: **False** ($CO_2 is a low-energy product; fuels like glucose provide energy).\n* **Mechanism Question:** Is resonance or the carbonyl role important in carbanion stabilization? Resonance allows electron displacement toward the oxygen atom, stabilizing the carbanion. The statement "The carbonyl plays no role" is **False**.\n* **Lactate Oxidation:** In the reaction Lactate \rightarrow$Pyruvate (via lactate dehydrogenase), lactate is being **oxidized** as electrons go from lactate to$NAD^+$to form$NADH$.$NADH is the reduced form.\n* **Redox Favorable?** Will the reduction of FAD$by$NADH at standard state be favorable?\n * E'^{\circ}$for$FAD + 2H^+ + 2e^- \rightarrow FADH_2$is$-0.219\,V.\n * E'^{\circ}$for$NAD^+ + H^+ + 2e^- \rightarrow NADH$is$-0.320\,V.\n * \Delta E'^{\circ} = (-0.219) - (-0.320) = +0.101\,V.\n * Since \Delta E'^{\circ}$$ is positive, the reaction is spontaneous and favorable.