Chapter 6: Metabolism (Energy) - Comprehensive Notes

Chapter 6: Metabolism (Energy)

6.1 Energy and Metabolism

• Most life on Earth is sustained by energy from the sun, which is captured by photosynthesizing organisms.
• Bioenergetics is the study of energy flow through living systems.

Energy & Energetics of the Cell

• Many cellular processes release heat, which isn't always a useful form of energy for transfer.
• Cells can convert energy from one form to another (e.g., mechanical to chemical).
• Photosynthetic organisms convert solar radiation (photons) into organic molecules through carbon fixation (autotrophic).
• All cells, including plants and animals, obtain energy through the oxidation of organic molecules via cellular respiration in the mitochondria, which is a breakdown process.

Metabolism

• Metabolism encompasses all chemical reactions within a cell or organism.
• A metabolic pathway is a series of biochemical reactions converting substrates into a final product.
• Photosynthesis captures solar energy to convert carbon dioxide (CO2) and water (H2O) into glucose (C6H{12}O_6).
• Cellular respiration releases the energy stored in glucose, regenerating CO2 and H2O.

Metabolic Pathways

• Anabolic pathways require energy to synthesize larger molecules.
• Catabolic pathways release energy by breaking down large molecules into smaller ones.

Evolution of Metabolic Pathways

• Different life forms share some metabolic pathways, suggesting common ancestry.
• Over time, these pathways diverged, with organisms developing specialized enzymes to adapt to their environments.

Anabolic and Catabolic Examples

• Anabolic: smaller molecules + energy --> larger molecules
• Catabolic: larger molecules --> smaller molecules + energy

Photosynthesis Pathway

• Photosynthesis is an anabolic pathway.
• It uses sunlight to convert carbon dioxide and water into carbohydrates.

6.2 Types of Energy

• Energy is the ability to do work.
• Kinetic energy is the energy of objects in motion.
• Potential energy is the energy possessed by objects with the potential to move.

Examples of Energy Types in Cells

• Energy of chemical/electrochemical gradients across the plasma membrane.
• Chemical energy is stored in chemical bonds (potential) and released when bonds are broken (kinetic).

Potential Energy Example

• The potential energy in gasoline's chemical bonds converts to kinetic energy, powering a car.

Energy: G

• Chemical reactions proceed towards a loss of free energy.
• Enzymes lower the energy needed to start spontaneous reactions.
• The net free-energy change determines reaction spontaneity.
• \Delta G changes as a reaction proceeds toward equilibrium.
• The standard free-energy change, \Delta G°, allows comparison of energetics between reactions.

Gibb’s Free Energy (G)

• Gibb’s Free Energy (G) represents the amount of energy available to do work.
• \Delta G represents the change in free energy after a reaction.
• \Delta G = \Delta H - T\Delta S
  • \Delta H is the change in the total energy of the system.
  • T is the temperature in Kelvin.
  • \Delta S is the change in entropy (energy lost to disorder).

Free Energy

• Exergonic reactions release energy, indicated by \Delta G < 0.
  • Products have less free energy than substrates.
  • These reactions are spontaneous but don't necessarily occur quickly.
• Endergonic reactions require energy input, indicated by \Delta G > 0.
  • Products have more free energy than substrates.

Activation Energy

• Activation energy is the energy required for a reaction to proceed.
• It contorts and destabilizes reactants, enabling bonds to break or form at the transition state.
• Heat energy is the main source for activation energy in a cell.
• Catalysts lower activation energy.

Example of Activation Energy

• Rusting of iron happens slowly because of activation energy requirements.
• Gasoline breakdown needs a spark to exceed activation energy.

6.3 The Laws of Thermodynamics

• Thermodynamics is the study of energy and energy transfer involving physical matter.
• The first law of thermodynamics states that energy cannot be created or destroyed; the total amount of energy in the universe is constant.
• The second law of thermodynamics states that energy transfer is not completely efficient, leading to energy loss as heat and increased entropy (disorder).

Laws of Thermodynamics Example

• Kids convert chemical energy from ice cream to kinetic energy while riding a bike, releasing heat.
• Plants also release heat energy when using sunlight during photosynthesis.

6.4 ATP: Adenosine Triphosphate

• ATP hydrolysis typically provides the energy for a cell's endergonic reactions.

Activated Carriers and ATP

• Formation of an activated carrier is coupled to an energetically favorable reaction; making ATP requires significant energy input.
• ATP is the most widely used activated carrier in the cell.
• NADH and NADPH are activated carriers of electrons with different roles in cells.
• Synthesis of biological polymers and complex molecules requires energy input.

ATP Structure

• ATP consists of an adenosine backbone with three phosphate groups attached.
• Adenosine is a nucleoside composed of adenine and ribose.
• The phosphate groups are labeled alpha, beta, and gamma.
• Bonds between phosphate groups are high-energy bonds; their breakage releases energy.

ATP Hydrolysis

• \Delta G = -7.3 \text{ kcal/mol}
• ATP is an unstable molecule that hydrolyzes quickly.
• If hydrolysis isn't coupled with an endergonic reaction, energy is lost as heat.
• When coupled, much of the energy can drive the reaction.
• ATP hydrolysis is reversible: ATP + H2O \rightarrow ADP + Pi + \text{free energy}

The Sodium-Potassium Pump

• The sodium-potassium pump exemplifies energy coupling.
• Energy from ATP hydrolysis powers the integral protein to pump 3 sodium ions out and 2 potassium ions into the cell.

6.5 Enzymes

• Enzymes are protein catalysts that accelerate reactions by lowering activation energy.
• Enzymes bind with reactant molecules, promoting bond-breaking and bond-forming processes.
• Enzymes are highly specific, catalyzing single reactions.
• Ribozymes are non-protein enzymes.

Enzyme-Substrate Specificity

• The 3D shape of enzymes and substrates determines specificity.
• Substrate molecules interact at the enzyme’s active site.
• Enzymes catalyze varied reactions, either bonding two substrates or breaking one molecule into smaller products.

Induced Fit

• Induced fit involves a slight shape change at the active site to optimize reactions.
• It maximizes catalysis and is an expansion of the lock-and-key model.

Protein Structure Revisited

• A protein's 3D shape is determined by its amino acid sequence.
• Active site amino acids are crucial for enzyme function and substrate binding.
• The cellular environment affects enzyme function.
  • Suboptimal temperatures can denature enzymes.
  • Suboptimal pH levels can reduce substrate-enzyme binding.

How Enzymes Lower Activation Energy

• Enzymes help substrates reach the transition state by:
  • Positioning substrates for perfect alignment.
  • Providing an optimal environment (e.g., acidic or polar).
  • Contorting/stressing the substrate.
  • Temporarily reacting with the substrate.
• After a catalyzed reaction, the product is released, and the enzyme is ready for another reaction.

Enzyme Regulation

• Regulation of enzyme activity helps cells control their environment.
• Enzymes can be regulated by:
  • Modifications to temperature and/or pH.
  • Production of molecules that inhibit or promote enzyme function.
  • Availability of coenzymes or cofactors.

Enzyme Inhibition

• Competitive inhibitors have a shape similar to the substrate, competing for the active site.
• Noncompetitive inhibitors bind to the enzyme at a different location, slowing the reaction rate.

Enzyme Inhibition (Figure 6.17)

• Competitive inhibitors slow reaction rates but do not affect the maximal rate.
• Noncompetitive inhibitors slow rates and reduce the maximal rate.
• Maximal rate is the reaction speed when the substrate is not limited.

Enzyme Regulation (Figure 6.18)

• Allosteric inhibitors modify the active site, reducing or preventing substrate binding.
• Allosteric activators modify the active site, increasing the affinity for the substrate.

Enzyme Cofactors

• Some enzymes need cofactors or coenzymes to function.
• Cofactors are inorganic ions (e.g., Fe^{+2}, Mg^{+2}, Zn^{+2}).
• DNA polymerase requires Zn^{+2}.
• Coenzymes are organic molecules, including ATP, NADH^+, and vitamins, primarily from the diet.

Feedback Inhibition in Metabolic Pathways (Figure 6.21)

• Metabolic pathways are a series of reactions catalyzed by multiple enzymes.
• Feedback inhibition, where the end product inhibits an upstream step, is an important regulatory mechanism.
• ATP is an allosteric inhibitor for some enzymes involved in cellular respiration.