Lecture 1

Introduction to Metabolism

Definition of Metabolism

Metabolism encompasses all biochemical reactions that occur within living organisms, comprising a group of coordinated cellular activities designed to:

• Synthesize compounds essential for cellular function.

• Decompose compounds that are no longer necessary for cellular activities.

• Harvest energy either through photosynthesis (in autotrophs) using sunlight or through the degradation of nutrients (in heterotrophs) derived from organic materials.

Cell Requirements

Fundamental Needs

• Energy: Required for all cellular processes, including growth, repair, movement, and synthesis of molecules.

• Source of Carbon: Organisms need carbon for building organic molecules.

• Source of Nitrogen: Essential for synthesizing amino acids and nucleic acids.

Autotrophs vs. Heterotrophs

• Autotrophs: Organisms that can utilize carbon dioxide (CO₂) as their sole carbon source to build organic compounds. Examples include plants and certain bacteria that conduct photosynthesis or chemosynthesis.

• Heterotrophs: Organisms that cannot use CO₂ as their sole carbon source. They must obtain carbon by consuming other organic compounds, such as glucose from plants or other animals.

Nitrogen Cycling

Role of Bacteria and Archaea

• Nitrogen-Fixing Bacteria and Archaea: These microorganisms convert atmospheric nitrogen (N₂) into ammonia (NH₃), making it available for incorporation into organic molecules.

Key Players in Nitrogen Cycling

• Denitrifying bacteria, archaea, and fungi: Convert ammonia (NH₃) back to nitrogen (N₂), thus completing the nitrogen cycle and returning nitrogen to the atmosphere.

• Nitrifying bacteria: Convert ammonia to nitrite (NO₂) and subsequently to nitrate (NO₃), which plants can absorb and utilize for synthesizing amino acids.

• Plants and Animals: Plants absorb nitrates to synthesize amino acids, which are essential for protein production. Animals, in turn, derive necessary amino acids by consuming these plants or feeding on other animals.

Metabolic Divisions

• Catabolism: The metabolic pathway that breaks down complex compounds into simpler molecules, releasing energy stored in chemical bonds. For example, the breakdown of glucose during cellular respiration.

  • Energy-containging nutrients (Carbohydrates, Fats, Proteins ) → Energy depleted end products (CO2, H2O, NH3)

• Anabolism: The pathway that builds complex molecules from simpler precursors, which requires an input of energy. This includes processes like protein synthesis and DNA replication. LOOK AT SLIDE

Metabolic Pathways

• Dual Pathways: Most compounds have both synthetic (anabolic) and degradation (catabolic) pathways, which allows for tight regulation of metabolism depending on cellular needs and environmental conditions. important for synthesis of biomolecules

Principles of Bioenergetics

Metabolism is driven by energy requirements, which include (cells need energy for):

• Synthesis of macromolecules: Proteins, lipids, nucleic acids, and polysaccharides.

• Establishing and maintaining concentration gradients: Essential for cellular transport and communication.

• Generating electrical gradients: Particularly crucial in nerve and muscle cells for signaling and coordination.

• Movement: Contraction of muscle fibers and transportation of materials across membranes.

• Heat production: Thermoregulation in warm-blooded animals.

• Light generation: Found in organisms like fireflies, through bioluminescence, where chemical energy is converted into light energy.

→ Ultimate source of this energy on Earth is Sunlight

Bioenergetics

Bioenergetics is the study of how organisms obtain, convert, and utilize energy for various biochemical processes, emphasizing the laws of thermodynamics that govern these transformations.

Unique Organisms: Giant Tube Worms

• Riftia pachyptila: (Deep underwater) (No need for sunlught to live) These marine organisms thrive in harsh environments near hydrothermal vents and rely on chemosynthetic bacteria as their primary food source.

• Energy Source: Chemosynthetic bacteria inside the worms derive energy from methane and hydrogen sulfide, allowing them to survive without sunlight, thus illustrating alternative metabolic strategies in extremophiles.

Laws of Thermodynamics

1. First Law (Conservation of Energy): Energy cannot be created or destroyed; it can only be transfered/change form. This principle highlights that the total energy in any isolated system remains constant.

2. Second Law (Universe tends towards increasing disorder): In natural processes, systems will tend to move towards greater entropy (disorder). For complex macromolecules to form, energy must be inputted, thus decreasing order in other parts of the system, as seen in metabolic processes.

Free Energy and Equilibrium Constant

• Gibbs Free Energy (G): (At Constant T&P) A thermodynamic quantity that predicts the spontaneity of a reaction and the energy change associated with it. Joules/Mole or Calories/Mole

  • A negative ∆G indicates an exergonic (energy-releasing) reaction (Always spntaneous) , while a positive ∆G signifies an endergonic (energy-consuming) reaction.

• Entropy (S): A measure of disorder within a system; while local decreases in entropy can occur (such as in living cells), the overall entropy of the universe is always increasing.

  • Gain in Entropy → Products are less complex and more disordered than reactants

  • Living organisms take free energy from the environment (nutrients and sunlight) and return heat and entropy.

Chemical Reaction Energetics

Free energy calculations can help predict reaction direction, assess equilibrium positions, and determine the work potential in biological systems:

• Example: The standard free-energy change for hydrolysis reactions:

[\text{ATP} + \text{H}_2\text{O} \rightarrow \text{ADP} + \text{Pi} \quad (\Delta G'° = -30.5 \text{ kJ/mol})]

• The equilibrium constant (Keq) provides a measure of the ratio of products to reactants at equilibrium:

  • A higher Keq (>1) correlates with a negative standard free energy change, while a lower Keq (<1) indicates a positive standard free energy change.

Coupled Reactions

Coupling exergonic and endergonic reactions allows for the validation of thermodynamic favorability, thereby facilitating processes that are not energetically favorable by linking them to favorable reactions.

Practical Applications of Energy Calculations in Cells

In living systems, the actual free energy change (ΔG) may not align with theoretical conditions due to varying substrate and product concentrations. Enzymes play a critical role in enhancing reaction rates by lowering activation energy without altering the equilibrium constants.

ATP and Phosphorylation

• Adenosine Triphosphate (ATP): Recognized as the central energy currency of cells, hydrolysis of ATP serves as a frequent energy source for numerous biosynthetic reactions.

• Phosphoryl Group Transfers: ATP donates phosphate groups to various substrates, facilitating their transformation during biochemical reactions.

  • Hydrolysis of ATP not only releases energy but also decreases electrostatic repulsion among its phosphate groups and stabilizes the phosphate-bearing products through resonance.

Modeling Reaction Couples and Equilibrium

The free energy changes are additive for sequential reactions, enabling unfavorable reactions to take place in conjunction with highly favorable ones. This coupling significantly increases the overall favorability of processes, as exemplified by ATP hydrolysis.

Considerations for Hydrolysis of Phosphorylated Compounds

The hydrolysis of phosphorylated compounds like ATP exhibits substantial standard free energy changes due to the release of electrostatic repulsion and the stabilization of products via resonance. Multiplicative relationships enhance our understanding of the influence of equilibrium constants across sequential reactions within biochemical pathways.

Conclusion

Understanding the laws of thermodynamics, the principles of bioenergetics, and the concept of free energy enables a comprehensive approach to analyzing metabolic processes, guiding further exploration within the fields of biochemistry and cellular biology.