Study Notes for Energy, Catalysis, and Biosynthesis

Energy – Catalysis – Biosynthesis

Instructors and Reference

  • Instructor: Ioannis D. Kyriazis, PhD
  • Faculty of Medicine, University of Thessaly
  • Reference: Rigoulet et al., 2020 BBA – Bioenergetics

Learning Objectives

Students should understand:

  1. The biological order within cells
  2. The chemical reactions leading to biological order (metabolism, enzymes)
  3. The characterization of chemical reactions (energy favorable or unfavorable reactions)
  4. The molecules that carry energy to carry out chemical reactions
  5. The necessity of constant energy supply for the maintenance of living organisms

Biological Orders and Structures

  • All living organisms generate ORDER at every level, from the structure of an organism to the organization of atoms in different molecules, constructing biomolecules that characterize the cells and eventually consist of the organism.
  • This specific property of organisms to create and maintain orders differentiates them from inanimate matter.
2nd Law of Thermodynamics
  • The degree of disorder (entropy) in the universe or any single system can only increase.
  • Entropy: Quantitative expression of disorder. The greater the disorder, the greater the entropy.
  • All systems tend to spontaneously change to states of higher entropy (disorder).

Order in Living Cells

  • To survive, grow, and create complex organisms, living cells require order.
  • Order is achieved through energy uptake from the environment and the controlled release of thermal energy from the cells.
  • Question Raised: Do cells violate the 2nd Law of Thermodynamics?

Energy Intake and Biological Order

  • Energy is taken in through food or photons from sunlight.
  • Molecules tend to appear in a disorganized state inside and outside the cell.
  • Release of Heat: Increases order within the cell and increases disorder in the cell's environment.
  • Matter Reservoir: The extracellular environment serves as a reservoir for matter as cells create order.

Metabolism as a Chemical Factory

  • Metabolism: The set of chemical reactions that a cell carries out in order to survive, grow, and reproduce, involving the many molecules that form cells, the building blocks for biosynthesis.
  • Metabolic Pathways:
    • Comprise both catabolic and anabolic pathways.
    • Catabolism: Major portion of energy stored in chemical bonds of food molecules is dissipated as heat.
    • Anabolism: Some energy is used to drive the synthesis of new molecules.
Temperature and Enzymes
  • Most chemical reactions require a higher temperature than that prevailing inside the cells.
  • Enzymes: Specialized proteins that catalyze specific chemical reactions.
    • Each enzyme speeds up or catalyzes only one chemical reaction.

Metabolic Pathways

  • Metabolic Pathways: A series of interconnected chemical reactions catalyzed by enzymes.
    • Linear Pathway: Initial reactant (A) is gradually converted to product (D).
    • Two-Way Reactions: One direction expresses catabolism (right), the reverse represents anabolism (left).
    • Cyclic Pathway: The original reactant (A) is regenerated at the end of the cycle.

Catalysis of Reactions by Enzymes

  • Enzymes convert a substrate into a product without changing the substrate itself.
  • Active Site: Each enzyme has a specific site to which the substrate binds via weak bonds (hydrogen bonds, van der Waals attractions, electrostatic attractions).
  • The enzyme participates in the reaction but remains unchanged.
Steps of Enzyme Reaction
  1. Binding of the substrate forming an enzyme-substrate complex.
  2. Conversion of substrate to product.
  3. Release of product, regeneration of enzyme.
Factors Influencing Reaction Speed
  • The speed of an enzymatic reaction depends on the efficiency of the enzyme catalyzing it.
  • Reaction rate increases with substrate concentration until Vmax is reached, where all active sites are occupied.
  • Km Constant: Determines binding strength of enzyme to substrate.
    • Defined as the substrate concentration at which enzyme velocity = 1/2 Vmax.
    • Higher Km indicates weak binding; Lower Km indicates strong binding.
Enzyme Activity Regulation
  • Enzyme activity and reaction speed is influenced by factors like inhibitors.
  • Competitive Inhibitors: Bind to active site, limiting substrate binding.
  • Diagram: ES complex where only substrate binds.

First Law of Thermodynamics

  • Energy cannot be created or destroyed; it can only be converted from one form to another.
  • There is adherence to the 2nd Law of Thermodynamics, which indicates an increase in overall disorder of the universe.

Photosynthesis and Cellular Respiration

Photosynthesis
  1. First Stage: Energy from sunlight is temporarily stored as chemical bond energy in activated carriers (e.g., ATP, NADPH).
  2. Second Stage: Energy from activated carriers is converted into the energy of chemical bonds in sugars and organic molecules with CO2 as raw material.
Cellular Respiration
  • The oxidation of organic compounds to extract energy.
  • Consumption of O2: Essential for the process; produces H2O and CO2 as byproducts.
Complementarity of Photosynthesis and Cellular Respiration
  • Photosynthesis produces sugars from CO2 using sunlight, while respiration uses O2 to oxidize food molecules, releasing CO2 back into the atmosphere.

Carbon Recycling in the Biosphere

  • Continuous cycle of carbon atoms through the biosphere.
  • Photosynthetic Activity: Incorporates carbon into organic molecules.
  • Oxygen is released but individual carbon atoms are restored to the atmosphere through respiration or combustion.

Characterization of Chemical Reactions

  • Chemical reactions increasing entropy occur spontaneously.
  • Free Energy Change (ΔG):
    • Defined as ΔG = Gproducts - Greactants.
    • Negative ΔG → reaction occurs spontaneously.
    • Example: Hydrolysis of sucrose into glucose and fructose shows a negative ΔG value.
Energetically Favorable Reactions
  • Spontaneously occurring reactions decrease free energy and increase entropy.
  • Enzymes lower activation energy needed for reactions.
Energetically Unfavorable Reactions
  • Reactions requiring energy input (ΔG > 0) lead to biological order.
  • Coupling to energetically favorable reactions facilitated by enzymes can drive energetically unfavorable reactions.
  • Included Diagram: Shows coupled reactions involving energetically favorable and unfavorable components.

Activated Carriers and Energy Storage

  • Activated Carriers: Store energy in readily exchangeable forms for use in biosynthesis.
  • Must be formed through enzyme-catalyzed reactions and coupling to energetically favorable reactions.
ATP (Adenosine Triphosphate)
  • Primary activated energy carrier.
    • Usage in Cells: Powers pumps for active transport, muscle contraction, and neuronal transport.
ATP Synthesis and Hydrolysis
  • Synthesis of ATP: Involves coupling energetically unfavorable reactions (adding a phosphate to ADP).
  • Hydrolysis: Highly favorable reaction releasing energy (ATP to ADP + Pi).

Biosynthesis and ATP

  • Example of biosynthesis includes the two-step conversion of glutamic acid to glutamine facilitated by ATP hydrolysis.
  • ATP's role in providing energy for unfavorable biosynthetic reactions is essential.
Alternative Pathways of ATP Hydrolysis
  • A specific route forming pyrophosphate prior to breakdown can release more energy.

Polynucleotide Biosynthesis

  • Involves activation of nucleoside monophosphates by ATP hydrolysis to form nucleoside triphosphates, aiding in DNA and RNA synthesis.

Activated Carriers NADH and NADPH

  • Specialized for transport of high-energy electrons and participate in redox reactions.
  • Support anabolic reactions and differ by structures designed for specific enzymatic interactions.
Activation and Roles
  • NADH is pivotal in catabolic processes, whereas NADPH supports anabolic synthesis like cholesterol production.
Summary
  • Encapsulates vital activated carriers (NAD+, NADP+, FAD, ADP, NADH, NADPH, FADH, ATP) and macromolecules like carbohydrates, lipids, proteins, DNA, and RNA.