Chemical Reaction

Aka: Chemical Reaction, Entropy, Thermodynamics, Enzyme Activity

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II. Definitions

  1. Chemical Reaction
    1. Chemical change in which two or more substances are modifed to result in one or more new substances
    2. Reactions affect the rearrangement of atoms or molecules
    3. Results in substances with different properties from the original substances
  2. Thermodynamics
    1. Energy relationships between different states of a system
    2. Properties (heat, work, Temperature, equilibrium) affect the conversion from one state to another

III. Physiology

  1. Thermodynamics
    1. Energy is conserved (First Law of Thermodynamics)
      1. Energy is equivalent on each side of a chemical equation
    2. Entropy (Second Law of Thermodynamics)
      1. Natural, normal progression and breakdown from a state of order to one of disorder and randomness
      2. Measured as the amount of heat or energy unavailable to do work
      3. Examples: Heat flows to colder regions, Chemical Reactions favor energy loss
  2. Chemical Reaction
    1. Reaction Direction
      1. Reactions follow pathways of net energy loss or release, and stable substances with stronger bonds
      2. Higher substance concentration also impact reaction direction (toward decreasing concentration)
      3. When reactions involve a cascade of sub-reactions, the net result is energy loss and stability
      4. Complex biosynthesis in organisms (including humans) requires significant energy loss
      5. Two-way reactions typically involve different mechanisms and enzymes for the different directions
      6. In vivo reactions are limited to the cells that contain the needed substrates and enzymes
        1. Many reactions are limited to certain tissues (e.g. liver, Muscle)
      7. Only one reaction direction is typically active at one time (to prevent wasted activity)
        1. For example, Glycolysis and Gluconeogenesis do not occur simultaneously
        2. Biosynthesis of a substance often occurs in different organs than its biodegradation
        3. Simultaneous, bidirectional reactions result in wasted energy, typically lost as heat
    2. Reaction Rate
      1. Rate is largely determined by the energy needed to trigger the reaction (energy of activation)
      2. Rate increases with warmer Temperatures and higher substrate concentrations, and when enzyme facilitated
      3. Rate decreases with colder Temperatures and higher reaction product concentrations
      4. Rate is independent of the potential energy loss from a given reaction
  3. Substrate
    1. Substrate concentration depends on multiple factors
      1. Rate of substrate precursor uptake (e.g. diet) versus excretion
      2. Substrate biosynthesis rate from precursors
      3. Substrate entrance into the cell (e.g. receptor-mediated)
  4. Enzymes (Proteins) and Ribozymes (RNA) facilitate Chemical Reactions
    1. Lower the energy of activation for a specific reaction, significantly speeding (catalyzing) the overall reaction
    2. Reactions are often built from multiple sub-steps of cascading enzyme activation
      1. Example: Clotting Pathway
    3. Enzyme efficiency is impacted by several factors
      1. Substrate concentration
      2. Enzyme concentration
      3. Enzyme amount in the active state (in contrast to its inactive precursor state or Zymogen)
      4. Feedback regulation
    4. Enzyme Categories
      1. Oxidoreductases (Redox Reaction, e.g. dehydrogenase, reductase enzymes)
        1. Transfer electrons from one molecule to another
        2. Molecules lose electrons in oxidation, and gain electrons in reduction
        3. Example: Pyruvate dehydrogenase (Glycolysis)
          1. Pyruvate is oxidized to Acetyl Coenzyme A.
      2. Transferases (e.g. transferase, synthase enzymes)
        1. Functional groups are transferred from one molecule to another
        2. Example: Phosphotransferase (Glycolysis)
          1. Phosphorylation of Glucose to Glucose-6P
      3. Hydrolases (e.g. amylase, Lipase, beta lactamase)
        1. Break apart covalent bonds (and molecules) with the use of water (hydrolysis)
        2. Example: Fumerase (TCA Cycle)
          1. Fumarate is catalyzed to Malate
          2. Fumarate's double bond becomes a single bond, as hydroxide is added
      4. Lyases (e.g decarboxylase, cyclase)
        1. Dissociates or breaks apart molecules
        2. Performed without water (unlike hydrolases), or oxidation/reduction (Redox Reaction)
        3. Example: Aldolase lyses Fructose-1, 6-bisphosphate into 2 products (Glycolysis)
          1. Glyceraldehyde-3-phosphate
          2. Dihydroxyacetone phosphate
      5. Isomerases
        1. Rearrange molecular bonds, creating an isomer (same chemical formula, different arrangement)
        2. Example: Phosphoglucomutase (Glycolysis)
          1. Catalyzes the rearrangement of phosphate in Glucose-1-phosphate to Glucose-6-phosphate
      6. Ligases
        1. Join molecules together, creating covalent bonds
        2. Example: Pyruvate Carboxylase (Gluconeogenesis)
          1. Catalyzes pyruvate to oxalocetate in the mitochondria (costing 1 ATP and bicarbonate)
      7. Images
        1. Glycolysis and TCA Cycle
          1. Glycolysis.png
        2. Gluconeogenesis
          1. gluconeogenesis.png

IV. References

  1. Goldberg (2001) Biochemistry, Medmaster, Miami, p. 4-12, 28-9

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