Ground Rules of Metabolism

  1. Energy and the Underlying Organization of Life
    1. Energy
      1. Potential energy – measured in kcals.
      2. Kinetic energy - includes heat energy.
      3. Metabolism.
    2. How Much Energy Is Available?
      1. First law of thermodynamics.
      2. A cell cannot produce energy; it can only be borrowed.
      3. Energy can be well channeled or lost as heat…(efficiency).
    3. The One-Way Flow of Energy
      1. Second law of thermodynamics (Entropy) (H ® L quality forms)
      2. Each conversion releases heat energy that is unavailable for work.
      3. The world of life (plant and animal) maintains a high degree of organization only because it is being resupplied with energy from the sun. Nobel Prize - 1970’s…T-1 exception
  2. The Directional Nature of Metabolism
    1. Which Way Will a Reaction Run?
      1. AB + CD ® AC + BD… « …
      2. depends on [ ] and the collision of molecules (heat).
      3. When a reaction approaches chemical equilibrium, the forward and reverse reactions proceed at equal rates
        1. There is no net change in concentrations.
        2. Every reaction has its own ratio of products to reactants at equilibrium.
    2. Conservation of Mass
      1. The law of conservation of mass states that the total mass of all substances entering a reaction equals the total mass of all the products. (Not true!)
      2. Balance chemical equations.
      3. Exergonic
      4. Endergonic
  3. Energy Transfers and Cellular Work
    1. The Structure of ATP
      1. Before cells can use the energy of sunlight or that stored in carbohydrates, they must transfer the energy to molecules of ATP.
      2. ATP is composed of adenine, ribose, and three phosphate groups.

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    1. Phosphate-Group Transfers
      1. Energy input links phosphate to ADP to produce ATP (phosphorylation). (phosphodiester bonds)
      2. ATP can in turn donate a phosphate group to another molecule, which then becomes primed and energized for specific reactions. (glucose-6 phosphate, AT…)
      3. ADP « ATP very rapidly in the ATP/ADP cycle.
    2. ATP Output and Metabolic Pathways
      1. Metabolic pathways form series of reactions that regulate the concentration of substances within cells by enzyme-mediated linear and circular sequences.
      2. In biosynthetic pathways, small molecules are assembled into large molecules; for example, simple sugars are assembled into complex carbohydrates.
      3. In degradative pathways, large molecules such as carbohydrates, lipids, and proteins are broken down to form products of lower energy. Released energy can be used for cellular work.
      4. Participants in metabolic pathways are defined as follows:
        1. Substrates are substances that enter reactions (reactants).
        2. Intermediates are the compounds formed between the start and the end of a pathway.
        3. End products are the substances present at the conclusion of a pathway.
        4. Energy carriers are mainly ATP.
        5. Enzymes are proteins that catalyze (speed up) reactions.
        6. Cofactors are small molecules and metal ions that help enzymes by carrying atoms or electrons.
        7. Transport proteins are membrane-bound proteins that participate in adjusting concentration gradients that will influence the direction of metabolic reactions.

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  1. Enzyme Structure and Function
    1. Enzymes
      1. Catalysts
      2. Recyclable
      3. Specificity - molecular recognition (directionality)
    2. Enzyme-Substrate Interactions
      1. Enzymes increase V by lowering activation energy.
      2. The active site is a crevice where the substrate; in Koshland’s induced-fit model, structural changes during binding allow a more precise fit.

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  2. Factors Influencing Enzyme Activity
    1. Enzymes and Environmental Conditions
      1. T° disrupts the bonds that maintain 3D shape (denaturation)
      2. pH – optimal near 7 (pepsin in the stomach is an exception);
    2. Control of Enzyme Function
      1. Genetic control regulates the number of enzyme molecules available by speeding up/slowing down their synthesis.
      2. Allosteric enzymes have (in addition to active sites) regulatory sites where control substances can bind to alter enzyme activity; if this control substance is the end product in the enzyme’s metabolic pathway, feedback inhibition occurs.
    3. Enzyme Helpers
      1. Cofactors are nonprotein groups that bind to many enzymes and make them more reactive.
      2. Coenzymes are large organic molecules such as NAD+, FAD, and NADP+ that transfer protons and electrons from one substrate to another.
      3. Heavy metals (ions) such as Fe++ also serve as cofactors when assisting membrane cytochrome proteins in their electron transfers in chloroplasts and mitochondria.

     

  3. Electron Transfers Through Transport Systems
    1. Energy is released from storage molecules (such as glucose) in controlled steps via a series of intermediate molecules.
      1. Electrons released during bond breaking are transferred stepwise through the components of electron transport systems located on various cell membranes.
      2. Each time a donor gives up an electron it is oxidized; if it gains, it is reduced.
    2. Electron transport systems are similar to staircases where electrons flow down the steps from the top (most energy) to the bottom (least energy), releasing a small amount at each step.
    3. The energy is harnessed to move hydrogen ions, which in turn establish pH and electric gradients necessary for ATP production.