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Ch8-9 (Metabolism (Free energy (A very useful function called the Gibbs…

- - - - Metabolic pathway begins with a specific molecule and ends with a product
      - Enzymes catalyze reactions in intersecting metabolic pathways
        
        Which may be catabolic pathways (breaking down molecules, releasing energy)
        
        Can also be anabolic pathways (building molecules, consuming energy)
      - Energy is fundamental to all metabolic processes
        
        Energy is the capacity to cause change; some forms of energy do work by moving matter
        
        Thermodynamics is the study of energy transformations
        
        The first law of thermodynamics, the energy of the universe is constant: Energy can be transferred and transformed, but it cannot be created or destroyed. (Also called the principle of conservation of energy)
        
        The second law of thermodynamics: Every energy transfer or transformation increases the entropy of the universe.
        
        Spontaneous processes, those requiring no outside input of energy; they can happen quickly or slowly. (For a process to occur spontaneously it must increase the entropy of the universe)
        
        Entropy is a measure of molecular disorder, or randomness
        
        The evolution of biological order is perfectly consistent with the laws of thermodynamics
        
        Organisms are islands of low entropy in an increasingly random universe
        
        Organisms replace ordered forms of matter and energy in their surroundings with less ordered forms
  - - - Free energy is a measure of a system's instability, its tendency to change to a more stable state
      - A spontaneous process occurs with no energy input; during such process, free energy decreases and the stability of a system increases
      - At a maximum stability, the system is at equilibrium and can do no work
    - - The change in free energy (ΔG) during a biological process is related directly to enthalpy change (ΔH) and to the change in entropy (ΔS): ΔG= ΔH - TΔS. Organisms live at the expense of free energy
      - ΔG is negative for all spontaneous processes; processes with zero or positive ΔG are never spontaneous
  - - - Loses free energy
      - magnitude of ΔG represents the maximum amount of work the reaction can perform
    - - Stores free energy
      - Magnitude of ΔG is the quantity of energy required to drive the reaction
  - - - Like most systems a living cell is not in equilibrium; they are open systems experiencing a constant flow of materials
      - Systems at a equilibrium are at a minimum of G and can do no work, a cell that has reached metabolic equilibrium is dead
  - - - Chemical work
        
        Pushing endergonic reactions. Do not occur spontaneously
      - Transport work
        
        Pumping substances against the direction of spontaneous movement
      - Mechanical work
        
        Such as contraction of muscles
      - Powered by the hydrolysis of ATP
    - - Hydrolysis of its terminal phosphate yields ADP and Pi and releases free energy
      - ATP is a renewable resource that is regenerated by addition of a phosphate group to adenosine diphosphate (ADP)
      - The energy to phosphorylate ADP comes from catabolic reactions in the cell
      - Catabolic pathways drive regeneration of ATP from ADP + Pi
    - - Through energy coupling, the exergonic process of ATP hydrolysis drives endergonic reactions by transfer of a phosphate group to specific reactants, forming a phosphorylated intermediate that is more reactive
      - Most energy coupling in cells is mediated by ATP
      - ATP hydrolysis (sometimes with protein phosphorylation) also causes changes in the shape and binding affinities of transport and motor proteins
- - - - Every chemical reaction between molecules involves bond breaking and bond forming
      - The initial energy needed to start a chemical reaction is called the free energy of activation, or activation energy (EA)
        
        In a chemical reaction, the energy necessary to break the bonds of the reactants is the activation energy, (EA)
        
        Activation energy is often supplied in the form of thermal energy that the reactant molecules absorb from their surroundings
  - - - It cannot make an endergonic reaction exergonic
      - Enables cell to have a dynamic metabolism
  - - - While bound, the activity of the enzyme converts substrate to product
      - The reaction catalyzed by each enzyme is very specific
      - Each enzyme has a unique active site that binds one or more substrate(s), the reactants on which it acts. It then changes shape, binding the substrate(s) more tightly (induced fit)
      - Induced fit of a substrate brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction
    - - The active site can lower an (EA) barrier by
      - orienting substrates correctly
      - straining substrate bonds
      - providing a favorable microenvironment
      - covalently bonding to the substrate
  - - - Competitive inhibitors bind to the active site
      - Noncompetitive inhibitor binds to a different site on the enzyme
  - - - Many enzymes are subject to Allosteric regulation: Regulatory molecules, either activators or inhibitors, bind to specific regulatory sites, affecting the shape and function of the enzyme
      - In cooperativity, binding of one substrate molecule can stimulate binding or activity at other active sites
      - In feedback inhibition, the end product of a metabolic pathway allosterically inhibits the enzyme for a previous step in the pathway
- - - - Location: Cytoplasm to mitochondria
      - Oxygen requirement: No oxygen required
      - Step 3: Krebs Cycle
        
        Location: Mitochondrial matrix
        
        Oxygen requirement: no oxygen
        
        Step 4: Electron Transport Chain
        
        Location: Inner mitochondrial membrane
        
        Oxygen requirement: aerobic
        
        Which conducts the electrons to O2 in energy-releasing steps. The energy that is released is used to make ATP
- - - - Breakdown of glucose to carbon dioxide is completed
      - Stage 3: Oxidative phosphorylation
        
        Electron transport an chemiosmosis
        
        Along the electron transport chain electron transfer causes protein complexes to move H+ from the mitochondrial matrix
        
        As H+ diffuses back into the matrix through ATP synthase, its passage drives the phosphorylation of ADP to form ATP called chemiosmosis
      - compound called CoA enters the cycle
      - Dehydrogenases transfer electrons from substrates to NAD+ or the related electron carrier FAD, forming NADH or FADH2