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Chap 8 & 9: Metabolism, and Cellular Respiration and Fermentation (The…

- - - - Second law of thermodynamics
        
        Entropy: used by scientist to measure molecule disorder
        
        Every energy transfer or transformation increases the entropy of the universe
      - First law of thermodynamics
        
        the energy of the universe is constant.
        
        a plant converts sunlight to chemical energy, a plant acts as an energy transformer, not an energy producer.
      - Biological Order and Disorder
        
        Organism also take in organized forms of matter and energy from the surroundings and replace them with less ordered forms.
        
        Entropy in a particular system may decrease as long as the total entropy of the universe, the systems plus its surroundings increases.
      - The Study of the energy transformation that occur in a collection of matter.
    - - Kinetic Energy; relative motion of objects
      - Thermal Energy; the random movement of atoms or molecules
        
        Heat; thermal energy transfer from one object to another
      - The capacity to cause change. Ex. can be used to do WORK
      - Potential Energy; an object not presently moving may still possess energy.
      - Chemical Energy; the potential energy available for in a chemical reaction.
    - - Catabolic pathways(Downhill)
        
        Breakdown pathways or degradative process
        
        major pathway of catabolism is cellular respiration
        
        Sugar glucose and other organic fuels are broken down in the presence of oxygen to carbon dioxide and water.
      - Anabolic Pathways(Uphill)
        
        Biosynthetic pathways
        
        Ex. the synthesis of an amino acid from simpler molecules and the synthesis of a protein from amino acids.
        
        In contranst to catabolic pathways, consumes energy to build complicated molecules from simpler ones.
      - Steps resulting in a certain product. Begins with a specific molecule.
      - Bioenergetics
        
        the study of how energy flows through living organisms.
    - - an emergent property of life that arises from orderly interactions between molecules.
      - totality of an organism's chemical reactions.
  - - - In 1878, J. Willard Gibbs, created the Gibbs free energy of a system.
      - Free Energy the portion of a system's energy that can perform work when temperature and pressure are uniform throughout the system.
      - This principle is very important in the study of metabolism, where a major goal is to determine which reactions can supply energy for cellular work.
      - Equilibrium; state of maximum stability
      - An important relationship between free energy and equilibrium, including chemical equilibrium
      - Systems that equilibrium are at a minimum of G and can do no work, a cell that has reached metabolic equilibrium will be done.
  - - - Ribozymes
      - Catalyst or chemical agent that speeds up a reaction without being consumed by the reaction.
        
        Catalysis; a process by which a catalyst selectively speeds up a reaction without itself being consumed.
      - RNA Molecules
    - - Without affect the free energy change for a reaction, an enzyme speeds the reaction by reducing its activation energy.
    - - The reactants AB and CD must absorb enough energy from the surroundings to reach the unstable transition state where bonds can break.
      - after bonds have broken new bonds from releasing energy to the surroundings.
    - - Most human enzymes have optimal temperatures of about 35-40C
      - Thermophilic bacteria that live in hot springs contain enzymes with optimal temperatures of 70C or higher
      - Optimal pH values for most enzymes fall in the range of pH 6-8
  - - - Activator: a regulatory site stabilizes the shape that has functional active sites.
      - Inhibitor: stabilizes the inactive from of the enzyme.
      - Cooperativity is the mechanism amplifies the response of enzymes to substrates: One substrate molecule primes an enzyme to act on additional substrate molecules.
- - - - Alcohol Fermentation: pyruvate is converted to ethanol (ethyl alcohol) in two steps.
        
        Ex. Yeast used for brewing, winemaking, and baking.
      - Lactic acid fermentation: pyruvate is reduced directly by NADH to form lactate as an end product, regenerating NAD+ with no release of CO2
        
        Ex; Human muscle cells make ATP by lactic acid fermentation when oxygen is scarce.
    - - The cells of most eukaroytic and many prokaryotic organisms can carry out aerobic respiration.
    - - In Aerobic respiration the final acceptor is oxygen
      - In Anaerobic respiration the final acceptor is another molecule that is electronnegative, although less so than oxygen.
      - In Fermentation the electron acceptor is an organic molecule such as PYRUVATE or ACETALDEHYDE.
- - - - Oxidizing "Uphill" with oxygen at the bottom of the chain
    - - Built into the inner membrane of the Mitochondria of Eukaryotic Cells
      - Located in the plasma membrane of respiring prokaryotes.
  - - - NAD+: Oxidized form
        
        Functions as an oxidizing agent during respiration
      - NADH: reduced form
        
        Molecule formed during respiration represents stored energy
    - - Oxidation
        
        Substance Y, the electron acceptor
      - Reduction: the addition of electrons to another substance.
        
        Substance Xe-, the electron donor
  - - - Eukaroyotes, Pyruvate process is called acetyl CoA
      - Prokaryotes, the Pyruvate process begins in the Cytosol
- - - - "Dance" between subtly different shapes in a dynamic equilibrium.
      - the enzyme changes shape slightly due to interactions between the substrate's chemical groups.
      - Active site
        
        typically a pocket or groove on the surface of the enzyme where catalysis occurs.
    - - only a restricted region of the enzyme molecule actually binds to the substrate.
      - reactant an enzyme acts on
      - Two or more reactants
  - - - The reverse process of Exergonic reaction (Downhill)
        
        Reversible process cannot be downhill in both directions
      - G= -686Kcal/mol is the conversion of carbon dioxide and water to glucose and oxygen.
      - Absorbs the free energy from its surroundings
    - - Loses free energy because of chemical mixture
      - Occurs spontaneous
        
        the released free energy can be harnessed to do work.
      - proceeds with a net release of free energy
  - - - the enzyme that makes ATP from ADP and inorganic phosphate.
      - Ion pump use ATP as an energy source to transport ions against their gradients.
      - Enzymes can catalyze a reaction in either direction.
    - - the capacity of the gradient to perform work
      - H+ is accepted from the mitochondrial matrix and deposited in the intermembrane.
      - H+ gradient
    - - energy stored in the form of hydrogen ion gradient across a membrane is used to drive cellular work.
      - The synthesis of ATP
      - Couples the electron transport chain to ATP synthesis