The Design of Metabolism                                       
key concepts
            or How Biological Order Comes About...

METABOLISM.... the catalytic reactions (run by enzymes) of cells.....
                                             metabolic pathways [A --> B --> C --> D --> E]

  2 Categories catalytic reactions -
        CATABOLISM...  chemical oxidation of food stuffs or Cell Respiration
                 1)    digestion of polymers (foods)  [hydrolysis reactions] to glucose
                 2)   GLYCO-LYSIS   glucose ---> pyruvate    [splitting of sugar]
                 3)   KREBS cycle    oxidation of Acetyl-CoA  --->  CO2 + NADH ----> H2O
                 4)   ELECTRON TRANSFER ----> NADH + O2  ---->  H2O +  H+ gradient
                 5)   ATP SYNTHASE ---> use a H+ gradient to phosphorylate P + ADP ----> ATP
   5 steps*
       ANABOLISM...   Biosynthesis, often via...
                                      coupled reactions - energetically unfavored  w  favored reactions
  flag18.gif (924 bytes)          1)   PHOTOSYNTHESIS    reduction of CO2 to CH2O







ENERGY - capacity or ability to do work 
       kinds:   KINETIC - motion
                   POTENTIAL - stored energy; capacity to do work (eventually);
                   HEAT - assoc with movement of molecules in a body of matter;
                                       most random form of energy (wasted).   
                                       Student Media Activities -
chapter 6A - Energy Transformations
                                EXAMPLES            general:  heat,  light,  sound,  mechanical
                                   of energy:       biological:  synthetic,  osmotic,  mechanical,
        molecules in living cells have potential energy to do work...
                               because of the arrangement (orientation) of their atoms
                               in space... we call this chemical bond energy
                               the energy of cells is stored in the covalent bonds of their molecules.

HOMEOSTASIS ...most of cell's energy is needed to maintain a steady state.
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 BIOENERGETICS - is study of energy transformations (changes) in Biological systems is based on


                   1st LAW = Conservation of Energy (energy is a constant)
                                   energy can not be created or destroyed, only transformed
                                           ... experimental caloric data says this LAW is true
 combustion of glucose releases 686 kilocalorie/mole of heat

                   2nd LAW = Energy transformations reduce the order of the universe
                                     it's directional --- > toward equilibrium (toward maximum disorder)
                                           ... ENTROPY = amount of disorder in a system -

       The Rules of Universe are simple :
                   Cities crumble, stars go Supernova, & we're all dying... (equilibrium...izing)
                                             law of ENTROPY says... Degree of disorder of the Universe
                                                     (its randomness - its entropy) CAN ONLY INCREASE.
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  Cells obey Laws of Chemistry & Physics

         yet CELLS.....  WOW !   .......become more highly ORDERED as they grow...
               fertilized egg ---> wing of bird,  a spider's web,  the human eye,  dividing cells,  etc...
                                 from fertilized egg cell... which  Feeds, Grows & Differentiates  =  HOW?

               for part of a system to become more ordered - lose entropy - (such as a cell),
                                             its surroundings must become more disordered - gain entropy -

FOODs (light & covalent bond energy)

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cell reactions give increased order within cell

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with release of HEAT

flag22.gif (924 bytes)                  HEAT (most disordered form of energy) = max entropy





                How do we measure energy changes in cells...

        Gibbs FREE ENERGY Equation      DG      =     DH        -   T DS
                                                   free energy     enthalpy         entropy

         DG is measures amount energy change in system that is able to do Work...
         DG is a numerical measure of how far a reaction is from equilibrium...
                        Disorder Increases (Entropy Increases)... when useful energy,
                                          that which could be used to do work, is dissipated as heat...
                 cells are ISOTHERMAL  -  (-2o to 37o)  - thus DH = 0 above
                                   Enthalpy may be thought of as
heat content of a system
                                   cells function within a very narrow temp range [23o-37oC],
                                   and thus
DH is negligible
DG can PREDICT...    the Direction of Cellular Reactions...
                                  TOWARD EQUILIBRIUM...     toward Maximum ENTROPY
flag23.gif (924 bytes)                                                                             toward a release of free energy

 CHEMICAL REACTON    A <---> B     Which Way is toward more Disorder?

                   DG  = DG0 RT ln  [p]/[r]

      change in free energy content of a reaction...depends upon:
            1.  energy is stored in molecule's covalent bonds
            2. temperature is negligible... cells are isothermal, i.e.,

DG       =    actual free energy at any time in a reaction
DGo'    =    standard free energy   [free energy change under standard conditions]
                    R          =    gas constant ( 2 x 10-3 Kc/mol)
                    T          =    absolute temp (-273oK)
                    ln          =    natural log (conversion to log10 = 2.303)

at equilibrium by definition    DG = 0   and  we call   [p]/[r]  =  Keq

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Free Energy Equation... 

    ΔG  =   ΔG0'   +   RT  ln [P]/[R]
       @ equilibrium  ΔG  =  0                     0  =   ΔG0'   +   RT  ln [P]/[R]
                       .... thus  rearranging     
ΔG0'  =  -RT ln [P]/[R]                 

       @ equilibrium         [P] / [R]   =   Keq

  &  @ 250C ... -RT ln Keq =  -(2.0) (298) (2.303) lg10 Keq  =   -[1372] lg10 Keq

                                  thus..........   ΔG0'  =  - [1372]   lg10 Keq  

                                                                                                   R  =  gas constant ( 2 x 10-3 Kc/mol)
                                                                                                   T  =  absolute temp (-273
                                                                                            ln =  natural log (conversion to log
10 = 2.303)





   The difference between   
ΔG   and    ΔG0'
    ΔG0' is a fixed value under idealized conditions for a given reaction and
                  indicates in which direction that reaction will proceed at standard conditions

                            standard condition do not exist within a cell, but ΔG0' may be
                            used to predict the direction of a reaction at a specific given time.

ΔG   is determined by the concentrations present at a given time and
                  is a measure of how far a reaction is from equilibrium then.
                            Cell metabolism is essentially a non-equilibrium condition.

         Metabolism works by changing the relative concentrations of reactants
                       and products to favor the progress of non-favored catalytic reactions.  

   when we solved above equation for DGo'  we could see relationship* of Keq to DGo’









 CHEMICAL REACTIONS    A <----> B      Which Way & Why?

    EXERGONIC REACTION - is one which releases free energy    [ -
DG ]
        Product (B)  <<< energy  REACTANT  (A)    [energy stored in covalent bonds]
            ex:    burning wood (cellulose)
                             glucose polymer...  potential energy.
                             breaks bonds, release heat & light ---> CO2 & H2O    fig 9.5*
                     cell respiration - cellular burning of glucose molecules.
                             slower,   multi-step process that captures & releases
                                          some energy... as ATP

    ENDERGONIC REACTION - requires input of energy for  A --> B
        Product (B) >>>  energy than   REACTANT (A)                 [  +
DG  ]
            ex:      photosynthesis (autotrophy)
                      glucose is made from  CO2
 +  H2O --light-->  C6H12O6
                                                      energy poor      vs.       energy rich

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 CELL METABOLISM is then a mix of...

           Exergonic  &  Endergonic  reactions that occur inside of cells...
                                          Concept Activities -
chapter 8.3 - Chemical Reactions and ATP

   How does Cell Metabolism really work energetically?
              for RX's which share one or more intermediates (a pathway)...   [ A-->B-->C-->D ]
              the overall free energy change (
DG) is the sum of indiv DG's
            Glu + Fruc     --->    Sucrose                                 + 5.5 Kc/m
                     ATP     --->    ADP + P                                 - 7.3 Kc/m
            Glu + ATP     --->     G-1-P + Fruc ----> Suc + P      - 1.8Kc/m

                     COUPLED REACTIONS - involves say... the linking of the hydrolysis of ATP
                                  (a favored rx)  to a thermodynamically unfavored reaction,
                                   thereby creating biological order (greater molecular structure).
   flag26.gif (901 bytes)                                    another ex:    synthesis of glutamine*




WHY ATP ? ? ?   shouldn't any nucleotide work?
    ... the ENERGY MOLECULE of CELLS is  ATP
             over the period of evolution,  cells favored enzymes that
             bound ATP & used its hydrolysis to drive endergonic reactions.

        adenosine triphosphate figure 6.8  * its structure is its source of energy
                                                        Concept Activities - chapter 8.3 - The Structure of ATP*
                1.  electrostatic repulsion       2.  resonance       3.  sphere of hydration 
   HYDROLYSIS of ATP  ATP    DG0'     =      -7.3 Kc/m     [ exergonic by some -7,300 cal/mol ]

         How ATP works -    phosphorylation*   &    metabolic ATP coupling*
Concept Activities - chapter 8.3 - Chemical Reactions & ATP.
                  next Lecture:    How cells make ATP*           a paradigm
key concepts*
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flag27.gif (901 bytes) the material below is covered elsewhere under proteomics &  enzymes

What catalyzes the metabolic reactions in cells..... ENZYMES

   Enzyme (from Gk... meaning roughly)  "in yeast" are proteins...
        History of Biochemistry is tied to history of enzymes
            First described in 1850's in Pasteur's lab in Paris as "ferments"
            and in 1926 Urease was crystalized by James Sumner

   Catalyze chemical reactions (A ---> B) in cells by breaking old
        covalent bonds and forming new covalent bonds'.

   Function as biological catalysts  (but, differs from metal catalysts)
           1.  have complex, specific structures (sequence of aa's)
           2.  act only upon a specific substance (substrate)
           3.  do not change the direction (energetics) of a reaction
                    only enhance rate of a chemical reaction A ---> B
                 without being used up in reaction
   flag33.gif (932 bytes)



    many require cofactor or coenzyme

        cofactor - small inorganic ion that catalyzes reaction
                    Cu+2 , Mg+2 , Mn+2, ,,etc...
        coenzyme - smaller,   non-protein ligand (9.4)  which catalyzes rx
                    gains/loses e- ; transfers group ; breaks bond.

   have an
Active Site  (6.12) - portion of enzyme protein that attaches the
                substrate by means of weak chemical bonds
                        (H-bonds, ionic bonds, hydrophobic forces, etc...)

   In chemical reaction   (6.9)  enzymes function  inertia
                              by lowering the Energy of Activation (6.10) - Ea
                              by bringing reactants together

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   Reaction path: E + S <---> ES <---> E + P

         enzymes are proteins with a specific 3-D shape,
         that binds substrate to its ACTIVE SITE

         shape of enzyme is critical to its ability to convert A ---> B
                change enzyme's 3D shape - won't bind substrate

        What will change shape of a protein (denaturation) ?
        1.  temp - increases kinetic motion, breaks H-bonds
        2.  pH - changes charges = alters shape
        3.  inhibitors - chemicals that bind to enzyme
                    & change its activity  [competitive/non-competitive]
        4.  poisons - organophosphorous compounds
                    (many insecticides) bind to enzymes of nervous system & kill
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   mathematical and/or graphical expression of the
   reaction rates of enzymes   ex: Catalase  2 H2O2 ---> 2 H2O + O2

wpe2.jpg (13204 bytes)

flag28.gif (873 bytes)   rate = ml of O2 per min  a) 0.35  b) 0.6    c) 1.125

Some Characteristic Enzyme Curves:
        or how to determine if the reaction A —> B is enzymatic


Rate (0.8 ml O2/min)  Vs. [E]


Rate (optimum) Vs. pH


Rate (optimum) Vs. Temperature


Rate (saturates) Vs. [S]


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Lenoir Michaelis - Maude Menten Enzyme Kinetics

wpe5.jpg (12335 bytes)

flag27.gif (901 bytes)   A plot of rate (amount of product per unit time) vs [S]
           1.   saturates..... at [S] = Vmax (maximum velocity)
           2.  Km = substrate concentration at which rate is one-half
                    the maximal velocity (in above Km = 2 mg per min)
                    a measure of affinity of enzyme for its substrate
                     amount of [S] needed to reach 1/2 Vmax



  Enzyme Inhibition - a reduction in enzyme activity

        Competitive (6.14).      binds to active site ...reversible
                                         lower Km same Vmax

        Noncompetitive         binds to an allosteric site
                                        same Km lower Vmax

        Feedback inhibition (6.16) - end product inhibits an initial enzyme

    Enzyme Cooperativity and Allosteric Regulation
                     enhancing enzyme activity by improving conformations
                     fig 6.15    and   fig 6.17
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     The NAMING of ENZYMEs
4 digit Numbering System []
                    1st     Major Class of Activity
                    2nd    Subclass (type of bond acted upon)
                    3rd    Subclass (group acted upon, cofactor required, etc...)
                    4th     Serial number ... sequence order

       Six MAJOR CLASSES of Enzymes           (Sigma Enzyme Index)

1. Oxidoreductases    [dehydrogenases] ....
    catalyze oxidation reduction reactions, often w coe NAD+/FAD
        Alcohol dehydrogenase [EC]   
                ethanol + NAD+ -------> acetaldehyde + NADH
flag19.gif (911 bytes) 2. Transferases    .... catalyze the transfer of functional groups
        Hexokinase [EC]
                D-glu + ATP ----------> D-glu-6-P + ADP

3. Hydrolyases .... catalyze hydrolytic reactions
                           add water across C-C bonds
        Carboxypeptidase A [EC]
                [aa-aa]n + H2O ---->    [aa-aa]n-1  +  aa
4. Lyases .... add or remove groups to  C= C  bonds
        Pyruvate decarboxylase [EC]
               PYR -----> acetaldehyde + CO2
5. Isomerases [mutases] .... catalyze isomerizations
            Maleate isomerase [EC5.2.1.1.]   (cis-trans isomerization)
                maleate   ----->   fumarate
flag21.gif (938 bytes) 6. Ligases .... condensation of 2 substrates with splitting of ATP
            Pyruvate carboxylase [EC]
                PYR + CO2 + ATP ------> OAA + ADP + P







                Charles Mallery,
                Department of Biology,
                University of Miami,
                Coral Gables, FL 33124

                Last Update - 06/03/2008