D) chapter 3: "Formal Enzymology (equalibria and kinetics" pgs.…
D) chapter 3: "Formal Enzymology (equalibria and kinetics" pgs. 93-103--Tony
2. Delta G changes as a reaction proceeds toward equilibrium
pay attention to Figure 3-17: reaction coupling can drive an energetically unfavorable reaction
reactions will proceed not only on the amount of energy stored in each individual molecule, but also on the
of the molecules in the reaction mixutre
because delta G changes as products accumulate and reactants deplete, chemical reactions will generally proceed until they reach a state of
. when this happens, the rates of the forward and revers reactions are equal, and there is no further net change in the concentration of substrate or product.
however, reaching an equilibrium in chemical reactions within the body, well that is compatable with life. living cells avoid reaching a state of complete chemical equilibrium because they are constantly exhanging materials with their environment.
replenishing nutrients and eliminating waste products; many of the individual cell's complex metabolic network also exist in disequilibrium because the products of one reaction are continually being siphoned off to become the substrates in a subsequent reaction. rarely do products and substrates reach concentrations at which the forward and reverse reaction rates are equal.
3. the standard free-energy change, delta G, makes possible to compare the energetics of different reactions
pay attention to Figure 3-18 which depicts equilibrium among reactions
1. The free energy change for a reaction determines whether it can occur
according to the second law of thermodynamics, a chemical reaction can proceed only if it results in a net (overall) increase in the disorder of the universe.
disorder increases when useful energy that could be harnessed to do work is dissipated as heat.
useful energy in a system is also known as
which is denoted
A system that is more orders as more useful energy, thus an ordered system contains more free energy vs. a disordered system.
reactions are those that decrease in useful energy or free energy, thus they have a
and occur in less ordered systems, whether they be reactant or product. these kinds of favorable reactions are said to be
, however, this does not mean that a favorable reaction will be quick
reactions increase useful energy, thus free energy, therefore resulting in a
because they are bringing about more order in the universe.
enzymes are respectfully important in this sense because they can create biological order by coupling energetically unfavorable reactions with energetically favorable ones, thus keeping the delta G overall negative and producing a "desired reaction"
4. thermal motion allows enzymes to find their substrates
enzymes and their substrates are both present in relatively small amounts in the cytosol of a cell.
enzymes do extremely well binding to substrate, releasing a product and then rebinding because they are so fast.
this is because there is constant heat energy in molecules within the cytosol and this constant motion helps for rapid binding.
this process is called
, which occurs throughout the cytosol
now, diffusion is a great way for smaller molecules to reach there targets, but proteins for instance are much larger, thus they take more time diffusing.
so this means that the rate at which an enzyme will encounter its substrate depends on the concentration of the substrate.
the random encounters with a substrate and its enzyme is called the
. this complex is stabilized by noncovalent, weak interactions such as hydrogen bonds, van der waal attractions, and electrostatic attractions (chapter 2)--these bonds persist until thermal motion causes dissociation.
in the end, these weak noncovalent interactions help keep the enzyme and substrate together long enough for the substrate to either break or form a covalent bond.
5. Vmax and Km measure enzyme performance
to catalyze a reaction, an enzyme must first bind its substrate. the substrate then undergoes a reaction to form the product, which initially remains bound to the enzyme. finally, the product is released and diffuses away, leaving the enzyme free to bind another substrate molecule and catalyze another reaction (see figure 3-15).
the rates of the different steps vary widely from one enzyme to another, and they can be measured by mixing purified enzymes and substrates together under carefully defined conditions in a test tube.
in such experiments, the substrate is introduced in increasing concentrations to a solution containing a fixed concentration of enzyme.
however, as more and more enzyme molecules become occupied by substrate, this rate increase tapers off, until at a very high concentration of substrate it reaches a maximum value, termed
because there is no clearly defined substrate concentration at which the enzyme can be deemed fully occupied, biochemists instead use a different parameter to gauge the concentration of substrate needed to make the enzyme work efficiently. this value is called
michaelis constant or Km
the Km of an enzyme is defined as the concentration of substrate at which the enzyme works at half its maximum speed.
in general, a
indicates that substrate binds very tightly--a
indicates that substrate bind very loosely