Thermodynamics in "Real state"

The Java program above has three panels. This is the same program we used in the kinetics pages, but here with a different purpose. Instead of concentrating on the enzyme kinetics this time..

1. PLEASE SELECT THE "[P]>0" RADIO BUTTON.
2. please slide the kcat/KM slider about halfway up to make the concentrations change at an appreciable rate.
3. Now grab the "DG" slider and move. This directly controls a pair of bar graphs in the upper right. The equilibrium position for your reaction.

Immediately to the left of this are three bars. The current [S], current [P] and observed rate of conversion (red bar).

What to look for.

1. Set the DG to some value
2. Watch [S] and [P] change until it reaches the same ratio as the red bars in the upper right
3. The rate bar starts high and decreases (NOTE: THIS IS A NET RATE OF CONVERSION OF S TO P)
4. You should see that when the current [S] and [P] are at the same ratio as the red bars the NET rate of conversion is 0
5. This means that the forward rate = reverse rate.
6. Increase the [P] slider. and observe what happens to [S]. note; if you start with [P] very high the observed rate is negative (S is forming faster than P)

Notes

• The top depicts a graph of the Enzyme rate vs. [S]. There are two lines on the first graph here:
  • Black: is a reference graph whose Data (K_m and V_max) ALWAYS remain unchanged even as the scale on the graph changes.
  • RED represents the data that you manipulate with the sliders.
  • A relative scale of the graph is indicated at the top.
• The two bar graphs on the top right represent formation about the current conditions chosen
  • The panel at top right gives a bar graph representation of the current [S], [P], and enzyme rates as well as
  • The log of the final equilibrium position.
• The middle panel provides numerical representation of the same data.
  • units for the parameters
  • all concentrations ([S], [P], [E]) are in M/l (Molar)
  • k_cat = sec^-1
  • enzyme rates (v_max and v_o=Rate of [P]) = moles/sec (moles of product produced per sec)
  • K_m = Molar
  • k_cat/K_m = Molar sec
  • K_eq is unitless
• The bottom panel provides some interaction.

• Sliders on the bottom panel allow you to independently alter the [S], [P], [E], k_cat, K_m, V_max, k_cat/K_m, K_eq and the Hill coefficient independently to observe the effects.
• The Radio buttons on the right allow you to maintain the [P]= 0 or allow [P] to accumulate.

In the latter case you should observe that eventually the ratio of [S] and [P] will come to the same ratio as indicated in the "final equilibrium position" window. This final equilibrium position can be altered by changing the DG of the reaction.