Notes on usage of the Thermodynamics tutorial
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..
- PLEASE SELECT THE "[P]>0" RADIO BUTTON.
- please slide the kcat/KM slider about halfway up to make the concentrations change at an appreciable rate.
- 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.
- Set the DG to some value
- Watch [S] and [P] change until it reaches the same ratio as the red bars in the upper right
- The rate bar starts high and decreases (NOTE: THIS IS A NET RATE OF CONVERSION OF S TO P)
- 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
- This means that the forward rate = reverse rate.
- 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)
- 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 (Km and Vmax) 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)
- kcat = sec-1
- enzyme rates (vmax and vo=Rate of [P]) = moles/sec (moles of product produced per sec)
- Km = Molar
- kcat/Km = Molar sec
- Keq is unitless
- The bottom panel provides some interaction.
- Sliders on the bottom panel allow you to independently alter the [S], [P], [E], kcat, Km, Vmax, kcat/Km, Keq 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.
| The bar graphs update in at a rate 10 times faster than "real time" this is solely to make the changes in the graph visible and more interesting to watch.
| Alter each parameter one at a time. Observe what the changes are in values that are linked as well as what happens to the graph itself.|
| Notes: the kcat/Km, kcat, Km, Vmax and [E] values are linked computationally observe what happens to each as you alter any of the one of the set.