Biological systems obey the rules of chemistry and physics.  They involve complex networks of chemical reactions which together produce the behavior we call life.

Thermodynamic analyses tells us the extent to which a particular reaction can proceed under specific conditions.  Every reaction is characterized by its equilibrium constant - K_eq.

Reaction kinetics tells us the rate at which the reaction actually occurs under these conditions. 

It is a mistake, however, to think that a system at equilibrium is static.   If we were to peer into the system at the molecular level we would find that even at equilibrium, reactants can be combining to form products and products are rearranging to form reactants.

At equilibrium these two processes are balanced, the net flux = 0.

If, at equilibrium, a reaction has gone almost to completion, there will be very little of the reactants left and lots of the products.

The product of the forward rate constant times the small reactant concentrations will equal the product of the backward rate constant times the high product concentration.

If a reaction's K_eq is greater than one, there will be more product than reactant at equilibrium.

If the K_eq is less than one there will be more reactant than product.

Coupled Reactions: 

Reactions can be coupled together if they share a common intermediate.

In this example, the two reactions share the component "D".

Lets assume that the first reaction has an K_eq << 1, while the K_eq for the second reaction is >> 1.

What will happen? Most of the D formed by the first reaction (which is not much), will react with E (assuming E is present) and be removed from the system.

This will inhibit the C+D back reaction, while the A+B forward reaction will continue.

More D will be produced, even though the reaction that produces it is unfavorable.

• A reaction is at equilibrium and we increase the amount of reactant, what happens in terms of the amount of reactant and product?
• A reaction is at equilibrium and we increase the amount of product, what happens in terms of the amount of reactant and product?
• Consider the coupled reaction above (A+B ⇔ F); what will happen to the concentrations of A,B,C,D, E and F if we somehow remove C from the system?  What happens if we add E to the system?

Reaction rates:  What does the equilibrium constant tell us about how long it will take for a reaction to reach equilibrium?

The somewhat surprising answer is nothing! 

To understand why, consider the factors that determine the equilibrium constant and reaction rates.  The rate of the reaction is determined by the molecular pathway that connects the reactants and the products.

We will examine one such reaction pathway using the transport of a molecule across a membrane as an example.

Consider the reaction

A is a hydrophilic molecule at high concentration outside the cell.

There is a major energy barrier, known as the activation energy, associated with the movement of A through the hydrophobic region of the lipid bilayer.

This barrier is high enough that A molecules rarely, if ever, pass through the membrane, even though the basic reaction itself is quite favorable. (What is that basic reaction?)

Now, consider how adding a channel to the membrane alters the reaction kinetics.

The channel catalyzes the reaction; it lowers the energy barrier between the two states, but is not itself used up when the reaction occurs.

The rate of a chemical reaction is determined not by the difference in the free energy between the reactants and the products, but (as a first approximation) by the difference in free energy between the reactants and the highest energy transition state or reaction intermediate.

This is the rate limiting step in the reaction

The vast majority of biological reactions require a catalyst to occur - catalysts act by reducing the free energy of the transition state.

In the system we have been considering, the channel is the catalyst.

Most, but not all, biological catalysts are proteins.

Protein catalysts are known as enzymes.  RNA catalysts are known as ribozymes.

• Why does a catalyst not change the equilibrium state of the system?
• What does the addition of a catalyst do to a system already at equilibrium
• What does the addition of a catalyst do to a system far from equilibrium?  
• Where does the energy come from to reach the activation state/reaction intermediate?