BCHM104B Notes

Overview:
This course consists of 4 modules. The first two are basic concepts in thermodynamics while the
other two are applications of the concepts and formulas in simple biochemical situations. The first
module reviews basic concepts in chemical thermodynamics. These concepts include heat,
temperature, entropy, enthalpy, gibbs free energy, equilibrium constant and the equations relating
these variables. Here, it is necessary to be clear about the relationship between similar concepts
(e.g. why does adding heat not always increases temperature, what is the difference between
equilibrium constant and reaction quotient). These equations are then used to solve simplified
biochemical models such as protein folding (the focus of module 3). In the second module, the
basic principles of electrostatics are reviewed in a biochemical context. The basic coulomb force
and energy formulas are modified so that they are applicable in biochemical situations ( e.g.
addition of dielectric constants). Then, electrostatics and thermodynamics are used together to
consider dissociation of charges from amino acids. Here, the basic idea behind multiple equilibria
is introduced ( the focus of module 4). In module 3, the molecular interactions behind protein
foldings are introduced ( the L-J potential and the hydrophobic effects). These ideas along with the
formulas from the previous 2 modules are used to solve the thermal denaturation of protein. In
module 4, the model for multiple equilibria is developed starting from the simplest one reaction
case. Different biochemical reactions are used to motivate more complex models. The calculation
of the fraction of a specific state is discussed for each model. Finally, these models are applied to
solve two models of hemoglobin cooperativity ( the MWC model and the Hill model).