Glossary of biochemical terms

Thermodynamics Glossary of biochemical terms

| First Law | Second Law | Free energy equation | Questions |

Glossary of biochemical terms

Biochemistry is a science of living cells. A living cell synthesizes complex molecules. These molecules may be shuttled out of the cell or from one compartment to another. To accomplish these activities, energy is required. Bioenergetics is a quantitative analysis of how cells gain and use energy. The objective of this chapter is to introduce you to the concepts of thermodynamics as applied to biochemistry.

1. First Law of Thermodynamics: The law states that total energy of a system and its surroundings remains constant. Energy is neither created nor destroyed but may be used to do useful work on the system or surroudings. For example, energy produced by the digestion and breakdown of proteins may be used by the organism to synthesize other molecules, be used to keep the temperature of the organism constant etc. This law is represented as:

E= q- w ----- (1)

where delta E is the change in internal energy of the system.

q is positive number when heat is absorbed by the system from its surroundings and a negative number when heat iis absorbed by the surroundings from the system.

w is positive when work done by the system and negative when the work is done by the surroundings. Since the concept of w generally applies to gaseous systems where partial pressure or volume of the system may vary, it is generally ignored for reaction in solution e.g cellular reactions. Under these conditions, delta E is essentially change in heat content of the system. Therfore E = H (the change in enthalpy of the system).

2. Second Law of Thermodynamics: Direction of Reactions:

The first law is essentially keeps track of energy produced and spent and these must balance. The second law helps us understand why certain processes can proceed in a reversible manner whereas others essentilly are unidirectional. For example, it is poosible to convert water to ice and vice versa but if we burn a piece of cloth to carbon dioxide and water, it is not reversible. This concept can be understood if we realize that not all the energy or heat content of the system (delta H) in solution may not be availavle for useful work i.e. some of the energy may be lost in non-productive manner. Thus delta H may be defined as:

H = G + T S------ (2)

where G is the free energy change in the system and is the energy available to do useful work (convert a substrate to a product) and delta S is change in the entropy of the system (entropy is defined as degree of randomness of the components of the system). These are conditions of constant pressure, volume, and absolute temperature in degrees Kelvin (T= 273 + degree centigrade). This equation is generally written as:

G = H - T S ------- (3)

It is clear and logical to think that if the free energy of the product is less than that of the reactants, then the reaction will be favored in the forward direction. However, if G is positive then the backward reaction will be favored. Negative values of G can be achieved if dH is negative and dS is positive. Such reactions are considered as Enthalpy Driven and/or Entropy Driven. However, depending upon the magnitude, it is possible to have negative value for G even if H is positive or S is negative. An example is melting of ice to water. The H for this system is positive whereas dS is highly positive which compensates for the positive dH. On the other hand when water freezes to ice, S is negative (less randomness in the structure of water) but positive TS value is compensated for by negative enthalpy change. It must be remembered that favorable reactions must have a negative value for dG. Such reactions are called Exergonic. Reactions with positive G are not favored in the forward direction and are called Endergonic.

Since reactions are driven by overall free energy changes, let us see if thermodynamics can explain the cellular processes. Considering a cellular process: S ----> P, the free energy of substrate and product can be described as:

Gs = G0s+ RT ln {S} and

Gp = G0p + RT ln {P}

G0p and G0s are standard free energy changes and represent the free energy of product and substrate when they are present at 1M concentrations. For biochemical reactions, standard free energy changes are normalized to pH 7 because many of the biochemical reactions involve {H+} as one of the components of the reaction and it is simpler not to have to include {H+} as one of the components of the reaction. Thus G0 are represented as G0'. Therefore, change in free energy of a reaction can be represented by:

G= (Gp-Gs)= (Gp0'-Gs0') + RT(ln {P}- ln {S})

G= G0' + RT ln {P}/{S} (1)

When the reaction reaches equilibrium, there is no net change in the concentrations of substrate and product; therefore no useful work is done by the system and G =0. Under these conditions:

0=G0' + RT ln {P}e/{S}e or G0' = - RT ln {P}e/{S}e = -RT ln Keq or G0' = -RT ln Keq

Thus knowing standard free energy change for a reaction, one can calculate equilibrium constant. For these calculations, R is 1.98 cal/mole/degree Kelvin and T is (273 + Degree centigrade) (in recent literature, the heat energy is represented by Joules or KiloJoules; it is easy to convert calories or kilocalories to Joules: 1 cal = 4.184 joules). Based on these calculations, one can predict the magnitude of Keq. Thus

Go' = 0 Keq = 1

Go' is negative Keq > 1

Go' is positive Keq < 1

Keq values also indicate whether the reaction is favored in a particular direction. Keq =1 means that the reaction is equally favored in both directions. Keq greater than one means that the reaction is favored in the forward direction whereas Keq of less than one means that the reaction is favored in the backward direction.

Usefulness of G0'

(1) Used for calculating Keq for a variety of reactions as dGo' values can be calculated.

(2) Can predict the direction of a reaction when reactant and product concentrations are equal or are 1 M each.

(3) Go' values for two reactions having a common intermediate are additive.

Let us see if thermodynamics can explain how some physiological reactions in the cell. Consider the physiological reaction:

Glucose + ATP ------- > Glucose--6--Phosphate + ADP G0' = -- 4 K cal/mole

This is a combination of two reactions;

Glucose + phosphate ------- > Glucose--6--Phosphate G0' = +3.3 Kcal/mole (a)

ATP -------- > ADP + Phosphate G0' = --7.3 Kcal/mole (b)

Reaction a would not occur without the participation of second reaction. Since reactions a and b have one of reactants and products in common, the standard free energies can be added, giving the overall energetics of the overall reaction. In addition to the negative standard free energy change, the reaction is further favored by continuous siphoning of the product, glucose-6-phosphate, in subsequent reactions of the glycolytic cycle. This gives a G value which is more negative than -4 K cal/mole. Another clear example of usefulness of additive aspects of G0' is the reaction:

D-Fructose-1,6,-bisphosphate --------- > Dihydroxyacetone-phosphate+ D-Glyceraldehyde--3--phosphate G0' = +5.77 Kcal/mole

The only reason this reaction proceeds in glycolysis is because under physiological conditions in the cell, the concentrations of products are much smallet than the reactant and when these concentrations are substituted in equation 1, the value of G comes out to be --0.32 Kcal/mole.

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