BOND MAKING AND BREAKING

The H for Reactions in terms of Bond Energies (Bond Dissociation Enthalpies).

This segment of EXBAN presents a brief review of the H for reactions in terms of bond breaking and making events. This is done to emphasize the large energies required to break bonds in comparison with overall H values for reactions that can be negative or positive depending on the energy balance of the bonds ruptured and formed. Two factors that must be kept in mind:

(a) In the present depiction bonds are “pulled apart” and the fragments “snap” together to form new bonds in “tinker-toy” fashion. The overall H for reactions can always be represented in this way, or in terms of the balance of bond breaking and making events employing appropriate bond dissociation enthalpies. The path the reaction actually takes for the transition between reactants and products will, of course, be quite different, and depend on the mechanism, e.g. whether the reaction is uncatalyzed, or catalyzed, etc.

(b) The misconception considered in this website is connected with the energy associated with bond breaking. The reactions here, including the coupled reaction, are examined, therefore, in terms of the H’s of the processes involved. Entropic contributions often contribute to the spontaneity of reactions, and can become the principal driving force for reactions or phase changes. It is, indeed, entropy that is responsible for the concentration dependence of reactions. However, bond breaking and making, as with the examples given here, is often the main factor in determining the spontaneity of reactions.

The H of hydrolysis of ATP in terms of a balance of bond breaking and making processes.

Due to the relatively weak phosphoanhydride linkage (high energy phosphate bond) the magnitude of the energy required to break the bonds in the reactants is seen to be more than offset by the corresponding decrease from bond formation in the products

Rupture of an O-H bond in water requires a very significant (~ 490 kJ/mole) input of energy. (The arrow depicting bond rupture appears with a break inserted in that the energy involved (bond dissociation enthalpy), is more than an order of magnitude larger than the H for the overall reaction.)

Breaking a phosphoanhydride bond requires considerably less but still cost energy. At this point the bond breaking is complete with an input of > 750 kJ of energy.

Energy begins to decrease with bond making. The magnitude of the decrease (blue) due to formation of the P-O bond here is much greater than the input (red) involved in breaking P~O anhydride bond.

The reaction is complete with the formation of an O-H bond.

The overall decrease of ~24 kJ/mole occurs, is the H of hydrolysis. The value of this exothermic process is at least an order of magnitude smaller than the input needed to break even the weakest bond, i.e. the phosphoanhydride, or “high energy phosphate” bond..

In this second example formation of the phosphodiester link in DNA shown here is the reverse of a hydrolysis reaction. The endothermic nature of this condensation is again examined in terms of bond breaking and making.

The reaction again begins with bond rupture in the reactants.

Almost as much energy is required to break the alcoholic O-H bond as an O-H bond in water.

Rupture of the P-O bond in the phosphate group also requires a significant energy input It is considerably greater than that required to break the phosphoanhydride bond in ATP.

The P-O bond in the phosphodiester link, is also significantly weaker (blue) than the phosphate P-O bond (red).

As a result, even with formation of a strong O-H that results in the production of water, the reaction remains endothermic.

The reaction requires a larger input of energy to break the bonds in the reactants than the decrease due to the weaker bonds, in particular the phosphodiester link, that are formed in the products.

The hydrolysis of a phosphoanhydride linkage in ATP that was considered in the first example is more exothermic and spontaneous, than hydrolysis of a phosphodiester linkage in DNA.

The more negative G for ATP hydrolysis derives primarily from its more exothermic nature (neg. H). The greater exothermicity associated with ATP hydrolysis is a consequence of the smaller input of energy (enthalpy) required to rupture the weaker phosphoanhydride linkage in comparison with the phosphodiester link in DNA:

H(hydrolysis) (kJ/mole)

ATP + H2O → ADP + Pi -24.2

DNA + H2O → 5’DNA + 3’DNA -12.0

so that reversing the 2nd reaction in the direction of DNA formation:

ATP + H2O → ADP + Pi -24.2

5’DNA + 3’DNA → DNA + H2O 12.0

results in an overall exothermic process if the condensation of the 2 DNA fragments can be coupled to the ATP hydrolysis reaction:

5’DNA + 3’DNA + ATP → DNA + ADP + Pi -11.8

.

In this coupled process the reactants are the 2 DNA fragments and a molecule of ATP. Note that water does not become involved as a reactant or product here.

The bond dissociation enthalpy for the 3’O-H is large…

followed by the rupture of the P-O bond on the phosphate of the 5’ terminal DNA stand.

The enthalpy increase ends with breaking a weak P-O phosphoanhydride (high energy phosphate bond) in ATP.

The enthalpy decrease depicted here starts with formation of the phosphodiester linkage. Note that the decrease (blue) is larger in magnitude than the input required to rupture the phosphoanhydride bond (red).

A much larger decrease in enthalpy occurs with formation of the P-O bond at the exterior of the pyrophosphate group. (There is still an anhydride P-O bond in the interior of the pyrophosphate.)

Coupling produces an exothermic (and exergonic) process resulting in the spontaneous formation of the phosphodiester linkage. This relatively weak bond was formed by breaking one that was even weaker (phosphoanhydride).

Coupling produces an exothermic (and exergonic) process resulting in the spontaneous formation of the phosphodiester linkage. This relatively weak bond was formed by breaking one that was even weaker (phosphoanhydride).

DNA synthesis or the joining, or splicing, of 2 single strands occurs in coupled overall exothermic (and exergonic) processes. In the splicing reaction, catalyzed by DNA ligase, ATP (NAD+ in the E.coli enzyme) as a cofactor (cosubstrate) is required to drive the reaction.

The anhydride linkage in the cofactor does not combine with a solvent molecule in its conversion to products. It can be thought of as drawing the H and OH groups, instead, from the ends of the DNA strands allowing them to collapse into a phosphodiester bond.

The mechanism again does not involve, as depicted here, complete rupture of bonds prior to bond formation with the huge energy barrier that would imply. New bonds form as old bonds are broken.

Not only do common intermediates involving e.g.,. formation of a phosphoanhydride linkage at the end of the 3’ DNA strand, appear to be implicated, but so does weak bonding of the cosubstrate to the enzyme (Lehman, I.R. (1974) Science, 186, 790-797).

For a proposed mechanism for DNA ligation involving the E coli enzyme with NAD+ as cosubstrate see: Horton, H.R., Moran, L.S., Ochs, R.S., Rawn.J.D. and Scrimgeour, K.G.; Principles of Biochemistry, 3rd Ed., p.643, Prentice Hall, Saddle River, N.J., 2002.

The End