BOND MAKING AND BREAKING

1
BOND MAKING AND BREAKING
The DH for Reactions in terms of Bond Energies
(Bond Dissociation Enthalpies). This
segment of EXBAN presents a brief review of the
DH 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 DH 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
2

• (a) In the present depiction bonds are
  pulled apart and the fragments snap together
  to form new bonds in tinker-toy fashion. The
  overall DH 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 DHs 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.

3
The DH of hydrolysis of ATP in terms of a balance
of bond breaking and making processes.
4
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
5
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 DH for the overall
reaction.)
6
Breaking a phosphoanhydride bond requires
considerably less but still cost energy. At this
point the bond breaking is complete with an input
of gt 750 kJ of energy.
7
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 PO anhydride
bond.
8
The reaction is complete with the formation of an
O-H bond.
9
The overall decrease of 24 kJ/mole occurs, is
the DH 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..
10
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.
11
The reaction again begins with bond rupture in
the reactants.
12
Almost as much energy is required to break the
alcoholic O-H bond as an O-H bond in water.
13
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.
14
The P-O bond in the phosphodiester link, is also
significantly weaker (blue) than the phosphate
P-O bond (red).
15
As a result, even with formation of a strong O-H
that results in the production of water, the
reaction remains endothermic.
16
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.
17
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.
18
The more negative DG for ATP hydrolysis derives
primarily from its more exothermic nature (neg.
DH). 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
DH(hydrolysis) (kJ/mole) ATP
H2O ? ADP Pi -24.2
DNA H2O ?
5DNA 3DNA -12.0 so that
reversing the 2nd reaction in the direction of
DNA formation ATP H2O ? ADP
Pi -24.2 5DNA 3DNA ?
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 5DNA 3DNA ATP
? DNA ADP Pi -11.8 .
19
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.
20
The bond dissociation enthalpy for the 3O-H is
large
21
followed by the rupture of the P-O bond on the
phosphate of the 5 terminal DNA stand.
22
The enthalpy increase ends with breaking a weak
P-O phosphoanhydride (high energy phosphate bond)
in ATP.
23
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).
24
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.)
25
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).
26
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).
27
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.

28
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.
29
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).
30
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.
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The End