The history of the "high-energy phosphates" and "high-energy
phosphate bond" terms along with the squiggle bond and their connection
with the flow of energy in biological systems, are outlined elsewhere
in this Website. The role of these terms in fostering and maintaining
the decades-old misconception of "exothermic bond breaking" are a primary
focus of EXBAN. These terms, however, are not the sole semantic impediments
to an understanding of bioenergetics, and of the molecular basis of energy
changes in chemical reactions and physical processes in general. Other
troublesome terms or phrases lend support to the misconception that the
rupture of chemical bonds is accompanied by an energy release. Several
of these are listed below.
|"Cutting and Splicing"
These are terms associated, in particular,
with recombinant DNA technology and are therefore presently fashionable.
The term "cutting" in this context refers to the hydrolysis of
phosphodiester linkages in DNA or RNA, often at base-specific
sites along the polymer chain. The single-strand breaks in the
phosphodiester linkages that result from hydrolysis reactions
catalyzed by restriction enzymes occur either at exactly
opposite positions on the two strands to give rise to "blunt ends",
or offset at specific palindromic sequences generating "sticky
ends". These hydrolysis reactions are exothermic and spontaneous
in the thermodynamic sense, as are hydrolysis reactions of nucleic
acids and proteins in general. However, these hydrolysis reaction
are catalyzed with appropriate enzymes, although RNA does undergo
a slow hydrolysis in alkaline solution. The use of the shorthand
term "cutting", while emphasizing the significant aspect of the
reaction, i.e. breakage of the DNA strand, supports the widespread
misconception that it is the bond breaking that produces the energy
release. However, those students who have been convinced that
bond breaking requires an input of energy, are likely to conclude,
as evidenced by responses to exam questions, that the "cutting
process" must be endothermic. The term "cutting" tends to disguise
the hydrolytic nature of the reaction in which both bond making
and breaking are occurring.
It is in reality
the reverse, the condensation or "splicing" reaction, in which the
relatively-weak phosphodiester bond has to be formed following rupture
of the stronger bonds at the ends of the 2 DNA stands, that is endothermic
and endergonic. Emphasis only on the phosphodiester bond formation
inherent in the term "splicing" suggests, erroneously again, that
it is the bond formation that requires energy. Those students again,
who know that bond formation is exothermic, are likely to conclude,
again incorrectly, that the splicing reaction resulting in the phosphodiester
linkage must therefore be exothermic. It would seem that students
are "damned if they do and damned if they don't". In the same manner
as with the overall synthesis of DNA and proteins, joining two DNA
strands, or closing the nick with the "splicing reaction", is in
fact endothermic and endergonic, i.e. it does not occur spontaneously.
It must be pushed by coupling to a reaction that is spontaneous.
The "splicing" reaction requires more than just DNA ligase
as a catalyst for it to occur. The free energy of hydrolysis of
the phosphoanhydride linkage of the NAD+ or ATP cofactor is required
to drive the process. The manner in which this coupling can occur
as viewed from a bond breaking and making perspective is considered
in the "Bond Making and Breaking Tutorial".
to the discussion of sterol biosynthesis found in many texts Prof.
Ray Fort finds that, perhaps with some sense of frustration,
there is some "woofing
and tweeting about energy-rich bonds". In his course website
he points out that there is no such thing as an energy-rich bond
and discusses the chemical basis of the Acetyl CoA as an acetyl
This widely used term is analogous to
"cutting ", but with a somewhat longer history, with both referring
essentially to the same process. The term "cleavage" is, more
often than not, employed in describing the result of a hydrolysis
reaction. The term "hydrolytic cleavage", in this case, is also
frequently encountered, and is less ambiguous.
|"Energy Stored in Bonds"
This phrase tends to be encountered in
general chemistry texts but can be found in physical chemistry
texts as well. It represents as with the other terms listed here,
a convenient shorthand for a process that demands a more lengthy
description to appreciate. Consider the following situation. A
non-chemist interested in the environment and energy sources in
the future, asks a chemist why hydrogen represents a good fuel.
They understand that the molecule is simply composed of two hydrogen
atoms bonded together, and want to know where the energy comes
from. The response, without further elaboration, could well be
that "the energy is stored in the bond". It is not difficult to
imagine that the non-chemist would conclude that "if the energy
is stored in the bond", then if there were no bond there would
be no energy. It would seem entirely reasonable to conclude that
energy release associated with hydrogen as a fuel must derive
from breaking the bond. A distinctly clearer response would require
that it be pointed out that good chemical fuels involve molecules
in which the bonds holding them together are relatively weak,
so that in reactions, e.g. involving oxygen (O2(g)), those weaker
bonds are replaced by stronger ones in the products, water (H2O)
in the case of the combustion of hydrogen.
It is not difficult to understand
why it is often suggested that students would be better off if left
with their inconsistencies; i.e. to live with the convenient misconception
that bond breaking is exothermic in their biology courses, but endothermic
when dealing with problems in chemistry. There are, however, inconsistencies
in this matter within biology itself. Retaining the misconception
that the rupture of , e.g. the high-energy phosphate bond
is exothermic, more often than not, it would.be conceded that the
rupture of H-bonding in the denaturation of DNA or the melting of
ice, does requires an input of energy.