A relevant reaction is one that makes use of an available substrate and converts it to a useful product. However, even a potentially relevant reaction may not occur. Some chemical transformations are too slow (have activation energies that are too high) to contribute to living systems, even with the aid of powerful enzyme catalysts. The reactions that do occur in cells represent a toolbox that evolution has used to construct metabolic pathways that circumvent the “impossible” reactions. Learning to recognize the plausible reactions can be a great aid in developing a command of biochemistry.

Even so, the number of metabolic transformations taking place in a typical cell can seem overwhelming. Most cells have the capacity to carry out thousands of specific, enzyme-catalyzed reactions: for example, transformation of a simple nutrient such as glucose into amino acids, nucleotides, or lipids; extraction of energy from fuels by oxidation; and polymerization of monomeric subunits into macromolecules.

More than a thousand chemical reactions take place in even as simple an organism as Escherichia coli. The array of reactions may seem overwhelming at first glance. However, closer scrutiny reveals that metabolism has a coherent design containing many common motifs. These motifs include the use of an energy currency and the repeated appearance of a limited number of activated intermediates. In fact, a group of about 100 molecules play central roles in all forms of life. Furthermore, although the number of reactions in metabolism is large, the number of kinds of reactions is small and the mechanisms of these reactions are usually quite simple. Metabolic pathways are also regulated in common ways.


The spontaneous formation of a bond between two atoms always involves the release of some of the internal energy of the unbonded atoms and its conversion to another energy form. The stronger the bond, the greater is the amount of energy released upon its formation. The bonding reaction between two atoms A and B is thus described by

 A + B  –>  AB + energy,

 where AB represents the bonded aggregate. The rate of the reaction is directly proportional to the frequency of collision between A and B. The unit most often used to measure energy is the calorie, the amount of energy required to raise the temperature of 1 g of water from 14.58C to 15.58C. Because thousands of calories are usually involved in the breaking of a mole of chemical bonds, most energy changes within chemical reactions are expressed in kilocalories per mole (kcal/mol). However, atoms joined by chemical bonds do not remain together forever, because there also exist forces that break chemical bonds.

By far the most important of these forces arises from heat energy. Collisions with fastmoving molecules or atoms can break chemical bonds. During a collision, some of the kinetic energy of a moving molecule is given up as it pushes apart two bonded atoms. The faster a molecule is moving (the higher the temperature), the greater is the probability that, upon collision, it will break a bond. Hence, as the temperature of a collection of molecules is increased, the stability of their bonds decreases. The breaking of a bond is thus always indicated by the formula

 AB + energy —> A + B

The amount of energy that must be added to break a bond is exactly equal to the amount that was released upon formation of the bond. This equivalence follows from the first law of thermodynamics, which states that energy (except as it is interconvertible with mass) can be neither made nor destroyed.

Here are the five most energy rich bonds :-

1st phosphoanhydride bond

  • It is a bond which is present in ATP. Formed between 2 molecules of  phosphoric acid. Its hydrolysis liberates about 7.3 kcal/ mol bond approx.
  • In ATP there are two high energy releasing diphosphate bonds. The third bond between phosphate and ribose is not energy rich bond, it is phosphate ester bond.
  • ATP serves as immediate donor of energy in biological processes it provides very high amount of energy such as in muscle contraction and in active transport across the membrane.
  • Other than ATP for different metabolic pathway energy of diphosphate bond of GTP, UTP, and CTP can be used.
FIGURE DEPICTING :- Phosphoanhyride bond between phosphate.

2nd enol phosphate bond

  • Enol phosphate bond forms when to double bonded carbon phosphate attached hydroxyl group bound.
  • It liberates about 64kj / mol bond energy
  • This bond is also energetically very rich
  • This bond is present in phosphenol pyruvate  which formed during breakdown of glucose in glycolysis.

3rd acyl phosphate bond

  • It is formed when carboxylic acid reacts with phosphate group
  • Its hydrolysis liberates 49kj/mol bond of energy
  • This type of bond is present in 1,3biphosphoglcerate which is also formed during glycolysis.
  • This type of high energy bond is also formed during activation of fatty acid and amino acid.

4th guanidine phosphate bond

  •  When phosphate group is attached to guanidine group at that time this bond is formed.
  • Its energy of hydrolysis is 43 kj/ mol bond.
  • The most important compound with this bound is phosphocreatine
  • Phosphocreatine is first of all forms in muscles cell where it serves as reservoir of energy.
  • In some animal as storage form of energy is arginine phosphate where phosphate group is bound to guanidine group of arginine.

5th thioester bond

  • Succinyl-CoA, like acetylCoA, has a thioester bond with a strongly negative standard free energy of hydrolysis (ΔG′° ≈ −36 kJ/mol).
  • It is present in acetyl coA  formed between sulfur of the critical thioester bond between the acetyl moiety and coenzyme A.
FIGURE DEPICTING :- Thioester bond in acetyl coA


The covalent bonds and functional groups of a biomolecule are, of course, central to its function, but so also is the arrangement of the molecule’s constituent atoms in three-dimensional space—its stereochemistry. Carboncontaining compounds commonly exist as stereoisomers, molecules with the same chemical bonds and same chemical formula but different configuration, the fixed spatial arrangement of atoms. Interactions between biomolecules are invariably stereospecific, requiring specific configurations in the interacting molecules.

The identifying characteristic of stereoisomers is that they cannot be interconverted without temporarily breaking one or more covalent bonds.  There is also isomerism in the configurations of maleic acid and its isomer, fumaric acid. These compounds are geometric isomers, or cis-trans isomers; they differ in the arrangement of their substituent groups with respect to the nonrotating double bond (Latin cis, “on this side”—groups on the same side of the double bond; trans, “across”—groups on opposite sides).

Maleic acid (maleate at the neutral pH of cytoplasm) is the cis isomer and fumaric acid (fumarate) the trans isomer; each is a well-defined compound that can be separated from the other, and each has its own unique chemical properties. A binding site (on an enzyme, for example) that is complementary to one of these molecules would not be complementary to the other, which explains why the two compounds have distinct biological roles despite their similar chemical makeup.

FIGURE DEPICITNG Geometric isomerism between maleic acid and fumaric acid.
FIGURE DEPICITNG :- Geometric isomerism between maleic acid and fumaric acid.

In the second type of stereoisomer, four different substituents bonded to a tetrahedral carbon atom may be arranged in two different ways in space—that is, have two configurations—yielding two stereoisomers that have similar or identical chemical properties but differ in certain physical and biological properties. A carbon atom with four different substituents is said to be asymmetric, and asymmetric carbons are called chiral centers (Greek chiros, “hand”; some stereoisomers are related structurally as the right hand is to the left).

A molecule with only one chiral carbon can have two stereoisomers; when two or more (n) chiral carbons are present, there can be 2 n stereoisomers. Stereoisomers that are mirror images of each other are called enantiomers . Pairs of stereoisomers that are not mirror images of each other are called diastereomers.


For some molecules, more than one pattern of covalent bonding can be written. For example, benzene can be written in two equivalent ways called resonance structures. Benzene’s true structure is a composite of its two resonance structures. A molecule that can be written as several resonance structures of approximately equal energies has greater stability than does a molecule without multiple resonance structures. Thus, because of its resonance structures, benzene is unusually stable. Chemical reactions entail the breaking and forming of covalent bonds. The flow of electrons in the course of a reaction can be depicted by curved arrows, a method of representation called “arrow pushing.” Each arrow represents an electron pair.

A carbon chain can include double bonds. If these are on alternate carbon atoms, the bonding electrons move within the molecule, stabilizing the structure by a phenomenon called resonance. Alternating double bonds in a ring can generate a very stable structure.

FIGURE DEPICTING Benzene resonance structure
FIGURE DEPICTING :- Benzene resonance structure

In one of the early steps in cholesterol biosynthesis, the enzyme prenyltransferase catalyzes condensation of isopentenyl pyrophosphate and dimethylallyl pyrophosphate to form geranyl pyrophosphate. The reaction is initiated by elimination of pyrophosphate from the dimethylallyl pyrophosphate to generate a carbocation, stabilized by resonance with the adjacent C=C bond.


Cells possess a variety of molecular energy transducers, which convert the energy of electron flow into useful work.

Every time we use a motor, an electric light or heater, or a spark to ignite gasoline in a car engine, we use the flow of electrons to accomplish work. In the circuit that powers a motor, the source of electrons can be a battery containing two chemical species that differ in affinity for electrons. Electrical wires provide a pathway for electron flow from the chemical species at one pole of the battery, through the motor, to the chemical species at the other pole of the battery.

Because the two chemical species differ in their affinity for electrons, electrons flow spontaneously through the circuit, driven by a force proportional to the difference in electron affinity, the electromotive force, emf. The emf (typically a few volts) can accomplish work if an appropriate energy transducer—in this case a motor—is placed in the circuit.

The motor can be coupled to a variety of mechanical devices to do useful work. Living cells have an analogous biological “circuit,” with a relatively reduced compound such as glucose as the source of electrons. As glucose is enzymatically oxidized, the released electrons flow spontaneously through a series of electron-carrier intermediates to another chemical species, such as O2 . This electron flow is exergonic, because O2 has a higher affinity for electrons than do the electron-carrier intermediates. The resulting emf provides energy to a variety of molecular energy transducers (enzymes and other proteins) that do biological work.

In the mitochondrion, for example, membrane-bound enzymes couple electron flow to the production of a transmembrane pH difference and a transmembrane electrical potential, accomplishing chemiosmotic and electrical work.

The proton gradient thus formed has potential energy, sometimes called the proton-motive force by analogy with electromotive force. Another enzyme, ATP synthase in the inner mitochondrial membrane, uses the proton-motive force to do chemical work: synthesis of ATP from ADP and Pi as protons flow spontaneously across the membrane. Similarly, membrane-localized enzymes in E. coli convert emf to proton-motive force, which is then used to power flagellar motion. The principles of electrochemistry that govern energy changes in the macroscopic circuit with a motor and battery apply with equal validity to the molecular processes accompanying electron flow in living cells.

The transfer of phosphoryl groups is a central feature of metabolism. Equally important is another kind of transfer: electron transfer in oxidation-reduction reactions, sometimes referred to as redox reactions. These reactions involve the loss of electrons by one chemical species, which is thereby oxidized, and the gain of electrons by another, which is reduced. The flow of electrons in oxidation-reduction reactions is responsible, directly or indirectly, for all work done by living organisms.

In nonphotosynthetic organisms, the sources of electrons are reduced compounds (foods); in photosynthetic organisms, the initial electron donor is a chemical species excited by the absorption of light. The path of electron flow in metabolism is complex. Electrons move from various metabolic intermediates to specialized electron carriers in enzymecatalyzed reactions.


  • The process of energy transduction takes place through a highly integrated network of chemical reactions called metabolism. Metabolism can be subdivided into catabolism (reactions employed to extract energy from fuels) and anabolism (reactions that use this energy for biosynthesis).
  • Metabolism is characterized by common motifs. A small number of activated carriers, such as ATP, NADH, and acetyl CoA, are used in many metabolic pathways. NADPH, which carries two electrons at a high potential, provides reducing power in the biosynthesis of cell components from more-oxidized precursors. ATP and NADPH are continually generated and consumed. Most transfers of activated groups in metabolism are mediated by a recurring set of carriers. Moreover, key reaction types are used repeatedly in metabolic pathways.
  • Most of the reactions that lead to the biosynthesis of nucleic acids and other biomolecules are not thermodynamically favorable under most conditions; they require an input of energy to proceed. Thus, they can proceed only if they are coupled to processes that release energy.


  • Lehninger  principles of biochemistry seventh edition By  David L. Nelson and Michael M. Cox
  • voets and voets biochemistry 4th edition
  • Life sciences  fundamental and practices sixth edition, pathfinder publication By Pranav Kumar and Usha Mina
  • Essential cell biology (fourth edition) by ALBERTS, BRAY, HOPKIN, JOHNSON, LEWIS, RAFF, ROBERTS, WALTER

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