Tumkur University

University college of Sciences

Tumakuru

Notes on -“ Biological oxidation ”

By

Mrs. BHAGYALAKSHMI.M

Department of Chemistry

Assistant professor

University College of science

Tumkur University, B H Road, Tumkur-572103

India
 Biological oxidation

Introduction

Bioenergetics is the part of biochemistry concerned with the energy involved in making and
breaking of chemical bonds in the molecules found in biological organisms. It can also be
defined as the study of energy relationships and energy transformations and transductions in
living organisms.

Biological oxidation is the combination of oxidation-reduction transformations of substances in

living organisms. Oxidation-reduction reactions are those which take place with a change in
the oxidation state of atoms through the redistribution of electrons between them.

or

Biological oxidation is catalysed by enzymes which function in combination with coenzymes

and/or electron carrier proteins.

The differences between biological oxidation and combustion

Free energy

A process will only happen spontaneously, without added energy, if it increases the entropy of
the universe as a whole (or, in the limit of a reversible process, leaves it unchanged) – this is
the Second Law of Thermodynamics. But to me at least, that's kind of an abstract idea. How can
we make this idea more concrete and use it to figure out if a chemical reaction will take place?

Basically, we need some kind of metric that captures the effect of a reaction on the entropy of the
universe, including both the reaction system and its surroundings. Conveniently, both of these
factors are rolled into one convenient value called the Gibbs free energy.

The Gibbs free energy (G) of a system is a measure of the amount of usable energy (energy that
can do work) in that system. The change in Gibbs free energy during a reaction provides useful
information about the reaction's energetics and spontaneity (whether it can happen without added
energy). We can write out a simple definition of the change in Gibbs free energy as:

ΔG=Gfinal–Ginitial

In other words, ΔG is the change in free energy of a system as it goes from some initial state,
such as all reactants, to some other, final state, such as all products. This value tells us the
maximum usable energy released (or absorbed) in going from the initial to the final state. In
addition, its sign (positive or negative) tells us whether a reaction will occur spontaneously, that
is, without added energy.

When we work with Gibbs free energy, we have to make some assumptions, such as constant
temperature and pressure; however, these conditions hold roughly true for cells and other living
systems.

Gibbs free energy, enthalpy, and entropy

In a practical and frequently used form of Gibbs free energy change equation, ΔG is calculated
from a set values that can be measured by scientists: the enthalpy and entropy changes of a
reaction, together with the temperature at which the reaction takes place.

ΔG=ΔH−TΔS
Let‟s take a step back and look at each component of this equation.

∆H is the enthalpy change. Enthalpy in biology refers to energy stored in bonds, and the change
in enthalpy is the difference in bond energies between the products and the reactants. A negative
∆H means heat is released in going from reactants to products, while a positive ∆H means heat is
absorbed. (This interpretation of ∆H assumes constant pressure, which is a reasonable
assumption inside a living cell).

∆S is the entropy change of the system during the reaction. If ∆S is positive, the system becomes
more disordered during the reaction (for instance, when one large molecule splits into several
smaller ones). If ∆S is negative, it means the system becomes more ordered.

Temperature (T) determines the relative impacts of the ∆S and ∆H terms on the overall free
energy change of the reaction. (The higher the temperature, the greater the impact of the ∆S term
relative to the ∆H term.) Note that temperature needs to be in Kelvin (K) here for the equation to
work properly.

Reactions with a negative ∆G release energy, which means that they can proceed without an
energy input (are spontaneous). In contrast, reactions with a positive ∆G need an input of energy
in order to take place (are non-spontaneous). As you can see from the equation above, both the
enthalpy change and the entropy change contribute to the overall sign and value of ∆G. When a
reaction releases heat (negative ∆H) or increases the entropy of the system, these factors make
∆G more negative. On the other hand, when a reaction absorbs heat or decreases the entropy of
the system, these factors make ∆G more positive.
By looking at ∆H and ∆S, we can tell whether a reaction will be spontaneous, non-spontaneous,
or spontaneous only at certain temperatures. If a reaction both releases heat and increases
entropy, it will always be spontaneous (have a negative ∆G), regardless of temperature.
Similarly, a reaction that both absorbs heat and decreases entropy will be non-spontaneous
(positive ∆G) at all temperatures. Some reactions, however, have a mix of favorable and
unfavorable properties (releasing heat but decreasing entropy, or absorbing heat but increasing
entropy). The ∆G and spontaneity of these reactions will depend on temperature, as summarized
in the table at right.

Endergonic and exergonic reactions

Reactions that have a negative ∆G release free energy and are called exergonic reactions. (Handy
mnemonic: exergonic means energy is exiting the system.) A negative ∆G means that the
reactants, or initial state, have more free energy than the products, or final state. Exergonic
reactions are also called spontaneous reactions, because they can occur without the addition of
energy.

Reactions with a positive ∆G (∆G > 0), on the other hand, require an input of energy and are
called endergonic reactions. In this case, the products, or final state, have more free energy than
the reactants, or initial state. Endergonic reactions are non-spontaneous, meaning that energy
must be added before they can proceed. You can think of endergonic reactions as storing some of
the added energy in the higher-energy products they form^11start superscript, 1, end superscript.

It‟s important to realize that the word spontaneous has a very specific meaning here: it means a
reaction will take place without added energy, but it doesn't say anything about how quickly the
reaction will happen^22squared. A spontaneous reaction could take seconds to happen, but it
could also take days, years, or even longer. The rate of a reaction depends on the path it takes
between starting and final states (the purple lines on the diagrams below), while spontaneity is
only dependent on the starting and final states themselves. We'll explore reaction rates further
when we look at activation energy.
Differences between exergonic and endergonic reaction

Energy coupling reaction

Reaction Coupling reaction in which the released energy drives an endergonic reaction

“Most biochemical pathways involve coupled reactions. In cells, an exergonic reaction is

coupled to an endergonic reaction to give it free energy to drive the reaction”.

Example:

Exergonic (spontaneous) reaction

ATP Hydrolysis reaction:

ADP + Pi + H→ ATP + H2O ∆G = ~ -30 kJ

Endergonic (nonspontaneous) reaction

Phosphorylation of Glucose reaction:

Glucose + Pi + H→Glucose-6-Phosphate + H2O ∆G = ~ +14 kJ

Coupled Reaction (showing just the key reactants & products):

Glucose + ATP → Glucose-Phosphate net ∆G = ~ -16 kJ

High energy compounds and energy rich bond (~):

Any bond, which on hydrolysis gives a minimum free energy of 7.4 Kcal/mol, is known as
energy rich bond and the compound which has an energy rich bond is known as high energy
compound. Ex. ATP, pyrophosphate, 1, 3-diphosphoglyceric acid, phosphoenol pyruvate,
creatine phosphate and acetyl-CoA.

Adenosine triphosphate (ATP):

ATP is also known as the „energy currency‟ of the living cell, because it transfers energy from
energy yielding sources to the energy requiring cell processes. ATP has two pyrophosphate
bonds. On hydrolysis of each of the terminal two phosphate groups there is release of more than
7.4 Kcal/mol of energy but the third bond yields only 3 Kcal/mol of energy, hence it is not a high
energy bond. On hydrolysis ATP is converted to ADP and to AMP.
Electron transport chain(ETC)

Transfer of electrons from substrate to molecular oxygen through a chain of electron carriers is
called electron transport chain or respiratory chain. Mitochondria contains a series of catalysts
forming the respiratory chain which are involved in the transfer of electrons and hydrogen and
their final reaction is with oxygen to form water. The components of respiratory chain are
arranged sequentially in the order of increasing redox potential.

Electrons flow through the chain in a stepwise manner from lower redox potential to higher
redox potential. Some amount of energy is liberated with transfer of electron from one
component to another. Whenever there is a release of 7.4 Kcal of energy or a little more, then
ATP formation takes place there. NADH forms 3 ATPs whereas FADH2 forms only 2 as it
enters ETC at the site beyond the first site of ATP formation.

The/three sites of ATP formation in the ETC or respiratory chain are:

1. Between NADH dehydrogenase (flavoprotein) and ubiquinone (coenzyme Q).

2. Between cytochrome-b and cytochrome-c1.

3. Between cytochrome-a and cytochrome-a3 (cytochromes oxidase).

Figure: The components of ETC, their redox potential and their sequence is
Phosphorylation:

Esterification of a phosphate through a high energy bond (7.4 Kcal) is known as

phosphorylation. Combination of inorganic phosphate (Pi) with any other compound through
high energy bond is known as phosphorylation. Or formation of ATP from ADP and phosphate
or NTP from NDP and Pi is known as phosphorylation.

P/O ratio

It is ratio of the number of molecules of ADP converted to ATP to the number of oxygen atoms
utilized by respiratory chain. • It is a measure to the efficiency of oxidative phosphorylation. • It
is 3/1 if NADH+H+ is used and 2/1 if FADH2 is used.

There are two types of phosphorylation:

1. Substrate level phosphorylation:

Formation of high energy phosphate bond at the level of a substrate without the involvement of
the respiratory chain is known as substrate level phosphorylation. Ex. Phosphoenolpyruvate is
converted to pyruvate by pyruvate kinase where ATP is formed from ADP.

2. Oxidative phosphorylation:

The enzymatic phosphorylation of ADP to ATP coupled with electron transport from a substrate
to molecular oxygen is known as oxidative phosphorylation or respiratory chain phosphorylation.

Mechanism of oxidative phosphorylation

Mechanism of oxidative phosphorylation was explained by three theories out of which only two
theories are mentioned

There are 2 theories: 1.The chemical theory.

2.The chemiosmotic theory.

1. Chemical theory:It suggests that there is a direct chemical coupling of oxidation and
phosphorylation through high-energy intermediate compounds. •This theory is not accepted, as
postulated high-energy intermediate compounds were never found.
2. Chemiosomotic theory

It suggest that the transfer of electrons through the electrons transport chain causes protons to be
translocated (pumped out) from the mitochondrial matrix to the intermembrane space at the three
sites of ATP production (i.e. it acts as a proton pump) resulting in an electrochemical potential
difference across the inner mitochondrial membrane.

Salient features of Chemiosomotic theory

 The electrical potential difference is due to accumulation of the positively charged

hydrogen ions outside the membrane.
 The chemical potential difference is due to the difference in pH, being more acidic
outside the membrane.
 This difference forces ATP synthase to generate ATP from ADP and inorganic
phosphate.

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