6

1. Metabolism is the term used to describe all the biochemical reactions
that take place inside a cell; it includes those reactions that release
energy into the cell, and those that make use of that energy.
Catabolism is the term used to describe reactions that break down
large molecules, usually coupled to a release of energy.
Anabolism is the term used to describe reactions involved in the
synthesis of macromolecules, usually requiring an input of energy.

3. Most microorganisms obtain their energy from the nutrients they
take into the cell; these may come from an organic or an inorganic
source. Once inside the cell, these nutrients must then be
biochemically processed by reactions that trap some of their
chemical energy, at the same time breaking them down into smaller
molecules. These then serve as building blocks for the synthesis of
new cellular components. Chemical compounds contain potential
energy within their molecular structure, and some of this can be
released when they are broken down. In other metabolic types,
energy is obtained from the sun by means of photosynthesis; once
again, however, the energy is used for synthetic purposes.

4. Enzymes
Central to the metabolic processes of any cell are enzymes. Without
them, the many biochemical reactions referred to above simply
wouldn’t take place at a fast enough rate for living cells to maintain
themselves.

5. Enzyme
Enzymes are globular proteins that act as biological catalysts. They
increase the rate of biochemical reaction without themselves being
chemically altered.
An enzyme is a cellular catalyst; it makes biochemical reactions proceed
many times more rapidly than they would if uncatalysed. The
participation of an enzyme can increase the rate of a reaction by a
factor of millions, or even billions.
Traditionally, all enzymes have been thought of as globular proteins,
but in the 1980s it was demonstrated that certain RNA molecules also
have catalytic properties. These ribozymes, however, are very much in
the minority, carrying out specific cut-and-splice reactions on RNA
molecules.

6. Like any other catalyst, an enzyme remains unchanged at the end of a reaction. It
must, however, at some point during the reaction bind to its substrate (the
substance upon which it acts) to form an enzyme–substrate complex by multiple
weak forces such as electrostatic forces and hydrogen bonding. Only a small part of
the enzyme’s three-dimensional structure is involved in this binding; these few
amino acids make up the active site, which forms a groove or dent in the enzyme’s
surface, into which the appropriate part of the substrate molecule fits (Figure 6.3).
The amino acid residues that go to make up the active site may be widely separated
in the enzyme’s primary structure, but by means of the secondary and tertiary
folding of the molecule, they are brought together to give a specific three-
dimensional conformation, complementary to that of the substrate. It is this
precise formation of the active site that accounts for one of the major
characteristics of enzymes, their specificity. You should not think, however, that
these few residues making up the active site are the only ones that matter; the
enzyme can only fold in this way because the order and arrangement of the other
amino acids allow it.

7. Certain enzymes have a non-protein component
Many enzymes require the involvement of an additional, non-protein
component in order to carry out their catalytic action. These ‘extra’
parts, or cofactors, are usually either metal ions (e.g. Mg2 + , Zn2 + ) or
complex organic molecules called coenzymes. Some of the most
important coenzymes act by transferring electrons between substrate
and product in redox reactions.
Prosthetic group: A prosthetic group is a tightly bound, specific non-
polypeptide unit required for the biological function of some proteins.
The prosthetic group may be organic (such as a vitamin, sugar, or lipid)
or inorganic (such as a metal ion), but is not composed of amino acids.

8. • The purely protein component of an enzyme is known as the
apoenzyme.
• The complex of apoenzyme and cofactor is called the holoenzyme.
The apoenzyme on its own does not have biological activity.

9. Mechanism of Enzyme Actions
An enzyme pulls substrates to its active site, catalyses the chemical
reaction that produces the products, and then enables the dissociation
of the products (detach from the enzyme surface). The enzyme and
substrate complex is the interaction between an enzyme and its
substrates.

12. Most enzymes have names that end in the suffix -ase. The first part
of the name often gives an indication of the substrate; for example,
urease and pyruvate decarboxylase. Other enzymes have names
that are less helpful, such as trypsin, and others have several
alternative names to confuse the issue further. To resolve such
problems, an internationally agreed system of nomenclature has
been devised. All enzymes are assigned initially to one of six broad
groups according to the type of reaction they carry out. Each
enzyme is then placed into successively more specific groupings,
each with a number. Thus regardless of any colloquial or
alternative names, each enzyme has its own unique and
unambiguous four-figure Enzyme Commission ‘signature’ (pyruvate
decarboxylase, mentioned above, is EC 4.1.1.1).

13. Major classes of enzymes

14. Oxidoreductases do not catalyse reactions involving hydrolysis, and
hydrolases do not catalyse processes involving both oxidation and
reduction. As a result, an enzyme can catalyse a specific chemical
reaction and various substances that are similar to it.
Even though enzymes have high levels of specificity, cofactors can be
used by numerous apoenzymes. For instance, nicotinamide adenine
dinucleotide (NAD) serves as a hydrogen acceptor in a large number of
dehydrogenase activities and is a coenzyme for those reactions.

15. Only suitably structured molecules may act as substrates for a specific
enzyme because the substrate must fit into the active site of the enzyme
preceding catalysis. An enzyme will often react with one naturally existing
compound. The concept of enzyme specificity will be demonstrated using
two oxidoreductase enzymes.
First, alcohol dehydrogenase (ADH) reacts with alcohol, and then lactate
dehydrogenase (LDH) reacts with lactic acid. Despite being oxidoreductase
enzymes, the two actions are not interchangeable. It indicates that alcohol
dehydrogenase cannot catalyse a process involving lactic acid and vice versa.
This is because each substrate has a specific structure that makes it
impossible to fit into the active site of a different enzyme.
Enzyme specificity is significant since it recognises the various metabolic
pathways consisting of a large number of enzymes.

16. Back in the 1950s
• The number of known enzymes was increasing rapidly
• No guiding authority
• The same enzymes became known by several different names, and
• The same name was sometimes given to different enzymes
• Names often conveyed little or no idea of the nature of the reactions
catalyzed

18. • Each of the six main classes is further subdivided
• The subclass generally contains information about the type of
compound or group involved (e.g. 1.1. acts on the CH–OH group of
donors whereas 1.3. acts on the CH–CH group of donors)
• The sub-subclass further specifies the type of reaction involved. (e.g.
for the oxidoreductases, 1.-.1. indicates that NAD or NADP is the
acceptor, 1.-.2. has cytochrome as the acceptor, etc
• The fourth digit is a serial number that is used to identify the
individual enzymes within a sub-subclass

19. The nomenclature of enzyme
The nomenclature of enzyme: Except for some of the originally studied
enzymes such as pepsin, rennin, and trypsin, most enzyme names end in
“ase”.
Enzyme
Endoenzyme: enzymes that function within cells e.g. metabolic enzymes like
cytochrome oxidase
Exoenzyme: enzymes that catalyse reactions outside cell e.g. digestive
enzymes like amylase, lipase, protease

20. Enzyme Specificity
The ability of an enzyme to select a specific substrate from a range of
chemically similar compounds is known as specificity. Since the enzyme
and substrate exhibit complementary structural and conformational
properties, specificity is a molecular identification process. Different
enzymes exhibit different levels of substrate specificity.

21. There are usually four different categories of specificity.
• Absolute specificity – The enzyme catalyses only one reaction.
• Group specificity – The enzyme acts only on molecules having specific
functional groups, like phosphate, amino, and methyl groups.
• Linkage specificity – The enzyme acts on a specific type of chemical
bond regardless of the remaining molecular structure.
• Stereochemical specificity – The enzyme acts on a certain optical or
steric isomer.

22. Allosteric enzymes
Some enzymes have an additional site - allosteric site which is
separated from active site and is important for their regulation. This
site interacts with special molecules, they are called the effectors,
which can change the enzyme activity.
• Positive effectors
• Negative effectors

23. Activation energy
For any chemical reaction to take place there must be a small input of
energy. This is called the activation energy, and is often likened to the
small push that is needed to loosen a boulder and allow it to roll down
a hill. It is the energy needed to convert the molecules at the start of a
reaction into intermediate forms known as transition states, by the
rearrangement of chemical bonds. The great gift of enzymes is that
they can greatly lower the activation energy of a reaction, so that it
requires a smaller energy input, and may therefore occur more
readilyBy lowering the amount of energy that must be expended in
order for a reaction to commence, enzymes enable them to proceed
much more quickly.

24. An enzyme lowers the activation energy of a
reaction

25. Disruption of an enzyme’s three-dimensional
structure causes denaturation
Disruption of the bonds that form the secondary and tertiary protein
structure of an enzyme (a) lead to a loss of catalytic activity, as the
amino acids forming the active site are pulled apart (b).

26. Environmental factors affect enzyme activity
The rate at which an enzyme converts its substrate into product is
called its velocity (v), and is affected by a variety of factors.
• Temperature
• pH
• Substrate concentration

27. Temperature
The rate of any chemical reaction increases with an increase in
temperature due to the more rapid movement of molecules, and so it
is with enzyme-catalysed reactions, until a peak is reached (the
optimum temperature) after which the rate rapidly falls away. What
causes this drop in the velocity? The very ordered secondary and
tertiary structure of a protein molecule is due to the existence of
numerous weak molecular bonds, such as hydrogen bonds. Disruption
of these by excessive heat results in denaturation, that is, an unfolding
of the three-dimensional structure. In the case of an enzyme, this leads
to changes in the configuration of the active site, and a loss of catalytic
properties.

28. Effect of temperature on enzyme activity

29. Below the optimum temperature, the rate of reaction increases as the
temperature rises. Above the optimum, there is a sharp falling off of
reaction rate due to thermal denaturation of the enzyme’s three-
dimensional structure.

30. pH
Enzyme velocity is similarly affected by the prevailing pH. Once again,
this is due to alterations in three-dimensional protein structure.
Changes in the pH affect the ionization of charged ‘R’-groups on amino
acids at the active site and elsewhere, causing changes in the enzyme’s
precise shape, and a reduction in catalytic properties. As with
temperature, enzymes have an optimum value at which they operate
most effectively; when the pH deviates appreciably from this in either
direction, denaturation occurs, leading to a reduction of enzyme
activity

32. Enzyme activity is influenced by substrate concentration

33. Cont…
The initial rate of reaction (Vo) is proportional to substrate
concentration at low values of [S]. However, when the active sites of
the enzyme molecules become saturated with substrate, a maximum
rate of reaction (Vmax) is reached. This cannot be exceeded, no matter
how much the value of [S] increases. The curve of the graph fits the
Michaelis–Menten equation.

34. Substrate concentration
Under conditions where the active sites of an enzyme population are
not saturated, an increase in substrate concentration will be reflected
in a proportional rise in the rate of reaction. A point is reached,
however, when the addition of further substrate has no effect on the
rate. This is because all the active sites have been occupied and the
enzymes are working flat out; this is called the maximum velocity
(Vmax). A measure of the affinity an enzyme has for its substrate (i.e.
how closely it binds to it) is given by its Michaelis constant (Km). This is
the substrate concentration at which the rate of reaction is half of the
Vmax value. Values of Vmax and Km are more easily determined
experimentally by plotting the reciprocals of [S] and v to obtain a
straight line.