enzymes

Digestive enzymes are referred to in sets because of the speciﬁc nature of proteins. Each protein

has a very speciﬁc shape that determines its very speciﬁc function. For example, diﬀerent

amylases are required for the branched and unbranched portions of starch, and the amylase

that hydrolyses unbranched portions of starch (made of α-glucose molecules) cannot hydrolyse

cellulose (made of β-glucose molecules). Carbohydrates such as sucrose (a molecule made up

of a glucose and a fructose joined together), which are made of other monosaccharides, cannot

be digested by the same amylases that digest starch. The speciﬁcity of enzymes is what makes

biochemical processes so complex and diseases so diﬃcult to treat.

The discovery of enzymes

Towards the end of the 19th century, the German chemist Eduard Buchner was experimenting

to ﬁnd a way of preventing yeast extracts from going bad. In one trial, he added sugar to

yeast extract and, rather than preventing change, he found that the sugar was fermented and

converted to alcohol. Louis Pasteur had already demonstrated that yeast was responsible for the

fermentation of sugar, but Buchner took the research further. He showed that the juice extracted

from living yeast cells was responsible for fermentation, not the yeast cells themselves. The

term ‘enzyme’ (from the Greek word en-zumē, meaning ‘within leaven/yeast’), which was ﬁrst

used by German physiologist Wilhelm Kühne, has come to refer to any protein that functions

as a catalyst.

Enzymes control metabolic processes

Without enzymes, biochemical reactions would be so slow as to hardly proceed at all, and life

in its current form would never have evolved. Thousands of diﬀerent reactions take place in a

cell. The functional organisation required for this is achieved by a highly controlled system of

metabolism, where speciﬁc enzymes are in particular places within the cell acting as catalysts

for each individual reaction.

Enzymes are divided into two broad groups based on where they act: inside or outside the cell.

Intracellular enzymes act inside cells, where they speed up and control metabolic reactions.

Extracellular enzymes are produced by cells but achieve their eﬀects outside the cells. These

include the digestive enzymes, which break down food in the stomach and small intestine.

Enzyme structure and function

Enzymes, like all proteins, have a highly

speciﬁc shape formed by their tertiary

structure (Figure 4.3.1). It is this shape that

allows it to bind with a speciﬁc reactant,

called its substrate. Enzymes are generally

named according to the substrate they

catalyse with the suﬃx ‘-ase’; for example,

sucrase, lipase and maltase. When an

enzyme-controlled reaction takes place, the

enzyme and substrate molecules join for a

short time to form an enzyme–substrate

complex. The substrate is converted to the

end product by the action of the enzyme.

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catalyst a substance that

speeds up a chemical

reaction but is not used

up in the reaction

intracellular enzyme an

enzyme that functions

inside the cell that

produces it, to speed up

and control metabolic

reactions

extracellular enzyme an

enzyme that is produced

by cells but functions

outside of the cell

substrate a substance

that enters a reaction;

also called reactant or

precursor

Tertiary protein

structure

Active site

Substrate

Catalytic

site

enzyme–substrate

complex a substance

formed when an

enzyme and a substrate

molecule join

end product a substance

that is formed by the

action of an enzyme

FIGURE 4.3.1 The basic structure of an

enzyme. The active site is a small cleft where

the substrates bind and catalysis occurs, while

the rest of the shape is required to create and

support the active site.

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CHAPTER 4 | BIOMOLECULES AND ENZYMES

The enzyme is unchanged by the reaction and can be used again. This means enzymes are

often only needed in small quantities within a cell. The process of enzyme catalysis can

be summarised as:

active site the place

on the surface of an

enzyme molecule where

substrate molecules

attach

lock-and-key model an

old model suggesting

that the shape of an

enzyme’s active site is

an exact, static ﬁt for the

shape of its substrate

molecule

enzyme + substrate(s) → enzyme–substrate complex → enzyme + end product(s)

Lock-and-key model

Within each enzyme’s shape is a precise area to which the substrate can become attached, called

the active site. In 1894, German chemist Emil Fischer proposed the lock-and-key model to

explain the substrate-speciﬁcity of enzymes (Figure 4.3.2). It involved viewing the enzyme

as a lock that can only be operated by inserting a particular substrate or key. Unfortunately,

this model assumes that the enzyme’s shape is static and it cannot explain how the enzyme is

actually catalysing the reaction from substrate to end product.

Substrate

molecule

Product

molecules

Active site

induced-ﬁt model a

model of enzyme activity

in which an enzyme’s

active site undergoes

speciﬁc changes,

induced by the substrate,

to achieve a high degree

of speciﬁcity with the

substrate

conformation the shape

of a molecule that is

determined by the three-

dimensional arrangement

of its atoms and bonds;

important for molecular

functioning

Enzyme–substrate

complex

FIGURE 4.3.2 The lock-and-key model of enzyme action, from 1894. This model proposed that the

substrate ﬁts into a speciﬁc, static active site on the surface of the enzyme.

Induced-ﬁt model

In 1958, in response to many experiments that demonstrated that enzymes changed their

shape after they bound to their substrate, Daniel Koshland, an American biochemist, proposed

a new model of enzyme action. It combined this shape change with the understanding that

an enzyme–substrate complex must do something to catalyse the reaction. Known as the

induced-ﬁt model of enzyme action (Figure 4.3.3), it proposes that the unbound enzyme is

in a relaxed conformation, much like a hand waiting to hold its substrate. Many molecules

Products are released

and enzyme is available

for another reaction.

Products

Active site

Enzyme

Substrate

Enzyme and

substrate are

available.

Conformational change

occurs and substrate

is converted to products.

Enzyme–substrate

complex

Enzyme undergoes conformational

change to enable full binding

of the substrate.

FIGURE 4.3.3 The induced-ﬁt model of enzyme action. The substrate enters the enzyme’s active

site, causing the enzyme to change its shape and bring about catalysis of the reaction.

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can enter the active site, but only its speciﬁc substrate can activate all the parts of the active site

required to trigger catalysis. When the substrate enters the active site, the enzyme undergoes

a conformational change, much like a hand closing over an object. This brings the substrate

into contact with the catalytic site, which converts the substrate to the end product. This end

product is a slightly diﬀerent shape from the substrate, so it no longer activates all the required

parts of the active site and the enzyme relaxes back into its original conformation, releasing

the end products.

The induced-ﬁt model more accurately reﬂects the ways enzymes and substrates interact

with each other. The bonds that form between an enzyme and its substrate at the active site

modify the shape of the enzyme so that the substrate can be fully accommodated and brought

to the catalytic site. This change in conformation stretches the bonds within the substrate

molecule, which lowers the activation energy required to initiate the reaction.

Activation energy

The mechanism that occurs in the active site of the enzyme is complex and still being researched,

but evidence shows that it provides a reaction pathway that requires less energy to activate.

Lowering the activation energy for a reaction means that the reactants don’t need as much

energy from the cell to begin the process of becoming products, which makes the reaction faster

and more eﬃcient for the cell.

Consider a match. A reaction can quickly convert the thin stick of wood to charcoal, but

without the energy input of a spark, the match will remain unchanged for years. The spark

that lights the match provides the activation energy for the reaction to proceed. In a similar

way, hydrogen peroxide (H2

O2), a toxic by-product of metabolism, remains unchanged in the

body for hours; 71 kJ of energy is required to kickstart the reaction that converts hydrogen

peroxide to water and oxygen:

2H2O2 → 2H2

O + O2

hydrogen peroxide → water and oxygen

Given its toxicity, it is essential that the cell removes hydrogen peroxide as fast as possible.

In the liver, an enzyme called catalase lowers the activation energy for the reaction to just 8 kJ

by stretching the bonds of hydrogen peroxide within its active site. In the presence of catalase,

this reaction can proceed up to 100 million times faster than without it (Figure 4.3.4).

activation energy the

energy required to initiate

a reaction

Reactant

Activation energy without

enzyme (energy input 5 71 kJ)

Activation energy

with enzyme

(energy input 5 8 kJ)

Progress of reaction

FIGURE 4.3.4 The effect of catalase on the activation energy required for the decomposition of

hydrogen peroxide

Product

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LEARNING CHECK 4.3

DESCRIBING

1 Describe the physical structure of an enzyme.

2 Describe what happens to an enzyme after it has catalysed a reaction.

3 State a deﬁnition for the ‘enzyme–substrate complex’.

APPLYING

4 Explain how enzymes affect the activation energy required for a reaction to occur.

5 Explain why complex chemical reactions in cells require multiple enzymes.

ANALYSING

6 Compare the induced-ﬁt model of enzyme action with the original lock-and-key model.

7 Compare intracellular and extracellular enzymes.

4.4 Factors affecting enzyme function

Enzymes, like all proteins, function most eﬃciently within an optimal range of pH and temperature.

This is because the action of an enzyme depends critically on its shape, and its shape is provided

by the bonds of the polypeptide backbone and the amino acid side chains in its tertiary protein

structure (see section 4.1). These side chain bonds are based on three key interactions:

• positive and negative side chains attracting each other

• polar side chains orienting towards water and non-polar side chains orienting away from water

• large side chains taking up a considerable amount of space in the structure.

When a change in environment, such as temperature or pH, aﬀects any of these three

interactions, the shape of the enzyme changes, which aﬀects its ability to function eﬀectively.

Worksheet

Enzyme reaction

rate: temperature

denaturation the process

by which the functional

structure of a protein is

lost due to factors such

as pH and temperature

Temperature

As temperature increases, molecules move more and collide more often. With more frequent

collisions, there are more opportunities for a substrate to bump into its enzyme so that it binds

at the active site. Therefore, the rate of reaction generally increases as temperature increases.

However, an increased temperature causes the atoms, including those in the side chains of the

enzyme, to move and vibrate more. Most side chain interactions can survive minor increases

in temperature, but large increases cause so much movement that the bonds begin to break.

Breaking those interactions aﬀects how much space there is for large side chains and allows

water to enter parts of the structure that are meant to be non-polar. When these key interactions

are broken, the enzyme loses its functional shape in a process called denaturation. Often,

denatured proteins cannot regain their functional shape, even when conditions return to optimal.

Denaturation of enzymes by temperature increases can be a useful tool for the body.

Syllabus link

Chapter 11 discusses

the role of fever in

immunity.

During infection, a fever raises the body temperature in an attempt to denature the enzymes

in the pathogen. However, if a fever gets out of control, our own critical enzymes could also be

denatured, leading to seizures and death.

Enzymes are not denatured at low temperatures because the shape is not disrupted

with a decrease in movement. However, low temperatures reduce the reaction rate because

slower molecules have less energy and will not encounter the active site as often.

Enzymes have evolved to work optimally in the temperature range of their organism

(Figure 4.4.1). In general, human enzymes work best at about 37°C. Psychrophiles are

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Key

Enzyme from a psychcrophile

found in Arctic sediment

Enzyme from human intestine

Enzyme from a thermophile

found on geothermal seabed

Temperature (°C) (not to scale)

FIGURE 4.4.1 Optimal activity ranges for enzymes of different organisms. Activity gradually increases until

enzymes begin to denature and the reaction rate decreases.

micro-organisms that live in near-freezing environments such as the wind-blasted rocks on

snow-covered mountains. Their enzymes have evolved to operate at very low temperatures.

Alternatively, the micro-organism Pyrodictium lives in geothermal-heated areas of the sea ﬂoor.

It is a thermophile and its enzymes operate best at temperatures of 95–105°C.

Taq polymerase is an enzyme from another thermophile, Thermus aquaticus. It operates

at a temperature of 70–90°C, which makes it useful in a biotechnological technique called the

polymerase chain reaction (PCR), which ampliﬁes DNA fragments for analysis.

The pH of the surrounding environment depends on the presence of H+

(hydrogen) ions and/

or OH– (hydroxide) ions. The charges on these ions aﬀect interactions of positive and negative

R group side chains on the enzyme. For example, too many H+

ions

will pull the positive side chains away, which has the same eﬀect.

Diﬀerent enzymes have diﬀerent optimum pH ranges (Figure 4.4.2). Some enzymes can

function in a broad range of pH environments, whereas others are very sensitive and only

function in a narrow pH range. The change in reaction rate that results from changing pH is not

ions will pull the negative side

chains away from their positive side chain partners and denature the protein by destroying the

bonds that would otherwise have kept the protein in its functional shape. Too many OH–

Weblink

Enzyme simulation

Key

Human pepsin in stomach

Human alkaline phosphatase

in bone

Human salivary amylase

1 2 3 4 5 6 7 8 9 10 11 12

Acidic

Basic

FIGURE 4.4.2 The optimum pH range for three human enzymes: pepsin, alkaline phosphatase

and amylase

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Rate of reaction

related to how fast the enzyme is working or how often the substrate encounters the active site,

as is the case for changing temperature. Instead, the change in reaction rate is directly caused

by the denaturation of the enzyme.

Substrate concentration

saturation point the point

at which all active sites

are ﬁlled with substrate,

resulting in maximum

reaction rate

Although substrate concentration does not aﬀect the function of an enzyme and cannot denature

an enzyme, it does aﬀect the reaction rate. The concentration of substrate in a reaction mix can

change the amount of product made. Increasing substrate concentration results in faster production

until all the enzyme active sites are working at their maximum capacity (Figure 4.4.3). At this

saturation point, increasing the substrate concentration no longer increases the reaction rate

because there are no more free enzymes in the solution.

Saturation point; all

enzyme is being used

Maximum

activity

Substrate concentration

FIGURE 4.4.3 The effect of increasing substrate concentration on the rate of an enzyme-

catalysed reaction

Inhibitors

inhibition the process of

blocking enzyme activity

inhibitor a molecule that

blocks enzyme activity

Enzyme production is expensive for a cell, which makes denaturation a wasteful method of

turning oﬀ their function. Enzyme inhibition is the process of blocking enzyme activity

by inhibitors rather than by denaturation.

For example, when a cell is low in energy, an enzyme called phosphofructokinase-1 (PFK-1)

works with other enzymes in cellular respiration to produce adenosine triphosphate (ATP) as

energy for the cell. When the cell has plenty of energy, the excess ATP binds to PFK-1 to change

its shape and inhibit its function, stopping cellular respiration only until the cell needs energy

again. Many substances that are toxic to humans, including those produced by animals and

plants in defence, are enzyme inhibitors that turn oﬀ vital functions in our cells.