C 1.

1 – Enzymes & Metabolism

”In what ways do enzymes interact with other molecules?

“What are the interdependent components of metabolism?”

C1.1.1 Enzymes as catalysts Students should understand the benefit of increasing rates of reaction in cells.
Students should understand that metabolism is the complex network of interdependent
Role of enzymes in and interacting chemical reactions occurring in living organisms. Because of enzyme
C1.1.2
metabolism specificity, many different enzymes are required by living organisms, and control over
metabolism can be exerted through these enzymes.
Examples of anabolism should include the formation of macromolecules from monomers
Anabolic and catabolic by condensation reactions including protein synthesis, glycogen formation and
C1.1.3
reactions photosynthesis. Examples of catabolism should include hydrolysis of macromolecules into
monomers in digestion and oxidation of substrates in respiration.

Enzymes as globular proteins Include that the active site is composed of a few amino acids only, but interactions
C1.1.4 between amino acids within the overall three-dimensional structure of the enzyme
with an active site for catalysis ensure that the active site has the necessary properties for catalysis.
Interactions between
Students should recognize that both substrate and enzymes change shape when binding
C1.1.5 substrate and active site to occurs.
allow induced-fit binding
Role of molecular motion and Movement is needed for a substrate molecule and an active site to come together.
C1.1.6 substrate-active site collisions Sometimes large substrate molecules are immobilized while sometimes enzymes can be
in enzyme catalysis immobilized by being embedded in membranes.
Relationships between the
structure of the active site,
C1.1.7 Students should be able to explain these relationships.
enzyme–substrate specificity
and denaturation
Effects of temperature, pH and
C1.1.8 substrate concentration on The effects should be explained with reference to collision theory and denaturation.
the rate of enzyme activity
Measurements in enzyme- Students should determine reaction rates through experimentation and using secondary
C1.1.9
catalysed reactions data.

Effect of enzymes on Students should appreciate that energy is required to break bonds within the substrate &
C1.1.10 that there is an energy yield when bonds are made to form the products of an enzyme
activation energy catalysed reaction. Students should be able to interpret graphs showing this effect.
Enzymes as catalysts
The enzyme helicase
Enzymes are catalysts which are effective
in small amounts. They speed up a
biological reaction but are itself unchanged
by the reaction. Without enzymes,
reactions would occur very slowly.
The enzyme amylase

In Biology, enzymes are globular

proteins composed of one or
more polypeptides, and their 3D
structure is affected by changes
in temperature and pH.
Enzymes as catalysts
The rate of reaction is the amount of product produced per unit
time. It is the speed at which a biochemical reaction is taking place.

Reaction with
enzyme

Reaction
without enzyme
The role of enzymes in metabolism

Metabolism is the
complex network of
interdependent and
interacting
biochemical
reactions occurring
in living organisms.
The role of enzymes in metabolism
The use of enzymes in organism makes biochemical reactions happen
faster, making a lot of processes more efficient. Enzymes are also
important because….

….Enzymes are
specific to their
substrate (the

https://www.nature.com/scitable/topicpage/cell-metabolism-14026182/
reactant), so a
large number of
enzymes are
required in
organism.

….And all the different metabolic reactions (anabolic and

catabolic) can carefully be controlled with the help of enzymes.
Anabolic and catabolic reactions
Metabolism, as the complex network of interdependent and interacting
chemical reactions occurring in living organisms, can be further divided
into anabolic and catabolic reactions.
 Anabolic and catabolic reactions Cell respiration

DNA
replication

Photosynthesis Decompositio
Building muscles Protein synthesis
Digestion
 Anabolic and catabolic reactions
Anabolism Catabolism

https://www.khanacademy.org/science/ap-biology/cellular-energetics/cellular-energy/a/overview-of-metabolism
Explanation

• Protein synthesis • Digestion of food (mouth, stomach, and

• DNA synthesis during replication small intestine)
• Photosynthesis (building up starch • Cell respiration where glucose or lipids are
Examples

from inorganic compounds) oxidized to carbon dioxide and water

• Synthesis of complex carbohydrates • Decomposition of complex carbon
(glycogen) compounds in dead organic matter.
Enzymes are globular proteins with an active site
An enzyme, such as
helicase during DNA
replication, is a
globular protein which
acts as a catalyst for
biochemical reactions.

Proteins are composed

of building blocks
called amino acids
which form long chains
that twist into globular
molecules.
Enzymes are globular proteins with an active site
An enzyme has an active site – a region of polar
amino acids on the surface of the enzyme to which
substrates bind and which catalyzes the reaction.

http://images.slideplayer.com/1/277615/slides/slide_46.jpg
The substrate is a reactant in a The enzyme-substrate complex is
biochemical reaction. Together a temporary structure formed
with the enzyme it forms the when a substrate binds to the
enzyme-substrate complex. active site of an enzyme.
Interactions between the structure of the active site …
and enzyme-substrate specificty
The overal three-dimensional
structure and the enzyme’s active site
amino acid sequence of the
active site is specific to the
substrate. This ensures that
the active site binds to the
substrate molecule, holds on
to it and lowers the activation The enzyme changes its
energy for the reaction. shape slightly to adapt to the
substrate (induced fit)
Interactions between the structure of the active site …
and enzyme-substrate specificty
The enzyme is highly specific
and the induced shape change
of the enzyme and substrate
upon binding results in a
proper alignment of the
catalytic groups on its surface
which allows the enzymatic
reaction to take place.

This process is referred to as the

induced-fit model, and it superseeds
the lock-and-key model which
describes a more restrictive shape of
enzyme and substrate (where only one
“key” (substrate) unlocks a “lock”
Interactions between the structure of the active site …
and enzyme-substrate specifity
Enzyme activity is the catalysis of a reaction by an enzyme:
There are three stages:

http://ejdio.weebly.com/uploads/3/0/7/8/30785041/373284_orig.jpg
1. The substrate(s) 2. While the substrates are bound 3. The products separate
binds to the active site to the active site, bonds in the from the active site,
of the enzyme because substrate are stressed or leaving it vacant for
of its structural and weakened causing it to change substrates to bind again.
chemical specificity. into different chemical substances
(products of the reaction).
Molecular motion & substrate-active site collisions
While some enzymes are embedded and immobilized within a
membrane, most enzymes and their substrates are found in solutions
(cytoplasm).

Immobilized enzymes

For a substrate and an active

site to come together molecular
movement is needed so that
substances can collide. The
greater the kinetic energy of
enzyme and substrate, the
greater the chance of collisions.
Molecular motion & substrate-active site collisions
When enzymes and substrates are in solutions both are doing the
movement. When an enzyme is immobilized within a membrane, the
substrate has to do all the movement.

Immobilized enzymes are also used as cell-free

preparations industrially in the preparation of
lactose free milk. Enzymes are attached to an
insoluble material or membrane with the
substrate moving over it. This is convenient, as
it allows reuse of the enzyme and avoids
havint to add the enzyme to the sample.
 Molecular motion & substrate-active site collisions
The formation of an enzyme-substrate complex overall depends on
three important aspects…
http://www.chemhume.co.uk/ASCHEM/Unit%203/14%20Reaction%20rates/collisions_orientation.jpg

1. water
The molecular motion of both, enzyme and molecules

substrate, which causes random collisions substrates

between molecules. All metabolic reactions
occur in an aqueous solution, which
enables the molecule’s continual motion.
2. part of enzyme
The correct alignment and angle between substrate
and enzyme affects the success of the collision.

3.
The speed of movement which is affected by the molecule`s size –
substrates are usually smaller than enzymes, so their movement is faster.
Molecular motion & substrate-active site collisions

1. Open the enzyme

simulation using this link
https://www.biologysimulat
ions.com/enzymes

2. The simulations shows two substrates – starch and maltose. For simplicity we will only focus
on one type of substrate now (maltose). Move the slider for “starch” all the way to 0. Also, move
the slider for “amylase” all the way to 0. Change the slider for maltose and maltase to 3.5, and
adjust the temperature to 25°C. Leave everything as it is. Click “Run Simulation” and observe the
changes to the concentrations of substrates and products.
Active site, enzyme–substrate specificity & denaturation
Since enzymes are proteins, their structure can be altered by changes
in pH or temperature. If the shape of the active site is changed
considerably it is said to have become denatured. It will not function
anymore, and the enzyme-substrate specificity is compromised.
High temperature causes denaturation as the extra energy leads to increased
vibration with the molecule, breaking intra-molecular bonds within the protein.

Changes in pH lead to a higher or lower concentration of hydrogen ions in the

solution – as a consequence, hydrogen bonds within the enzyme are broken.

http://www.pnas.org/content/100/9/5142/F5.expansion.html
 http://images.slideplayer.com/1/277801/slides/slide_27.jpg
The effect of temperature on enzyme activity
A thermophile, such as bacteria at deep-
sea vents, is an organism that is able to
withstand much higher temperatures
before its enzymes denature.

• As temperature increases, the rate of

reaction increases as molecules have more
kinetic energy.

• Enzyme and substrate molecules move

faster, increasing the chances of colliding
more frequently with the active site of the
enzyme. Enzyme activity is increasing.

• When enzymes are heated above

optimum, the chance of bonds breaking
within the molecule increases. The
structure changes, denaturing the enzyme.
The effect of pH on enzyme activity
Digestive enzymes have their
optimum pH at different ranges,
depending on where their activity
is the highest.

pH is a measure for the number of hydrogen ions in a solution. The higher

the concentration, the lower the pH. The pH scale is logarithmic, a change in
pH by one unit means a tenfold rise in hydrogen ions.
When the pH is
above or below the

http://avonapbio.pbworks.com/f/Denaturation.png
optimum (acidic or
alkaline), the
structure of the
enzyme (incl. active
site) is altered –
denatured.
The effect of substrate concentration on enzyme activity
Increasing substrate
concentration increases
the rate of reaction,
because the chances of

http://bioserv.fiu.edu/~walterm/Fund_Sp2004/lec3_cell_metab/cell_metabolism_files/image014.jpg
molecular (successful)
collisions between active
site of the enzyme and
substrate have increased.

At the optimum
concentration of substrate
molecules, all active sites
are full and working at
maximum efficiency.
Any increase in concentration beyond the optimum will have no added effect
as there are no extra active sites to be used – a greater and greater
proportion of substrate-active site collisions are blocked.
Effect of enzymes on activation energy
Most chemical or biological reactions require energy in order to occur. This
energy is called activation energy. With the help of enzymes reactions can be
carried out with a lower investment into the activation energy. This will allow
more product to be produced – the rate of reaction is increased.

Activation energy
is the minimum
amount of energy

https://www.nagwa.com/en/explainers/248185482685/
required for a
chemical reaction
to occur.
Enzymes lower the activation energy

https://1drv.ms/v/s!Au8ZKE_EDcrQhJAvAo-fDKmrrpzXeg?e=jm1hEq
Enzymes lower the activation energy An enzyme lowers the
activation energy by
Energy is required weakening bonds
to reach a already, and therefore
transition state less energy is needed
for an exothermic
before completing
reaction to occur. After
a reaction. the products have
been formed, energy
is released.
The transition state
is an intermediate
state before being
converted into
products, e.g. bonds
need to be broken
or weakened in a
substance. This is
what the activation
energy is used for.
Uses and applications of enzymes in industry

Nowadays, more
than 500
(immobilized)
enzymes have
commercial uses.

Research on
some

http://www.abpischools.org.uk/cnt/txt/177/1/milk.gif
examples!
Uses and applications of enzymes in industry

Enzymes are used in medicine & biotechnology for

contact lens cleaners (proteases to remove proteins on In the brewing industry, Detergents contain
lenses to avoid infections) and genetic engineering enzymes help a number proteases and lipases
(restriction enzymes, ligase, polymerase) for PCR and of processes, including to help breakdown
forensic science. the clarification of beer. proteins and fat stains

Enzymes are widely used in the food industry Paper production uses enzymes for the pulping of
• Fruit juice, pectinase to increase juice yield from fruit wood (amylase, cellulase, lignase). These enzymes
• Fructose is used as a sweeter, it is converted from degrade starch to lower viscosity and coating
glucose by isomerase paper; cellulase smoothens fibers, enhance water
• Rennin is used to help cheese production. drainage, and promote ink removal
Uses and applications of enzymes in industry
Measurements in enzyme-catalysed reactions
When measuring the rate of enzyme-catalysed reactions, we record
the amount of substrate that has disappeared from a reaction mixture
or the amount of product that has accumulated in a unit of time.

The shape of the curve indicates the rate

of the reaction is not constant during the
reaction but is fastest at the start and
slows down as the reaction proceeds.
Measurements in enzyme-catalysed reactions

The gradient (=the rate) is

therefore not constant
and so can only be given
for a particular value of
time (instantaneous rate
of reaction). This rate can
be measured by drawing
a tangent to the curve at
the specified time and
dividing the change in
product (P) by the
change in time (T).

When the instantaneous rate of reaction is calculated at t=0 we call it the initial
rate of reaction. In enzyme reactions this is what most commonly is used.
Measurements in enzyme-catalysed reactions

https://exchange.iseesystems.com/public/jon-darkow/lactase-enzyme-simulation-with-data-analysis/index.html?fbclid=IwAR0uB1RvucCscBHmYvqfvlfrCC8T2HBXi3pe0sDTEXyXbcOc2i9elOpnmMo