REVIEW

Levels of Protein Structure

Primary structure/ sequence:
Linear sequence of amino acids
primary structure is held together by covalent bonds
such as peptide bonds
 Levels of Protein Structure
Secondary structure/ substructure:
Folding or coiling of the polypeptide
into a repeating configuration.
H-Bonds

Alpha helix
Beta pleated sheet
 Levels of Protein Structure
Tertiary/polypeptide shape:

3D configuration
determined by the interaction
bonds between side chains

Quaternary/protein shape:

Two or more polypeptides

e.g. Hemoglobin (Hb)
Objectives:
The learners shall be able to:
Describe the components of an enzyme
STEM_BIO11/12-Ii-j-17

Determine how factors such as pH, temperature,

and substrate affect enzyme activity.
STEM_BIO11/12-Ii-j-19
Benedictine Hallmark:
Stewardship

Values Integration:
Recognize and appreciate
the different types of
enzymes.
ENZYMES
Enzymes
• Most enzymes are proteins.
• Most enzymes are three
dimensional tertiary globular
proteins.
• Enzymes are molecules that
act as catalysts.
• Functions:
1. Increased the rate of
chemical reactions to speed
up biological reactions
2. Decreases the activation of
energy to start a chemical
reaction.
Enzyme
• All reactants need to have a certain energy before they
will react.
• Activation Energy – amount of energy to start a reaction
• All catalysts ONLY lower the energy barrier and allowing
the reactants (substrates) to react faster forming the
products.
• Enzymes do not participate in the reaction.
In lowering the activation energy of a
reaction, enzymes decrease the barrier to
starting a reaction.
 Enzymes Structures
• Enzymes shape attracts specific
molecules
• The compound on which an
enzyme acts is the substrate.
• Substrate – molecules that bind
to the enzyme.
• Enzymes can break a single
structure into smaller
components or join two or
more substrate molecules
together.
Enzymes
• Enzymes have a specific region
where the substrate binds and
where catalysis occurs. This is called
the active site.
• Active site – location on the
enzymes where the substrate bind
to the enzyme.
• Enzymes are substrate-specific,
although specificity varies from
enzyme to enzyme.
• When a substrate binds to an
enzyme’s active site, an enzyme-
substrate complex is formed.
Enzyme Active Sites
Substrate molecule:
Substrate molecules are the
chemicals that an enzyme
acts on. They are drawn into
Active site:
the cleft of the enzyme.
The active site contains both binding
and catalytic regions. The substrate
is drawn to the enzyme’s surface and
the substrate molecule(s) are
positioned in a way to promote a
reaction: either joining two molecules
Enzyme molecule: together or splitting up a larger one.
The complexity of the
active site is what makes
each enzyme so specific
(i.e. precise in terms of the
substrate it acts on).

This model (above) is an enzyme called

Ribonuclease S, that breaks up RNA
molecules. It has three active sites (arrowed).
• An example of a catabolic enzyme is amylase.
Amylase converts starch into maltose.
• An example of an anabolic enzyme is DNA
polymerase. This enzyme repairs (rebuilds) DNA
 Enzyme Examples
Enzyme Role

Stomach enzyme used to

break protein down into
Pepsin
peptides. Works at very acidic
pH (1.5).

Digestive enzymes which act

Proteases on proteins in the digestive
system

A family of enzymes which

Amylases assist in the breakdown of
carbohydrates

A family of enzymes which

3D molecular structures for the Lipases
enzymes pepsin breakdown lipids
 Enzyme Examples
• One of the fastest enzymes in the
body is catalase.
• Catalase breaks down hydrogen
peroxide, a waste product of cell
metabolism, into water and oxygen.
• Accumulation of hydrogen peroxide
is toxic so this enzyme performs an
important job in the body.
 Enzymes names
• Enzymes are named by their substrate. The letters ase are
added to the substrates name.
• Examples are:

1. lactase – breaks down lactose (milk sugars)

2. diastase – digests vegetable starch
3. sucrase – digests complex sugars and starches
4. maltase – digests disaccharides to monosaccharides
(malt sugars)
5. glucoamylase – breaks down starch to glucose
6. protease – breaks down proteins found in meats,
nuts, eggs, and cheese
7. lipase – breaks down fats found in most dairy
products, nuts, oils, and meat
8. cellulase – breaks down cellulose, plant fibre; not
found in humans
 Enzymes facts

Many fruits contain enzymes

that are used in commercial
processes. Pineapple
(Ananas comosus) contains
the enzyme papain which is
used in meat tenderization
processes and also
medically as an anti-
inflammatory agent.
Lock and Key Model
The lock and key model of enzyme action, proposed earlier this century,
proposed that the substrate was simply drawn into a closely matching
cleft on the enzyme molecule.

Products
Substrate

Symbolic representation of the lock and key model of enzyme action.

1. A substrate is drawn into the active sites of the enzyme.
Enzyme 2. The substrate shape must be compatible with the enzymes active site
in order to fit and be reacted upon.
3. The enzyme modifies the substrate. In this instance the substrate is
broken down, releasing two products.
Induced Fit Model
More recent studies have Two substrate
molecules are
revealed that the process is drawn into the cleft
much more likely to involve of the enzyme.

an induced fit.
The enzyme
The enzyme or the reactants changes shape,
(substrate) change their shape forcing the substrate
slightly. molecules to
combine.
The reactants become bound to
enzymes by weak chemical bonds.

This binding can weaken bonds

within the reactants themselves,
allowing the reaction to proceed The resulting end
product is released
more readily. by the enzyme
which returns to its
normal shape, ready
to undergo more
reactions.
 substrate enzymes products

lactose lactase glucose + galactose

maltose maltase Glucose

cellulose cellulase Glucose

lipid lipase Glycerol + fatty acid

starch amylase Maltose

protein protease Peptides + polypeptide

Changing the Active Site
• Changes to the shape of the active site will result in a
loss of function.
• Enzymes are sensitive to various factors such as
temperature & pH.

• When an enzyme has lost its characteristic 3D shape, it

is said to be denatured.
• Some enzymes can regain their shape while in others,
the changes are irreversible.
 Enzyme Activity
Temperature
pH
Four Variables
Enzyme Concentration

Substrate Concentration
The Effect of Temperature on Enzyme
Action • Speeds up all reactions, but the
rate of denaturation of
Optimum
enzymes also increases at
Temperature higher temperatures.
for enzyme Too hot for
Enzyme to
work • High temperatures break the
disulphide bonds holding the
tertiary structure of the
enzyme together thus changing
Too cold for the shape of the enzyme.
Enzyme to
work
• This destroys the active sites &
therefore makes the enzyme
non – functional.
The Effect of Temperature on Enzyme
Action
• Lactase functions best between
roughly 70 and 120 degrees
Fahrenheit or room temperature,
with its function optimized at
around 115 degrees Fahrenheit.
those above 135 degrees
Fahrenheit, for example -- lactase
can become denatured, or lose
its shape. A protein's shape is
responsible for its function, so
when it becomes denatured,
lactase loses its ability to
function.
• Cooler temperatures slow the
rate of lactase’s function, while at
extremely high temperatures.
The Effect of pH on Enzyme Action
Like all proteins, enzymes are
denatured by extremes of pH
(acidity/alkalinity).
 The optimal pH for lactase
performance is around 6, but
lactase can function in an
acidic environment ranging
between a pH of 2 to 7, which
corresponds to the typical pH
of the human small intestine.
Deviations in pH outside of
this range, particularly to the
high basic levels of 10 to 12,
can cause the lactase enzymes
to become denatured.
The Effect of Enzyme Concentration on
Enzyme Action
• Assuming that the
amount of substrate is
not limiting, an increase
in enzyme concentration
causes an increase in the
reaction rate.
The Effect of Substrate Concentration on
Enzyme Action
• At low substrate concentration, the rate of reaction
if proportional to the substrate concentration-
there are plenty of active sites available to bind the
substrate
• As the substrate concentration increases, the rate
of reaction decrease and is no longer proportional
to the substrate concentration--- some of the active
sites are occupied by substrate
• At high substrate concentration, the rate of
reaction is constant and independent of the
substrate concentration.
The Effect of Substrate Concentration on
Enzyme Action
Co-factors
Co-factor is the non protein molecule
which carries out chemical reactions
that can not be performed by standard
20 amino acids.
Co-factors are of two types:
➢Organic co-factors
➢Inorganic cofactors
 Inorganic co-factors
Examples:
1. Enzyme carbonic anhydrase requires Zn for it’s activity.
An enzyme present in red blood cells, carbonic anhydrase, aids in the
conversion of carbon dioxide to carbonic acid and bicarbonate ions.
2. Hexokinase has co-factor Mg
Hexokinase is an enzyme that phosphorylates hexoses, forming
hexose phosphate.

ORGANIC CO-FACTORS
Example:
Glycogen phosphorylase requires the small organic
molecule pyridoxal phosphate.
Glycogen phosphorylase catalyzes the hydrolysis of glycogen
 Types of Organic
co-factors
Prosthetic Group Coenzyme
o A prosthetic group is a tightly o A coenzyme is loosely bound
bound organic co-factor e.g. organic co-factor. E.g. NAD +
Flavins, heme groups and biotin.
The Effect of Cofactors on Enzyme
Action
• Cofactors are substances that are essential to the
catalytic activity of some enzymes.
• Cofactors may alter the shape of enzymes slightly
to make the active sites functional or to complete
the reactive site.
 The Nature of Enzyme Inhibitors
Enzyme inhibitor is a molecule that binds to
an enzyme and decreases its activity.
 The Nature of Enzyme Inhibitors
Enzyme inhibitors may or may not act reversibly:

Reversible: the inhibitor is temporarily bound to the

enzyme, thereby preventing its function (used as a
mechanism to control enzyme activity).

Irreversible: the inhibitor may bind permanently to the

enzyme causing it to be permanently deactivated.
 The Nature of Enzyme Inhibitors
a. Non-specific inhibitiors include any physical or chemical
changes which ultimately denatures the protein portion of the
enzyme and are therefore irreversible.
Ex. Acid, Base, Temperature, Alcohol, Heavy Metals, Reducing
Agents

b. Specific Inhibitors exert their effects upon a single enzyme.

Ex. Poison, Drugs
1. Competitive Inhibitor -Block the substrate from interfering
the active site. Reduce the enzyme activity.
2. Non-competitive – bind the enzyme other than the active
site, change the shape, prevent the substrate in binding
 Summary: Enzymes
1. Enzymes work very rapidly and help to speed
up biological reactions.
2. Enzymes work in decreasing the activation
energy.
3. Enzymes are usually specific to one particular
substrate.
4. Enzymes can be used multiple times (however
they do degrade eventually).
5. Enzymes have optimal temperatures and pH
that they will operate. Beyond these optimum
ranges they will either not work or become
denatured (unfolded/breakdown).