Chapter 5

Enzymes

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 Enzymes the bio-catalyst

Enzyme have double roles -

Protein + Catalyst
Catalyst – lower the activation
energy of a reaction
Protein – controls the catalytic
activity by changing its shape
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 Lowering Activation Energy

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 How catalysis in monitored by
enzyme structures?
 Enzymes are specific to a
substrate
 Enzyme has specific binding
site for the substrate – known
as active site
 The enzyme changes shape
upon binding of the substrate
the active site– known as
induced fit
 After the reaction is over
enzyme retains its initial shape
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 Naming of Enzymes
 Each Enzyme has unique name
 The first part of an enzyme’s name
– name of the substrate
 The second part of an enzyme’s name
– type of the reaction it catalyze
 All enzyme names end in the suffix
– -ase
 Examples:
– DNA polymerase; Glycogen synthetase

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 Enzymes require precursors for
their functioning
 Some enzymes need special molecules to help them
function correctly.
– Called cofactors
 Cofactors can be inorganic ions, such as zinc or iron.
 Some cofactors are organic molecules.
– Called coenzymes
 Vitamins are the precursors for many coenzymes.
– Vitamin B2 is made into FAD.
– Niacin is made into NAD.
 Vitamins must be acquired from the diet, since cells
cannot make them.
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 The Role of Coenzymes

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 Turnover number of enzymes
 Turnover number is the maximum number of
substrate molecules that an enzyme can
convert (to the product molecule) per
catalytic site per unit of time (turnover rate)
 The turnover number of an enzyme is
maximized under the ideal conditions for that
enzyme.

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 How the Environment Affects
Enzymes
Each enzyme has ideal conditions that include:
Temperature
pH
Substrate concentration

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 Temperature
 Temperature has two effects on enzymes.
– Changes the rate of molecular motion
 Increasing temperature increases molecular motion.
– Increases the rate of catalysis
 Optimum temperaturethe temperature at which the enzyme
has the highest rate of catalysis.
 Decreasing temperature decreases molecular movement.
– Decreases the rate of catalysis
– Causes changes in the shape of an enzyme
 Temperature changes above optimum will denature the
enzyme.
 This changes its shape, and it can no longer bind substrate
and catalyze the reaction.
 This is why a high fever is potentially dangerous.
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 The Effect of Temperature
on Turnover Number

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 pH
 In the three-dimensional shape of an enzyme
– Some amino acid side chains are exposed to the
environment.
 In a basic environment
– The acidic side chains could donate protons.
 In an acidic environment
– The basic side chains could accept protons.
 Both of these events may change the shape of the
enzyme
– Making it less able to bind substrate, thus less able to
catalyze the reaction

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 The Effect of pH on the Turnover
Number

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 Enzyme-Substrate Concentration

 The rate of catalysis increases as the amount

of
– Enzyme increases
– Substrate increases
 However, once all of the enzymes are
occupied, the rate of catalysis will not
increase
– Even if more substrate is added

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 Enzyme substrate saturation

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 Regulation of enzyme activity

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 Enzymatic Competition for Substrate
 Enzymatic competition
– Occurs when more than
one enzyme interacts
with the same substrate
 Each enzyme converts
the substrate to a
different product.
 The enzyme that “wins”
is the one that is the
most abundant at the
time.
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 Gene Regulation
 Enzymes are proteins.
– Protein production is controlled by genes.
 Certain chemicals in the cell turn particular
enzyme-producing genes on or off depending
on the situation.
– Called gene-regulator proteins
 Those that decrease the amount of an enzyme made
are called gene-repressor proteins.
 Those that increase the amount of an enzyme made are
called gene-activator proteins.
 Example: Malate synthetase

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 Enzyme Inhibition
 Inhibitors are molecules
that attach to enzymes
and make them unable
to bind to substrate.
 Many drugs, pesticides
and herbicides target
enzymes.
 Types of inhibition
– Competitive inhibition
– Negative-feedback
inhibition
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 Competitive Inhibition
 Competitive inhibitors
closely resemble the
substrate.
– Therefore, they bind
to the active site of
the enzyme.
– They block the
substrate from
binding.
 Example:
– Anti-herpes drugs

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 Negative-Feedback Inhibition

 Occurs within enzyme-catalyzed reactions

that occur in a sequence

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 Negative-Feedback Inhibition
 As the end-product of the sequence accumulates,
– Those molecules feedback and bind to an
enzyme early in the sequence.
– They inhibit that enzyme, and stop the sequence.
– This decreases the amount of end-product made.
 This functions to keep levels of the end-product
within a certain range.

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 Review Enzyme: Q1
 The amount of energy it takes to get a
chemical reaction to occur is known as -
– Starting energy
– ATP
– Activation energy
– Denaturation

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 Review Enzyme: Q2
 A molecule that is acted upon by an enzyme
is a
– Cofactor
– Binding site
– Vitamin
– Substrate

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 Review Enzyme: Q3
 Vitamins are precursor to -
– Cofactor
– Co-enzyme
– Enzyme
– Substrate

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 Review Enzyme: Q4
 In your biology laboratory, you have heated
an enzyme and added to the substrate. The
substrate failed to produce the product
molecule. This is because the enzyme is -
– Competitively inhibited
– Anabolized
– Killed
– Denatured

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 Review Enzyme: Q5
 Whenever there are several different
enzymes available to combine with a given
substrate, _________________ results.

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 Review Enzyme: Q6
 If a cleaning agent contains an enzyme that
will get out stains that are protein in nature, it
can also be used to stains caused by oils.
– True or False; Justify

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 Review Enzyme: Q7
 Organophosphate pesticides are capable of
attaching to the enzyme
acetylcholinesterase. Since
acetylcholinesterase is necessary for normal
nerve cell function, organophosphates
pesticides are nerve position and kills
organisms.
– Explain the mechanism how organophosphate
pesticides are poison to nerve cells.

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 Review Enzyme: Q8

Read the paragraph 

Why the coat
below carefully. cannot form below
Answer the 18C?
following questions 
What possible kind
in terms of their of enzyme is
enzyme activities - involved in this coat
A lowering of the formation?
atmospheric 
Explain why the
temperature from coat formation stops
5-30
22C to 18C causes when the cell needs
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 Look at this picture carefully and
explain the phenomenon

Enzyme 1
Enzyme 2 Enzyme 3

5-31 Justify,Copyright
whether this is an example of competitive inhibition.
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 Competitive versus non-
competitive inhibition

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 Cells Use Enzymes to Process
Energy and Matter
 Organisms obtain
energy through
enzyme-catalyzed
biochemical reactions.
– These reactions break
chemical bonds,
releasing their internal
potential energy.
– Example: burning wood

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 What a living wood (plant) will
do?

Living wood will not allow exhaust all its
energy at a time.

Rather, energy will be released in stepwise
manner.

Enzymes are involved in each step to
facilitate energy release.

In addition to enzymes some other molecules
assist in energy production.

All these together are known as biochemical
5-34 pathway.
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 Biochemical Pathways
 A series of enzyme-catalyzed reactions
 Also called metabolic pathways
– Catabolism-the breakdown of compounds
– Anabolism-the synthesis of new, larger compounds
 Examples: photosynthesis, respiration, protein synthesis, etc.

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 Basic Biochemical pathways are
same across the organisms

Basic biochemical pathways are more or less
the same across different organisms.

Hence, these organisms share same set of
enzymes.

As enzymes are proteins and proteins are
produced by genes, E. coli and human share
1000 of common genes among themselves

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 Generating Energy in a Useful
Form: ATP
 ATP
– Is the molecule that
organisms use to fuel
anabolic reactions
– Is an adenosine + three
phosphates
 The bonds between the
phosphates contain a lot of
potential energy.
– Called high energy
phosphate bonds
 Breaking those bonds
releases a lot of energy.
– ATP - 1 phosphate = ADP
– ADP – 1 phosphate = AMP

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 ATP: The Power Supply for Cells

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 Basic biochemical pathways and
electron carriers

Biochemical pathways involve stepwise
reactions, breaking or formation of bonds

Breaking of bonds -

Energy absorbed, electron in the outermost
shell is excited and released

These free electrons are potentially
hazardous to the cell.

Because, they can combine with any
macromolecule and modify or destroy it.
5-39 
Hence, there should be some molecules
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 Electron carrier molecules

These molecules receive electrons

Electron receivers are themselves reduced

Example, NAD+, NADP+, FAD

As they receive electron their charges alter

Now these molecules are capable of
receiving H atoms

Hence, electron carrier molecules are both
receivers of electron and hydrogens
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 Electron Transport
 Oxidized electron carriers NADH, NADPH, FADH2
can revert back to their original forms NAD+, NADP+
etc., once the reaction is over.
 Hence, these molecules are recyclable inside the
cell.
 They carry both e-/H+ from one molecule to the
other
 Are electron carriers enzymes?
 Are they co-factors?

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 Proton Pumps
 The energy released by the transfer of electrons can
be used to pump protons.
– This is accomplished by proton pumps.
– This concentrates protons in a small space.
– The “pressure” created by this concentration gradient drive
the diffusion of the protons.
 The protons diffuse through a special protein called
ATP synthase.
 The ATP synthase uses the energy released from
the diffusion of the protons to make ATP.

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 Electron Transport and Proton
Gradient

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