Chapter 5

Lecture Outline
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 How Cells Use Enzymes

 Organisms need energy and nutrients

to grow and reproduce.
 Organisms mobilize nutrients for
energy through biochemical reactions.
 Catalysts are chemicals that speed up
the rate of biochemical reactions.
 Enzymes are catalytic proteins.

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 How Enzymes Speed
Chemical Reactions
 Enzymeslower the activation energy of
biochemical reactions.
– The reactants in an enzyme-catalyzed
reaction are called substrates.
 Enzymes have a specific shape that fits
with the substrate shape.
– When the substrate and enzyme interact,
an enzyme-substrate complex is formed.
– This destabilizes the bonds in the substrate,
speeding up the reaction.

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 Lowering Activation Energy

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 How Substrates Bind to
Enzymes
 Enzymes only catalyze one or a few reactions.
– They are specific because they have a particular shape that only
fits particular substrates.
 The enzyme has a binding site for the substrate.
– Called the active site
 Induced fit
– When the substrate binds to the active site, the enzyme changes
shape to fit it perfectly.

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 How Enzymes Are Usually
Named

 Since each enzyme catalyzes a specific reaction

– Each has a unique name
 The first part of an enzyme’s name
– Is the name of the substrate
 The second part of an enzyme’s name
– Indicates the type of reaction it will catalyze
 All enzyme names end in the suffix
– -ase
 Examples:
– DNA polymerase
– Glycogen synthetase

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 Why Enzymes Need Vitamins
 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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 How the Environment
Affects Enzymes
 The rate at which an enzyme can bind to a
substrate is called the turnover number.
 The turnover number of an enzyme is
maximized under the ideal conditions for that
enzyme.
 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 will 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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 How the Cell Controls
Enzymes

 A cell must be able to control when and how often its

biochemical reactions take place.
– It does this by controlling enzymes.
 Coordination ensures that reactions happen in the
correct order.
 Regulation ensures that reactions happen at the
correct rate and controls the amount of product that
is made.
 Cells coordinate and regulate the activity of their
enzymes by:
– Enzymatic competition for substrate
– Gene regulation
– Enzyme inhibition
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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.
 Certainchemicals 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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 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
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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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 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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 Electron Transport
 Electrons in the outer energy level of atoms can be
lost to the other atoms
– If they receive energy and become excited
 Special molecules can receive the excited electrons
and harness that energy.
– They are called electron carriers.
 NAD, FAD
– The transfer reactions are called oxidation-reduction
reactions.
 Molecules losing electrons become oxidized.
 Molecules receiving electrons become reduced.

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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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