AP Biology

1.3 ENZYME STRUCTURE

& FUNCTION
UNIT 1 THE CHEMISTRY OF LIFE
 Topics: (click one to jump to that section)
(1) How Enzymes Work
(2) Factors Affecting Enzyme Activity
(3) Regulation of Enzymes

Unit 1.3 Self-Assessment Questions

TOPIC 1
UNIT 1.3 ENZYME STRUCTURE & FUNCTION

HOW ENZYMES WORK

Chemical Reactions
● Chemical reactions occur when
molecules become new molecules
through the breaking and reforming of
chemical bonds between atoms.
● A chemical equation summarizes a
chemical reaction.
● Reactants are the molecules on the left
side of the arrow, which are the
substances present at the start of a rxn.
● Products are the molecules on the right
side of the arrow, which are the new
substances formed from the rxn.
Activation Energy
● Every chemical reaction between Chem Rxn: AB + CD → AC + BD
molecules involves bonds breaking and
bonds forming.
● The activation energy (EA) is the initial
amount of energy needed to be absorbed
by the reactants in order for a chemical
reaction to occur.
● This energy is typically supplied in the form
of heat from the surroundings.
● Reactions that have high activation
energies, occur slowly. Reactions that have
small activation energies, occur quickly.
How Enzymes Work
● Enzymes are proteins that act as
catalysts in cells and organisms.
○ A catalyst is a chemical that
speeds up a reaction without
being consumed by the
reaction.
● Enzymes speed up metabolic
reactions by lowering the
activation energy (which makes
the reaction occur more “easily”
and thus go faster).
How Enzymes Work Protein
Folding
● Enzymes (like all proteins) are made of a
sequence of amino acids, which folds
into a specific shape.
● The shape of an enzyme allows it to bind
to the reactants needed for a chemical
reaction and assist in the breaking and
forming of new bonds.
● The reactant an enzyme binds to is
known as the enzyme’s substrate.
● The region on the enzyme where the
substrate binds to is called the active
site. enzyme-substrate complex
How Enzymes Work
● The binding of the enzyme and
substrate forms an enzyme-substrate
complex.
● The binding of a substrate(s) to the
active site creates an induced fit, in
which the enzyme changes shape to
embrace the substrate(s) to ensure it
does not detach until the reaction is
complete.
● Enzymes are not chemically changed
or “used-up” in a chemical reaction
and can be used over and over again.
Enzyme Specificity
● Enzymes have a specific shape and active
site that only binds to a specific substrate. Maltose
Thus, enzymes control very specific
reactions. Ex: Lactase can hydrolyze the disaccharide lactose
(glucose and galactose), but cannot hydrolyze the
● Substrates binds to the active site on disaccharide maltose (glucose and glucose).
enzymes through weak interactions, such
as ionic bonds (+/- charges), hydrogen
bonding, and polar/nonpolar interactions.
● For an enzyme-mediated chemical
reaction to occur, the shape and charge of Amylase

the substrate must be compatible with the Ex: Amylase can break the glycosidic linkages
between glucose in starch, but not the glycosidic
active site of the enzyme. linkage between glucoses in cellulose.
Enzyme Specificity
● The name of an enzyme always end with
the suffix “-ase” and typically refer to the
substrate they bind to or the type of
reaction they catalyze.
○ EX: Lactase catalyzes the hydrolysis
of lactose into glucose and
galactose.
○ EX: ATP Synthase catalyzes the
reaction that synthesizes ATP in the
cell.
Identify the reactants and products in the reaction
described in the equation below.
6 CO2 + 6 H2O → C6H12O6 + 6 O2

Interactive Notes
Label the activation
energy on the graph.

Draw a new line on the

graph that shows how
the reaction would
change with the addition
of an enzyme.

Interactive Notes
How do enzymes (and catalyst in general) speed up
chemical reactions in a cell?

Enzymes are _______________ which are made up

of monomers called ______________________.

Interactive Notes
On the diagram below, label the enzyme, active
site, substrates and products.

How does the previous diagram demonstrate an

induced fit?

Interactive Notes
Determine if the statements below or true (T) or
false (F). Correct the statements that are false.
___ Enzymes speed up chemical reactions by providing energy to
reactions.

___ The rate of a reaction is faster when the activation energy is lower.

___ Enzymes bind to substrates by forming strong covalent bonds with the
substrate.

___ There is only one specific reaction that an can be catalyzed by a

certain type of enzyme.

Interactive Notes
Describe enzyme specificity, using lactase OR
amylase as an example.

Interactive Notes
TOPIC 2
UNIT 1.3 ENZYME STRUCTURE & FUNCTION

FACTORS AFFECTING
ENZYME ACTIVITY
 All enzymes working
Increasing Substrate Concentration at max speed.

● The rate of enzyme activity can be

sped up by increasing the substrate
concentration in a solution.
● When all enzyme molecules in a
solution are bonded with substrate,
the enzymes are said to be
saturated.
● At enzyme saturation, the enzymes
are all working at max speed and
the rate of the reaction can only be
increased by adding more enzyme.
Environmental Conditions and Denaturation
● The structure and function of enzymes, like all
proteins, are sensitive to changes in environmental
conditions, which can cause them to denature.
● Specifically, if the structure of an enzyme’s active
site is altered, it’s ability to bind to substrates and
catalyze a chemical reaction will also be affected.
● Enzymes have an optimum pH and temperature at
which they have evolved to fold into the correct
conformation (shape).
○ The optimal pH and temp are unique to each
enzyme and depends on where that enzyme is
meant to function.
Environmental Conditions and Denaturation
● Increasing temperature generally increases the
rate of a reaction, because it causes molecules to
move faster and increases the number of
collisions between enzymes and their substrate.
○ However at some point the increased
temperature will affect the stability of the
enzyme’s structure, causing it to denature.
○ Ex: Most human enzymes have optimal
temperatures of about 35-40 °C (close to
human body temperature) and do not
function outside that range due to
denaturing.
Environmental Conditions and Denaturation
● The optimal pH values for most
enzymes fall in the range of pH 6-8,
but there are some exceptions.
○ Ex: Pepsin, a digestive enzyme
in the stomach, works best at a
pH of 2.
○ Ex: Trypsin, a digestive enzyme
in the intestines, works best at a
pH of 8.
Mutations
● Mutations change the amino acid sequence of a protein. A mutation in a DNA
region that codes for an enzyme can alter its structure and function.
● If an amino acid found in the active site of enzyme is changed, it can lead to
the enzyme no longer being able to bind to the substrate.
● A change in an amino acid outside the active site can also affect the folding of
the enzyme and the shape of its active site.
Cofactors & Coenzymes
● Many enzymes require non-protein helpers
called cofactors to help them catalyze reactions.
There are inorganic and organic cofactors
○ Inorganic cofactors include things such as
metal ions (zinc, iron, and copper).
○ Organic cofactors, called coenzymes,
include things such as vitamins.
● Enzymes only become active when all the
appropriate cofactors and coenzymes are
present and bind to the appropriate sites on
the enzyme.
Inhibitors
● Enzyme inhibitors are chemicals that selectively attach to an enzyme and
inhibit it from binding to its substrate, causing a reduction in reaction rate.
● There are two types of inhibitors: competitive and noncompetitive.
● Competitive inhibitors: reduce the productivity of enzymes by attaching to the
enzyme’s active site and thus blocking substrates from attaching.
○ Competitive inhibitors have similar chemical properties as the enzyme’s
substrate, allowing it to bind to the active site.
Inhibitors
● Noncompetitive inhibitors: bind to the enzyme at a location that is not the
active site, causing the enzyme (and its active site) to change shape and thus
preventing the enzyme’s active site from attaching to the substrate.
Inhibitors
● Inhibitors can bind reversibly or irreversibly.
○ Reversible inhibitors temporarily
associate with the binding site of the
enzyme, without forming any permanent
bonds. Eventually they fall off.
○ Irreversible inhibitors form covalent
bonds with the enzyme at the binding Inhibitor covalently bonds
to active site.
site and do not unattach, permanently
inhibiting the enzyme.
Inhibitors
● Reversible competitive inhibitors can be overcome by increasing the
concentration of substrate, but noncompetitive inhibitors cannot be overcome
by increasing the substrate concentration.
Create a graph showing the effect of substrate
concentration on reaction rate. Label the axes.

Interactive Notes
What might happen to a bacteria taken from a
stream with 20 °C water if it was placed in a hot
spring with 50 °C? Explain.

Interactive Notes
Base off the graph below, which enzyme (1, 2, or 3)
would you most likely find in bacteria that thrive in
the acidic environment near hydrothermal vents in
the ocean? Why?

Interactive Notes
Describe a mutation in an enzyme that would likely
not affect its function.

Interactive Notes
People who are severely vitamin C deficient
develop scurvy, a disease resulting from the body’s
inability to produce collagen. There are multiple
enzymes involved in the synthesis of collagen.
Propose a possible explanation for why vitamin C
deficiency causes scurvy.

Interactive Notes
Draw a picture of a competitive inhibitor acting on
an enzyme.

Draw a picture of a noncompetitive inhibitor acting

on an enzyme.

Interactive Notes
Molecule A catalyzes the conversion of Molecule B to
Molecule C. The reaction is inhibited by Molecule D, which
resembles Molecule B. Increasing the ratio of Molecule B to
Molecule D reduces the inhibitory effect of Molecule D.
Identify each molecule:
_____ Substrate
_____ Product
_____ Enzyme
_____ Inhibitor
Is the inhibitor a competitive or noncompetitive inhibitor?

Interactive Notes
TOPIC 3
UNIT 1.3 ENZYME STRUCTURE & FUNCTION

REGULATION OF
ENZYMES
Allosteric Regulation of Enzymes
● Reactions taking place in a cell need to be carefully regulated (controlled).
● For this reason, enzymes have active and inactive conformations (shapes),
meaning they can be turned “on” and “off.”
● Allosteric regulation is the term used to describe any case in which a protein’s
function at one site is affected by binding of a regulatory molecule at another
site.
○ Enzymes change shape when regulatory molecules bind to specific sites,
affecting the enzyme’s function.
● Allosteric regulation can either activate or inhibit an enzyme’s activity.
Allosteric Regulation of Enzymes
● Allosteric Activation is a form of allosteric regulation that stimulates
(increases) enzyme activity.
○ Occurs when the binding of a regulatory molecule, called an activator,
stabilizes the active conformation of the enzyme.
Allosteric Regulation of Enzymes
● Allosteric Inhibition is a form of allosteric regulation that inhibits (decreases)
enzyme activity. This is the same thing as noncompetitive inhibition.
○ Occurs when the binding of a regulatory molecule, called an inhibitor,
stabilizes the inactive form of the enzyme, in which substrates cannot bind
to the active site of the enzyme.
Metabolic Pathways & Feedback Inhibition
● Often in organisms, a series of chemical reactions are needed to take a certain
substrate and turn it into a desired final product. This is called a metabolic
pathway.
● Each chemical reaction involved in the pathway is catalyzed by a different
enzyme.
Metabolic Pathways & Feedback Inhibition
● A process called feedback inhibition regulates metabolic pathways. This
process involves the end product shutting down the metabolic pathway by
binding to and inhibiting an enzyme that is used earlier in the pathway.
● Feedback inhibition prevents a cell form synthesizing more product than is
needed and wasting chemical resources.
Metabolic Pathways
& Feedback Inhibition

Example: In certain organisms, a metabolic pathway

exists that turns the amino acid, threonine, into the
amino acid, isoleucine. This pathway is made up of
five reactions, catalyzed by five different enzymes.
When the end product, isoleucine, starts to
accumulate in the cell, it starts binding to and
inhibiting threonine deaminase (the first enzyme in the
metabolic pathway).
Enzyme Localization in a Cell
● Cells compartmentalize where certain reactions take place within the cell,
meaning that different reactions take place in different areas (“compartments”)
of the cell.
○ This increases the efficiency of the cell, such as by preventing conflicting
types of reactions from competing with one another.

ATP Synthase
Inner mitochondrial
membrane
Enzyme Localization in a Cell
● Cells accomplish this by making sure that certain enzymes are localized to
certain areas within the cell.
○ Many enzymes are incorporated into specific membranes within the cell.
○ Some are contained in solutions enclosed within a specific
membrane-bound organelle.
○ EX: the enzyme ATP synthase is embedded in the inner membrane of the
mitochondria, the organelle where ATP synthesis occurs.
ATP Synthase
Inner mitochondrial
membrane
An allosteric activator stimulates an enzyme by…

An allosteric inhibitor inhibits an enzyme by…

Interactive Notes
One type of metabolic pathway that takes place in
cells is the synthesis of isoleucine from threonine,
which requires 5 different enzymes. According to
the diagram in the slides, what happens when there
is an excess of isoleucine produced in the cell?
Explain why this outcome would be beneficial.

Interactive Notes
Many chemical reactions only take place in certain
locations within a cell. How do cells accomplish
this?

Interactive Notes
UNIT 1.3 ENZYME STRUCTURE & FUNCTION

SELF-ASSESSMENT
QUESTIONS
Self-Assessment Questions
1. Vioxx and other prescription nonsteroidal anti-inflammatory drugs (NSAIDs) are
potent inhibitors of the cyclooxygenase-2 (COX-2) enzyme. High substrate
concentrations reduce the efficacy of inhibition by these drugs. These drugs are

A. competitive inhibitors.
B. noncompetitive inhibitors.
C. allosteric regulators.
D. prosthetic groups.
E. feedback inhibitors.
Self-Assessment Questions
2. If you were designing an organism, and a critical chemical reaction occurred too
slowly at the organism’s body temperature, what would you need to add to the
design?

A. an enzyme
B. a catalyst
C. a molecule that lowers the activation energy of the reaction
D. A, B, or C
E. A or C
Self-Assessment Questions
3. If you took a bacterium living in a stream with 20°C water and placed it in a hot
spring with 50°C water, what might happen?

A. It would thrive, with more thermal energy to speed reactions.

B. It would die because its enzymes would malfunction at high temperature.
C. It would grow as usual, since temperature has little effect on bacteria.
D. It would die because faster reactions would deplete cellular ATP.
E. B and D
Self-Assessment Questions
4. If a mechanic tries to change as many tires as possible in a short time by
bringing car after car into the garage before previously repaired cars can be
removed, eventually no more work can be done until the fixed cars are removed.
What enzyme function is this like?

A. allosteric activation
B. denaturation
C. optimal temperature
D. feedback inhibition
E. noncompetitive inhibition
Self-Assessment Questions
5. Imagine that you have discovered a new enzyme, but when you isolate it for
further study, it does not work properly. What might have been lost?

A. a cofactor
B. an inhibitor
C. bound reactant
D. A and B
E. A, B, and C
Self-Assessment Questions
6. The enzyme glucose oxidase binds the 6-carbon sugar glucose and catalyzes
its conversion to glucono-1,5-lactone. Mannose is also a 6-carbon sugar, but
glucose oxidase cannot bind mannose. The specificity of glucose oxidase is based
on the

A. free energy of the transition state.

B. activation energy of the reaction.
C. change in free energy of the reaction.
D. three-dimensional shape and structure of the active site.
Self-Assessment Questions
7. Which of the following statements best helps explain the reaction specificity of
an enzyme?

A. The free energy of the reactants is greater than the free energy of the
products.
B. The equilibrium constant of the reaction is much greater than 1.
C. The shape and charge of the substrates are compatible with the active site of
the enzyme.
D. The concentration of the enzyme inside living cells is greater than the
concentration of substrate.
Self-Assessment Questions
8. Enzymes with their highest activity at
an alkaline (basic) pH are represented by
which of the following graphs?

A. I only
B. II only
C. III only
D. I and III only
E. I and IV only
Self-Assessment Questions
9. A tissue culture of vertebrate muscle was provided with a constant excess supply of
glucose under anaerobic conditions starting at time zero and the amounts of pyruvic acid and
ATP produced were measured. The solid line in the graph above represents the pyruvic acid
produced in moles per liter per minute. ATP levels were also found to be highest at points A
and C, lowest at B and D. A second culture was set up under the same conditions, except that
substance X was added, and the results are indicated by the dotted line.

It is most reasonable to hypothesize that, in the

breakdown of glucose, substance X is
A. An activator
B. An inhibitor
C. A substrate
D. A coenzyme
E. A cofactor
Self-Assessment Questions
10. Which of the following best explains
why pepsin functions poorly at a neutral
pH?

A. The primary sequence of pepsin

changes at a neutral pH
B. The shape of pepsin’s active site
changes at a neutral pH
C. The substrate that pepsin binds to is
not stable at neutral pH
D. Both A and B
E. All of the above
ANSWERS TO SELF-ASSESSMENT QUESTIONS
1. A
2. D
3. B
4. D
5. A
6. D
7. C
8. B
9. B
10. B