CONCEPT 3: ANALYZING CELL
METABOLISM AND ENZYME
FUNCTION (CH 8, AP Inv 13)
Holtzclaw: “Metabolism” pg 58-62; 324-325
Campbell: Read pg 142-145, 155-156
Look at figures on pg 147, 157-159
Online Activities
Fig. 8-1
CONCEPT 3: LEARNING INTENTIONS


An Introduction to Energy Metabolism
 Examples of endergonic and exergonic reactions.
 The key role of ATP in energy coupling.
 That enzymes work by lowering the energy of activation.
 The catalytic cycle of an enzyme that results in the production
of a final product.
 The factors that influence the efficiency of enzymes.
Investigation: Enzyme Activity
 The factors that affect the rate of an enzyme reaction such as
temperature, pH, enzyme concentration.
 How the structure of an enzyme can be altered, and how pH
and temperature affect enzyme function.
BUT FIRST…
Basic Metabolism
 Forms of Energy
 Laws of Thermodynamics
 Order vs Disorder
 Free Energy

METABOLISM

Metabolism is the totality of an organism’s chemical
reactions

Catabolic pathways release energy by breaking down
complex molecules into simpler compounds


Ex: Cellular respiration
Anabolic pathways consume energy to build complex
molecules from simpler ones

Ex: The synthesis of protein from amino acids
METABOLISM
A metabolic pathway begins with a specific molecule
and ends with a product
 Each step is catalyzed by a specific enzyme

Enzyme 1
A
Reaction 1
Starting
molecule

Enzyme 2
B
Enzyme 3
C
Reaction 2
D
Reaction 3
Product
In order to have these reactions occur, what do you need?
ENERGY!
What
is energy?
 Energy
is the capacity to cause
change!
 For example… hold up your pen…
Fig. 8-2
A diver has more potential
energy on the platform
than in the water.
Climbing up converts the kinetic
energy of muscle movement
to potential energy.
Diving converts
potential energy to
kinetic energy.
A diver has less potential
energy in the water
than on the platform.
FORMS OF ENERGY


Energy exists in various forms, some of which can
perform work
Kinetic energy is energy associated with motion


Potential energy is energy that matter possesses
because of its location or structure


Heat (thermal energy) is kinetic energy associated with
random movement of atoms or molecules
Chemical energy is potential energy available for release in
a chemical reaction
Energy can be converted from one form to another
THE LAWS OF ENERGY TRANSFORMATION


Thermodynamics is the study of energy
transformations
Organisms are energy transformers
When you climb a cliff and then dive off… what are the
energy transformations?
 How did you get the energy to
climb the hill in the first place?

THE LAWS OF ENERGY TRANSFORMATION

Think: Describe the forms of energy found in an apple as
it grows on a tree, then falls and is digested by someone
who eats it.
THE FIRST LAW OF THERMODYNAMICS

According to the first law of thermodynamics, the
energy of the universe is constant:
– Energy can be transferred and transformed, but it cannot be
created or destroyed

For example, BC Hydro does NOT create energy… they
transform it to a form that we use in our homes.
THE SECOND LAW OF THERMODYNAMICS


During every energy transfer or transformation, some
energy is unusable, and is often lost as heat
According to the second law of thermodynamics:
– Every energy transfer or transformation increases the
entropy (disorder/randomness) of the universe
Think: What are some examples
(biological or non-biological)
of the second law?
Fig. 8-3
Heat
Chemical
energy
(a) First law of thermodynamics
CO2
+
H2O
(b) Second law of thermodynamics
THE SECOND LAW OF THERMODYNAMICS

Chew on this one:

Every energy transfer increases the entropy of the
universe
 Therefore, the universe is unstoppable in its
increasing randomness!!!

What is the impact on Biological systems?***
BIOLOGICAL ORDER AND DISORDER

Cells create ordered structures from less ordered
materials
BIOLOGICAL ORDER AND DISORDER
Cells create ordered structures from less ordered
materials
 Organisms also replace ordered forms of matter
and energy with less ordered forms

BIOLOGICAL ORDER AND DISORDER
Cells create ordered structures from less ordered
materials
 Organisms also replace ordered forms of matter and
energy with less ordered forms
 Energy flows into an ecosystem in the form of light
and exits in the form of heat

BIOLOGICAL ORDER AND DISORDER

The evolution of more complex organisms does not
violate the second law of thermodynamics

Entropy (disorder) may decrease in an organism, but the
universe’s total entropy increases

“Organisms are islands of low entropy in an increasingly
random universe.” (Campbell, p145)
FREE-ENERGY CHANGE, G
A living system’s free energy is energy that can do
work when temperature and pressure are uniform, as in
a living cell
 It can be thought of as a measure
of instability.


For example… on which platform
would you have the greatest ability
to do work? Which one would you
feel most stable?
EXERGONIC AND ENDERGONIC REACTIONS IN
METABOLISM

An exergonic reaction proceeds with a net release of
free energy and is “spontaneous”
Spontaneous
change

Spontaneous
change
An endergonic reaction absorbs free energy from its
surroundings and is nonspontaneous
Fig. 8-6
Reactants
Free energy
Amount of
energy
released
(∆G < 0)
Energy
Products
Progress of the reaction
(a) Exergonic reaction: energy released
Free energy
Products
Amount of
energy
required
(∆G > 0)
Energy
Reactants
Progress of the reaction
(b) Endergonic reaction: energy required
NOW…
ATP in energy coupling
 Energy of Activation
 Catalytic Cycle
 efficiency of enzymes

HOW DOES A CELL DO WORK?
A
cell does three main kinds of work:
Chemical ex) Building glycogen
 Transport ex) active transport across a cell membrane
 Mechanical ex) beating cilia in the trachea

 To
do work, cells manage energy resources by
energy coupling, the use of an exergonic
process to drive an endergonic one
 Most energy coupling in cells is mediated by
ATP – a molecule with a very high free energy
The bonds between the phosphate groups of ATP’s tail
can be broken by hydrolysis
 Energy is released from ATP when the terminal
phosphate bond is broken
 This release of energy comes from the chemical change to
a state of lower free energy, not from the phosphate
bonds themselves
Adenine

Phosphate groups
Ribose
Fig. 8-9
P
P
P
Adenosine triphosphate (ATP)
H2O
Pi
+
Inorganic phosphate
P
P
+
Adenosine diphosphate (ADP)
Energy

FYI: ATP drives endergonic reactions by
phosphorylation, transferring a phosphate group to some
other molecule, such as a reactant
Adenine
Phosphate groups
Ribose
THE REGENERATION OF ATP
ATP is a renewable resource that is regenerated by
addition of a phosphate group to ADP
 The rate of renewal is VERY fast!


10 millions ATP molecules are turned over every second in
every one of your cells… if this didn’t happen you would use
up your body weight in molecules in one day.
ATP + H2O
Energy from
catabolism (exergonic,
energy-releasing
processes)
ADP + P i
Energy for cellular
work (endergonic,
energy-consuming
processes)
ENZYMES


A catalyst is a chemical agent that speeds up a reaction
without being consumed by the reaction
An enzyme is a catalytic protein

Hydrolysis of sucrose by the enzyme sucrase is an example of
an enzyme-catalyzed reaction

Even though the reaction is “spontaneous”/exergonic/
releases free energy, it would happen WAY to slow (years)
without help from the enzyme due to its very high energy of
activation. With the enzyme, the reaction takes seconds.
Fig. 8-13
Sucrose (C12H22O11)
Sucrase
Glucose (C6H12O6)
Fructose (C6H12O6)
THE ACTIVATION ENERGY BARRIER



Every chemical reaction between molecules involves
bond breaking and bond forming
The initial energy needed to start a chemical reaction is
called the free energy of activation, or activation
energy (EA) (to contort the bonds)
Activation energy is often supplied in the form of heat
from the surroundings
Fig. 8-14
A
B
C
D
Transition state
A
B
C
D
EA
Reactants
A
B
∆G < O
C
D
Products
Progress of the reaction
HOW ENZYMES LOWER THE EA BARRIER

Enzymes catalyze reactions by lowering the EA barrier;
they do not affect the change in free energy (∆G)
Animation: How Enzymes Work
Fig. 8-15
Course of
reaction
without
enzyme
EA
without
enzyme
EA with
enzyme
is lower
Reactants
Course of
reaction
with enzyme
∆G is unaffected
by enzyme
Products
Progress of the reaction
SUBSTRATE SPECIFICITY OF ENZYMES
The reactant that an enzyme acts on is called the
enzyme’s substrate
 The enzyme binds to its substrate, forming an enzymesubstrate complex
 The active site is the region on the enzyme where the
substrate binds



Induced fit of a substrate brings chemical groups of the
active site into positions that enhance their ability to
catalyze the reaction
Most enzymes are capable of 1000 substrate actions per
second!
Fig. 8-16
Substrate
Active site
Enzyme
(a)
Enzyme-substrate
complex
(b)
CATALYSIS IN THE ENZYME’S ACTIVE SITE

In an enzymatic reaction, the substrate binds to the
active site of the enzyme.
Think of four mechanisms which allow the active site to
lower an EA barrier…
CATALYSIS IN THE ENZYME’S ACTIVE SITE

Four mechanisms which allow the active site to lower an
EA barrier:
Orienting substrates correctly – providing a place for
reactants to find each other
 Straining substrate bonds – contorting reactants towards
transition state through weak H and ionic interactions from
the R groups in the protein
 Providing a favorable microenvironment – ex) acidic
conditions via acidic R-groups
 Covalently bonding to the substrate – this covalent
bonding is temporary… it is released in subsequent reactions

Fig. 8-17
1 Substrates enter active site; enzyme
changes shape such that its active site
enfolds the substrates (induced fit).
2 Substrates held in
active site by weak
interactions, such as
hydrogen bonds and
ionic bonds.
Substrates
Enzyme-substrate
complex
6 Active
site is
available
for two new
substrate
molecules.
Enzyme
5 Products are
released.
4 Substrates are
converted to
products.
Products
3 Active site can lower EA
and speed up a reaction.
EFFECTS OF LOCAL CONDITIONS ON ENZYME
ACTIVITY

An enzyme’s activity can be affected by:

Substrate concentration: activity increases with increasing
substrate concentration until the saturation point is reached
(where all active sites are occupied)

General environmental factors, such as temperature and pH

Chemicals that specifically influence the enzyme
EFFECTS OF TEMPERATURE AND PH
Each enzyme has an optimal temperature in which it can
function
 Each enzyme has an optimal pH in which it can function

Fig. 8-18
Rate of reaction
Optimal temperature for
typical human enzyme
Optimal temperature for
enzyme of thermophilic
(heat-tolerant)
bacteria
40
60
80
Temperature (ºC)
(a) Optimal temperature for two enzymes
0
20
Optimal pH for pepsin
(stomach enzyme)
100
Optimal pH
for trypsin
Rate of reaction
(intestinal
enzyme)
4
5
pH
(b) Optimal pH for two enzymes
0
1
2
3
6
7
8
9
10
COFACTORS
Cofactors are nonprotein enzyme helpers
 Cofactors may be inorganic (such as a metal in ionic
form) or organic
 An organic cofactor is called a coenzyme
 Coenzymes include vitamins

ENZYME INHIBITORS
Competitive inhibitors bind to the active site of an
enzyme, competing with the substrate
 Noncompetitive inhibitors bind to another part of an
enzyme, causing the enzyme to change shape and
making the active site less effective


Examples of inhibitors include toxins, poisons,
pesticides, and antibiotics
Fig. 8-19
Substrate
Active site
Competitive
inhibitor
Enzyme
Noncompetitive inhibitor
(a) Normal binding
(b) Competitive inhibition
(c) Noncompetitive inhibition
REGULATION OF ENZYME ACTIVITY HELPS CONTROL
METABOLISM
Chemical chaos would result if a cell’s metabolic
pathways were not tightly regulated
 A cell does this by switching on or off the genes that
encode specific enzymes or by regulating the activity of
enzymes

ALLOSTERIC REGULATION OF ENZYMES
Allosteric regulation may either inhibit or stimulate
an enzyme’s activity
 Allosteric regulation occurs when a regulatory molecule
binds to a protein at one site and affects the protein’s
function at another site

ALLOSTERIC ACTIVATION AND INHIBITION
Most allosterically regulated enzymes are made from
polypeptide subunits
 Each enzyme has active and inactive forms
 The binding of an activator stabilizes the active form of
the enzyme
 The binding of an inhibitor stabilizes the inactive form of
the enzyme

Fig. 8-20
Active site
Allosteric enyzme
with four subunits (one of four)
Regulatory
site (one
of four)
Activator
Active form
Stabilized active form
Oscillation
NonInhibitor
functional Inactive form
active
site
Stabilized inactive
form
(a) Allosteric activators and inhibitors
Substrate
Inactive form
Stabilized active
form
(b) Cooperativity: another type of allosteric activation
Cooperativity is a form of allosteric regulation that can
amplify enzyme activity
 In cooperativity, binding by a substrate to one active site
stabilizes favorable conformational changes at all other
subunits

Fig. 8-20b
Substrate
Inactive form
Stabilized active
form
(b) Cooperativity: another type of allosteric activation
IDENTIFICATION OF ALLOSTERIC REGULATORS
Allosteric regulators are attractive drug candidates for
enzyme regulation
 Inhibition of proteolytic enzymes called caspases may
help management of inappropriate inflammatory
responses

FEEDBACK INHIBITION
In feedback inhibition, the end product of a metabolic
pathway shuts down the pathway
 Feedback inhibition prevents a cell from wasting
chemical resources by synthesizing more product than is
needed

Fig. 8-22
Initial substrate
(threonine)
Active site
available
Isoleucine
used up by
cell
Threonine
in active site
Enzyme 1
(threonine
deaminase)
Intermediate A
Feedback
inhibition
Isoleucine
binds to
allosteric
site
Enzyme 2
Active site of
enzyme 1 no
longer binds Intermediate B
threonine;
pathway is
Enzyme 3
switched off.
Intermediate C
Enzyme 4
Intermediate D
Enzyme 5
End product
(isoleucine)
SPECIFIC LOCALIZATION OF ENZYMES WITHIN THE
CELL
Structures within the cell help bring order to metabolic
pathways
 Some enzymes act as structural components of
membranes
 In eukaryotic cells, some enzymes reside in specific
organelles; for example, enzymes for cellular respiration
are located in mitochondria
