LECTURE PRESENTATIONS
For CAMPBELL BIOLOGY, NINTH EDITION
Jane B. Reece, Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minorsky, Robert B. Jackson
Chapter 8
An Introduction to Metabolism
Lectures by
Erin Barley
Kathleen Fitzpatrick
© 2011 Pearson Education, Inc.
Overview: The Energy of Life
• The living cell is a miniature chemical factory where
thousands of reactions occur
• The cell extracts energy and applies energy to perform
work
– e.g. plants can extract the energy from sunlight and use it
make sugars – energy in sugars can be extracted by other
organisms and used to perform work
• Some organisms even convert energy to light, as in
bioluminescence
An organism’s metabolism transforms matter and energy,
subject to the laws of thermodynamics
Metabolism: the Chemistry of Life
• Metabolism is the totality of an organism’s chemical reactions
– an emergent property of life
– arises from orderly interactions between molecules within the cell
• manages the material and energy resources of the cell
• organized into a complex “roadmap” of metabolic reactions
– reactions are organized as metabolic pathways
• metabolic pathway begins with a specific molecule and ends with a product
– each step is catalyzed by a specific enzyme
Enzyme 2
Enzyme 1
A
Starting
molecule
D
C
B
Reaction 1
Enzyme 3
Reaction 2
Reaction 3
Product
Metabolism: Catabolism and Anabolism
• Catabolic pathways release energy by breaking down complex
molecules into simpler compounds
– “downhill” component of metabolism
• e.g. cellular respiration = the breakdown of glucose in the presence
of oxygen
• the energy stored in the organic molecules are now available to
perform the work of the cell
Metabolism: Catabolism and Anabolism
• Anabolic pathways consume energy to build complex molecules
from simpler ones
– “uphill” component of metabolism
•
•
•
•
also referred to a biosynthesis or biosynthetic pathways
e.g. synthesis of protein from amino acids
e.g. gluconeogenesis – the synthesis of glucose de novo
energy of catabolism can be stored and used to power biosynthesis
• how the organism manages their energy resources = Bioenergetics
– i.e. how energy flows through organisms
Forms of Energy
• Energy is the capacity to cause change
– ability to rearrange a collection of matter
• exists in various forms
• some of which can perform work
Animation: Energy Concepts
• Kinetic energy = energy associated with
motion
– e.g. contraction of leg muscles powering a
bicycle
A diver has more potential
energy on the platform
than in the water.
Diving converts
potential energy to
kinetic energy.
• Heat (thermal energy) = kinetic energy
associated with random movement of
atoms or molecules
• Potential energy = energy that matter
possesses because of its location or
structure
– energy that is not kinetic is potential
– molecules possess potential energy because of
the arrangement of electrons in bonds
• Chemical energy = potential energy
available for release in a chemical
reaction
– in catabolism – bonds are broken and other
formed
– energy is released as thermal energy
– lower chemical energy products results
Climbing up converts the kinetic
energy of muscle movement
to potential energy.
A diver has less potential
energy in the water
than on the platform.
• energy can be converted from one form to
another BUT CANNOT BE CREATED OR
DESTROYED
• how is energy converted from one form to
another?
• study of energy transformations in a
collection of matter = THERMODYNAMICS
(woohoo!)
The Laws of Energy Transformation
• system = used to denote matter under study
• an isolated system = system isolated from its
surroundings
– e.g. liquid in a thermos
– also known as a closed system
• open system = energy and matter can be transferred
between the system and its surroundings
– absorption of light or chemical energy and the release of
heat and metabolic waste products to the surroundings
• Organisms are open systems
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
• The first law is also called the principle of conservation of
energy
• e.g. brown bear converts the chemical energy of the fish to the
kinetic energy of running
Heat
Chemical
energy
(a) First law of thermodynamics
(b) Second law of thermodynamics
The Second Law of Thermodynamics
• during every energy transfer or transformation, some energy is not
available to do work
– this energy is often lost as heat - lost to the surroundings
– all living cells unavoidably convert organized forms of energy to less
organized forms – i.e. heat
– a system can put this heat to work if there is a temperature gradient
– BUT - in organisms where temperatures are constant – the purpose of this
heat is to warm the organism
• the logical consequence of this loss of usable energy = the universe
becomes less ordered
• disorder can be measured = entropy
• according to the second law of thermodynamics
– Every energy transfer or transformation increases the entropy
(disorder) of the universe
– “you can’t put the toothpaste back in the tube”
• understanding entropy helps in understanding why
certain reactions and processes occur without any
input of energy
• spontaneous processes - occur without energy input
–
–
–
–
spontaneous does NOT mean fast
these processes can happen quickly or slowly
but they do not require energy to proceed
so spontaneous really means energetically favorable
• for a process to occur spontaneously (without
energy)input - it must increase the entropy of the
universe
Biological Order and Disorder
• living systems ultimatelyincrease the entropy of their surroundings
• it is true that cells create ordered structures from less ordered materials
• BUT - organisms also replace ordered forms of matter and energy with less
ordered forms
• so while an organism may form by increasing its order (decreasing entropy)–
the ultimate effect on the universe is a decrease in order (increasing entropy)
• the evolution of more complex organisms does not violate the second law of
thermodynamics
– as long as the overall entropy of the universe increases
The free-energy change of a reaction tells us
whether or not the reaction occurs
spontaneously
• Biologists want to know which reactions occur
spontaneously and which require input of energy
• need to determine energy changes that occur in
chemical reactions
Free-Energy Change, G
• A living system’s free energy (G) = energy that can do work when
temperature and pressure of a system are uniform – e.g. within a cell
• The change in free energy (∆G) during a process is
related to the change in enthalpy, or change in total
energy (∆H), change in entropy (∆S), and temperature
in Kelvin (T)
∆G = ∆H – T∆S
G & G
• another way of looking at free energy change ∆G= difference in the
free energy of a system’s final state minus the free energy of the
system’s initial state
∆G = G final state – G initial state
• when a process occurs spontaneously – ∆G is negative
– ∆G is negative when the process involves a loss of free energy as the initial
state of the system becomes the final state of the system
– the system in its final state is more stable and less likely to change than the
system in its initial state
• so free energy is a measure of a system’s instability
• in terms of biochemistry:
– the higher the G of a compound – the more unstable it is
– more stable compounds have a lower G
– e.g. glycolysis – glucose is more unstable and likely to breakdown than its
products – higher G than the products it produces
Free Energy, Stability, and Equilibrium
• Free energy = a measure of a
system’s instability
– its tendency to change to a more
stable state
• during a spontaneous change free energy decreases and the
stability of a system increases
• equilibrium = a state of
maximum stability
• More free energy (higher G)
• Less stable
• Greater work capacity
In a spontaneous change
• The free energy of the system
decreases (G  0)
• The system becomes more
stable
• The released free energy can
be harnessed to do work
• Less free energy (lower G)
• More stable
• Less work capacity
• as a reaction proceeds toward equilibrium – the free energy of
the reactants and products decreases
• G is at its lowest possible value in that system
• equilibrium is like a “free-energy valley”
– a process is spontaneous and can perform work only when it
is moving toward equilibrium – going “downhill”
– to “climb” out of this valley will have a positive ∆G and will
not be spontaneous
– so systems never move spontaneously away from
equilibrium
Free Energy and Metabolism
(a) Exergonic reaction: energy released, spontaneous
Reactants
Amount of
energy
released
(G  0)
Free energy
• the concept of free energy can be
applied to the chemistry of life’s
processes
• based on their ∆G values – two kinds
of chemical reactions
• 1. exergonic reaction - proceeds with
a net release of free energy and is
spontaneous
Energy
Products
Progress of the reaction
(b) Endergonic reaction: energy required, nonspontaneous
– negative ∆G
– positive ∆G
Free energy
• 2. endergonic reaction - absorbs free
energy from its surroundings and is
non-spontaneous
Products
Amount of
energy
required
(G  0)
Energy
Reactants
Progress of the reaction
Exergonic reactions
• e.g. cellular respiration
• overall – the ∆G = -686 kcal/mol
• exergonic, spontaneous reaction
(a) Exergonic reaction: energy released, spontaneous
Reactants
Free energy
– for each mole of glucose, 686 kcal (2,870
kJ) of energy are made available for work
– the products store 686kcal less energy per
mole than the reactants
– 686kcal less energy stored in their
chemical bonds
Amount of
energy
released
(G  0)
Energy
Products
Progress of the reaction
Initial state
Final state
-less stable
-more stable
-higher G
-lower G
∆G = G final state – G initial state
Endergonic reactions
– chloroplasts convert light energy into
chemical energy
– the chemical energy is then used to make
sugars – exergonic process
– PHOTOSYNTHESIS
(b) Endergonic reaction: energy required, nonspontaneous
Products
Free energy
• absorbs free energy from the
surroundings
• reaction stores free energy in the
chemical bonds of the products
• ∆G is positive – is the amount of
energy required to drive the reaction
• so technically – to reverse cellular
respiration and build sugars from CO2
and water = need to put in 686kcal of
energy per mole sugar you want to
create
• how do plants make sugars?
• get the required energy from the
sunlight
Amount of
energy
required
(G  0)
Energy
Reactants
Progress of the reaction
Equilibrium and Metabolism
• reactions in a closed/isolated
system eventually reach
equilibrium and then do no work
• BUT: cells are not in equilibrium
– they are open systems experiencing
a constant flow of materials
• in organisms - metabolism is
never at equilibrium
– flow of materials in and out of the
cell prevents reaching equilibrium
– metabolism in a cell is more like a
multi-step open system
G  0
G  0
(a) An isolated hydroelectric system
(b) An open hydroelectric system
G  0
G  0
G  0
G  0
(c) A multistep open hydroelectric system
ATP powers cellular work by coupling
exergonic reactions to endergonic reactions
• a cell does three main kinds of work
– Chemical – the “pushing” of endergonic reactions
• e.g. building of a polymer from monomers
– Transport – the pumping of substances against a
concentration gradient
– Mechanical – the beating of cilia, contraction of
muscle cells, movement of chromosomes in mitosis
• to do this work - cells use energy coupling
– usign an exergonic process to drive an endergonic one
• most energy coupling in cells is mediated by ATP
– the exergonic process makes ATP
– the endergonic process uses it
The Structure and Hydrolysis of ATP
Adenine
• ATP = adenosine triphosphate
• ATP - composed of ribose (a sugar),
adenine (a nitrogenous base), and three
phosphate groups
• the phosphate groups are held together
by high-energy phosphate bonds
– don’t really store a lot of energy
themselves
Phosphate groups
Ribose
• called high energy bonds - release of
energy comes from the chemical change
to a state of lower free energy
– not from the phosphate bonds
themselves
– ATP is less stable and has a higher G vs.
ADP and Pi
• the bonds can be broken through
hydrolysis
• breaking of the phosphate bond
provides energy to power endergonic
reactions
Adenosine triphosphate (ATP)
Inorganic
phosphate
Energy
Adenosine diphosphate (ADP)
Hydrolysis of ATP – ATP + H20  ADP + Pi (-7.3 kcal/mol)
How the Hydrolysis of ATP Performs Work
• the energy from the exergonic reaction of ATP hydrolysis can be
used to drive an endergonic reaction
• overall - the coupled reactions are exergonic
Glutamic acid conversion to glutamine
NH3
Glu
Glutamic
acid
Glu
NH2
Glutamine
Ammonia
Glutamic conversion coupled to ATP hydrolysis
NH3
P
1
Glu
GGlu = +3.4 kcal/mol
Glu
ATP
ADP
2
Phosphorylated
intermediate
Glutamic
acid
Glu
NH2
Glutamine
GGlu = +3.4 kcal/mol
Glu
NH3
GGlu = +3.4 kcal/mol
Free-energy
change for + GATP = 7.3 kcal/mol
coupled
Net G = 3.9 kcal/mol
reaction
ATP
Glu NH2
GATP = 7.3 kcal/mol
ADP
Pi
ADP
Pi
•
ATP drives endergonic reactions by
phosphorylation
– transferring a phosphate group to some
other molecule
•
the recipient molecule is now called a
phosphorylated intermediate
– this intermediate is less stable/more
reactive than the unphosphorylated
counterpart
– so the phosphorylated glutamine is less
stable & more likely to assume a more
stable final state
Transport protein
ATP
Pi
Solute transported
(a) Transport work: ATP phosphorylates transport proteins.
Cytoskeletal track
Vesicle
phosphorylation also couples transport in
the cell
– phosphorylation leads to a change in
shape in a pump (more stable
conformation)
•
ADP P i
P
• NH3 replaces the Pi group
• the resulting glutamine is more stable
(lower G)
•
Solute
phosphorylation drives mechanical work
in a cell
– ATP is bound to a motor protein – shape
change, motor protein binds cytoskeleton
– ATP hydrolysed & the ADP and Pi are
released – more shape changes and the
motor protein “walks”
ATP
ATP
ADP P i
Motor protein Protein and
vesicle moved
(b) Mechanical work: ATP binds noncovalently to motor
proteins and then is hydrolyzed.
The Regeneration of ATP
• ATP is a renewable resource that is regenerated by addition of a phosphate group
to adenosine diphosphate (ADP)
• endergonic reaction – not spontaneous
• energy must be spent
• free energy to phosphorylate ADP comes from catabolic reactions in the cell
• shuttling of inorganic phosphate and energy = ATP cycle
• ATP cycle is a revolving door through which energy passes during its transfer from
catabolic to anabolic pathways
ATP
Energy from
catabolism (exergonic,
energy-releasing
processes)
ADP
H2O
Pi
Energy for cellular
work (endergonic,
energy-consuming
processes)
Enzymes speed up metabolic reactions by
lowering energy barriers
•
thermodynamics tell us about what and will not happen chemically BUT tell us nothing
about the rate
– spontaneous does NOT equal fast!!!!
– hydrolysis of sugar is exergonic – but could take years!
– need some kind of catalyst to speed things up
•
•
•
catalyst = chemical agent that speeds up a reaction without being consumed by the reaction
enzyme = catalytic protein
hydrolysis of sucrose by the enzyme sucrase is an example of an enzyme-catalyzed reaction
Sucrase
Sucrose
(C12H22O11)
Glucose
(C6H12O6)
Fructose
(C6H12O6)
The Activation Energy Barrier
the chemical reactions of a cell’s
metabolism involve both bond breaking
and bond forming
– changing one molecule to another
involves transforming the starting
molecule into a highly unstable state
before the reaction can proceed
– the bonds absorb energy from the
surroundings to achieve this unstable
state
– when the newer bonds form – the
product is more stable (lower G) and the
excess energy released as heat
•
•
the initial energy needed to do create
these unstable bonds (i.e. to start a
chemical reaction) = free energy of
activation or activation energy (EA)
activation energy is often supplied in the
form of thermal energy that the reactant
molecules absorb from their
surroundings and use to transform into
the unstable transition state
A
B
C
D
Transition state
Free energy
•
A
B
C
D
EA
Reactants
A
B
G  O
C
D
Products
Progress of the reaction
How Enzymes Lower the EA Barrier
Course of
reaction
without
enzyme
• enzymes catalyze reactions by lowering
the EA barrier
• enzymes do not affect the change in free
energy (∆G)
– instead, they hasten reactions that would
occur eventually
EA with
enzyme
is lower
Reactants
Free energy
– allow the reactants to easily absorb
enough energy to reach their unstable
transition state
– so they can reach this state even at
moderate temperatures and faster too!
EA
without
enzyme
G is unaffected
by enzyme
Course of
reaction
with enzyme
Products
Progress of the reaction
Animation: How Enzymes Work
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 enzyme-substrate complex
– the active site is the region on the enzyme where the substrate binds
– 3D shape of the active site is unique and fits with the 3d shape of the substrate
• enzymes are not stiff structures
–
–
–
–
the are thought to “dance” between subtly different shapes
each change in shape is like a different “pose”
the shape that best fits the substrate isn’t always the one with the lower G
but one of these “poses” will be able to bind the substrate
• the active site is also not stiff
– binding of the substrate can change the active site shape as chemical groups
interact between substrate and active site – mostly Hydrogen and ionic bonds
– this interaction makes the active site fit the substrate better  Induced fit theory:
Substrate
Active site
Enzyme
(a)
(b)
Enzyme-substrate
complex
Substrates enter active site
1 Induced fit at active site due
to S-E interaction
2 Substrates are held
in active site by weak
interactions.
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
Active site can
lower EA and speed
3
up a reaction
several ways
1.orienting the substrates
(multi-substrate reactions)
2.stressing the substrate
bonds toward their transition
state form – making it easier
to reach
3. providing a good
microenvironment for the
reaction to take place
e.g. pocket of low
pH for a reaction
4. participating directly in
the reaction by being part
of the transition state
Catalysis in the Enzyme’s Active Site
• SO the active site can lower an EA barrier by
–
–
–
–
Orienting substrates correctly
Straining substrate bonds
Providing a favorable microenvironment
Covalently bonding to the substrate
Effects of Local Conditions on Enzyme Activity
• an enzyme’s activity can be affected by
– general environmental factors - temperature and
pH
– chemicals that specifically influence the enzyme
Effects of Temperature and pH
– temperature can influence how many
substrates collide with the active site of
an enzyme
– too high of a temp and the bonds that
form and stabilize the active site are lost
– even higher and the entire protein loses
its 3D shape - denaturation
Rate of reaction
• each enzyme has an optimal
temperature in which it can function
Optimal temperature for
Optimal temperature for
typical human enzyme (37°C)enzyme of thermophilic
(heat-tolerant)
bacteria (77°C)
0
• optimal conditions favor the most active
shape for the enzyme’s active site
40
60
80
Temperature (°C)
120
100
(a) Optimal temperature for two enzymes
Optimal pH for pepsin
(stomach
enzyme)
Optimal pH for trypsin
(intestinal
enzyme)
Rate of reaction
• each enzyme has an optimal pH in which
it can function
– pH can affect the 3D shape of an active
site
– most operate a neutral pHs
– except for pepsin and lysosomal enzymes
20
0
1
2
3
4
5
pH
(b) Optimal pH for two enzymes
6
7
8
9
10
Cofactors
• Cofactors are non-protein enzyme helpers
– many enzymes require these co-factors to work optimally or work
at all
• function in many ways – but the all perform a critical
chemical function
• may be inorganic - such as a metal in ionic form
– e.g. iron, zinc and copper the most common in cells
• may also be organic = coenzyme
– include vitamins
Enzyme Inhibitors
• in order to study enzyme function – researchers can use agents that
inhibit their function
• two kinds of enzyme inhibitor:
– 1. Competitive inhibitors - bind to the active site of an enzyme
• compete with the substrate
– 2. Noncompetitive inhibitors - bind to another part of an enzyme
• causing the enzyme to change shape and making the active site less effective
• examples include toxins, poisons, pesticides, and antibiotics
(a) Normal binding
(b) Competitive inhibition
(c) Noncompetitive
inhibition
Substrate
Active
site
Competitive
inhibitor
Enzyme
Noncompetitive
inhibitor
The Evolution of Enzymes
•
•
Enzymes are proteins encoded by genes
THEORY: mutations in genes lead to changes in amino acid composition of an
enzyme
– Altered amino acids in enzymes may alter their substrate specificity
– Under new environmental conditions a novel form of an enzyme might be favored
Two changed amino acids were
found near the active site.
•
•
•
Beta-galactosidase enzyme
used in a lab model that
mimicked evolution in E.coli
introduced random mutations
and then tested the enzyme
ability
looked for the best enzymes
over several rounds of
mutations
Two changed amino acids
were found in the active site.
Active site
Two changed amino acids
were found on the surface.
Regulation of enzyme activity helps control
metabolism
• chemical chaos would result if all of a cell’s metabolic pathways
were running at the same time
– i.e. were not tightly regulated – temporally and spatially
• a cell does this by
– 1. switching on or off the genes that encode specific enzymes
– 2. by regulating the activity of enzymes once they are made
• Allosteric regulation of enzymes
• each enzyme has active and inactive forms
• allosteric regulation may either inhibit or stimulate an enzyme’s
activity by switching the enzyme between distinct 3D forms
• occurs when a regulatory molecule binds to a protein at one site
– this affects the protein’s function at another site
Allosteric Regulation of Enzymes: Activators and Inhibitors
(a) Allosteric activators and inhibitors
Allosteric enzyme
with four subunits
Active site
(one of four)
Regulatory
site (one
of four)
• Allosteric - binding of a molecule at
one site on the enzyme affects the
activity of another site on the enzyme
• the binding of an activator stabilizes
the active form of the enzyme
Activator
Stabilized active form
Active form
– from active to stabilized active form
• the binding of an inhibitor stabilizes
the inactive form of the enzyme
Oscillation
– from inactive to stabilized inactive
form
Nonfunctional
active site
Inactive form
Inhibitor
Stabilized inactive
form
• most allosterically regulated enzymes
are made from polypeptide subunits
(complex of proteins)
– so binding one subunit with a
regulator can affect the others
Allosteric Regulation of Enzymes: Cooperativity
(b) Cooperativity: another type of allosteric activation
• Cooperativity - form of
allosteric regulation that can
amplify enzyme activity
• a substrate molecule primes an
enzyme to act on other
substrate molecules more
readily
• cooperativity is allosteric
because binding by a substrate
to one active site affects
catalysis in a different site
Substrate
Inactive form
Stabilized active
form
Identification of Allosteric Regulators
EXPERIMENT
Caspase 1
• allosteric regulators are attractive
drug candidates for enzyme
regulation because of their
specificity
• inhibition of proteolytic enzymes
called caspases may help
management of inappropriate
inflammatory responses
• experiments done to identify
allosteric inhibitors (or activators) of
caspases
• these activators and inhibitors can
be used study caspase function in
cells
Active
site
Substrate
SH
Active form can
bind substrate
SH
Known active form
SH Allosteric
binding site
Allosteric
Known inactive form
inhibitor
Hypothesis: allosteric
inhibitor locks enzyme
in inactive form
RESULTS
Caspase 1
Inhibitor
Active form
Allosterically
inhibited form
Inactive form
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
Active site
available
Isoleucine
used up by
cell
Active site of
Feedback
enzyme 1 is
inhibition
no longer able
to catalyze the
conversion
of threonine to
intermediate A;
pathway is
switched off. Isoleucine
binds to
allosteric
site.
Initial
substrate
(threonine)
Threonine
in active site
Enzyme 1
(threonine
deaminase)
Intermediate A
Enzyme 2
Intermediate B
Enzyme 3
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