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Chapter 8:
An Introduction
to Metabolism
Metabolism
• total of an organism’s chemical reactions
– It manages the material and energy resources of the cell.
• Two types of Metabolic Pathways
– Catabolic Pathways –
• breakdown reactions that release stored energy for cellular work;
Ex. cellular respiration
– Anabolic Pathways
• building of complex molecules from simpler ones; consumes energy;
Ex. photosynthesis, amino acids to proteins
• Energy released from the catabolic pathways can be
stored and later used to drive anabolic pathways
• Reactions are linked in metabolic pathways
Enzyme 1 Enzyme 2 Enzyme 3
A B C D
Reaction 1 Reaction 2 Reaction 3
Starting Product
molecule
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Forms of energy:
• Energy = capacity to do work or cause
change
• 1) Kinetic energy = energy of motion
– Ex. water through a dam;
– Heat or thermal energy = KE associated
i d
with random motion of atoms/molecules
• 2) Potential energy = stored energy
– Ex. water behind a dam
– Chemical energy = energy stored in
chemical bonds
• Cellular respiration and other catabolic
pathways
th transform
t f the
th (chemical)
( h i l) energy
in food to kinetic energy
• The energy in food was derived from Light
energy by green plants during
photosynthesis.
The Laws of Energy Transformations:
• Thermodynamics = study of energy transformations that
occur in a collection of matter.
• Organisms are open systems
First Law ((Principle
p off Conservation off
Energy) states:
à energy cannot be created or destroyed, but can
be transferred or transformed from one form to
Chemical another.
energy
à i.e. Amount of energy in the universe is
constant.
(a) First law of thermodynamics
Every
E energy transfer
f or Heat
transformation increases the Entropy
(degree of disorder) of the universe. CO2
+
H2O
In most energy transformations, a large
amount of energy is released as heat
(the most random form of energy).
(b) Second law of thermodynamics
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• Spontaneous processes occur without energy input; they
can happen quickly or slowly
• For a process to occur without energy input, it must
increase the entropy of the universe
• Cells create ordered structures from less ordered
materials;
t i l but
b t replace
l ordered
d d forms
f off matter
tt andd energy
with less ordered forms
• Ex.: Food is broken down to CO2 + H2O + energy
• Energy flows into an ecosystem in form of light and exits
in the form of heat.
1st and 2nd laws put together:
The quantity of energy in the
universe is constant, but its
quality is not.
Free Energy Change (ΔG) of a reaction
• tells us whether or not the reaction occurs spontaneously
• Free energy (G) = the portion of a system's energy
available to perform work when the temperature and
pressure are uniform throughout the system (as in a living
cell).
ll)
• Free Energy = G = H - TS
– {where H =total energy (enthalpy); S = entropy;
& T = absolute temperature (K = oC+273)}
• Change in free energy = ΔG = Gfinal state - Gstarting state
• For a SPONTANEOUS reaction to occur, ΔG must be less
than 0 (i.e. negative) since
• If ΔG is zero or greater (i.e. positive), the process is
NONSPONTANEOUS.
NONSPONTANEOUS
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Free Energy, Stability and Equilibrium:
• G is a measure of a system’s instability.
– Higher G means higher instability;
– Lower G means more stability
• Equilibrium
E ilib i = state
t t off maximum
i stability.
t bilit
• ΔG = Gfinal state - Gstarting state
• At equilibrium, ΔG = 0
– Therefore,, a system
y at equilibrium
q performs no work.
p
• ΔG decreases as reaction proceeds towards
equilibrium but increases when a reaction is pushed
away from equilibrium.
Free energy, work capacity & spontaneous change
• In any spontaneous process, the free energy of a system decreases
• A system is spontaneous and can perform work when sliding
towards equilibrium.
• Movement away from equilibrium is nonspontaneous and will
need energy input to proceed
• More free energy (higher G)
• Less stable
• Greater work capacity
In a spontaneous change
• The free
f energy off 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
(a) Gravitational motion (b) Diffusion (c) Chemical reaction
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Free Energy and Metabolism
• An Exergonic Reaction proceeds with a net release of free energy
– ΔG < 0 (negative); occurs spontaneously
– Ex. Cellular Respiration: C6H12O6 6CO2 + 6H2O; ΔG = -686 kcal/mol
• An Endergonic Reaction absorbs energy from its surroundings
– ΔG > 0 (p
(positive);
); are nonspontaneous
p
– Ex. Photosynthesis: 6CO2 + 6H2O C6H12O6; ΔG = +686 kcal/mol
• Magnitude of ΔG = quantity of energy required to drive the reaction
Reactants
Products
Amount of
energy
released Amount of
energy
Free energy
(∆G < 0)
Free energy
required
Energy Energy
Products (∆G > 0)
Reactants
Progress of the reaction
Progress of the reaction
(a) Exergonic reaction: energy released
(b) Endergonic reaction: energy required
Equilibrium and Metabolism
• For a living cell, constant flow of materials in and out maintains
lack of equilibrium, as the metabolic pathways cannot reach
equilibrium.
• To sustain the ‘lack of equilibrium’ the product of one reaction
b
becomes the
h reactant for
f the
h next step in
i the
h pathway.
h
∆G < 0 ∆G = 0 In a closed system,, energy
flow stops when reactions
reach a static equilibrium.
equilibrium.
(a) An isolated hydroelectric system
i.e. ΔG = 0; ex. dead cell
In an open system, ,
In an open system ∆G < 0
∆G < 0 ∆G < 0
incoming energy ∆G < 0
drives continuous
reactions: dynamic
reactions: dynamic
equilibrium
Open hydroelectric system A multistep open hydroelectric system
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Energy Coupling: Cells use energy from exergonic reactions
to power endergonic reactions.
Coupling requires and energy transfer molecule
molecule.
Adenine
The most common one is Adenosine
Triphosphate (ATP), which has 2 high-energy
phosphate bonds.
Phosphate groups
Ribose
Hydrolysis of ATP to release the tail Phosphate group in an exergonic reaction
Under standard conditions,
– ATP + H2O ADP + P; ΔG = -7.3 kcal/mol or -31kJ/mol
However, in the cell ΔG ~ -13kcal/mol
P P P
ATP is recycled ATP + H2O
in the cell Adenosine triphosphate (ATP)
Ribose
HO 2
Inorganic
Energy for cellular phosphate
Energy from catabolism
(exergonic, work (endergonic, Pi + P P + Energy
energy-consuming
ADP + Pi
energy-releasing
processes) processes) Adenosine diphosphate (ADP)
How ATP performs cellular work
( - by coupling exergonic to endergonic reactions)
NH2
1. Chemical Work: NH3 ∆G = +3.4 kcal/mo
Glu
+ Glu
Ex. Synthesis of glutamine
Glutamic acid Ammonia Glutamine
(an endergonic process) is
(a) Endergonic reaction
coupled to ATP hydrolysis 1
ATP phosphorylates P
by phosphorylating glutamic acid, + ATP + ADP
making the amino Glu Glu
glutamic acid, making it acid less stable.
NH2
2
more reactive ((less stable)) Ammonia displaces P NH3 + Pi
the phosphate group,
than the original molecule. forming glutamine. Glu + Glu
(b) Coupled with ATP hydrolysis, an exergonic reaction
(c) Overall free-energy change
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3 kinds of Cellular work:
• 2. Transport work - Membrane protein
across membranes
against the direction
off spontaneous
P Pi
movement. Solute transported
Solute
(a) Transport work: ATP phosphorylates
• 3. Mechanical work transport proteins ADP
ATP +
– Ex. Pi
Vesicle Cytoskeletal track
– beating of cilia,
– muscle cell
contraction, ATP
– movement of
chromosomes Motor protein Protein moved
during cell division (b) Mechanical work: ATP binds noncovalently to motor
proteins, then is hydrolyzed
ENZYMES speed up metabolic reactions by lowering energy barriers:
• A spontaneous chemical reaction is very slow.
• A catalyst is a chemical agent that increases the
rate of a reaction but remains unchanged at the end
of the reaction.
Biological catalysts
à Include:
à Enzyme = catalytic protein;
à Ribozyme = catalytic RNA
Sucrose ((C12H22O11)
Most
M enzyme names end d iin ~ase
Hydrolysis of Sucrose is Sucrase
Exergonic
spontaneous,
but s l o w . . .
Glucose (C6H12O6) Fructose (C6H12O6)
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The Activation Energy (EA) Barrier:
• Activation Energy
– the energy required to break bonds in the reactant molecules
– Or, energy required to push reactants over an energy barrier or hill.
• At the Transition State, the reactants are in a highly unstable
condition.
condition
A B
This reaction would Unstable, bonds
ready to break
C D
occur spontaneously, Transition state
but very slowly
Adding heat would A B EA
speed up ALL cellular C D
reaction Reactants
Relatively A B
Cells use enzymes to stable ∆G < O
lower EA and speed up C D
specific reactions Products
Progress of the reaction
Effect of an Enzyme on Activation energy
An enzyme cannot change the
Course of ΔG of a reaction or make an
reaction endergonic reaction exergonic.
without EA
enzyme without
enzyme
e y e EA with
enzyme
is lower
Reactants
Course of
∆G is unaffected
reaction
by enzyme
with enzyme
Products
Progress of the reaction
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Substrate Specificity of Enzymes:
• The Substrate (S) of an enzyme is the reactant
the enzyme acts on.
• An Enzyme acts by binding to its specific
Substrate.
– The specificity is determined by
• the shape of the 3-dimensional folded structure of the
enzyme (a protein) and
• the shape of the substrate.
Catalysis in the Enzyme’s Active Site:
1 Substrates enter active site; enzyme
changes shape such that its active site 2 Substrates held in
enfolds the substrates (induced fit). active site by weak
interactions, such as
hydrogen bonds and
ionic bonds.
Substrates
Enzyme-substrate
complex 3 Active site can
lower EA and speed
up a reaction.
6
Active
site is
available Active site = restricted
for two new region that binds the
region that binds the
b t t
substrate
molecules. substrate
Enzyme
5 Products are 4 Substrates are
released. converted to
products.
Enzyme Products Enzyme-substrate complex
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Catalysis in the Enzyme’s Active Site:
• The process is very fast,
– ~ 1000S/E as enzyme is recycled many times over.
• Most
M t metabolic
t b li reactions
ti are reversible
ibl
– an enzyme can catalyze both the forward and backward
reactions depending on which direction has a negative ΔG.
• The rate of catalysis is a function of
– the initial concentration of substrate upp to when the
enzyme becomes saturated.
– At this point, rate can only be increased by adding more
enzyme.
Effects of Local Conditions on Enzyme activity:
• 1. Temperature (T):
– Rate increases as T is increased up to the Optimal Temperature.
– Beyond that point, rate drops drastically as the enzyme active
conformation is denatured. Each enzyme has its optimal T.
– For most Human enzymes, it is between 35-40°C (body T= 37°C)
– Thermophilic bacteria live in hot springs and have optimal T of
70°C or higher.
Optimal temperature for Optimal temperature for
typical human enzyme enzyme of thermophilic
Optimal temperature for Optimal temperature for
(heat-tolerant)
of reaction
typical human enzyme enzyme of thermophilic
bacteria
(heat-tolerant)
of reaction
bacteria
RateRate
40 0 6020 80 100
Temperature (ºC)
0 20 40 60 80 100
(a) Optimal temperature for two enzymes
Temperature (ºC)
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2. pH:
Optimal pH for pepsin Optimal pH
• Each enzyme has its (stomach enzyme) for trypsin
(intestinal
Optimal pH.
Rate of reaction
enzyme)
• Most fall in the
range of pH 6-8, but
there are exceptions.
– Ex. pepsin - optimal 0 4
1 52 3 6 7 8 9 10
pH
pH 2 (functions in (b) Optimal pH for two enzymes
acidic stomach).
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3. Cofactors
Non-protein helpers;
à Inorganic cofactors include ions of zinc, iron, copper etc.
à Coenzymes are organic cofactors.
Ex. most vitamins
4. Enzyme inhibitors
• chemicals that selectively inhibit the action of specific enzymes
– Irreversible inhibitors attach by covalent bonds. Ex. toxins and poisons
– Reversible inhibitors attach by weak bonds or interactions.
• Competitive Inhibitors are reversible inhibitors that resemble the
normal Substrate and compete for the active site.
site
• Noncompetitive Inhibitors bind to another part of the enzyme causing a
change in conformation so the active site no longer fits S.
– Ex. antibiotics function by inhibiting key enzymes in bacteria.
Substrate
Active site
Competitive
inhibitor
Enzyme
Noncompetitive inhibitor
(a) Normal binding (b) Competitive inhibition (c) Noncompetitive inhibition
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Regulation of enzyme activity helps
Control Metabolism
• A cell regulates its metabolic pathways
– either by switching genes for specific enzymes on and off,
– or by regulating the activity of already made enzymes.
Allosteric Regulation Allosteric enzyme Active site Allosteric activator
with four subunits (one of four) stabilizes active form
• a protein’s function at
one site is affected by
the binding of a
regulatory molecule to a Regulatory
different site site (one
Activator
of four))
• Allosteric
All i regulators
l Active form Stabilized active form
may inhibit or
stimulate the enzyme Oscillation
activity.
Allosteric inhibitor
stabilizes active form
• Such enzymes are
usually multisubunit
with an active site on
each unit.
• Cells control enzyme
activity by controlling Non- Inhibitor
functional Inactive form Stabilized inactive
concentrations of active form
site
activator and inhibitor (a) Allosteric activators and inhibitors
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Cooperativity: - a type of allosteric activation.
• The Substrate is the Activator
• Cooperativity amplifies enzyme response to
substrate.
bt t
– Ex. hemoglobin with 4 subunits, binding of O2 on
one activates the other subunits
Substrate
Inactive form Stabilized active form
(b) Cooperativity: another type of allosteric activation
Initial substrate
Feedback Inhibition Active site
(threonine)
available
Threonine
in active site
• end product of a Enzyme 1
metabolic pathway acts Isoleucine
(threonine
deaminase)
as an inhibitor of an used up by
cell
early enzyme in the Intermediate A
Feedback
pathway, thus inhibition Active site of
Enzyme 2
enzyme 1 no
switching off the longer binds Intermediate B
threonine;
pathway pathway is
switched off.
Enzyme 3
Intermediate C
• It prevents the cell Isoleucine
binds to Enzyme 4
from wasting chemical allosteric
site
resources to produce a Intermediate D
product that is not Enzyme 5
needed.
End product
(isoleucine)
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Specific Localization of enzymes within the cell:
• Some enzymes and Mitochondria
enzyme complexes
h
have fi
fixedd locations
l ti
within the cell.
– Some are structural
components of
membranes,
– others are in solution
within organelles. Ex.: Enzymes that catalyze
the reactions of cellular
respiration occur only in
the mitochondria
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