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CHAPTER 3
Bioenergetics, Enzymes, and
Metabolism
3.1 Bioenergetics
• The study of the various types of energy
transformations that occur in living
organisms.
The Laws of Thermodynamics and
the Concept of Entropy
• Energy – capacity to do work, or the
capacity to change or move something.
• Thermodynamics – the study of the
changes in energy that accompany events
in the universe.
The First Law of Thermodynamics
(1)
• The first law of
thermodynamics – the
law of conservation of
energy.
• Energy can neither be
created nor destroyed.
• Transduction –
conversion of energy
from one form to another.
• Electric energy can be
transduced to mechanical
energy when we plug in a
clock.
The First Law of Thermodynamics
(2)
• Cells are capable of
energy transduction.
• Chemical energy is
stored in certain
biological molecules,
such as ATP.
• Chemical energy is
converted to mechanical
energy when heat is
released during muscle
contraction.
The First Law of Thermodynamics
(3)
• Energy transduction
in the biological world:
conversion is the
conversion of sunlight
into chemical energy
– photosynthesis.
• Animals, such as
fireflies and luminous
fish, are able to
convert chemical
energy back to light.
The First Law of Thermodynamics
(4)
• The universe can be divided into system
and surroundings.
– The system is a subset of the universe under
study.
– The surroundings are everything that is not
part of the system.
– The energy of the system is called the internal
energy (E), and its change during a
transformation is called ΔE.
The First Law of Thermodynamics
(5)
• The first law of thermodynamics: ΔE = Q – W,
where Q is the heat energy and W is the work
energy.
• When there is energy transduction (ΔE) in a
system, heat content may increase or
decrease.
– Reactions that lose heat are exothermic.
– Reactions that gain heat are endothermic.
– The first law does not predict whether an energy
change will be positive or negative.
The First Law of Thermodynamics
(6)
The Second Law of
Thermodynamics (1)
• The second law of thermodynamics:
events in the universe tend to proceed
from a state of higher energy to a state of
lower energy.
– Such events are called spontaneous, they
can occur without the input of external energy.
– Loss of available energy during a process is
the result of a tendency for randomness to
increase whenever there is a transfer of
energy.
The Second Law of
Thermodynamics (2)
• Entropy is a measure of randomness or
disorder.
– It is energy not available to do additional
work.
– Loss of available energy equal TΔS, where
ΔS is the change in entropy.
The Second Law of
Thermodynamics (3)
• Every event is
accompanied by an
increase in the
entropy of the
universe.
– Entropy associated
with random
movements of
particles or matter.
– Living systems
maintain a state of
order, or low entropy
Free Energy (1)
• The first and second laws of
thermodynamics can be combined and
expressed mathematically.
– Equation: ΔH = ΔG + TΔS
– Free energy, ΔG, is the energy available to do
work.
– Spontaneity of the reaction is ΔG, if <0 the
reaction is exergonic, if >0 it is endergonic.
– Spontaneity depends on both enthalpy and
entropy.
Free Energy (2)
Free-Energy Changes in Chemical
Reactions (1)
• All chemical reactions are theoretically
reversible.
• All chemical reactions spontaneously proceed
toward equilibrium (Keq = [C][D]/[A][B]).
• The rates of chemical reactions are proportional
to the concentration of reactants.
• At equilibrium, the free energies of the products
and reactants are equal (ΔG = 0).
Free-Energy Changes in Chemical
Reactions (2)
• Free energy changes of reactions are
compared under standard conditions.
– The standard free energy changes, ΔG°’, are
described for each reaction under specific
conditions.
– Standard conditions are not representative of
cellular conditions, but are useful to make
comparisons.
– Standard free energy changes are related to
equilibrium: ΔG°’ = -RT ln K’eq
Calculation of free energy changes
(1)
• Non-standard conditions are corrected for
prevailing conditions.
– Equation: ΔG = ΔG°’ + RT ln Keq.
– Prevailing conditions may cause ΔG to be
negative, even when G°’ is positive.
– Making ΔG negative may involve coupling
endergonic and exergonic reactions in a sequence.
– Simultaneously coupled reactions have a common
intermediate.
– ATP hydrolysis is often coupled to endergonic
reactions in cells.
Calculation of free energy changes
(1)
Coupling Endergonic and
Exergonic Reactions
Coupling Endergonic and
Exergonic Reactions
Equilibrium versus Steady-State
Metabolism
• Cellular metabolism is nonequilibrium
metabolism.
• Cells are open thermodynamic systems.
• Cellular metabolism exists in a steady state.
– Concentrations of reactants and products remain
constant, but not at equilibrium.
– New substrates enter and products are removed.
– Maintaining a steady state requires a constant input
of energy, whereas maintaining equilibrium does not.
Steady State versus Equilibrium
3.2 Enzymes as Biological
Catalysts
• Enzymes are catalysts that speed up
chemical reactions.
• Enzymes are almost always proteins.
• Enzymes may be conjugated with
nonprotein components.
– Cofactors are inorganic enzyme conjugates.
– Coenzymes are organic enzyme conjugates.
Properties of Enzymes (1)
• Are present in cells in small amounts.
• Are not permanently altered during the course
of a reaction.
• Cannot affect the thermodynamics of
reactions, only the rates.
• Are highly specific for their particular reactants
called substrates.
• Produce only appropriate metabolic products.
• Can be regulated to meet the needs of a cell.
Properties of Enzymes (2)
Overcoming the Activation Energy
Barrier
• A small energy input,
the activation energy
(EA) is required for any
chemical
transformation.
– The EA barrier slows the
progress of
thermodynamically
unstable reactants.
– Reactant molecules that
reach the peak of the EA
barrier are in the
transition state.
Enzymes lower the activation
energy
• Without an enzyme,
only a few substrate
molecules reach the
transition state.
• With a catalyst, a
large proportion of
substrate molecules
can reach the
transition state.
The Active Site
• An enzyme interacts with
its substrate to form an
enzyme-substrate (ES)
complex.
• The substrate binds to a
portion of the enzyme
called the active site.
• The active site and the
substrate have
complementary shapes
that allow substrate
specificity.
The Active Site
Mechanisms of Enzyme Catalysis
(1)
• Substrate orientation
means enzymes hold
substrates in the
optimal position of the
reaction.
Mechanisms of Enzyme Catalysis
(2)
• Changes in the reactivity
of the substrate
temporarily stabilize the
transition state.
– Acidic or basic R groups on
the enzyme may change
the charge of the substrate.
– Charged R groups may
attract the substrate.
– Cofactors of the enzyme
increase the reactivity of
the substrate by removing
or donating electrons.
Mechanisms of Enzyme Catalysis
(3)
• Inducing strain in
the substrate.
– Shifts in the
conformation after
binding cause an
induced fit
between enzyme
and the substrate.
– Covalent bonds of
the substrate are
strained.
Mechanisms of Enzyme Catalysis
(4)
• Conformational changes
and catalytic
intermediates.
– Various changes in atomic
and electronic structure
occur in both the enzyme
and substrate during a
reaction.
– Using time-resolved
crystallography,
researchers have
determined the threedimensional structure of an
enzyme at successive
stages during a reaction
Mechanisms of Enzyme Catalysis
(4)
• Conformational changes
and catalytic
intermediates.
– Various changes in atomic
and electronic structure
occur in both the enzyme
and substrate during a
reaction.
– Using time-resolved
crystallography,
researchers have
determined the threedimensional structure of an
enzyme at successive
stages during a reaction
Enzyme Kinetics (1)
• Kinetics is the study of rates of enzymatic
reactions under various experimental conditions.
• Rates of enzymatic reactions increase with
increasing substrate concentrations until the
enzyme is saturated.
– At saturation every enzyme s working at maximum
capacity.
– The velocity at saturation is called maximal velocity,
Vmax.
– The turnover number is the number of substrate
molecules converted to product per minute per
enzyme molecule at Vmax.
Enzyme Kinetics (2)
• The Michaelis
constant (KM) is the
substrate
concentration at onehalf of Vmax.
– Units of KM are
concentration units.
– The KM may reflect
the affinity of the
enzyme for the
substrate.
Enzyme Kinetics (3)
• Plots of the inverses of velocity versus
substrate concentrations, such as the
Lineweaver-Burk plot, facilitate estimating
Vmax and KM.
• Temperature and pH can affect enzymatic
reaction rates.
Enzyme Kinetics (4)
Enzyme Kinetics (4)
Enzyme Inhibitors (1)
• Enzyme inhibitors slow the rates for
enzymatic reactions.
– Irreversible inhibitors bind tightly to the enzyme.
– Reversible inhibitors bind loosely to the enzyme.
• Competitive inhibitors compete with the enzyme for
active sites
– Usually resemble the substrate in structure.
– Can be overcome with high substrate/inhibitor ratios.
Enzyme Inhibitors (2)
Enzyme Inhibitors (3)
• Noncompetitive
inhibitors
– Bind to sites other
than active sites and
inactivate the enzyme.
– The maximum velocity
of enzyme molecules
cannot be reached.
– Cannot be overcome
with high
substrate/inhibitor
ratios.
The Human Perspective: The
Growing Problem of Antibiotic
Resistance (1)
• Antibiotics target human metabolism
without harming the human host.
– Enzymes involved in the synthesis of the
bacterial cell wall.
– Components of the system by which bacteria
duplicate, transcribe, and translate their
genetic information.
– Enzymes that catalyze metabolic reactions
specific to bacteria.
The Human Perspective: The
Growing Problem of Antibiotic
Resistance (2)
• Antibiotics have been misused with dire
consequences.
– Susceptible cells are destroyed, leaving rare and
resistant cells to survive and replicate.
– Bacteria become resistant to antibiotics by
acquiring genes from other bacteria by various
mechanisms.
3.3 Metabolism
• Metabolism is the collection of bio-chemical
reactions that occur within a cell.
• Metabolic pathways are sequences of chemical
reactions.
– Each reaction in the sequence is catalyzed by a
specific enzyme.
– Pathways are usually confined to specific locations.
– Pathways convert substrates into end products via a
series of metabolic intermediates.
An Overview of Metabolism (1)
• Catabolic pathways
break down complex
substrates into simple
end products.
– Provide raw materials
for the cell.
– Provide chemical
energy for the cell.
• Anabolic pathways
synthesize complex
end products from
simple substrates.
– Require energy.
– Use ATP and NADPH
from catabolic
pathways.
An Overview of Metabolism (2)
• Anabolic and catabolic
pathways are
interconnected.
– In stage I, macromolecules
are hydrolyzed into their
building blocks.
– In stage II, building blocks
are further degraded into a
few common metabolites.
– In stage III, small molecular
weight metabolites like
acetyl-CoA are degraded
yielding ATP.
Oxidation and Reduction: A Matter
of Electrons (1)
• Oxidation-reduction (redox) reactions
involve a change in the electronic state of
reactants.
– When a substrate gains electrons, it is reduced.
– When a substrate loses electrons, it is oxidized.
– When one substrate gains or loses electrons,
another substance must donate or accept those
electrons.
• In a redox pair, the substrate that donates electrons is a
reducing agent.
• The substrate that gains electrons is an oxidizing agent.
Oxidation and Reduction: A Matter
of Electrons (1)
The Capture and Utilization of
Energy
• Reduced atoms can be oxidized, releasing
energy to do work.
• The more a substance is reduced, the more
energy that can be released.
• Glycolysis is the first stage in the catabolism of
glucose, and occurs in the soluble portion of the
cytoplasm.
• The tricarboxylic (TCA) cycle is the second
stage and it occurs in the mitochondria of
eukaryotic cells.
Glycolysis and ATP Formation (1)
• Of the reactions of
glycolysis, all but
three are near
equilibrium (ΔG ~ 0)
under cellular
conditions.
• The driving forces of
glycolysis are these
three reactions.
Glycolysis and ATP Formation (2)
Glycolysis and ATP Formation (3)
• Glucose is phosphorylated to glucose 6phosphate by using ATP.
• Glucose 6-phosphate is isomerized to
fructose 6-phosphate.
• Fructose 6-phosphate is phosphorylated to
fructose 1,6-bisphophate using another
ATP.
• Fructose 1,6-bisphosphate is split into two
three-carbon phosphorylated compounds.
Glycolysis and ATP Formation (4)
• NAD+ is reduced to NADH when glyceraldehyde
3-phosphate is converted to 1,3bisphosphoglycerate.
– Dehydrogenase enzymes oxidize and reduce
cofactors.
– NAD+ is a nonprotein cofactor associated with
gluceraldehyde phosphate dehydrogenase.
– NAD+ can undergo oxidation and reduction at
different places in the cell.
– NADH donates electrons to the electron transport
chain in the mitochondria.
Glycolysis and ATP Formation (5)
Glycolysis and ATP Formation (5)
Glycolysis and ATP Formation (6)
• ATP is formed when 1,3bisphosphoglycerate is
converted to 3phosphoglycerate by 3phosphoglycerate kinase.
– Kinase enzymes transfer
phosphate groups.
– Substrate-level
phosphorylation occurs
when ATP is formed by a
kinase enzyme.
Glycolysis and ATP Formation (7)
• ATP formation is only
moderately endergonic
compared with other
phosphate transfer in
cells.
– Transfer potential shown
when molecules higher on
the scale have less affinity
for the group being
transferred than are the
ones lower on the scale.
– The less the affinity, the
better the donor.
Glycolysis and ATP Formation (8)
• 3-phosphoglycerate is converted to
pyruvate via three sequential reactions, in
one of them a kinase phosphorylates ADP.
• Glycolysis can generate a net of 2 ATPs
for each glucose.
• Glycolysis occurs in the absence of
oxygen, it is an anaerobic pathway.
• The end product, pyruvate, can enter
aerobic or anaerobic catabolic pathways.
Anaerobic Oxidation of Pyruvate:
The Process of Fermentation (1)
• Fermentation restores NAD+ from NADH.
– Under anaerobic conditions, glycolysis depletes
the supply of NAD+ by reducing it to NADH.
– In fermentation, NADH is oxidized to NAD+ by
reducing pyruvate.
– In muscle and tumor cells pyruvate is reduced to
lactate.
– In yeast and other microbes, pyruvate is reduced
and converted to ethanol.
– Fermentation is inefficient with only about 8% of
the energy of glucose captured as ATP.
Anaerobic Oxidation of Pyruvate:
The Process of Fermentation (2)
Reducing Power (1)
• Anabolic pathways require a source of
electrons to form larger molecules.
• NADPH donates electrons to form large
biomolecules.
– NADPH is a nonprotein cofactor similar to
NADH.
– The supply of NADPH represents the cell’s
reducing power.
– NADP+ is formed by phosphate transfer from
ATP to NAD+.
Reducing Power (2)
• NADPH and NADH are interconvertible, but
have different metabolic roles.
• NADPH is oxidized in anabolic pathways.
• NAD+ is reduced in catabolic pathways.
• The enzyme transhydrogenase catalyzes the
transfer of hydrogen atoms from one cofactor to
the other.
– NADPH is favored when energy is abundant.
– NADH is used to make ATP when energy is scarce.
Metabolic Regulation (1)
• Cellular activity is regulated as needed.
• Regulation may involve controlling key enzymes of
metabolic pathways.
• Enzymes are controlled by alteration in active sites.
– Covalent modification of enzymes regulated by
phosphorylation such as protein kinases.
– Allosteric modulation by enzymes regulated by
compounds binding to allosteric sites.
• In feedback inhibition, the product of the pathway
allosterically inhibits one of the first enzymes of the
pathway.
Metabolic Regulation (2)
Separating Catabolic and Anabolic
Pathways (1)
• Glycolysis and gluconeogenesis are the
catabolic and anabolic pathways of glucose
metabolism.
– Synthesis of fructose 1,6-bisphosphate is coupled
to hydrolysis of ATP.
– Breakdown of fructose 1,6-bisphosphate is via
hydrolysis by fructose 1,6-bisphosphatase in
gluconeogenesis.
– Phosphofructokinase is regulated by feedback
inhibition with ATP as the allosteric inhibitor.
– Fructose 1,6-bisphosphatase is regulated by
covalent modification using phosphate binding.
– ATP levels are highly regulated.
Separating Catabolic and Anabolic
Pathways (2)
Separating Catabolic and Anabolic
Pathways (3)
• Anabolic pathways do not proceed via the
same reactions as the catabolic pathways
even though they may have steps in
common.
– Some catabolic pathways are essentially
irreversible due to large ΔG°’ values.
– Irreversible steps in catabolic pathways are
catalyzed by different enzymes from those in
anabolic pathways.
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