Bioenergetics, Enzymes, and Metabolism

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CHAPTER 3

• Bioenergetics, Enzymes, and Metabolism

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3.1 Bioenergetics

• The study of the various types of energy
  transformations that occur in living organisms.

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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.

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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.

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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.

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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.

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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 ?E.

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The First Law of Thermodynamics (5)

• The first law of thermodynamics ?E Q W,
  where Q is the heat energy and W is the work
  energy.
• When there is energy transduction (?E) 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.

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The First Law of Thermodynamics (6)
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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.

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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 T?S, where ?S is
  the change in entropy.

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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

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Free Energy (1)

• The first and second laws of thermodynamics can
  be combined and expressed mathematically.
• Equation ?H ?G T?S
• Free energy, ?G, is the energy available to do
  work.
• Spontaneity of the reaction is ?G, if lt0 the
  reaction is exergonic, if gt0 it is endergonic.
• Spontaneity depends on both enthalpy and entropy.

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Free Energy (2)
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Free-Energy Changes in Chemical Reactions (1)

• All chemical reactions are theoretically
  reversible.
• All chemical reactions spontaneously proceed
  toward equilibrium (Keq CD/AB).
• The rates of chemical reactions are proportional
  to the concentration of reactants.
• At equilibrium, the free energies of the products
  and reactants are equal (?G 0).

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Free-Energy Changes in Chemical Reactions (2)

• Free energy changes of reactions are compared
  under standard conditions.
• The standard free energy changes, ?G, 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 ?G -RT ln Keq

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Calculation of free energy changes (1)

• Non-standard conditions are corrected for
  prevailing conditions.
• Equation ?G ?G RT ln Keq.
• Prevailing conditions may cause ?G to be
  negative, even when G is positive.
• Making ?G 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.

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Calculation of free energy changes (1)
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Coupling Endergonic and Exergonic Reactions
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Coupling Endergonic and Exergonic Reactions
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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.

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Steady State versus Equilibrium
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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.

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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.

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Properties of Enzymes (2)
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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.

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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.

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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.

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The Active Site
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Mechanisms of Enzyme Catalysis (1)

• Substrate orientation means enzymes hold
  substrates in the optimal position of the
  reaction.

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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.

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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.

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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 three-dimensional structure
  of an enzyme at successive stages during a
  reaction

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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 three-dimensional structure
  of an enzyme at successive stages during a
  reaction

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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.

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Enzyme Kinetics (2)

• The Michaelis constant (KM) is the substrate
  concentration at one-half of Vmax.
• Units of KM are concentration units.
• The KM may reflect the affinity of the enzyme
  for the substrate.

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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.

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Enzyme Kinetics (4)
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Enzyme Kinetics (4)
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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.

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Enzyme Inhibitors (2)
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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.

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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.

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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.

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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.

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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.

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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.

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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.

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Oxidation and Reduction A Matter of Electrons (1)
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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.

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Glycolysis and ATP Formation (1)

• Of the reactions of glycolysis, all but three are
  near equilibrium (?G 0) under cellular
  conditions.
• The driving forces of glycolysis are these three
  reactions.

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Glycolysis and ATP Formation (2)
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Glycolysis and ATP Formation (3)

• Glucose is phosphorylated to glucose 6-phosphate
  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.

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Glycolysis and ATP Formation (4)

• NAD is reduced to NADH when glyceraldehyde
  3-phosphate is converted to 1,3-bisphosphoglycerat
  e.
• 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.

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Glycolysis and ATP Formation (5)
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Glycolysis and ATP Formation (5)
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Glycolysis and ATP Formation (6)

• ATP is formed when 1,3-bisphosphoglycerate is
  converted to 3-phosphoglycerate by
  3-phosphoglycerate kinase.
• Kinase enzymes transfer phosphate groups.
• Substrate-level phosphorylation occurs when ATP
  is formed by a kinase enzyme.

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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.

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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.

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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.

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Anaerobic Oxidation of Pyruvate The Process of
Fermentation (2)
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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 cells
  reducing power.
• NADP is formed by phosphate transfer from ATP to
  NAD.

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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.

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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.

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Metabolic Regulation (2)
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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.

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Separating Catabolic and Anabolic Pathways (2)
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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 ?G values.
• Irreversible steps in catabolic pathways are
  catalyzed by different enzymes from those in
  anabolic pathways.