Energy, Enzymes, and Metabolism

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Energy, Enzymes, and Metabolism
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Energy, Enzymes, and Metabolism

• Energy and Energy Conversions
• ATP Transferring Energy in Cells
• Enzymes Biological Catalysts
• Molecular Structure Determines Enzyme Function
• Metabolism and the Regulation of Enzymes

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Energy and Energy Conversions

• To physicists, energy represents the capacity to
  do work.
• To biochemists, energy represents the capacity
  for change.
• Cells must acquire energy from their environment.
• Cells cannot make energy energy is neither
  created nor destroyed, but energy can be
  transformed.
• In life, energy transformations consist primarily
  of movement of molecules and changes in chemical
  bonds.

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Energy and Energy Conversions

• There are two main types of energy
• Potential energy is energy of state or
  positionit is stored energy.
• Kinetic energy is the energy of movement. Kinetic
  energy does work that alters the state or motion
  of matter.

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Figure 6.1 Energy Conversions and Work
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Energy and Energy Conversions

• Metabolism can be divided into two types of
  activities
• Anabolic reactions link simple molecules together
  to make complex ones. These are energy-storing
  reactions.
• Catabolic reactions break down complex molecules
  into simpler ones. Some of these reactions
  provide the energy for anabolic reactions.

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Energy and Energy Conversions

• The first law of thermodynamics states that
  During any conversion of forms of energy, the
  total initial energy will equal the total final
  energy. Energy is neither created nor destroyed.
• Although living cells are open systems (they
  exchange matter and energy with their
  surroundings), they still obey these laws.

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Figure 6.2 (a) The Laws of Thermodynamics
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Energy and Energy Conversions

• Second law of thermodynamics When energy is
  transformed, some becomes unavailable to do work.
  
• No physical process or chemical reaction is 100
  per cent efficient, that is, not all the energy
  released can be used to do work.

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Figure 6.2 (b) The Laws of Thermodynamics
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Energy and Energy Conversions

• In any system
• total energy usable energy unusable energy
• Or
• enthalpy (H) free energy (G) entropy (S)
• H G TS (T absolute temperature)
• Entropy is a measure of the disorder of a system.
• Usable energy
• G H TS

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Energy and Energy Conversions

• G, H, and S cannot be measured precisely.
• Change in each at a constant temperature can be
  measured precisely in calories or joules.
• DG DH TDS
• If DG is positive (), free energy is required.
  This is the case for anabolic reactions.
• If DG is negative (), free energy is released.
  This is the case for catabolic reactions.

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Energy and Energy Conversions

• If a chemical reaction increases entropy, its
  products are more disordered or random than its
  reactants are.
• An example is the hydrolysis of a protein to its
  amino acids. Free energy is released, DG is
  negative, and DS is positive (entropy increases).
• When proteins are made from amino acids, free
  energy is required, there are fewer products, and
  DS is negative.

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Energy and Energy Conversions

• The second law of thermodynamics also predicts
  that, as a result of energy conversions, disorder
  tends to increase.
• This tendency for disorder to increase gives a
  directionality to physical and chemical
  processes, explaining why some reactions proceed
  in one direction rather than another.

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Energy and Energy Conversions

• It may seem that highly complex organisms, such
  as the human body, are in apparent disagreement
  with the second law, but this is not the case.
• The metabolic processes that take place in living
  tissues produce far more disorder than the order
  present within the tissues.
• To maintain order, life requires a constant input
  of energy.

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Energy and Energy Conversions

• Anabolic reactions may make single products from
  many smaller units such reactions consume
  energy.
• Catabolic reactions may reduce an organized
  substance (glucose) into smaller, more randomly
  distributed substances (CO2 and H2O). Such
  reactions release energy.
• There is a direct relationship between the amount
  of energy released by a reaction (DG), or the
  amount taken up (DG), and the tendency of a
  reaction to run to completion without an input of
  energy.

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Energy and Energy Conversions

• A spontaneous reaction goes more than halfway to
  completion without input of energy, whereas a
  nonspontaneous reaction proceeds that far only
  with an input of energy.
• Spontaneous reactions are called exergonic and
  have negative DG values (they release energy).
• Nonspontaneous reactions are called endergonic
  and have positive DG values (they consume
  energy).
• If under certain conditions A B is spontaneous
  (exergonic), then B A must be nonspontaneous
  (endergonic).

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Figure 6.3 Exergonic and Endergonic Reactions
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Energy and Energy Conversions

• In principle, all reactions are reversible (A
  B).
• Adding more A speeds up the forward reaction, A
  B adding more B speeds up the reverse
  reaction, B A.
• At the point of chemical equilibrium, the
  relative concentrations of A and B are such that
  forward and reverse reactions take place at the
  same rate.
• Although no further net change occurs at this
  point, reactions of individual molecules continue.

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Energy and Energy Conversions

• An example of equilibrium can be seen in the
  cellular conversion of glucose 1-phosphate to
  glucose 6-phosphate.
• At pH 7 and 25C, the concentration of the
  product rises while the concentration of the
  reactant falls.
• Equilibrium is reached when the
  product-to-reactant ratio is 191.
• At this point the forward reaction has gone 95
  percent to completion.
• The further a reaction goes toward completion in
  order to reach equilibrium, the greater the
  amount of free energy released.

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Figure 6.4 Concentration at Equilibrium
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ATP Transferring Energy in Cells

• All living cells use adenosine triphosphate (ATP)
  for capture, transfer, and storage of energy.
• Some of the free energy released by certain
  exergonic reactions is captured in ATP, which
  then can release free energy to drive endergonic
  reactions.
• ATP is not an unusual molecule and it has other
  uses as well for example, it can be converted
  into a building block for DNA and RNA.

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Figure 6.5 ATP (Part 1)
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Figure 6.5 ATP (Part 2)
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ATP Transferring Energy in Cells

• ATP can hydrolyze to yield ADP and an inorganic
  phosphate ion (Pi).
• ATP H2O ADP Pi free energy
• The reaction is exergonic (DG 12 kcal/mol).
• Free energy of the PO bond is much higher than
  the HO bond that forms after hydrolysis.
• Phosphates are negatively charged, so energy is
  required to get them near each other to bond (to
  add a phosphate to ADP).

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ATP Transferring Energy in Cells

• The formation of ATP from ADP and Pi, is
  endergonic and consumes as much free energy as is
  released by the breakdown of ATP
• ADP Pi free energy ATP H2O
• ATP shuttles energy from exergonic reactions to
  endergonic reactions.
• Each cell requires millions of molecules of ATP
  per second to drive its biochemical machinery.
• Each ATP molecule undergoes about 10,000 cycles
  of synthesis and hydrolysis every day.

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Figure 6.6 The Energy-Coupling Cycle of ATP
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Figure 6.7 Coupling ATP Hydrolysis to an
Endergonic Reaction
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Enzymes Biological Catalysts

• A catalyst is any substance that speeds up a
  chemical reaction without itself being used up.
• Living cells use biological catalysts to increase
  rates of chemical reactions.
• Most biological catalysts are proteins called
  enzymes. Certain RNA molecules called ribozymes
  are also catalysts.

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Enzymes Biological Catalysts

• The direction of a reaction can be predicted if
  DG is known, but not the rate of the reaction.
• Some reactions are slow because there is an
  energy barrier between reactants and products.
• Exergonic reactions proceed only after the
  addition of a small amount of added energy,
  called the activation energy (Ea).
• In a chemical reaction, activation energy is the
  energy needed to put molecules into a transition
  state.
• Transition-state species have higher free energy
  than either reactants or products.

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Figure 6.8 Activation Energy Initiates Reactions
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Enzymes Biological Catalysts

• Exergonic reactions often are initiated by the
  addition of heat, which increases the average
  kinetic energy of the molecules.
• However, adding heat is not an appropriate way
  for biological systems to drive reactions.
• Enzymes solve this problem by lowering the
  energy barrier.

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Figure 6.9 Over the Energy Barrier
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Enzymes Biological Catalysts

• Enzymes bind specific reactant molecules called
  substrates.
• Substrates bind to a particular site on the
  enzyme surface called the active site, where
  catalysis takes place.
• Enzymes are highly specific They bind specific
  substrates and catalyze particular reactions
  under certain conditions.
• The specificity of an enzyme results from the
  exact three-dimensional shape and structure of
  the active site.

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Figure 6.10 Enzyme and Substrate
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Enzymes Biological Catalysts

• The names of enzymes reflect their function
• RNA polymerase catalyzes formation of RNA but not
  DNA.
• RNA nuclease hydrolyzes RNA polymers.
• Hexokinase accelerates phosphorylation of hexose.
  
• All kinases add phosphates. All phosphatases
  remove phosphates.

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Enzymes Biological Catalysts

• Binding a substrate to the active site produces
  an enzymesubstrate complex (ES).
• Hydrogen bonding, ionic attraction, or covalent
  bonding acting individually or together hold
  these complexes together.
• The enzymesubstrate complex (ES) generates the
  product (P) and free enzyme (E)
• E S ES E P

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Enzymes Biological Catalysts

• Enzymes lower activation energy requirements and
  thus speed up the overall reaction, but they do
  not change the difference in free energy (DG)
  between the reactants and the products.
• Thus they do not affect the final equilibrium.
• Enzymes can have a profound effect on reaction
  rates. Reactions that might take years to happen
  can occur in a fraction of a second.

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Figure 6.11 Enzymes Lower the Energy Barrier
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Enzymes Biological Catalysts

• At the active sites, enzymes and substrates
  interact by breaking old bonds and forming new
  ones.
• Enzymes catalyze reactions using one or more of
  the following mechanisms
• Orienting substrates
• Adding charges to substrates
• Inducing strain in the substrates

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Figure 6.12 Life at the Active Site
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Enzymes Biological Catalysts

• Enzymes orient substrates.
• While free in solution, substrates tumble and
  collide.
• The probability of collision at the angle
  necessary to change chemical interactions is low.
• When bound to enzymes, two substrates can be
  oriented such that a reaction is more likely to
  occur.

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Enzymes Biological Catalysts

• The R groups of an enzymes amino acids can make
  substrates more chemically reactive.
• In acid-base catalysis, acidic or basic R groups
  form the active site and transfer H to or from
  the substrate, destabilizing a covalent bond in a
  substrate.
• In covalent catalysis, a functional group side
  chain forms a temporary covalent bond with the
  substrate.
• In metal ion catalysis, metal ions gain or lose
  electrons without detaching from the protein,
  making them important participants in redox
  reactions.

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Enzymes Biological Catalysts

• Some enzymes induce strain in the substrate.
• For example, the carbohydrate substrate for the
  enzyme lysozyme enters the active site in a
  flat-ringed chair shape.
• The active site causes it to flatten out into a
  sofa shape.
• The stretching of the bonds decreases their
  stability, making them more reactive to water.

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Figure 6.13 Tertiary Structure of Lysozyme
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Molecular Structure Determines Enzyme Function

• Most enzymes are much larger than their
  substrate.
• The active site of most enzymes is only a small
  region of the whole protein.
• The specificity of an enzyme for a particular
  substrate depends on a precise interlock.
• In 1894, Emil Fischer compared the fit to that of
  a lock and key.
• In 1965, using X-ray crystallography, David
  Phillips observed a pocket in the enzyme lysozyme
  that neatly fit its substrate.

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Molecular Structure Determines Enzyme Function

• The change in enzyme shape caused by substrate
  binding is called induced fit.
• Induced fit at least partly explains why enzymes
  are so large.
• The rest of the macromolecule may have two
  functions
• To provide a framework so that the amino acids of
  the active site are properly positioned
• To participate in the small changes in protein
  shape that allow induced fit

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Figure 6.14 Some Enzymes Change Shape When
Substrate Binds to Them
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Molecular Structure Determines Enzyme Function

• Some enzymes require other molecules in order to
  function
• Cofactors are metal ions (e.g., copper, zinc,
  iron) that bind temporarily to certain enzymes
  and are essential to their function.
• Coenzymes are small molecules that act like
  substrates. They bind to the active site and
  change chemically during the reaction, then
  separate to participate in other reactions.
• Prosthetic groups are permanently bound to
  enzymes. They include the heme groups that are
  attached to hemoglobin.

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Figure 6.15 An Enzyme with a Coenzyme
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Molecular Structure Determines Enzyme Function

• The rate of an uncatalyzed reaction is directly
  proportional to the concentration of reactants.
• This is true up to a point with catalyzed
  reactions, but then the rate levels off.
• This is due to saturation of the enzyme, when all
  the enzyme molecules are bound to substrate.
• Turnover number is the number of substrate
  molecules converted to product per unit time.
• The turnover number ranges from 1 molecule every
  2 seconds for lysozyme, to 40 million per second
  for the liver enzyme catalase.

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Figure 6.16 Catalyzed Reactions Reach a Maximum
Rate
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Metabolism and the Regulation of Enzymes

• A major characteristic of life is homeostasis,
  the maintenance of stable internal conditions.
• Regulation of enzyme activity contributes to
  metabolic homeostasis.

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Metabolism and the Regulation of Enzymes

• An organisms metabolism is the total of all
  biochemical reactions taking place within it.
• Metabolism is organized into sequences of
  enzyme-catalyzed chemical reactions called
  pathways.
• In these sequences, the product of one reaction
  is the substrate for the next.
• A B C
  D

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Metabolism and the Regulation of Enzymes

• Some metabolic pathways are anabolic and
  synthesize the building blocks of macromolecules.
• Some are catabolic and break down macro-molecules
  and fuel molecules.
• The balance among these pathways can change
  depending on the cells needs, so a cell must
  regulate its metabolic pathways constantly.

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Metabolism and the Regulation of Enzymes

• Enzyme activity can be inhibited by natural and
  artificial binders.
• Naturally occurring inhibitors regulate
  metabolism.
• Irreversible inhibition occurs when the inhibitor
  destroys the enzymes ability to interact with
  its normal substrate(s).
• DIPF, a nerve gas, irreversibly inhibits
  acetylcholinesterase, an enzyme necessary for
  propagation of nerve impulses.

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Figure 6.17 Irreversible Inhibition
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Metabolism and the Regulation of Enzymes

• Not all inhibition is irreversible.
• When an inhibitor binds reversibly to an enzymes
  active site, it competes with the substrate for
  the binding site and is called a competitive
  inhibitor.
• When the concentration of the competitive
  inhibitor is reduced, it no longer binds to the
  active site, and the enzyme can function again.

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Figure 6.18 (a) Reversible Inhibition (Part 1)
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Figure 6.18 (a) Reversible Inhibition (Part 2)
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Metabolism and the Regulation of Enzymes

• When an inhibitor binds reversibly to a site
  distinct from the active site, it is called a
  noncompetitive inhibitor.
• Noncompetitive inhibitors act by changing the
  shape of the enzyme in such a way that the active
  site no longer binds the substrate.
• Noncompetitive inhibitors can unbind from the
  enzyme, making the effects reversible.

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Figure 6.18 (b) Reversible Inhibition (Part 1)
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Figure 6.18 (b) Reversible Inhibition (Part 2)
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Metabolism and the Regulation of Enzymes

• The change in enzyme shape due to noncompetitive
  inhibitor binding is an example of allostery.
• Allosteric enzymes are controlled by allosteric
  regulators.
• Allosteric regulators bind to an allosteric site,
  which is separate from the active site, and this
  changes the structure and function of the enzyme.
• Allosteric regulators work in two ways
• Positive regulators stabilize the active form.
• Negative regulators stabilize the inactive form.

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Figure 6.19 Allosteric Regulation of Enzymes
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Metabolism and the Regulation of Enzymes

• Allosteric enzymes usually have more than one
  type of subunit (quaternary structure).
• A catalytic subunit has an active site that binds
  the enzymes substrate.
• A regulatory subunit has one or more allosteric
  sites that bind specific regulators.
• In the active state, the active sites on the
  catalytic subunits can bind substrate.
• In the inactive state, the allosteric sites on
  the regulatory subunits can bind inhibitor.

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Metabolism and the Regulation of Enzymes

• Some allosteric enzymes have multiple active
  sites.
• When one binding site is occupied, it changes the
  other(s) so that they bind additional substrate
  molecules more readily.
• How the rate of a reaction changes with
  increasing substrate concentration depends on
  whether the enzyme is allosterically regulated.
• The enzymes catalytic rate becomes
  concentration-sensitive and concentration-responsi
  ve.

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Figure 6.20 Allostery and Reaction Rate
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Metabolism and the Regulation of Enzymes

• Metabolic pathways typically involve a starting
  material, intermediates, and an end product.
• The first step in the pathway is called the start
  up or commitment step.
• Once this step occurs, other enzyme-catalyzed
  reactions follow until the product of the series
  builds up.
• One way to control the whole pathway is to have
  the end product inhibit the first step in the
  pathway.
• This is called end-product inhibition or feedback
  inhibition.

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Figure 6.21 Inhibition of Metabolic Pathways
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Metabolism and the Regulation of Enzymes

• Rates of most enzyme-catalyzed reaction depend on
  the pH of the medium.
• Each enzyme is most active at a particular pH.
• pH can change the charges of the carboxyl and
  amino groups of amino acids. This affects the
  interactions of the amino acids and can change
  the structure of the protein.

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Figure 6.22 pH Affects Enzyme Activity
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Metabolism and the Regulation of Enzymes

• Temperature also affects enzyme activity.
• High temperature can inactivate enzymes by
  breaking non-covalent bonds.
• If the tertiary structure is disrupted the enzyme
  is called denatured.
• Some organisms that can live at different
  temperatures generate different forms of an
  enzyme, called isozymes.
• Enzymes adapted to warm temperatures usually have
  a tertiary structure of covalent bonds, such as
  disulfide bridges.

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Figure 6.23 Temperature Affects Enzyme Activity