Directions and Rates of Biochemical Processes

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Chapter 5
Directions and Rates of Biochemical Processes
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Key Questions

• What factors determine which way a reaction will
  go?
• What factors determine the rate of a chemical
  reaction?
• How do enzymes work?
• How can cells modify the activity of enzymes?

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Work and Energy

• Work movement of an object against a force
• Work can be stored as potential energy in a
  spring or battery
• Examples lifting something against gravity,
  winding a spring
• Energy ability to do work ability to promote
  change
• 2 forms
• Kinetic- associated with movement, rock falling
  or muscle contracting
• Potential- due to structure or location, can be
  gravitational, electrical, chemical
• Chemical energy- energy in molecular bonds
• Kinetic energy of molecules is heat

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Thermodynamics

• Rules of chemical energy change
• Used to predict the conversion of energy from one
  form to another
• Determines the direction of the changes
• First law The total amount of energy in any
  process stays constant
• Law of conservation of energy
• Energy cannot be created or destroyed
• Energy may change form from chemical to kinetic
• Ex. Doing a pushup Muscles contract (work)
  Energy from ATP becomes kinetic energy of
  movement and heat
• Second law entropy (chaos, disorder) continually
  increases in the universe
• Transfer or transformation of energy from one
  form to another increases entropy or degree of
  disorder of a system

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Energy and Chemical Reaction

• Chemical reactions one substance is changed into
  another, release store energy
• Reactants molecules entering into the chemical
  reaction
• Products changed molecules at the end of the
  reaction
• Free energy of activation Energy is needed to
  initiate the reaction between molecules
• Activation Energy
• Initial input of energy to start reaction
• Allows molecules to get close enough to cause
  bond rearrangement
• Can now achieve transition state where bonds are
  stretched
• Overcoming activation energy
• 2 common ways
• Large amounts of heat
• Using enzymes to lower activation
• energy

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Energy and Chemical Reaction

• Chemical reactions one substance is changed into
  another, release store energy
• Exergonic reaction Energy released from the
  reactants during the reaction
• Energy released due to reactions breaking down
  complex molecules into simpler molecules called
  catabolic reactions (????).
• Endergonic reactions Energy added to products
  during the reaction. DO NOT occur spontaneously
• Anabolic reactions (????) are endergonic
  reactions that use energy to build complex
  molecules from simpler molecules.
• Making bonds can store potential chemical energy

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Direction of Reactions

• Chemical reactions usually go in the direction
  that releases heat
• Heat is energy that is not available to do work
• Energy input is required to reverse these
  reactions
• H G TS
• H enthalpy or total energy
• G free energy or amount of energy for work
• S entropy or unusable energy
• T absolute temperature in Kelvin (K)
• Energy in a system that is available to do work
• Change in free energy determines direction
• Energy transformations involve an increase in
  entropy
• Entropy - a measure of the disorder that cannot
  be harnessed to do work

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Entropy

• Measure of disorder
• Second law of thermodynamics, implies that
  disorder will increase
• Going from ordered state to disordered releases
  energy to do work
• Going from disorder to order requires energy
• Concentration and Entropy
• Movement of molecules from concentrated to less
  concentrated increases entropy, releases energy

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?G ? H - T ? S

• Equilibrium and Free Energy
• Exergonic
• ?Glt0 or negative free energy change
• Spontaneous
• Occur without input of additional energy
• Not necessarily fast
• Key factor is the free energy change
• Endergonic
• ?Ggt0 or positive free energy change
• Requires addition of free energy
• Not spontaneous

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Sources of Free Energy

• Breaking of unstable bonds and formation of
  stable bonds
• ?G of product lower than ?G of reactants
• High energy bonds unstable
• Hydrolysis of ATP
• ?G -7.3 kcal/mole
• Reaction favors formation of products
• Energy liberated can drive a variety of cellular
  processes

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Coupled Reactions

• Cells use ATP hydrolysis
• An endergonic reaction can be coupled to an
  exergonic reaction
• Endergonic reaction will be spontaneous if net
  free energy change for both processes is negative

Glucose phosphate ? glucose-phosphate H2O ?G
3.3 Kcal/mole endergonic ATP H2O ? ADP
Pi ?G -7.3 Kcal/mole exergonic Coupled
reaction Glucose ATP ? glucose-phosphate
ADP ?G -4.0 Kcal/mole exergonic
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Enzymes Act as Catalysts

• Catalyst- agent that speeds up the rate of a
  chemical reaction without being consumed during
  the reaction
• Enzymes can accelerate reactions as much as 1016
  over uncatalyzed rates!
• Ex. Urease catalyzed rate 3x104/sec
• Uncatalyzed rate 3x10-10/sec
• Ratio is 1x1014 !
• Pepsin (protein digestion in stomach) works best
  at pH2 too much food dilutes acid, inhibits
  digestion
• Vinegar (acetic acid) denatures proteins in
  bacteria, killing them, preserving food (pickles,
  herring)

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Enzymes Features

• Catalyst- agent that speeds up the rate of a
  chemical reaction without being consumed during
  the reaction
• Enzymes- protein catalysts in living cells, speed
  up chemical reactions
• Do not affect free energy, cannot reverse a
  reaction
• Bind to reacting molecules (substrates) at the
  active site
• Binding is reversible (100,000 times per second)
• Binding is specific only do 1 kind of reaction
• Active site - location where reaction takes place
• Substrate- reactants that bind to active site
• Enzyme-substrate complex formed when enzyme and
  substrate bind
• Each enzyme has optimum conditions temperature,
  pH, salt concentration
• High temperatures denature proteins
• pH influences 3-D structure of protein
• Salt can interfere with binding of substrates
• Prosthetic groups - small molecules permanently
  attached to the enzyme
• Cofactor - usually inorganic ion that temporarily
  binds to enzyme
• Coenzyme - organic molecule that participates in
  reaction but left unchanged afterward

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Enzymes Lower Activation Energy of a Reaction

• Enzyme binds to substrate with non-covalent bonds
• Holds substrate in position for reaction
• Distorts substrate into a transition state
• Enzyme is unchanged at the end of a reaction
• Straining bonds in reactants to make it easier to
  achieve transition state
• Positioning reactants together to facilitate
  bonding
• Changing local environment
• Direct participation through very temporary
  bonding

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Enzyme Mechanism

• Substrate binding
• Enzymes have a high affinity or high degree of
  specificity for a substrate
• Used the example of a lock and key for substrate
  and enzyme binding
• Induced fit - interaction also involves
  conformational changes

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Regulation

• Factors that Affect Enzyme Activity
• Enzymes activity is sensitive to the change in
  their 3-dimensional shape.
• Temperature and pH are two factors that may make
  enzyme to lose its shape or denature. (antifreeze
  protein, hot spring protein)
• The 3-D shape of an enzyme can also be affected
  by the binding of specific chemicals called
  activators (facilitate chemical reactions) and
  inhibitors (turn-off chemical reactions).
• Steric inhibitors bind to active site and prevent
  substrate from binding can be overcome by
  increasing substrate concentration
• Allosteric (non-competitive) inhibitors bind at
  another site, change shape of enzyme some are
  reversible
• Enzyme activity within an organism is often
  regulated by inhibitors under the process called
  negative feedback
• End-product inhibition