AP Biology Chapter 6: An Introduction to Metabolism

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AP Biology Chapter 6An Introduction to
Metabolism
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Metabolism

• Totality of an organisms reactions
• (from Greek metabole, to change)
• An emergent property from interactions between
  chemicals within the environment of the cell
• Concerned with managing the material and energy
  resources of the cell

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Metabolism

• Made of two types of reactions
• Catabolic Pathways release energy by breaking
  down complex molecules into simpler compounds
  (e.g. cellular respiration)
• downhill reactions
• Anabolic Pathways consume energy to build
  complicated molecules from simpler ones (e.g.
  synthesis of proteins from amino acids)
• uphill reactions
• These reactions are coupled together

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Bioenergetics

• The study of how organisms manage their energy
  resources
• Energy the capacity to do workability to
  rearrange a collection of matter
• Kinetic energy of motion
• Potential stored energy
• Chemical form of potential energy stored in
  molecules as the result of the arrangement of
  atoms

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Thermodynamics

• Study of the energy transformations that occur in
  a collection of matter
• First Law of Thermodynamics energy is
  constantenergy can be transferred and
  transformed but it cannot be created nor
  destroyed
• Second Law of Thermodynamics every energy
  transfer makes the universe more disordered or
  random or increases the entropy (measure of the
  randomness)

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Entropy

• In most energy transformations, some of the
  energy stored is converted to heat (the most
  random form of energy)
• Organisms are open systems and exchange energy
  and materials with the surroundingstakes in both
  organized and unorganized forms of matter and
  energy and releases both into the environment
• Depletions of energy in organisms is due to the
  loss as heat.

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Free Energy

• The portions of a systems energy that is
  available to perform work when temperature is
  uniform throughout the system
• Not all of the energy in a system is available
  for work
• G H T S
• G Free EnergyH Total Energy (of the
  system)T Temperature (in Kelvin)S Entropy

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Energy Changes

• ?G ?H - T ?S
• For spontaneous, downhill reactions, ?G must be
  negative (?G lt 0)

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Free Energy and Metabolism

• Exergonic Reactions (energy outward) proceeds
  with a net release of free energy. ?G is
  negative. Reactions are spontaneous
• Endergonic Reactions (energy inward) absorbs
  free energy from its surroundings, stores free
  energy in molecules. ?G is positive. Reactions
  are nonspontaneous. Require energy to drive
  reaction

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Energy Changes
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Metabolic Disequilibrium

• Equilibrium ?G 0. There is no net change in
  the system. No work is being performed
• Reactions in closed systems will eventually reach
  equilibrium
• Living organisms are open systems and maintain
  disequilibrium by constantly flowing materials
  into and out of the cell
• Analogy hydroelectric systems

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Metabolic Disequilibrium
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What work do cells do?

• Mechanical Work beating cilia, contraction of
  muscles, movement of chromosomes during cell
  division
• Transport Work pumping substances across
  membranes against spontaneous movement
• Chemical Work pushing of endergonic reactions,
  synthesis of polymers
• All these works require energy in the form of
  ATP

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ATP

• Adenosine triphosphate is closely related to a
  nucleotide. It contains an adenine base,
  ribose, and 3 phosphate groups
• The phosphate groups are highly charged and when
  broken apart by hydrolysis releases large amounts
  of energy. (?G -13 kcal/mole)

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How ATP does work

• With the help of enzymes, the cell can couple the
  energy release of ATP hydrolysis with an
  endergonic process by transferring a phosphate
  group from ATP to another molecule.
• The recipient of the phosphate is phosphorylated
  and becomes a more reactive intermediate

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Regeneration of ATP

• An organism at work (alive) uses ATP
  continuously, but ATP is a renewable resource and
  can be regenerated from ADP by adding a phosphate
  (Pi)
• The energy required to phosphorylate ADP comes
  from the break down (catabolism) of molecules in
  the cell
• Very quick process?A working muscle cell
  regenerates ALL its ATP in under 1 minute (10
  million molecules/second)

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Catalysts

• Chemical agent that changes the rate of a
  reaction without being consumed by the reaction
• Enzymes are biological catalysts, most often made
  of protein (there are a few ribozymes made of
  RNA)
• Without enzymes, most reactions, even
  spontaneous, exothermic reactions, proceed VERY
  slowly.
• Example Sucrose in water will not break down

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Activation Energy Barrier

• Chemical reactions involve forming and breaking
  of bonds. Existing bonds in reactants must be
  broken and new bonds of products formed.
• Breaking bonds requires an input of energy
• The initial investment of energy for starting a
  reactionenergy required to break bonds is
  called the activation energy or free energy of
  activation (EA)

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Enzymes and Activation Energy

• Enzymes speed up reactions by lowering the EA
  barrier, so the transition state is within reach
  at moderate temperatures.
• They do not change the ?G of the reaction

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Enzymes are Substrate Specific

• The reactant a specific enzyme works on is called
  a substrate
• Enzymes bind to their substrate(s) allowing the
  catalytic action of the enzyme to create the
  products
• Substrate Enzyme Product
• Enzymes can distinguish their substrate by shape.
  The substrate must fit into the active site of
  the enzyme, a groove or pocket in the protein

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Enzyme-Substrate Cycle
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Induced Fit

• Active sites are not rigid like a lock-and-key
  but instead change shape slightly to fit snugly
  around the substratelike a handshake
• Induced fit brings chemicals together into
  positions that enhance their ability to catalyze

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Environmental Effects on Enzymes

• Enzyme activity is greatly affected by general
  environmental factors
• Enzymes have optimal conditions where they work
  best
• Temperature thermal agitation can disrupt
  conformation. Optimal temp allows greatest
  number of molecular collisions without
  denaturing (usually 35-40ºC)
• pH H concentration can also disrupt
  conformation. Optimal range for most enzymes is
  between pH 6-8

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Cofactors

• Many enzymes require non-protein helpers for
  catalytic activity, called cofactors which are
  bound to the active site
• They can be permanent or bind reversibly with the
  substrate
• Cofactors are inorganic such as iron, zinc, or
  copper
• Coenzymes are organic cofactors

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Enzyme Inhibitors

• Certain chemicals selectively inhibit the action
  of an enzyme by covalently bonding to the active
  site. Usually irreversibly
• Competitive Inhibition bind with the active
  site, competing with the substrate for access to
  the active site
• Can be overcome by increase the concentration of
  the substrate
• Noncompetitive Inhibition bind with the enzyme
  outside of the active site, changing the enzymes
  conformation and impeding the substrate binding
• Examples poisons, antibiotics

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Allosteric Regulation

• Reversible noncompetitive inhibitors are in
  charge of most of the control of metabolism
• Regulatory molecules (activators or inhibitors)
  bind at an allosteric site away from the active
  site to turn on/off an enzymes activity
• Allosteric enzymes have multiple subunits
  (polypeptide chains)

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Feedback Inhibition

• Products of a pathway can act as the allosteric
  inhibitors and switch off an enzyme in the
  catabolic process
• Example ATP is the allosteric inhibitor for the
  ATP-generating catabolic pathway

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Cooperativity

• Substrate molecules can stimulate an enzyme.
  Binding a substrate can induce the enzyme to
  change into a shape which is more favorable for
  binding at other sites
• Amplifies the response of enzymes to substrates

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Localization of Enzymes

• Organisms are more efficient because they can
  keep all the enzymes required for a pathway in
  one place, organ or organelle.
• Metabolic pathways can be assembled together into
  a multienzyme complex to keep everything
  organized and efficient