energetics and metabolism

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energetics and metabolism

• biology 1

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• The chemistry of life is organized into metabolic
  pathways
• Organisms transform energy
• The energy of transformation are subject to the
  Laws of Thermodynamics
• Organisms live at the expense of free energy
• Cellular work is driven by ATP
• Enzymes act as catalysts to reactions
• How Enzymes work, and how they are controlled

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The chemistry of life metabolism

• Metabolism is the sum total of an organisms
  chemical processes, requiring management of
• Materials
• Energy
• Metabolic pathways
• Catabolic pathways break down complex
  macromolecules to simpler products, releasing
  energy
• Anabolic pathways utilize energy to construct
  complex macromolecules from simpler ones
• Anabolism feeds catabolism, and visa-versa

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Organisms transform energy...

• Energy capacity to do work
• Potential energy energy inherent to matter due
  to location or arrangement
• Kinetic energy energy in the process of doing
  work through motion
• For example

Transformation via photosynthesis, using CO2, H20
Suns Energy C6H12O6
(chemical energy)
(kinetic energy)
(plants)
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Energy transformation conforms to the Laws of
Thermodynamics

• 1st Law Energy can neither be destroyed or
  created
• 2nd Law Energy transformations occur so as to
  maximize entropy
• Organisms can be considered open systems.
  Although metabolic processes may be considered to
  decrease entropy within the system, the net
  change to the system and its surroundings should
  reflect an increase in entropy

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Organisms live at the expense of free energy

• Not all of a systems energy is available to do
  work. The energy that is available is termed free
  energy (G), where
• G H - TS
• H total energy
• T absolute temperature
• S Entropy
• \TS energy not available to do work
• Amount of energy harvested from a reaction is
  equal to change in free energy from start to end
  of reaction
• DG DH - TDS
• Certain reactions occur spontaneously (dont need
  energy). Thus in these cases, DG lt 0

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Free energy and metabolism
DG 2870 kJ/mol
e.g., 6CO2 6H2O
C6H12O6 6O2
DG -2870 kJ/mol
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How does the cell harness energy

• ATP (adenosine triphosphate) is the immediate
  source of energy that drives cellular work
• Mechanical work (cilia, flagella, cytoplasmic
  flow, etc.)
• Transport work (pumps)
• Chemical work (anabolism)
• ATP is a nucleotide with unstable phosphate
  bonds. Hydrolysis of a phosphate group is an
  exergonic reaction that releases energy
• ATP H2O ADP Pi

DG -55 kJ/mol
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ATP

• Provides energy through phosphorylation (addition
  of temporary phosphate group to reactant forming
  transitional compound)
• Is continually being regenerated (107/sec).
  Regeneration is endergonic, needing energy (from
  cellular respiration)

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The role of enzymes in metabolism

• Enzymes act as catalysts
• Catalysts act to lower the activation energy of a
  reaction
• Activation energy of a reaction represents the
  energy needed to initially break chemical bonds
  in reactants
• Addition of activation energy (EA) raises free
  energy of reaction to a transitional state
• As new bonds form, free energy is released. DG
  for the reaction is the difference in free energy
  between the reactants and products

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Enzymes as catalysts

• Very selective to a specific substrate, as
  dictated by three-dimensional structure of
  protein
• Substrate binds to enzymes active site with weak
  hydrogen or ionic bonds (lock-and-key
  hypothesis), inducing a change shape of enzyme
• Active site may hold two or more reactants in
  place so that they may react
• Induced fit of enzymes active site may distort
  reactants chemical bonds, weakening them
• Active site may provide localized
  micro-environment conducive to reaction

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Enzyme activity

• Found freefloating in cytoplasm or bound within a
  membrane or organelle
• Activity is maximal under certain conditions of
  temperature (35-40C), pH (6-8), and substrate
  concentration (up to saturation)
• Some enzymes require a co-factor (inorganic Zn,
  Fe, Cu or organic co-enzymes, vitamins) that
  binds to enzyme to induce correct shape

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• Enzymes can be inhibited either reversibly or
  irreversibly
• Competitive inhibitors block the active site form
  the substrate by binding with it themselves
• Non-competitive inhibitors bind to sites other
  than the active site on the enzyme, changing its
  shape so that is no longer specific to original
  reaction (DDT, antibiotics)

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Regulation of enzyme activity

• Allosteric enzymes use non-competitive inhibitors
  that bind to sites that activate or inhibit the
  enzyme
• Binding of an activator to an allosteric site
  activates the enzyme
• Binding of an inhibitor to an allosteric site
  inhibits the enzyme
• Another common method of control is through
  feedback inhibition

Enzyme 1
Enzyme 2
Enzyme 3
Enzyme 4
Enzyme 5
Threonine A B C D isoleucine
Initial substrate
Endproduct and allosteric inhibitor of enzyme 1
Feedback inhibition