Bioenergetics

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Bioenergetics

• Study of energy transformations in living
  organisms
• Thermodynamics
• 1st Law Conservation of E
• Neither created nor destroyed
• 2nd Law Events proceed from higher to lower E
  states
• Entropy always increases
• Universe system surroundings

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Bioenergetics

• (E content of system) ?H (useful free E) ?G
  (E lost to disorder) T?S
• Gibbs Free Energy ?G ?H - T?S
• If ?G negative, then rxn is exergonic,
  spontaneous
• If ?G positive, then rxn is endergonic, not
  spontaneous
• Standard conditions (?G) 25oC, 1M each
  component, pH 7, H2O at 55.6M

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Bioenergetics

• A B lt--gt C D
• Rate of reaction is directly proportional to
  concentration of reactants
• At equilibrium, forward reaction backward
  reaction
• k1AB k2CD
• Rearrange
• k1/k2 (CD)/(AB) Keq
• Relationship between ?G and Keq is
• ?G -2.303 R T log Keq
• If Keq gt1, ?G is negative, rxn will go forward
• If Keq lt1, ?G is positive, rxn will go backward

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• ?G is a fixed value at standard conditions
• ?G under actual cellular conditions can be
  different
• e.g., for ATP hydrolysis inside a cell, can
  approach ?G -12 kcal/mol
• We will work with ?G values

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Coupling endergonic and exergonic rxns
Glutamic acid (Glu) NH3 --gt Glutamine
(Gln) ?G3.4 kcal/mol
ATP --gt ADP Pi ?G-7.3
kcal/mol -----------------------------------------
-----------------------------------------------
Glu ATP NH3 --gt Gln ADP
Pi ?G-3.9 kcal/mol Glutamyl phosphate is the
common intermediate
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ATP --gt ADP Pi ?G -7.3 kcal/mol ADP Pi
--gt ATP ?G 7.3 kcal/mol C(diamond) O2
--gt CO2 ?G -94.8 kcal/mol PEP --gt pyruvate
Pi ?G -14.8 kcal/mol C(graphite) O2 --gt
CO2 ?G -94.1 kcal/mol P-creatine --gt
creatine Pi ?G -11.0 kcal/mol G6-P --gt
glucose Pi ?G -3.0 kcal/mol 1,3-BPG --gt
3PG Pi ?G -12.5 kcal/mol ------------------
--------------------------------------------------
-------------------- What is ?G of PEP ADP
--gt pyruvate ATP ------------------------------
--------------------------------------------------
-------- What is ?G of G6-P ADP --gt glucose
ATP What is ?G of P-creatine ADP --gt
creatine ATP What is ?G of C(s, diamond) --gt
C(s, graphite)
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Equilibrium vs steady state

• Cells are open systems, not closed systems
• O2 enters, CO2 leaves
• Allows maintenance of reactions at conditions far
  from equilibrium

O2
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• Reqd in small amounts
• Not altered/consumed in rxn
• No effect on thermodynamics of rxn
• Do not supply E
• Do not determine product/reactant ratio (Keq)
• Do accelerate rate of reaction (kinetics)
• Highly specific for substrate/reactant
• Very few side reactions (i.e. very clean)
• Subject to regulation
• No relationship between ?G and rate of a reaction
  (kinetics)
• Why might a favorable rxn not occur rapidly?

Biological Catalysts
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Overcoming the activation energy barrier (EA)

• Bunsen burner CH4 2O2 --gt CO2 2H2O
• The spark adds enough E to exceed EA (not a
  catalyst)
• Metabolism burning glucose
• Enzyme lowers EA so that ambient fluctuations in
  E are sufficient

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Overcoming the activation energy barrier (EA)

• Bunsen burner CH4 2O2 --gt CO2 2H2O
• The spark adds enough E to exceed EA
• Metabolism burning glucose
• Enzyme lowers EA so that ambient fluctuations in
  E are sufficient

Catalyst shifts EA line to left lt---
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How to lower EA

• The curve peak is the transition state (TS)
• Enzymes bind more tightly to TS than to either
  reactants or products

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How to lower EA

• Mechanism form an Enzyme-Substrate (ES) complex
  at active site

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How to lower EA

• Mechanism form an Enzyme-Substrate (ES) complex
  at active site
• Orient substrates properly for reaction to occur
• Increase local concentration
• Decrease potential for unwanted side reactions

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How to lower EA

• Mechanism form an Enzyme-Substrate (ES) complex
  at active site
• Enhance substrate reactivity
• Enhance polarity of bonds via interaction with
  amino acid functional groups
• Possibly form covalent bonded intermediates with
  amino acid side chains

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How to lower EA

• Possibly form covalent bonded intermediates with
  amino acid side chains
• Serine protease mechanism

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How to lower EA

• Possibly form covalent bonded intermediates with
  amino acid side chains
• Serine protease mechanism

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How to lower EA

• Mechanism form an Enzyme-Substrate (ES) complex
  at active site
• Induce bond strain
• Alter bonding angles within substrate upon
  binding
• Alter positions of atoms in enzyme too Induced
  fit

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Induced fit
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Induced fit
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Enzyme kinetics The Michaelis-Menten Equation
S lt--gt P At low S, rate/velocity is slow,
idle time on the enzyme At very high S,
rate/velocity is maximum (Vmax), enzyme is
saturated V Vmax S/(S Km) Km S at
Vmax/2 A low Km indicates high enzyme affinity
for S (0.1mM is typical)
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Enzyme kinetics pH and temperature dependence
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Enzyme inhibitors

• Irreversible
• Form a covalent bond to an amino acid side chain
  of the enzyme active site
• Blocks any further participation of the enzyme in
  catalysis

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Enzyme inhibitors

• Reversible
• Competitive
• bind at active site
• Steric block to substrate binding
• Km increased
• Vmax not affected (increase S can overcome)

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Enzyme inhibitors

• Reversible
• Noncompetitive
• Bind at discrete site, not overlapping active
  site
• Subtly alter enzyme structure reducing catalysis
• Km not affected
• Vmax decreased, (increase S cannot overcome)

Noncompetitive
Competitive
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Drug discovery

• Average cost to market 1B
• Average time to market 13 years
• Size of market 170B per year in US
• S. aureus infections are a problem in hospital
  settings
• Drug targets
• Metabolic rxns specific to bacteria
• Sulfa drugs (folic acid biosynthesis)
• Cell wall synthesis
• Penicillin, methicillin, vancomycin
• DNA replication, transcription, translation
• Ciprofloxacin (DNA gyrase)
• Tetracyclins (ribosome)
• Zyvox (ribosome)
• Introduced in 2000, resistance observed within 1
  year of use