Bioenergetics and Enzymes

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Bioenergetics and Enzymes
Raffinose
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Carbon dioxide reduction is endergonic Glucose
oxidation is exergonic
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In the reaction 2 Na Cl2, 2 Na 2
Cl-, what is being oxidized and what is being
reduced?

• Na is being oxidized, Cl2 is being reduced
• Na is being reduced, Cl2 is being oxidized
• Both Na and Cl2 are being oxidized
• Both Na and Cl2 are being oxidized

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First law The energy content of the universe is
constant. Second law In all energy
transformations, entropy (disorder) increases
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Solar into chemical potential energy
chemical potential into kinetic energy
chemical potential into gradient energy
chemical potential into gradient energy
chemical potential into light energy
Kinetic into heat energy
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Entropy can decrease (order increase) in an open
system
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Biological organisms decrease entropy as they
develop (become more ordered), but in all energy
transformations, entropy increases! Therefore
biological organisms (cells) do not obey the
second law of thermodynamics (which says that
entropy increases).

• True
• False

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G Gibbs free energy H enthalpy (bond
energy) S entropy (disorder)
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Gibbs free energy (G)

• Free energy is a useful concept because it is an
  easy-to-measure indicator of whether or not
  chemical reactions are capable of occurring
  (going to the right) spontaneously.
• Free energy decreases in spontaneous (exergonic)
  reactions. Energy is released by the reaction.
• Free energy increases in reactions that cannot
  occur spontaneously (endergonic). Energy has to
  be put into the reaction to make it go forward
  (to the right).

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I Heart Cell Bio
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1138 a.m. EST on Jan. 28, 1986 Space shuttle
Challenger
Space Shuttle Booster Rocket O-Ring
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• The change in free energy for an reaction can be
  measured if we know
• the Keq of the reaction
• the molar concentration of reactants and
  products.
• the temperature.

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Standard conditions 1 M and STP
Starting at standard conditions, the reaction
will go to the right (exergonic) or to the left
(endergonic) to attain equilibrium.
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The standard free energy change for a reaction
with a Keq 1 is

• gt 0
• lt 0
• 0

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The standard free energy change for a reaction
with a Keq gt 1 is

• gt 0
• lt 0
• 0

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Exergonic Endergonic
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Standard conditions never prevail in the cell.
The standard free energy change is used to
calculate the free energy change at non-standard
conditions.
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non-standard conditions
This is a very important equation for cell
biologists since it allows one to predict the
direction of a chemical reaction from the actual
starting conditions that prevail in the cell.
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Which equation is used to determine if a reaction
in the cell will go forward?

• top
• bottom

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What is the meaning of a positive

• Reaction goes spontaneously to the left from
  standard conditions
• Reaction goes spontaneously to the left from
  standard conditions
• Reaction goes spontaneously to the left from
  prevailing conditions
• Reaction goes spontaneously to the right from
  prevailing conditions

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An exergonic reaction can drive an endergonic
reaction if the two reactions are coupled on the
surface of an enzyme.
The delta Gs are additive.
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The standard free energy change for the complete
oxidation of glucose is -686 kcal/mole. In
respiration, this oxidation is coupled to the
production of 30 ATPs. What is the standard free
energy change for the oxidation of glucose in the
cell?

• -686 kcal/mole
• -686 kcal/mole 30 (-7.3 kcal/mole)
• -686 kcal/mole 30 (7.3 kcal/mole)
• -686 kcal/mole - 30 (-7.3 kcal/mole)

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What does an enzyme do to the standard free
energy change of a reaction it catalyzes?

• Increases it
• Decreases it
• Nothing

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Product
Transition state
Substrate
Insert 5-8
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Picasso, Woman Seated in a Chair, 1941
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In the foregoing demonstration, what did the
chair represent?

• Product
• Reactant
• Enzyme
• Transition state

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Michaelis and Menten

• Learning how enzymes work
• from observing their kinetic behavior

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Initial velocity vo
Vo
y ax2 bx c dy/dx 2ax b at x0, dy/dx b
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Initial velocity vo
Vo
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E S ES E P
k1
k3
k2

• k1, k2, and k3 are rate constants (k4 is ignored)
• k1, k2, and k3 are related to the affinity of the
  enzyme for its substrate
• high k1 means high affinity
• high k2 and k3 means low affinity
• KM (k2 k3)/k1 (low KM high affinity)
• k3 is the turnover number (the maximal rate of
  product formation)
• k3.ET VMAX

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saturation
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Common sense definitions

• VMAX
• the highest rate that a given concentration of
  enzyme can work
• the rate of product formation when the active
  site of the enzyme is saturated
• KM
• the substrate concentration at which the vo is
  half-maximal
• the substrate concentration at which the active
  site is half-saturated (filled half the time)
• An approximation of the affinity of the substrate
  for the active site high KM means low affinity
  and vice versa

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The Michaelis-Menten equation
o

• vo increases as S increases
• at infinite S, vo equals VMAX
• as KM increases (affinity decreases), vo
  decreases

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Which of the following is false?

• At VMAX, the active site is saturated
• At VMAX, the reaction is at equilibrium
• At KM, the active site is half saturated.
• KM is inversely proportional to the affinity of
  the active site for its substrate.

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The affinity of the active site for the substrate
is the sum of all the bonds holding S in place
Cyclic AMP substrate
Phosphodiesterase enzyme
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Aminoacyl-tRNA synthetases add amino acids to
tRNA. Valine and threonine are two structurally
similar amino acids. What is the difference
between the bindings site of A)
valyl-tRNA-synthetase and B) threonyl-tRNA-synthet
ase?

• A has 1 polar binding site and 3 non-polar
  binding sites B has 2 and 2.
• A has 2 polar binding site and 2 non-polar
  binding sites B has 1 and 3.
• A has 2 polar binding site and 2 non-polar
  binding sites B has 3 and 1.
• A has 3 polar binding site and 1 non-polar
  binding sites B has 2 and 2.

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Lineweaver-Burk linear transformation
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Galactokinase catalyzes the phosphorylation of
galactose. The phosphate is from ATP. What is the
KM of galactokinase?

• 0.05 mM
• 0.01 mM
• 10 mM
• 20 mM

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Galactokinase catalyzes the phosphorylation of
galactose. The phosphate is from ATP. What is the
VMAX of galactokinase?

• 0.1 umole/min
• 0.05 umole/min
• 10 umole/min
• 20 umole/min

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Km is increased, Vmax is unchanged
Km is unchanged, Vmax is reduced
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Example of competitive inhibitors
ethanol ethylene glycol
Oxidized by alcohol dehydrogenase to pyruvate
Oxidized by alcohol dehydrogenase to toxic
oxalate which can cause kidney failure
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Example of non-competitive inhibitors
Heavy metals (lead, mercury) bind sulfhydral
groups (cysteine residues) outside of the active
site and change the conformation of the enzyme,
making it totally inactive
Remember that Vmax k3Et
A house painter affected by chronic lead
poisoning. Wasted muscles and wrist drop are
tell-tale symptoms of lead poisoning.
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Lineweaver-Burk linear transformation
Competitive inhibitor
Non-competitive inhibitor
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Two more important ways enzyme (protein) activity
can be controlled by the cell

• Allosterism Different shape. Quaternary
  structure. An allosteric subunit binds an
  allosteric effector and changes the shape of the
  catalytic subunit. KM is changed.
• Phosphorylation The addition of phosphate groups
  from ATP increases or decreases the Vmax of a
  protein.

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