Title: Lecture 5: Friday, January 16, 2009
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Biology 172
Lecture 15: Wednes day , February 26 , 202 5
Todays Outline
Free Energy
Announcements
Quiz 7 due Tuesday by
midnight
Energy and reactions
Free energy and G
Exergonic reactions
Endergonic reactions
Activation energy
Catalysts
Enzymes ENERGY Energy = the potential to do work
Potential energy - energy stored in an object
Kinetic energy - energy of motion - includes motion at the
molecular scale - i.e., temperature Free Energy
Energy that can be used to do work
Chemical reaction. In a
cell, a sugar molecule is
broken down into simpler
molecules.
Diffusion. Molecules
in a drop of dye diffuse
until they are randomly
dispersed.
(a) Gravitational motion.
Objects
move spontaneously from a
higher altitude to a lower one.
More free energy (higher G)
Less stable
Greater work capacity
Less free energy (lower G)
More stable
Less work capacity
In a spontaneously change
The free energy of the system
decreases ( G<0)
The system becomes more stable
The released free energy can
be harnessed to do work
(a) (b) (c)
More stable
Less concentrated
Less ordered
Lesser work
capacity
Less stable
More concentrated
More ordered
Greater work capacity
Higher free energy
Lower free energy
Objects tend to move from high free energy to lower free energy! Free Energy
> Diffusion. Molecules
> in a drop of dye diffuse
> until they are randomly
> dispersed.
> More free energy (higher G)
> Less stable
> Greater work capacity
> Less free energy (lower G)
> More stable
> Less work capacity
> In a spontaneously change
> The free energy of the system
> decreases ( G<0)
> The system becomes more stable
> The released free energy can
> be harnessed to do work
More stable
Less concentrated
Less ordered
Less work capacity
Less stable
More concentrated
More ordered
Greater work capacity
Higher free energy
Lower free energy
Objects tend to move from high free energy to lower free energy!
The reason molecules
move down their
concentration
gradients is because
each molecule at high
concentration has a
higher free energy
than a molecule at low
concentration Free Energy
Energy that can be used to do work
More stable
Less concentrated
Less ordered (high
entropy
Less work capacity
Less stable
More concentrated
More ordered (low
entropy)
Greater work capacity
Higher free energy
Lower free energy
Objects tend to move from high free energy to lower free energy !
O=C=O O=C=O
O=C=O
O=C=O
O=C=O O=C=O Low Entropy High Entropy Energy -releasing reactions are exergonic
Energy -consuming reactions are endergonic
SPONTANEOUS
NON -SPONTANEOUS
Change in free energy determines reaction
characteristics
Note: spontaneous does not mean instantaneous or
rapid -it means that overall, energy is released.
Reaction requires sustained input of energy.
> Which of these reactions goes from high free energy to low?
Exergonic reactants have
more energy than products
G < 0
Endergonic reactants
have less energy than
products G > 0
Reactants Products
(a) Exergonic reaction: energy released
Reactants
Products
Energy
Progress of the reaction
Amount of
energy
released ( G<0)
> Free energy
Energy
Products
Amount of
energy
consumed ( G>0)
Progress of the reaction
Reactants
> Free energy
(b) Endergonic reaction: energy required
Types of
Chemical
Reactions G = CHANGE in Free Energy
* That energy releasing reactions have
negative G can be confusing really get
this down so that the rest is not confusing
G < 0
G > 0 (a) Exergonic reaction: energy released
Reactants
Products
Energy
Progress of the reaction
Amount of
energy
released ( G<0)
> Free energy
Energy
Products
Amount of
energy
consumed ( G>0)
Progress of the reaction
Reactants
> Free energy
(b) Endergonic reaction: energy required
G = CHANGE in Free Energy Note: The height of each
bar does NOT represent
amount !
The bar represents free
energy
For this endergonic
reaction, which has
higher free energy ?
A. Reactants
B. Products Reaction Equilibrium
If [B] > [A], then K eq > 1
A B
If [B] < [A], then K eq < 1
Equilibrium Constant = K eq = [B]
[A]
The equilibrium constant is the proportion of products
over reactants when the reaction reaches equilibrium Which has higher free energy, a ball at the top or at the bottom?
Would a ball rolling down the hill be an exergonic or endergonic
reaction?
Assuming top = reactant and bottom = product, what is the Keq?
A B Equilibrium Constant = K eq = [B]
> [A]
> (bottom)
> (top)
> [A]
> [B]
Which has higher free energy, a ball at the top or at the bottom?
Would a ball rolling down the hill be an exergonic or endergonic
reaction?
Assuming top = reactant and bottom = product, what is the Keq?
top
bottom
>1
A B Equilibrium Constant = K eq =
> [B]
> [A]
> (bottom)
> (top)
Chemical Reactions
Exergonic reactants have more energy than products
G < 0
Reactants Products
Keq > 1
Keq G
Sucrose + H 2O glucose + fructose 140,000 - 7.0
Endergonic reactants have less energy than products
G > 0 Keq < 1
Acetic acid + H 2O acetate + H 3O+ 0.00002 +6.3
Keq G
> * This means at equilibrium, there are 140K glucose for every sucrose
How does synthesis (polymerization) ie protein synthesis
occur?
Amino acids -> Protein G > 0
A protein is more ordered , less stable , than its
amino acid subunits.
Which has a higher free energy, a protein or its
free amino acids?
This reaction should be endergonic , and non -spontaneous.
So, how do proteins get synthesized?
How do other endergonic reactions proceed?
Endergonic reactions are coupled to exergonic reactions
which allows endergonic reactions to take place. The bonds linking these
phosphate groups have
high potential energy.
Phosphate groups
Adenine
Ribose
Adenosine
Adenosine 5' monophosphate (AMP)
Adenosine 5' diphosphate (ADP)
Adenosine 5' triphosphate (ATP)
ATP Provides the Energy for Many Reactions in the Cell Energy coupling by ATP hydrolysis
G = +3.4 kcal/mol Glu Glu + NH 3
NH 2
> Glutamic
> acid
> Ammonia Glutamine
Coupled reactions: Overall G is negative; together, reactions are spontaneous.
In any biological reaction, always assume the overall reaction will be exergonic!
G = 7.3 kcal/mol ATP H2O+ ADP + P
G = 3.9 kcal/mol
endergonic,
not spontaneous
exergonic,
spontaneous
exergonic,
spontaneous
Overall reaction: Glutamic Acid + Ammonia + ATP Glutamine + ADP + P
G= -3.9 kcal/ mol Spontaneous reactions
Many spontaneous reactions with G < 0 do
NOT occur spontaneously. For example, if you
burn paper, that reaction has a negative G.
Paper + O 2 CO 2 + H 2O
Why doesnt this reaction occur immediately to
all paper? What do you need to start a fire?
G < 0 Transition states
Activation energy
(E A) energy
required for
reactants to reach
the transition state
(unstable
intermediate)
> A
> CD
> A
> A
> B
> B
> B
> C
> C
> D
> D
> Transition state
> Products
> Progress of the reaction
> G< O
> Reactants
> Free energy EA
The requirement
for a transition
state can greatly
impede exergonic
reactions Effect of a catalyst (enzyme) on a
reaction
- does not change
amount of energy
released (i.e., does
not change G)
- does not change
equilibrium
constant, K eq
- does increase the
rate of the reaction - is not itself changed by the reaction
- does lower the
energy of activation,
EABiological catalysts include enzymes
& ribozymes
## Catalysts
Proteins
Enzymes
RNA
> Ribozymes
Example of Exergonic Reaction
Reaction rate depends
on kinetic energy and
activation energy (E A)
energy required for
reactants to reach the
transition state (unstable
intermediate). Even if
G is negative, a reaction
will occur very slowly if
the activation energy is
high.
Transition state
Reactants
Products
Activation
energy
How can we lower Ea?
Transition state= old bonds broken, new bonds being formed Effect of a Catalyst (enzyme) on a
Reaction
A catalyst lowers the
activation energy of a
reaction by stabilizing
the transition state.
Catalysts do not
change G and
are not consumed in the
reaction.
A catalyst lowers
activation energy, thus
speeding up the rate of
reaction .Carboxylesterase
(Homo sapiens)
-ase
-ase
-ase
-ase
-ase
> ENZYMES
Enzymes
Enzymes are proteins
Enzymes act as catalysts by lowering activation
energy
Enzymes have substrate specificity they have
higher binding affinity and/or catalytic activity on
specific molecules
> This enzyme has
> the highest
> catalytic activity on
> Valine, but can
> also act on other
> compounds like
> Isoleucine
Enzymes are protein catalysts and typically catalyze
a single reaction .
Most biological chemical reactions occur at
meaningful rates only in the presence of an enzyme .
Enzymes bring substrates together in specific
positions that facilitate reactions and are very
specific as to which reactions they catalyze .
Cleft or groove on the enzyme where the substrate
binds is called the active site. Amino
acids
Unfolded
enzyme
Bound
substrate
Folded
enzyme
The amino acids that
form the active site are
often far apart in the
linear sequence of the
unfolded enzyme.
Protein folding brings
specific amino acids
close to each other
to form the active
site. Enzyme Active Site
Enzymes have an active site
The active site is where the substrate(s) bind and
where catalysis occurs
Binding between enzyme and substrate can cause a
shape change in the enzyme protein (this is called
induced fit ) enzymes are substrate -
specific
Characteristics of Enzyme Action
region that binds
substrate is active site
binding involves
interactions between
enzymes R -groups and
substrate
binding destabilizes
bond(s) in substrate
> Substrates
> Products
> Enzyme
> Enzyme -substrate
> complex
Active site and substrate specificity
Enzyme substrate specificity emerges from two
features:
1. How well does the active site match the shape
and chemistry of the substrate
2. How well does the enzyme drive catalysis for
that substrate
This pocket
matches the
shape and
chemistry
(hydrophobic) of
the benzene ring
This pocket
matches the
shape and
chemistry
(hydrophobic and
positive charge at
the end) of the
lysine R -group What do enzymes do?
Active site binds substrates (reactants) substrate -
specificity
Binding involves interactions between enzymes R-groups
and substrates
Binding destabilizes chemical bonds in substrate >
lowers the activation energy > reaction goes faster
Substrates (S)
Active site*
Products (P)
Enzyme (E) ES complex Interactions with R -groups at active
site stabilize the transition state
R-groups flanking
active site
R-groups interact
with substrate(s),
stabilizing transition
state
Reaction can
proceed with furthe
interactions with
R-groups Remember: Enzymes lower the activation energy of
a reaction. The reduction in activation energy is due
primarily to four things:
An enzyme holds reactants (substrates) close
together in the right orientation for the reaction,
which reduces the reliance on random collisions.
An enzyme may put a strain on existing bonds,
making them easier to break.
An enzyme provides a microenvironment that is
more chemically suited to the reaction.
Sometimes the active site of the enzyme itself is
directly involved in the reaction during the transition
states. Which of the following is true about
enzymes?
A) lower the G
B) increase activation energy (E a)
C) stabilize transition states
D) change the equilibrium constant
E) the enzyme is permanently changed
after the reaction Enzyme Kinetics
Basic enzymatic reaction:
Reaction Rate = amount of product formed
time
S + E ES E + P
Factors Affecting the Rate of a Reaction:
substrate concentration
enzyme concentration
temperature
pH
the presence/concentration
of other ions
> E = enzyme
> S = substrate
> P = product
Terms
Free energy
G
Exergonic/endergonic
Exothermic/endothermic
Non/spontaneous
Keq
Entropy
Activation energy
Catalysis
Enzyme
Substrate specificity
Active site
Reaction coupling Concepts
What characteristics can help you identify a higher free
energy or lower free energy state?
What type of reaction releases (consumes) energy? Is this
reaction going from low to high, or high to low free
energy? What is this reactions Keq ?
Why arent chemically spontaneous reactions always
spontaneous in the normal usage of that term?
What about a reaction does a catalyst change; what
doesnt it change?
How is a catalyst different than a substrate?
What determines substrate specificity?
How does catalysis occur?
How do endergonic reactions occur in biological systems?