Energy, ATP, and Enzymes

Part I: The Importance of ATP

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 Topic Outline

• The reason we need ATP to do work

• Hydrolysis of ATP releases free
energy
• ATP as an energy coupler
• Enzymes and ATP

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 Life is about work
(and not so much about fun)
:(
• The ability to acquire and use energy is a
fundamental property of all living organisms.

• In a cell, energy is the ability to do work.

• Some types of work:

Biosynthesis, mechanical activity, active transport (pumping across
a membrane), bioluminescence
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• All reaction pathways for biological work are
ultimately Endergonic (+ΔG). For example:
Monomer + Monomer Dimer + H2O

ΔG = +
• This condensation reaction spontaneously moves
left.
• Making this reaction move to the right requires
an input of energy.
• Many endergonic reactions are driven by free
energy released from the hydrolysis of the
nucleotide ATP. 4
Adenosine Triphosphate: ATP
H2O

ATP is the same ribonucleotide

triphosphate used in RNA!

Another fact favoring an ancient

RNA world? 5
 ATP as energy carrier
• ATP’s three phosphate groups are closely set and all
negatively charged. They repel each other, but are
held together by phosphoester bonds.

• Hydrolysis of the terminal phosphate group

requires some energy, but creates a much
more stable product.
– Going from a less-stable structure to a more-stable
structure releases free energy. 6
 ATP Hydrolysis
• One or more terminal phosphate groups
are removed from ATP by hydrolysis.

• ATP hydrolysis is highly

Exergonic.
/-G°' = –7,300 cal/mol (–7.3 kcal/mol) 7
 the dart gun analogy (with
demo!)
ADP PO42-
(already negative)

• Loading a dart in the barrel requires energy input to compress a spring

(like adding a third phosphate to ADP).

• Spring held compressed by trigger assembly (like phosphoester bond)

• Pulling trigger allows spring to decompress, do work (free energy

release) 8
 ATP as Energy Coupler
• Exergonic ATP hydrolysis is usually
coupled with a second, Endergonic
reaction.

• The coupled reactions moves forward ("to

the right") if |DG| of ATP hydrolysis (7.3
kcal/mol) > | D G| of the endergonic
reaction.

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 ATP as Energy
• Consider the following reaction:
Coupler
A+ B ↔︎C G C>GA+B DG +
– This reaction cannot move to the
right.
• Couple the reaction with ATP
Eq. 1: ATP  ADP + Pi DG1 = –
hydrolysis:
Eq. 2: A + B  C DG2 = +

• If |DG1| > |DG1| , then total reaction sequence

is Spontaneous (Exergonic).
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Example:
Synthesis of glutamine from glutamic acid

NH3
12
13
Part II: Proteins as Catalysts
 The Chemistry of Life
• All reactions are theoretically reversible.
A ↔︎B

• However, only “favorable” reactions can move

forward, and concentrations also matter.
• If a reaction is at Equilibrium, or Endergonic, it
cannot move forward.
• Some exergonic reactions still don’t happen,
however. Why?
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 A favorable cellular
reaction
Hydrolysis of Sucrose

• ΔG = –7,000 cal/mol
• Highly favorable!

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 A favorable cellular reaction
…that still doesn’t go.
• Sucrose + Water = Sucrose +
Water

– Nothing happens for many years!

– Remember: A reaction may be
thermodynamically “spontaneous” but not
occur at an appreciable rate.
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 When a negative DG isn’t enough

• The Laws of Thermodynamics can tell us if a

reaction can move forward or not.
• They tell us little or nothing about reaction rate.
• Most biochemical reactions progress too slowly
on their own to support life.
• Problem solved by using biological Catalysts.

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 What Is a
• Catalyst?
Catalysts accelerate a reaction w/o being consumed
or permanently changed
– Neither a substrate nor a product
• Biological catalysts are called Enzymes.
– Usually a protein
– May be a catalytic RNA
• Ribozyme
– Can be regulated: Up and Down

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 Enzymes Accelerate Reactions

• Reaction goes to completion in

seconds
• How does an enzyme make this
happen?
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 Anatomy of a Chemical
•Reaction
All chemical reactions involve breaking or
rearranging chemical bonds (e.g. covalent or
ionic).
• Process requires a higher-energy, unstable,
intermediate step called the Transition
State.
• Reactants must have sufficient energy to
reach the transition state if a bond is to be
formed or broken.

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 Energy Profile of a Favorable
Reaction
(Reactants) AB + CD → AC + BD (Products)

Activatio
n Energy

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 Energy Profile of a Favorable
Reaction
(Reactants) AB + CD → AC + BD (Products)

Activatio
n Energy

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 Activation Energy (EA)
• For a reaction to go to completion:
– Energy must be present and available to
raise reactants to the transition state.
• Transition state has more energy than reactants.
– Energy is released when old bonds are broken,
new bonds are formed, and the product
assumes a lower-energy, more-stable state.

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 Activation Energy (EA)
• Activation Energy serves as a barrier
to reaction progression and
completion.
– Low Barrier: Many reactant molecules
have sufficient energy.
• The reaction proceeds rapidly.
– High Barrier: Few reactant molecules
have sufficient energy.
• The reaction proceeds slowly.

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 Step 1: Energize reactants

Step 2: Convert reactants to

products and recover
activation energy + more

Step 3: Calculate net energy return

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 Accelerating Favorable
Reactions
• Most important favorable reactions
have significant EA barriers.
• How can get reactants across the
barrier
• Solution 1: Increase average energy
of reactants by increasing
temperature
– Increases the percentage of molecules
with sufficient energy to get over the
barrier 27
– Works well in lab; not in living systems
– Must increase temperature above
dangerous levels to work

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 Accelerating Favorable
• Reactions
Solution 2: Reduce the barrier
– More reactants will have sufficient energy at
the start of the reaction

• This is what enzymes do

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With help, enzymes can also enable
endergonic reactions
• Solution: add an ATP-binding function to
the enzyme.
• Enzyme couples ATP hydrolysis to a
otherwise unfavorable reaction to make it
favorable overall.
• ATP-dependent enzymes are still
essentially lowering EA: mixing ATP and
substrate alone does nothing.
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DNA ligase: an ATP-dependent enzyme

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Role of Enzymes

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 How Do Enzymes Lower EA?
• Enzymes and reactants
form an Enzyme–
Substrate (ES)
Complex.
E+S ↔ ES ↔ E +
P
• Substrate is converted to
the Product (P).
• Interaction between
enzyme and substrate 33
 The Active Site
• Substrates bind at the Active Site
– Groove or pocket exposed on the surface
of enzyme
– Not a rigid structure
– Small portion of enzyme protein structure

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 The Active Site
• Formed from noncontiguous amino
acids

• Great example of the importance of

shape
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 Specificity of Substrate
Binding

• Presence of substrate changes shape of enzyme

to form tight complex: “Induced Fit"
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 1 Substrates enter 2 Substrates are
active site. held in active
site by weak
interactions.

Substrates
Enzyme-substrate
complex
 1 Substrates enter 2 Substrates are
active site. held in active
site by weak
interactions.

Substrates
Enzyme-substrate
complex

3 Substrates are
converted to
products.
 1 Substrates enter 2 Substrates are
active site. held in active
site by weak
interactions.

Substrates
Enzyme-substrate
complex

4 Products are
released. 3 Substrates are
converted to
Products products.
 1 Substrates enter 2 Substrates are
active site. held in active
site by weak
interactions.

Substrates
Enzyme-substrate
complex

5 Active site
is available
for new
substrates.

Enzyme

4 Products are
released. 3 Substrates are
converted to
Products products.