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Assertion Reason question=2 points total

Short Answer= 2 points each
Clarity
Presents answer clearly and
concisely, in an organized
manner.
1 point
Presents information fairly clearly Uses some information from lectures
and concisely, may have minor
organization problems.
0.5 pts
Significant problems with clarity
and organization, making the
answer hard to understand.
0 pts
Knowledge
Demonstrates an accurate and
complete understanding of the
question, incorporates all pertinent
information with no extra information.
1 point
and assigned readings but not in an
overly thorough manner, some facts
may be missing.
0.5 pts
Merely restates the question and offers
an irrelevant or undeveloped response.
0 pts

REACTION MECHANISM

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III. How are enzymes affected by the

environment?

Why are enzymes sensitive to pH?

Why are enzymes sensitive to change in

temperature?

What types of changes would make an enzyme

function better at higher temperature?

Thermodynamics
Lecture 3

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Thermodynamics

I. What is energy?
II. What is an energy diagram?
III. What is equilibrium?
IV. What is ATP’s role in the cell?

I. What is energy?
Energy is neither created or destroyed
First Law of Thermodynamics

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Second Law of Thermodynamics

As energy changes form, there is an increase in disorder

(entropy, S); that is, some energy is converted into non-usable
forms
What are some less useful forms of energy?

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A side note:

Mass is also conserved!

Carbon atoms are recycled…you have carbons

from dinosaurs in your body!

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We can describe the total

energy in the system as
follows

H = G + TS
Enthalpy Gibbs Free Energy
(Measure of total (Energy available Entropy
energy) for change)
Temperature

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∆G = ∆H – T∆S

• Free energy = ∆G = energy available to do work

• In biological systems, T is relatively constant
• Phase changes (solid to liquid to gas) are
relatively uncommon
• Free energy can often be related to changes in
entropy alone

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Entropy (S) is a measure of

(dis)order
Second Law of Thermodynamics says:
Disorder/entropy tends to increases in
the universe

DECREASED
INCREASED ORDER
ORDER
ENTROPY DOWN
ENTROPY UP

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How does Fido become part of a tree?

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One can ask:

What happens to a system that starts out of
equilibrium?

Which way does the reaction run?

Can we make a prediction based on our

knowledge of free energy?

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II. What is an energy diagram?

Some reactions are energetically
unfavorable

∆G > 0 B
Free Energy

Reaction Coordinate
∆G = ∆H − T ∆S

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What does ∆G > 0 mean?

∆G = ∆H − T ∆S
Building large compounds from smaller ones
takes energy!

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Some reactions are energetically

favorable

A
Free Energy

∆G < 0 B

Reaction Coordinate
∆G = ∆H
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− T ∆S

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If a reaction is exergonic, then which

of the following statements is true?

A. The products have lower free energy than

the reactants.
B. Energy must be added continuously for
the reaction to proceed.
C. The products have lower entropy (are
more ordered) than the reactants.
D. The reaction occurs immediately.
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Energy landscapes for reactions

have “features” - they aren’t
smooth

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One key “feature” in reaction

energy landscapes is known as
the activation energy

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Break

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III. What is equilibrium?

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Equilibrium

• Reactions can run in both directions.

• ∆G=0 when equilibrium is reached.
• What is equilibrium?

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Consider a generic reaction:

A reacts to form B
A could be a hydrogen atom
B could be H2

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Example

• http://phet.colorado.edu/simulations/sim
s.php?sim=Reversible_Reactions
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We add 50 of reactant A. What will happen?

A. All the reactants will quickly overcome the

energy barrier and form products.
B. Only those reactants that have sufficient
energy to overcome the transition state will
form product.
C. The reaction will quickly reach equilibrium.

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If we re-run the experiment but this time started

with 50 molecules of B and no A, what result will
we see?

A. All the reactants quickly overcome the energy

barrier and form products.
B. None of the products have sufficient energy
to overcome the transition state.
C. The products (B) begin to form reactants (A)
but some cross back over the energy barrier to
reform (B) until equilibrium is reached.

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Besides adding heat, how else could you make

the reaction reach equilibrium more quickly?

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Catalysts lower the activation energy

barrier - but do not change deltaG

Is this affecting the forward or reverse reaction or both?

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Which of the following would be the same in an

enzyme catalyzed or non-catalyzed reaction?
A. B. C. D. E.
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Conclusions we can draw from this animation …

1. High energy of activation greatly reduces rate of

reaction
2. Continuous input of high quality energy is
necessary to push an uphill reaction forward

What does equilibrium mean, biologically?

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Inorganic Catalysts

The catalytic converter in your car is made of

metals (platinum).
It catalyzes the oxidation of hydrocarbons to
carbon dioxide, reducing “pollutants”.
Other metals can also act as catalysts.
Clay and pyrite (iron sulfide) provide a surface that
can orient organic molecules, causing them to
organize into chains (polymerize).
The surface is charged, attracting substrates.

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Catalysts as Surfaces
“Cage effect” – catalyst orients substrates, and
increases contact time between reactants
– Reactants held in active site by weak
interactions (e.g., hydrogen bonds)
– Increases contact time
– Controls angle of interaction
– R-groups of amino acids can interact with
the substrate to stabilize transition-state
– ALL cause lowering of energy of activation

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Life uses Enzymes

(not heat)

because….

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In biological systems ATP (along with cognate binding

sites on enzymes) is a common currency for energy
transfer

ATP
Adenosine
Tri-
phosphate

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IV. What is ATP’s role in the cell?

Cells store chemical energy in the form of high
energy carbohydrates and fats, but they also need
“cash” to make things happen.

Why does ATP have such extraordinarily high

potential energy?

ATP

Why is hydrolysis of these bonds favorable?

How many high energy bonds are present in the ATP molecule?

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Hydrolysis of ATP

deltaG ~ -30.5kJ/mol
deltaG ~ -7.3kcal/mol

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Thermodynamically favorable
deltaG = -7.5 kcal/mol
A B+C

D+E F
deltaG = +5 kcal/mol
Thermodynamically Unfavorable
What is the net deltaG for this reaction?

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Which endergonic reaction below can be coupled

to the hydrolysis of ATP (-7kcal/mol)?
a. A B (+9kcal/mol)
b. A B (+14kcal/mol)
c. A B (+4kcal/mol)
d. A B (- 4kcal/mol)
e. A B (- 9 kcal/mol)

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Evaluate the following claim:

“A great deal of energy is released when ATP is
hydrolyzed to ADP, and this released energy
drives events in the cell.”

1) The reaction is ATP + H2O ADP + Pi + 7.3 kcal; those calories

change endergonic reactions to exergonic ones.

2) The energy released by hydrolysis would be lost as heat or

mechanical energy—it wouldn’t do work.

3) The key isn’t the energy released by hydrolysis—it’s the potential

energy added to a substrate when it’s phosphorylated.

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