Enzyme Activity and Thermodynamics

Learning Objectives

Differentiate between activation energy and Gibbs free energy.
Be able to calculate the net ΔG of coupled reactions.
List the properties of enzymes.
Compare and contrast exergonic vs. endergonic (relate these to anabolic and catabolic).
Describe HOW enzymes speed up chemical reactions.
Describe and distinguish between active site and allosteric site.
Explain different ways that enzyme activity is regulated.
Differentiate between allosteric activators and inhibitors.
Differentiate between competitive and non-competitive inhibitors.

Gibbs Free Energy

Different molecules have different levels of energy in them.
Gibbs Free Energy (G) is defined as the energy available to do work or "useful" energy.

Chemical Reactions and Energy

Life runs on chemical reactions.

Reaction Example

Glutamic acid + ATP -> Glutamyl phosphate + ADP + P
Reactants: A + BC
Products: AB + C

Change in Free Energy (ΔG)

ΔG indicates whether a reaction is spontaneous.
- If products have lower energy than reactants, energy is released and the reaction can occur spontaneously.
- A negative ΔG indicates that the reaction is spontaneous.
- ΔG Formula:
- $ΔG = G{products} - G{reactants}$
- If ΔG < 0, the reaction CAN go, but the rate may be slow.
Enzymes help speed up reactions.

Types of Reactions

Exergonic Reactions

Exergonic reactions release energy.
ΔG is negative:
- $ΔG = G{products} - G{reactants}$

Endergonic Reactions

Endergonic reactions require energy.
ΔG is positive:
- $ΔG = G{products} - G{reactants}$

Free Energy and Reaction Progress

Graphical representation of energy changes:
- Exergonic reaction: Energy released (ΔG < 0).
- Endergonic reaction: Energy required (ΔG > 0).

ATP and Reaction Energetics

ATP hydrolysis releases energy:
- $ATP + H₂O → ADP + P_i ext{; } ΔG = -7.3 ext{ kcal/mol}$
Coupled reactions can make non-spontaneous reactions occur.

Coupled Reactions

Cells couple endergonic and exergonic reactions to drive reactions.
Energy coupling is defined as the transfer of energy to drive a second reaction.
For example:
- Glucose breakdown coupled with ATP synthesis.
- Net ΔG calculation:
- Example: $Net ΔG = (+3.4) + (-7.3) = -3.9 ext{ kcal/mol}$
Catabolic Pathway
- Definition: Complex molecules broken down to release energy ; Exergonic; Overall ΔG < 0.
Anabolic Pathway
- Definition: Complex molecules built from simpler molecules requiring energy; Endergonic; Overall ΔG > 0.

Enzymes

Definition and Characteristics

Enzymes are biological catalysts.
- Found in all living organisms.
- Specific three-dimensional shape (tertiary or quaternary structure).
- Specific to substrates; physically bind substrates.
- Unchanged by the reaction.
- Required in small amounts.
- Do not change thermodynamic values; they only accelerate thermodynamically favorable reactions.

Role of Enzymes

Enzymes lower activation energy (Ea).
- Activation energy is the energy required to initiate a reaction.
Without enzymes, most biological reactions would not occur.
Example:
- With enzyme: $A + BC → AB + C$
- Without enzyme: $A + BC$

Activation Energy Profiles

Enzymes provide a pathway for reactions to proceed at lower activation energy.
Example of glucose oxidation profile:
Activation energy barrier affects reaction speed significantly.

Mechanism of Enzyme Action

Substrates bind at the enzyme's active site.
Reaction occurs, forming products.
Products are released.
Enzyme can repeat the process.
Enzymes physically bind substrates to assist conversion:
- Align reactants correctly.
- Reactive groups initiate reactions.

Types of Enzymes

Oxidoreductases (EC 1.x.x.x)
- Functions: Catalyze oxidation-reduction reactions.
- Examples: Dehydrogenases, Hydrogenases.
Transferases (EC 2.x.x.x)
- Functions: Catalyze group transfer reactions.
- Examples: Aminotransferases, Phosphotransferases.
Hydrolases (EC 3.x.x.x)
- Functions: Catalyze hydrolysis reactions.
- Examples: Lipases, Peptidases.
Lyases (EC 4.x.x.x)
- Functions: Catalyze the addition/removal of groups to form double bonds.
Isomerases (EC 5.x.x.x)
- Functions: Catalyze isomerization changes.
Ligases (EC 6.x.x.x)
- Functions: Catalyze ligation of two substrates with ATP hydrolysis.

Enzyme Inhibition

Competitive Inhibition

Competitive inhibitor binds at the enzyme’s active site, preventing substrate binding.

Noncompetitive Inhibition

Noncompetitive inhibitor binds at a different site than the active site, altering the enzyme shape and preventing substrate binding.

Allosteric Inhibition

Noncompetitive inhibitors can also function as allosteric regulators.
Allosteric sites allow molecules to modulate enzyme activity.
Allosteric activators increase enzyme activity.

Feedback Inhibition

Feedback inhibition self-regulates pathways.
Example: Threonine deaminase pathway regulated by isoleucine.

Factors Influencing Enzyme Activity

Presence of inhibitors or activators.
Concentration of enzyme and substrate.
Temperature impacting reaction rates.
pH affecting protein folding and stability.

Enzyme Activity and Environmental Factors

Effect of Concentration

Rate of reaction increases with enzyme and substrate concentration until saturation points are reached.

Effect of pH

Enzymes like pepsin work at acidic pH, whereas trypsin works at neutral to basic pH.

Effect of Temperature

Increasing temperatures lead to enzyme denaturation, losing enzymatic activity.

Hydrolysis of ATP

Reaction: $ATP → ADP + P_i; ΔG = -7.3 ext{ kcal/mol}$
The reaction is exergonic and releases energy.

Creatine and Enzyme Regulation

Creatine supplementation can enhance ATP regeneration by phosphorylating ADP to ATP.

Conclusion on Enzyme Function

Enzymes accelerate reactions primarily by lowering activation energy.
They do not change reaction thermodynamics but facilitate faster reaction rates under favorable conditions.