Week 4 - Sept 26

Energy and Enzymes

Introduction to Energy and Enzymes

Enzymes are essential biological catalysts that accelerate chemical reactions in living organisms. They function by lowering the activation energy required for reactions, thereby increasing the rate at which products are formed without being consumed in the process.

Enzyme Function and Catalysis

Definition and Role of Enzymes

• Enzymes are proteins that catalyze (increase the rate of) chemical reactions.

• They are released unchanged at the end of the reaction and can be reused.

• Enzymes are highly specific for their substrates (the reactants they act upon).

Example: The enzyme glucokinase catalyzes the phosphorylation of glucose using ATP as a substrate.

How Enzymes Catalyze Reactions

• Bringing reactants (substrates) together in the correct orientation to facilitate the reaction.

• Lowering the activation energy (EA) required for the reaction to proceed.

Substrate Binding and the Active Site

• The active site of an enzyme is the region where substrate binding occurs.

• Binding is highly specific and often involves an induced fit, where the enzyme changes shape to accommodate the substrate.

• "Shape matters"—the conformation of the enzyme can change upon substrate binding, enhancing catalysis.

Activation Energy and Reaction Progress

Activation Energy (EA)

Activation energy is the minimum energy required to bring reactants to the transition state so that a reaction can occur.

• Enzymes lower the activation energy, allowing more reactant molecules to reach the transition state in a given time period.

• The overall change in free energy ($\Delta G$) of the reaction does not change with enzyme catalysis.

Equation:

$\Delta G = G_{products} - G_{reactants}$

Graphical Representation: Enzyme-catalyzed reactions have a lower peak (activation energy) on a free energy vs. reaction progress graph compared to uncatalyzed reactions.

Major Mechanisms for Lowering Activation Energy

• Orientation: Bringing reactants together in the correct orientation.

• Induced Fit: Changing the shape of the substrate, making it more reactive (e.g., straining or distorting bonds).

• Microenvironment: Creating an environment that promotes the reaction (e.g., providing charged groups or facilitating interactions between R groups and substrates).

How Enzymes Work: The Catalytic Cycle

1. Initiation: Substrates bind to the enzyme's active site, forming an enzyme-substrate complex.

2. Transition State Facilitation: The enzyme stabilizes the transition state, lowering the activation energy.

3. Termination: Products are released, and the enzyme is free to catalyze another reaction.

Example: When ATP and glucose bind to glucokinase, the enzyme changes shape, facilitating the transfer of a phosphate group to glucose.

Factors Affecting Enzyme Activity

Substrate Concentration

• As substrate concentration increases, the rate of product formation increases until the enzyme becomes saturated (maximum speed of reaction).

• At saturation, all enzyme active sites are occupied, and adding more substrate does not increase the rate further.

Enzyme Concentration

• The rate of reaction increases linearly with enzyme concentration, provided substrate is not limiting.

Temperature

• Enzyme activity increases with temperature up to an optimal point, after which activity decreases due to denaturation.

• Different enzymes have different temperature optima depending on the organism's environment.

pH

• Each enzyme has an optimal pH at which it functions best.

• Changes in pH can alter the ionization state of amino acid side chains, affecting enzyme shape and function.

• Enzymes from organisms in acidic environments have lower pH optima, while those from neutral environments have higher pH optima.

Effect of pH on Amino Acid Structure

The ionization state of amino acids changes with pH, which can affect enzyme structure and activity.

pH	Structure of Amino Acid
1	Both amino and carboxyl groups are protonated
3	Carboxyl group loses a proton
7	Both groups are in zwitterion form
10	Amino group loses a proton

Additional info: The specific ionization states influence the charge and shape of the enzyme, impacting substrate binding and catalysis.

Summary Table: Factors Affecting Enzyme Activity

Factor	Effect on Enzyme Activity
Substrate Concentration	Increases rate until saturation
Enzyme Concentration	Increases rate linearly (if substrate is not limiting)
Temperature	Increases rate up to optimum, then decreases due to denaturation
pH	Each enzyme has an optimal pH; deviations reduce activity