PROTEIN STRUCTURE

• Definition of Protein Structure: A protein's structure determines its function, involving complex arrangements of amino acids.

  • Key Components:

  • Active Site: The region on the enzyme where substrate molecules bind and undergo a chemical reaction.

  • Binding Sites: Locations on the enzyme for substrate attachment, including the active site.

  • Catalytic Site: The part of the enzyme where catalysis occurs, ultimately leading to the conversion of substrates into products.

ACTIVE SITE FUNCTIONS

• Active Site Functionality:

  • Binding and Orientation:

  • Enzymes bind substrates at the active site, which positions them correctly for the chemical reaction.

  • Reduction of Activation Energy:

  • Enzymes lower the activation energy needed for a reaction, facilitating faster reaction rates.

ENERGY CONCEPTS

• Energy and Chemical Reactions: Understanding energy change is crucial in biochemical processes.

  • Exergonic Reaction:

  • Characteristics: Reactions that release energy; characterized by a negative free energy change (ΔG < 0).

  • Graphical Representation:

    • Reactants have higher energy compared to products.

  • Endergonic Reaction:

  • Characteristics: Reactions that absorb energy; characterized by a positive free energy change (ΔG > 0).

  • Graphical Representation:

    • Products have higher energy compared to reactants.

LEARNING OBJECTIVE 13.1: ENZYME FUNCTION AND CHARACTERISTICS

1. Why 'Active Site' is Appropriate:

   • The term reflects its role as the specific region where substrate binding and catalysis occur.

2. Mechanisms Lowering Activation Energies:

   • Enzymes stabilize the transition state and provide an alternative reaction pathway with lower activation energy.

3. Specificity of Enzymes:

   • Most enzymes are highly specific due to the precise nature of their active sites, which are tailored for particular substrates.

4. Influence on Reaction Rates:

   • Enzymes increase the speed of reactions by lowering the activation energies but do not change the overall free energy of the reaction (do not make endergonic reactions exergonic).

LEARNING OBJECTIVE 13.2: GRAPH INTERPRETATION

• Understanding Reaction Progress Graphs:

  1. Identify Sections: Label the graph to show reactants, activation energy, and products.

  2. Energy Peaks during Transition State:

     • The peak represents the transition state where reactants are most unstable before forming products.

  3. Determine Reaction Type:

     • Assess if the reaction is exergonic (energy is released) or endergonic (energy is absorbed) based on ΔG values.

ENZYME SUMMARY FROM CODON LEARNING

1. Gene Encoding for Enzymes: Human genes encode information to produce over 2700 distinct enzymes.

2. Enzyme Specificity:

   • Each enzyme is specific to a single reaction, demonstrating the lock-and-key model.

3. Active Site Function:

   • The active site is where substrates bind and where bond-breaking and bond-making processes occur.

4. Speeding Up Reactions:

   • Enzymes facilitate reactions by positioning substrates in an optimal orientation.

5. Reaction Conditions:

   • Enzymes do not change the free energy levels of the reactants or products before and after the reaction.

LEARNING OBJECTIVE 13.3: GRAPH ANALYSIS OF ENZYME ACTIVITY

• Parameters influencing enzyme reactions:

  • pH, Temperature, Substrate Saturation: Understand how these factors impact enzyme activity.

  • Use reaction rate vs various conditions graphs to deduce the normal environment for specific enzymes in cells.

CHEMICAL STRUCTURES IN ENZYMATIC REACTIONS

• Common Molecules and Intermediates:

  • Citrate:

    • Structural Formula: COO

    • HO-C-COO¯

    • H-C-H

    • COO

  • Cis-Aconitate: Connection in the citric acid cycle.

  • Isocitrate: Another important substrate and intermediate in metabolic pathways.

• Overall Process: Enzymes facilitate the conversion of substrates through several intermediates, leading to the final products in various biochemical pathways.