Lecture_03_Proteins II

Protein Structure & Function Overview

Subject of the Lecture

Focus: Protein structure and functionCourse: Biology 3510, Chapter 4

Objectives

• Describe protein binding to ligands and enzyme roles: Enzymes lower activation energy for biochemical reactions, crucial for processes like digestion and energy production. Understanding how enzymes bind substrates and transition states is vital for grasping biological mechanisms.

• Discuss activation energy and free-energy change (ΔG): Activation energy is the energy needed to initiate a reaction, while ΔG indicates spontaneity; negative ΔG means a reaction releases energy, and positive ΔG requires energy input. These concepts are essential for metabolic regulation.

Enzyme Classes

• Major enzyme categories: Enzymes are classified by the reactions they catalyze, each playing a unique role in metabolism and regulation

Protein Regulation

• Types of regulation:

  • Feedback regulation: End products can inhibit earlier processes to maintain resource efficiency.

  • Allosteric effects: Effectors bind away from the active site, altering enzyme activity based on cellular needs.

  • Ligand interactions: Small molecules affect protein structure and function, impacting processes like signal transduction.

  • Kinases and phosphatases: Regulate activity by adding/removing phosphate groups.

Protein Visualization

• Antibody use: Techniques like immunofluorescence enable visualization of protein expression and localization. Fusion tags (e.g., GFP) allow real-time tracking of proteins in live cells.

Protein-Ligand Interactions

• Binding Dynamics: Ligands bond at specific protein sites, influencing function through non-covalent interactions:

  • Hydrogen bonds: Structural stability.

  • Ionic bonds: Stability between charged groups.

  • Hydrophobic interactions: Minimize water exposure.

  • Van der Waals forces: Stabilize short-range interactions.

Enzymatic Function

• Characteristics: Enzymes act as catalysts, enhancing reaction rates by lowering activation energy and maintaining specificity for substrates.

• Activation Energy and ΔG: Enzymes lower initiation energy, speeding up reactions without altering free-energy changes.

Classes of Enzymes

• Hydrolase: Cleave bonds (e.g., digestive enzymes).

• Nuclease: Cleave nucleic acids.

• Protease: Hydrolyze protein peptide bonds.

• Ligase: Join molecules, requiring energy.

• Isomerase: Rearrange molecular bonds.

• Polymerase: Synthesize nucleotide chains.

• Kinase: Transfer phosphate groups, important in signaling.

• Phosphatase: Remove phosphates.

• Oxido-reductase: Facilitate oxidation-reduction reactions.

• ATPase: Hydrolyze ATP, releasing energy.

Enzyme Kinetics

• Performance metrics:

  • Vmax: Maximum reaction rate at substrate saturation.

  • KM: Substrate concentration at half Vmax, indicating enzyme affinity.

Example: Lysozyme Function

• Substrate Binding: Lysozyme creates an enzyme-substrate complex (ES) to cleave polysaccharides in bacterial cell walls, essential for immune response.

• Cleavage and Product Formation: Cleaves specific bonds, forming oligosaccharides and regenerating free enzyme, showcasing catalytic efficiency.

Protein Functionality

• 3D Structure: The conformation of proteins is critical; for example, rhodopsin detects light through structural changes when retinal binds, initiating the visual signaling pathway essential for vision.