Molecules to Cells: Protein Structure

1. Four Levels of Protein Structure

• Primary Structure:

  • Description: The sequence of amino acids in a polypeptide chain.
  • Key Elements: Peptide bonds linking the amino acids.

• Secondary Structure:

  • Description: Local folding of the polypeptide chain into structures like alpha-helices and beta-sheets.
  • Key Elements: Hydrogen bonds between the backbone atoms.

• Tertiary Structure:

  • Description: The overall 3D shape of a single polypeptide chain.
  • Key Elements: Interactions between side chains (R groups) such as hydrogen bonds, ionic bonds, hydrophobic interactions, and disulfide bridges.

• Quaternary Structure:

  • Description: The arrangement of multiple polypeptide chains into a single functional protein.
  • Key Elements: Interactions between different polypeptide subunits.

2. Protein Folding and Roles of Accessory Factors

• Protein Folding:
  • Proteins fold into their functional 3D shapes based on the interactions of their amino acids.
  • Roles of Chaperones: Chaperones are proteins that assist in the correct folding of other proteins by preventing misfolding and aggregation.
  • Accessory Factors: Enzymes like protein disulfide isomerase and peptidyl prolyl isomerase help form correct disulfide bonds and isomerize proline residues, respectively.

3. Techniques to Purify, Identify, and Characterize Proteins

• Purification Techniques:

  • Affinity Chromatography: Uses specific binding interactions to isolate a protein of interest.
  • Ion Exchange Chromatography: Separates proteins based on charge.
  • Gel Filtration Chromatography: Separates proteins based on size.

• Identification Techniques:

  • Mass Spectrometry: Identifies proteins by measuring the mass of their peptides.
  • Western Blotting: Detects specific proteins using antibodies.

• Characterization Techniques[/strong>:

  • X-ray Crystallography: Determines the 3D structure of proteins at atomic resolution.
  • NMR Spectroscopy: Provides information on protein structure in solution.

4. Structure and Synthesis of Collagen

• Collagen Structure:

  • Collagen is a triple helix composed of three polypeptide chains.
  • Unique Structural Elements: Every third amino acid is glycine, which allows tight packing of the helix. Proline and hydroxyproline contribute to the stability of the triple helix.

• Synthesis:

  • Collagen is synthesized as a precursor called procollagen, which is modified (e.g., hydroxylation of proline and lysine) and then secreted from the cell.
  • The procollagen is cleaved to form mature collagen, which assembles into fibrils.

5. Structural Causes of Diseases Linked to Collagen Deficiency

• Osteogenesis Imperfecta:

  • Caused by mutations in genes encoding type I collagen, leading to brittle bones.
  • The mutations often disrupt the triple helix structure, reducing the strength of collagen fibers.

• Ehlers-Danlos Syndrome:

  • A group of disorders caused by defects in collagen synthesis or structure.
  • Results in hyperflexible joints, stretchy skin, and in severe cases, vascular issues due to weakened connective tissue.