26.9 Protein Structure

Proteins are the workhorses of life, performing countless functions in our bodies. Their structure is key to their function, with four levels of organization: primary, secondary, tertiary, and quaternary. Each level builds upon the previous, creating complex 3D shapes.

Understanding protein structure is crucial for grasping how they work and what happens when things go wrong. From alpha helices to beta sheets, various forces hold proteins together. When these structures break down, it can lead to serious health issues.

Protein Structure

Four levels of protein structure

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• Primary structure
  • Unique sequence of amino acids linked together by peptide bonds
  • Determined by the gene that codes for the protein
  • Amino acid sequence is specific to each protein (hemoglobin, insulin)
• Secondary structure
  • Local folding patterns of the polypeptide chain stabilized by hydrogen bonds
  • Occurs between the backbone atoms of nearby amino acids
  • Two main types are alpha helices and beta-pleated sheets (collagen, silk)
• Tertiary structure
  • Three-dimensional shape of the entire polypeptide chain
  • Stabilized by various interactions between amino acid side chains
  • Determines the overall structure and function of the protein (enzymes, antibodies)
  • May consist of multiple protein domains, which are distinct functional or structural units
• Quaternary structure
  • Arrangement of multiple folded polypeptide chains into a larger protein complex
  • Held together by the same types of interactions as tertiary structure
  • Not all proteins have quaternary structure (hemoglobin, DNA polymerase)

Alpha helices vs beta-pleated sheets

• Alpha helices
  • Spiral conformation of the polypeptide chain that coils to the right
  • Stabilized by hydrogen bonds between the carbonyl oxygen and amino hydrogen of amino acids spaced 4 residues apart
  • Each turn of the helix contains 3.6 amino acid residues with a rise of 1.5 Å per residue
  • Found in globular proteins (myoglobin) and fibrous proteins (alpha-keratin in hair)
• Beta-pleated sheets
  • Extended conformation of the polypeptide chain with amino acids spaced 3.5 Å apart
  • Stabilized by hydrogen bonds between the backbone atoms of adjacent polypeptide strands
  • Can be parallel with N-termini aligned or antiparallel with alternating N- and C-termini
  • Found in fibrous proteins (silk fibroin) and the core of many globular proteins (immunoglobulins)

Forces in tertiary structure

• Hydrogen bonds form between side chains and backbone atoms
• Disulfide bridges created by the oxidation of cysteine residues (insulin)
• Ionic interactions occur between positively and negatively charged side chains (salt bridges)
• Hydrophobic interactions between nonpolar side chains that avoid water (protein cores)
• Van der Waals forces arise from close packing of atoms
• Denaturation causes loss of tertiary structure by disrupting the stabilizing forces
  1. Changes in temperature (heating)
  2. Changes in pH (acid or base)
  3. Exposure to chemicals (urea, detergents)
• Denaturation often results in loss of protein function (enzyme inactivation)
• Some proteins can refold to their native state when denaturing conditions are removed (renaturation)

Protein Folding and Misfolding

• Protein folding is the process by which a polypeptide chain assumes its functional three-dimensional structure
• Chaperones are proteins that assist in the folding process, preventing misfolding and aggregation
• Misfolded proteins can form aggregates, leading to various diseases
• Prions are misfolded proteins that can induce misfolding in other proteins, causing neurodegenerative disorders