Amino Acids & Protein Structures

Amino Acid & Protein 2

• Proteins are composed of amino acids linked by peptide bonds.
• Forces influencing protein structure:
  • Hydrogen bonds between peptide groups.
  • Hydrogen bonds between side chains and peptide groups.
  • Hydrogen bonds between two side chains.
  • Hydrophobic interactions.
  • Ionic bonds.
  • Disulfide bonds.

Secondary Structures

• Alpha-helix:
  • Hydrogen bonds between C=O and N-H groups of neighboring peptide bonds.
  • Right-handed helix.
  • Approximately 11 amino acids per helix turn (range up to 53).
• Beta-sheet:
  • Hydrogen bonds between neighboring peptide bonds in the same or different chains.
  • Parallel or anti-parallel chains.
  • Forms a pleated sheet structure.
  • 2-15 amino acids per sheet (average 6).
  • Anti-parallel more common.
  • Slight right-handed twist.
  • Often found in the central core of globular proteins.

Tertiary Structures

• 3D structure of the polypeptide.
• Arrangement of secondary structures.
• Super-secondary structures (motifs).
• Hydrophobic amino acids usually found in the protein interior (e.g., valine, leucine, methionine).
• Polar and charged amino acids often found on the surface (e.g., glutamic acid, aspartic acid, histidine, lysine).
• Polar (uncharged) amino acids can be found both inside or outside globular proteins (e.g., serine, asparagine, tyrosine).
• Large globular proteins (>200 amino acids) often contain domains.
• Examples: myoglobin, hemoglobin, Concanavalin A.

Quaternary Structures

• Interaction of multiple polypeptide chains to form a larger protein molecule.
• Proteins with multiple chains are called oligomeric.
• Individual chains are called subunits or monomers.
• Structures: dimer, trimer, tetramer, etc.
• Subunits can be identical (homogeneous) or different (heterogeneous).
• Examples: muscle creatine kinase (dimer), hemoglobin (tetramer).

Central Dogma of Protein Folding

• Primary structure determines the tertiary structure.
• Protein folding is spontaneous.
• Folding likely starts with local secondary structures (e.g., alpha-helix, beta structures).
• Molecular chaperones (heat-shocked proteins) assist folding.

Fibrous Proteins

• Proteins with a long, rope-like structure
• Examples:
  • Keratin: Structural component of hair, nails, claws and hooves.
    • Coiled-coils.
    • Protofilaments.
    • Microfibrils.
    • Macrofibrils.
    • α-helix
  • Collagen: Most abundant protein in vertebrates.
    • Component of connective tissue (e.g., ligaments, tendons, cartilage).
    • Triple helix structure.
  • Silk: Forms spider webs and silkworms' cocoons.

Globular Proteins

• Proteins with a roughly spherical shape.
  • Hydrophobic amino acids inside.
  • Hydrophilic amino acids outside.
  • Examples:
    • Myoglobin: Oxygen-carrying protein in muscle tissue.
    • Hemoglobin: Oxygen-carrying protein in red blood cells.

Denaturing Proteins

• Breaking protein bonds.
  • Breaks the protein shape.
  • Prevents proper function.
• Causes: Changes in temperature; pH or salt concentration.
• Fibrous proteins lose structural strength.
• Globular proteins become insoluble and inactive.