Protein Structure and Function

Amino Acids - The Alpha Team

• Building blocks of proteins. General structure: central $\alpha$-carbon, amino group ($-NH_2$), carboxyl group ($-COOH$), H atom, & variable R-group (side chain).
• All (except Glycine) are chiral; L-isomers predominate in humans.
• Classified by R-group properties: Nonpolar, Aromatic, Polar uncharged, Positively charged (Basic), Negatively charged (Acidic).
• Essential AAs (dietary intake crucial): 📌 PVT TIM HALL (Phenylalanine, Valine, Threonine, Tryptophan, Isoleucine, Methionine, Histidine, Arginine, Leucine, Lysine).
• At physiological pH (approx. 7.4), exist as zwitterions (dipolar ions).
• Peptide bond: Covalent bond linking amino acids; formed by dehydration synthesis (loss of $H_2O$).

⭐ Aromatic amino acids (Tyrosine, Tryptophan, Phenylalanine) are responsible for UV light absorption by proteins, primarily at 280 nm (Tyr & Trp).

Protein Structure - Levels Unlocked

• Primary (1°): Linear sequence of amino acids.
  • Linked by peptide bonds.
  • Determines all higher structures; read N-terminus → C-terminus.
  • Example: Insulin.
• Secondary (2°): Local, regular folding of polypeptide backbone.
  • Stabilized by hydrogen bonds between backbone CO & NH groups.
  • α-helix: Right-handed coil; 3.6 residues/turn. (📌 Proline = Helix Breaker).
  • β-pleated sheet: Extended strands; parallel or antiparallel.
  • β-turns & loops: Connect α-helices and β-sheets.
• Tertiary (3°): Overall 3D conformation of a single polypeptide chain.
  • Maintained by R-group (side chain) interactions:
    • Hydrophobic interactions (major driving force).
    • Hydrogen bonds.
    • Ionic bonds (salt bridges).
    • Disulfide bonds (covalent; Cysteine-Cysteine).
  • Forms functional domains.
• Quaternary (4°): Arrangement of multiple polypeptide subunits (oligomeric proteins).
  • Held by non-covalent interactions & sometimes disulfide bonds.
  • Example: Hemoglobin (tetramer: 2α, 2β subunits).

⭐ The primary structure, the specific amino acid sequence, is the ultimate determinant of a protein's three-dimensional conformation and its biological function.

Protein Folding - Shape Shifters

• Process: Linear polypeptide chain → functional 3D structure. Primary sequence dictates folding.
• Chaperones (e.g., HSPs): Aid correct folding, prevent misfolding & aggregation.
  • HSP60 (chaperonins): Folding chambers.
  • HSP70: Bind nascent polypeptides.
• Misfolding consequences:
  • Degradation by Ubiquitin-Proteasome System (UPS).
  • Aggregation → Amyloid fibrils → Disease.
• Key Diseases: Alzheimer's (Aβ), Parkinson's (α-synuclein), Prion diseases (PrPSc), Cystic Fibrosis (CFTR).

⭐ Prion protein (PrP) misfolding into PrPSc (scrapie form) causes transmissible spongiform encephalopathies (e.g., CJD); PrPSc acts as a template for converting normal PrPC.

Hemoglobin & Myoglobin - Oxygen's Ride

• Hemoglobin (Hb):
  • Structure: Tetramer (α₂β₂ in HbA), 4 hemes, binds 4 O₂.
  • Function: O₂ transport in blood. Sigmoidal O₂ dissociation curve (ODC) due to cooperative binding.
  • Regulation (Right shift ODC = ↑O₂ unloading): ↑ 2,3-BPG, ↑ $PCO_2$ (Bohr), ↑ H⁺ (Bohr, ↓pH), ↑ Temp. 📌 CADET right shift!
• Myoglobin (Mb):
  • Structure: Monomer, 1 heme, binds 1 O₂.
  • Function: O₂ storage in muscle. Hyperbolic ODC, higher O₂ affinity than Hb.
• Fetal Hb (HbF - α₂γ₂): Higher O₂ affinity (poor 2,3-BPG binding) facilitates placental O₂ transfer.

⭐ Carbon monoxide (CO) binds Hb with ~200-250 times greater affinity than O₂, forming carboxyhemoglobin (COHb), impairing O₂ transport and causing a left shift of the remaining Hb's ODC.

High‑Yield Points - ⚡ Biggest Takeaways

• Primary structure (amino acid sequence) dictates higher-order structures and function.
• Secondary structures (α-helix, β-sheet) are stabilized by hydrogen bonds.
• Tertiary structure (3D folding) is stabilized by hydrophobic interactions, disulfide bonds, and ionic bonds.
• Quaternary structure involves multiple polypeptide subunits (e.g., hemoglobin).
• Protein misfolding can cause diseases like Alzheimer's (amyloid-β) and prion diseases.
• Enzymes (protein catalysts) lower activation energy, speeding reactions.
• Allosteric regulation involves binding at a site distinct from the active site, altering protein activity.