proteins

• amino acid

  amino acids are the monomers of proteins, linked in chains to form polypeptides
• types of amino acids: common amino acids

  encoded directly by DNA codons
• types of amino acids: derived amino acids


  modified enzymatically after being incorporated into a protein
• structure of amino acids

  alpha-carbon bonded to:

  • amino group (-NH3)
  • carboxyl group (-COOH)
  • Hydrogen atom
  • R group (side chain)
• what does the R group determine

  the amino acids physical and chemical properties eg.

  • polar
  • non polar
  • acidic
  • basic
• Key derived amino acids

  • cystine: formed from two cysteines vis a disulfide bond
  • hydroxyproline and hydroxylysine: post-translationally modified forms essential for collagen stability
• structure of primary proteins


  • sequence of amino acids linked by peptide bonds
  • eg. insulin (2 chains, 51 amino acids total)
  • post-translational modifications (eg. phosphorylation) may be considered part of this structure
• secondary structure of a protein: a-helix

  • stabilised by hydrogen bonds between the C=O of one amino acid and the N-H of another four residues away
  • proline acts as a helix breaker due to its unique ring structure
• secondary structure of a protein: b pleated sheets

  • parallel and antiparallel arrangements
  • stabilized by hydrogen bonds between backbone atoms
  • R groups extend above and below the plane
• tertiary structure of a protein

  • The three-dimensional structure of a single polypeptide.
  • Stabilized by:
  • Hydrophobic interactions
  • Hydrogen bonds
  • Salt bridges
  • Disulfide bonds
• quaternary structure of a protein

  • Assembly of multiple polypeptides into a functional protein.
  • Example: Hemoglobin (composed of four subunits).
• type 1 collagen

  • Most abundant collagen in the body (25% of total proteins).
  • Composed of heterotrimers: two α1(I) chains and one α2(I) chain.
• steps of collagen biosynthesis inside the cell:

  • Synthesis in Rough ER:
  • Hydroxylation of specific proline and lysine residues (requires vitamin C as a cofactor).
  • Glycosylation of some lysine residues.
  • Triple-Helix Formation:
  • Procollagen is formed with N- and C-terminal extension peptides.
• steps of collagen biosynthesis outside the cell

  • Cleavage:
  • Enzymes remove terminal peptides to form tropocollagen.
  • Cross-Linking:
  • Lysyl oxidase (copper-dependent) catalyzes cross-links between lysine residues, stabilizing fibrils.
• scurvy

  • Caused by vitamin C deficiency.
  • Leads to defective collagen synthesis (low levels of hydroxyproline, hydroxylysine).
  • Symptoms: Weakness, poor wound healing, gum disease, bleeding.
• globular proteins

  • Compact and water-soluble.
  • Example: Hemoglobin, enzymes.
  • Hydrophilic residues on the surface, hydrophobic residues inside.
• fibrous proteins

  • Insoluble and elongated.
  • Example: Collagen (structural strength) and elastin (elasticity).
  • Found in tendons, skin, cartilage.
• blood plasma proteins: albumin

  • Most abundant plasma protein.
  • Functions:
  • Maintains oncotic pressure.
  • Transports ions (Ca²⁺), hormones (thyroxine), fatty acids, and drugs.
• blood plasma proteins: haptoglobin

  • Binds free hemoglobin to prevent oxidative damage.
  • Useful in diagnosing hemolytic anemia.
• blood plasma proteins: transferrin

  • Iron transport protein.
  • Binds Fe³⁺ tightly at neutral pH but releases it in acidic vesicles inside cells.
• blood plasma proteins: ceruloplasmin

  • Copper-carrying enzyme.
  • Converts Fe²⁺ to Fe³⁺ for incorporation into transferrin
• purpose of the urea cycle

   Detoxifies ammonia by converting it into urea.
• key steps of urea cycle

  • ammonia incorporation
  • ornithine and citrulline transfer
  • argininosuccinate formation
  • urea formation
• ammonia incorporation

  Carbamoyl phosphate synthetase I catalyzes the formation of carbamoyl phosphate (requires ATP, Mg²⁺, and N-acetyl glutamate)
• Ornithine and Citrulline Transfer

  Ornithine transcarbamylase forms citrulline in mitochondria
• Argininosuccinate Formation

  Citrulline reacts with aspartate
• urea formation

  Arginase hydrolyzes arginine to produce urea and regenerate ornithine
• hyperammonemia

  • Causes: Deficiency in enzymes like carbamoyl phosphate synthetase or ornithine transcarbamoylase.
  • Symptoms: Vomiting, lethargy, developmental delays.
• protein degradation

  • ATP-Dependent Pathway:
  • Proteasome degrades short-lived or misfolded proteins tagged with ubiquitin.
  • ATP-Independent Pathway:
  • Lysosomal degradation of long-lived extracellular proteins.
• lipid rafts

  • Definition: Microdomains in cell membranes enriched in cholesterol, glycosphingolipids, and proteins.
  • Function:
  • Organizing centers for signaling molecules.
  • Facilitate receptor-effector interactions.