Biochemistry of Proteins

PROTEINS

Functions

  • As biological catalysts – enzymes.
  • Provide structural framework of cells.
  • Act as transport media in bloodstream.
  • Act as hormones.
  • Perform mechanical work in skelatal muscle and heart.
  • Act as antibodies.
  • Regulate gene expression.

Peptides

  • Short sequences of amino acids linked covalently, are known as peptides.
  • Peptide bond is formed by reaction of amino group of one amino acid with the carboxyl group of other.
  • On the basis of number of amino acids they are termed di, tri, tetra- peptides and so on.
Peptide Bond Formation

Biologically active peptides

Biologically Active Protein
Classification of Protein
Classification of Proteins

Bonds Responsible for Protein Structure.

  1. Covalent bond
  • Peptide bonds
  • Disulphide bond

2.  Noncovalent bond

  • Hydrogen bond
  • Hydrophobic bond or interaction
  • Electrostatic or ionic bond 
  • Van der Waals interactions.

Covalent Bond

  • Peptide bonds (–CO-NH–) : bond  formed by the condensation of the amino group of one amino acid with the carboxyl group of another amino acid with a removal of a water molecule
  • Disulfide bond (-S-S-) :  bond formed between the sulfhydryl group (-SH) of side chain of cysteine residues.

Noncovalent Bonds

  • Hydrogen bond : formed between -NH and -CO groups of peptide bond by sharing single hydrogen. Side chains of some amino acids can also form hydrogen bond.  
  • Hydrophobic bond or interaction : formed by interaction between nonpolar hydrophobic R groups (side chain) of amino acids like alanine, valine, leucine, isoleucine, methionine, phenylalanine and tryptophan.
  • Electrostatic or ionic bond or salt bond : formed between oppositely charged groups such as amino (NH3+) terminal and carboxyl (COO) terminal groups of the peptide and oppositely charged R-groups of polar amino acid residues.
  • Van der Waals interactions : include both an attractive and a repulsive forces (between both polar and nonpolar side chain of amino acid residues).
Non-Covalent Bond

Structure – function relationship

  • The following three proteins are considered; each belongs to a different class in the functional classification.
  1. Enzymes
  2. Transport proteins
  3. Structural proteins

Enzymes

  • The first step in enzymatic catalysis is the binding of the enzyme to the substrate. 
  • This, in turn, depends on the structural conformation of the active site of the enzyme, which is precisely oriented for substrate binding.
  • Eg. Carbonic anhydrase catalyses the reversible hydration of carbon dioxide.

Transport proteins

  • Eg. Haemoglobin – sickle cell anemia (HbS) This is formed when the glutamate residue at position 6 in the β chain is replaced by valine.
  • This amino acid residue is present on the surface of the haemoglobin molecule.
  • Replacement of the polar glutamate by nonpolar valine alters the surface properties of the haemoglobin molecule.
  • The nonpolar valine residue on the surface of one molecule attracts the nonpolar residue of another haemoglobin molecule.
  • This starts a chain reaction resulting in the aggregation of several hemoglobin molecules, which form a fibrous structure that distorts the erythrocyte into a sickle-shaped cell
  • Therefore, aggregation of haemoglobin molecules and sickling of erythrocytes occur when haemoglobin is present in the deoxygenated form i.e. at low oxygen tension.
  • Sickled erythrocytes are susceptible to premature destruction.
  • Rapid destruction of erythrocytes causes haemolytic anaemia

Sructural Proteins

  • Collagen is the most abundant protein in mammals and is the main fibrous component of skin, bone, tendon, cartilage and teeth.
  • In vitamin C deficiency, failure of hydroxylation of proline/lysine leads to reduced hydrogen bonding  and consequent weakness of collagen.
  • The quarter staggered triple helical structure of collagen is responsible for its tensile strength.

Properties of proteins

  • Colloidal nature

  Colloidal protein molecules exert osmotic pressure. 

  Colloidal osmotic pressure or oncotic pressure 

   exerted by protein maintain blood volume.

  •   Molecular weight

      Albumin = 6,9000 

      γ-Globulin = 1,60,000.

  • Solubility

     globular proteins, such as, albumin have higher solubility than elongated fibrous proteins. Moreover, smaller molecules are more soluble than larger molecules.

  • Shape of the protein

Scleroproteins like keratin, collagen are in the form of fibers. While soluble proteins tend to be of rounded shape and are called globular proteins.

  • Amphoteric nature
  • Isoelectric pH of the protein
  • Hydration of proteins

Shell-like layer of water, called the “solvation layer” or water envelope isheld around each protein particle in an aqueous medium.

Denaturation of protein

Disorganization of  primary, secondary, tertiary and quaternary structure by breaking of Hydrogen bond, ionic bond and hydro­phobic bond without breakage of any peptide linkage.

Denaturation of Protein

Significance of denaturation 

     Digestibility of native protein is increased. 

–     in blood analysis to eliminate the proteins of 

          the blood.

Coagulation

Irreversible denaturation.

For example boiled egg.

Other Biochemistry Notes

Carbohydrate Metabolism

VITAMIN PYRIDOXINE AND BIOTIN

Vitamin A

Pyrimidine metabolism

Purine Metabolism

Cardiac Biomarkers

VITAMIN D

. Blood Metabolism (Heme synthesis and breakdown)

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