BIOCHEMISTRY

• Nitrogen


  • Nitrogen is the most abundant element in the atmosphere. It constitutes 78% concentration in the air
  • Nitrogen is universally present in all organisms in different forms. It is a component of proteins, chlorophyll, enzymes, nucleic acids, hormones
• Nitrogen metabolism


  The biosynthesis of amino acids in plants and the animal body
• Processes in nitrogen metabolism

  • Nitrogen fixation
  • Nitrogen cycle
  • Biosynthesis and breakdown of amino acids
• Nitrogen cycle


  1. Nitrogen gas is converted into organic substances and then back to nature

  2. Ammonification

  3. Nitrification

  4. Nitrate assimilation

  5. Denitrification

  6. Nitrogen fixation
• Ammonification


  Organic Nitrogen is converted into ammonium ions by the microbes present in the soil
• Nitrification


  Ammonia is oxidized to nitrate and nitrite
• Nitrate assimilation


  Plants cannot observe the nitrates present in the soil; hence the nitrates are first reduced to nitrite bio enzyme nitrate reductase, and then the nitrite is converted into ammonia by a series of steps
• Denitrification


  Nitrate and nitrite are converted into ammonia, nitrogen gas and nitrous oxide
• Nitrogen fixation


  The conversion of molecular Nitrogen into beneficial Nitrogen compounds, such as ammonia
• Types of nitrogen fixation

  • Physical (abiological) nitrogen fixation
  • Biological nitrogen fixation
• Physical nitrogen fixation


  Nitrogen is reduced to ammonia without involving any living cell
• Types of physical nitrogen fixation

  • Industrial nitrogen fixation
  • Natural nitrogen fixation
• Biological nitrogen fixation


  The conversion of atmospheric nitrogen into nitrogenous compounds involving living organisms
• Organisms involved in biological nitrogen fixation


  • Symbiotic rhizobium and Frankia
  • Free-living Azospirillum and Azotobacter
  • Blue-green algae (BGA)
  • Aerobic bacteria - Azotobacter
  • Anaerobic photosynthetic bacteria - Clostridium, Rhodopseudomonas
  • Chemosynthetic bacteria - Desulfovibrio
  • Heterocystous Cyanobacteria - Nostoc, Anabaena, Calothrix
• Amino acids metabolism


  Proteins are broken down into their constituent amino acids in digestion inside the stomach
• There are altogether twenty standard amino acids involved in the process of translation
• Anabolism


  The sequence of enzyme-catalyzed reactions in which nutrients are used to form comparatively complex molecules in the living cells with moderately simpler structures
• Anabolic processes


  Control catabolic processes in growing cells. The balance exists between both in non-growing cells
• Enzymatic reaction


  Unlike most proteins, enzymes are reusable. Once they bind to a substrate and catalyse a reaction, enzymes will release the substrate and the active site will regain its shape, ready to bind to another set of substrates
• Substrate


  Enzyme
• Enzyme-substrate complex


  Product
• Denaturation of proteins


  Destruction of the tertiary structure of a protein molecule and the formation of random polypeptide chains
• Levels of protein denaturation

  • Quaternary structure: Subunits of proteins are dissociated from each other and get separate
  • Tertiary structure: 1. Disruption of covalent bonds, 2. Disruption of non-covalent dipole-dipole bonds, 3. Disruption of Van der Waals bonds
  • Secondary structure: Protein loses all repeating patterns such as alpha helix, beta pleated sheet, etc.
• Types of protein denaturation

  • Reversible denaturation
  • Irreversible denaturation
• Agents causing denaturation


  • Chemical factors: Organic solvents (Alcohol, acetone), Detergents (Sodium Dodecyl Sulfate), Extremes of pH, urea (Guanidine Hydrochloride)
  • Physical factors: Heat, UV Light, High Pressure, Violent Shaking
• Renaturation of proteins


  Conversion of a denatured protein back into its native 3D structure. Reconstruction of a protein molecule after losing its original structure.
• Renaturation


  • It is the inverse process of denaturation, but it is not common and easy as denaturation
  • One way of renaturing a protein is removing the SDS and denaturing agents following denaturation during PAGE or IEF protein identification. When the physiological conditions are placed back, the protein folding may occur and restore its original 3D conformation.
• Renaturing


  • The environment returns to optimal folding conditions (which may be different for different proteins)
  • The amino acids are undamaged and unchanged, and have not made new bonds
• Denaturation


  Proteins lose their functional and biologically active 3D structure
• Renaturation


  A denatured protein gets its native 3D structure back
• Denaturation of proteins


  Destruction of the tertiary structure of a protein molecule and the formation of random polypeptide chains
• Levels of protein denaturation

  • Quaternary structure: Subunits of proteins are dissociated from each other and get separate
  • Tertiary structure: Disruption of covalent bonds, non-covalent dipole-dipole bonds, and Van der Waals bonds
  • Secondary structure: Protein loses all repeating patterns such as alpha helix, beta pleated sheet, etc.
• Types of protein denaturation

  • Reversible denaturation
  • Irreversible denaturation
• Agents causing denaturation


  • Chemical factors: Organic solvents (Alcohol, acetone), Detergents (Sodium Dodecyl Sulfate), Extremes of pH, Urea (Guanidine Hydrochloride)
  • Physical factors: Heat, UV light, High pressure, Violent shaking
• Renaturation of proteins


  Conversion of a denatured protein back into its native 3D structure. Reconstruction of a protein molecule after losing its original structure.
• Renaturation


  • It is the inverse process of denaturation
  • It is not common and easy as denaturation
  • One way is removing the SDS and denaturing agents following denaturation during PAGE or IEF protein identification, and then placing the protein back in optimal folding conditions
• Renaturing - Proteins can return to their functional shape when the environment returns to optimal folding conditions (which may be different for different proteins), and the amino acids are undamaged and unchanged, and have not made new bonds
• Denaturation


  Proteins lose their functional and biologically active 3D structure
• Renaturation


  A denatured protein gets its native 3D structure back
• Denaturation of proteins


  Destruction of the tertiary structure of a protein molecule and the formation of random polypeptide chains