Elementary plant Biochemistry and Biotechnology (2+1)

RNA chain initiation

• Once the open promoter complex has formed, RNA polymerase is ready to initiate synthesis.
  
• RNA polymerase contains two nucleotide binding sites called the initiation site and the elongation site.
  
• The initiation site primarily binds to purine triphosphates, ATP or GTP.
  
• ATP is usually the first nucleotide in the chain.
  
• The initiating nucleoside triphosphate binds to the enzyme in the open-promoter complex and forma a hydrogen bond with the complementary DNA base.
  
• The elongation site (also called the catalytic site) is the filled with a nucleoside triphosphate that is selected by its ability to hydrogen-bond with the next base in the DNA strand.
  
• The two nucleotides are then joined together, the first base is released from the initiation site and initiation is complete.
  
• In some way, the details of which are not understood, the RNA polymerase and the template strand move relative to each other, so the binding sites and the catalytic sites are shifted by exactly one nucleotide.
• The drug, rifampicin is useful in studying initiation.
  
• It binds to the ß subunit of RNA polymerase blocking the transition from the chain initiation phase to the elongation phase.

Chain elongation

• After several nucleotides (~ 8) are added to the growing chain, RNA polymerase undergoes a conformational changes and loses the σ subunit.
  
• Thus now this process enters into elongation phase, and most elongation is carried out by the core enzyme of RNA polymerase.
  
• The core enzyme moves along the DNA, binding a nucleoside triphosphate that can pair with the next DNA base and opening the DNA helix as it moves.
• The DNA helix resumes its original shape as synthesis proceeds.
  
• The newly synthesized RNA is released from its hydrogen bonds with the DNA as the helix re-forms.