7. nucleic acids

• The process of transcription can be divided into three main steps: initiation, elongation and termination

  • In initiation, RNA polymerase binds to the promoter and causes the unwinding and separating of the DNA strands
  • Elongation occurs as the RNA polymerase moves along the coding sequence, synthesising RNA in a 5’ → 3’ direction
  • When RNA polymerase reaches the terminator, both the enzyme and nascent RNA strand detach and the DNA rewinds
• Post transcriptional events:

  • Capping - involves the addition of a methyl group to the 5’-end of the transcribed RNA. The methylated cap provides protection against degradation by exonucleases.
  • Polyadenylation - the addition of a long chain of adenine nucleotides (a poly-A tail) to the 3’-end of the transcript. Improves the stability of the RNA transcript and facilitates its export from the nucleus.
  • Splicing - removal of introns (removal of extrons is called alternative splicing)
• Modification of Histone Tails

  Typically the histone tails have a positive charge and hence associate tightly with the negatively charged DNA

  • Adding an acetyl group to the tail (acetylation) neutralises the charge, making DNA less tightly coiled and increasing transcription
  • Adding a methyl group to the tail (methylation) maintains the positive charge, making DNA more coiled and reducing transcription
• Types of Chromatin

  • When DNA is supercoiled and not accessible for transcription, it exists as condensed heterochromatin
  • When the DNA is loosely packed and therefore accessible to the transcription machinery, it exists as euchromatin
• Elongation of translation

  • A second tRNA molecule pairs with the next codon in the ribosomal A site
  • The amino acid in the P site is covalently attached via a peptide bond (condensation reaction) to the amino acid in the A site
  • The tRNA in the P site is now deacylated (no amino acid), while the tRNA in the A site carries the peptide chain
• Translocation of translation

  • The ribosome moves along the mRNA strand by one codon position (in a 5’ → 3’ direction)
  • The deacylated tRNA moves into the E site and is released, while the tRNA carrying the peptide chain moves to the P site
  • Another tRNA molecules attaches to the next codon in the now unoccupied A site and the process is repeated
• Termination of translation:

  The final stage of translation involves the disassembly of the components and the release of a polypeptide chain:

  • Elongation and translocation continue in a repeating cycle until the ribosome reaches a stop codon 
  • These codons do not recruit a tRNA molecule, but instead recruit a release factor that signals for translation to stop
  • The polypeptide is released and the ribosome disassembles back into its two independent subunits
• A polysome (or a polyribosome) is a group of two or more ribosomes translating an mRNA sequence simultaneously

  • The polysomes will appear as beads on a string (each 'bead' represents a ribosome ; the ‘string’ is the mRNA strand)
  • In prokaryotes, the polysomes may form while the mRNA is still being transcribed from the DNA template
  • Ribosomes located at the 3’-end of the polysome cluster will have longer polypeptide chains that those at the 5’-end
• • Ribosomes are made of protein (for stability) and ribosomal RNA (for catalytic activity)
  • They consist of a large and small subunit:
  • The small subunit contains an mRNA binding site
  • The large subunit contains three tRNA binding sites – an aminoacyl (A) site, a peptidyl (P) site and an exit (E) site
• Transfer RNA (tRNA) have 4 key regions

  • The acceptor stem (3’-CCA) carries an amino acid
  • The anticodon associates with the mRNA codon (via complementary base pairing)
  • The T arm associates with the ribosome (via the E, P and A binding sites)
  • The D arm associates with the tRNA activating enzyme (responsible for adding the amino acid to the acceptor stem)