LC 05: Translation

• Translation involves reading frames starting with the 5' most AUG codon, where three nucleotides are read at a time to define the amino acid sequence
• The genetic code consists of codons, which are mRNA triplets encoding for amino acids; it includes redundancy with multiple codons for most amino acids, a start codon (AUG), and stop codons
• The genetic code is not the sequence of DNA that makes up an organism (genome); it refers to the codons that specify which amino acids are coded for by three nucleotides
• Ribosomes start translation at the 5' end, skipping until the first AUG codon, which codes for methionine, then continue reading three nucleotides at a time until a stop codon is reached
• TRNAs recognize the codon on mRNA and bring the proper amino acid
• TRNAs are approximately 80 nucleotides long
• TRNAs have both 5' and 3' ends and are transcribed as usual
• TRNAs base pair with themselves in regions, forming double helical structures
• The amino acid gets attached at the 3' end of the TRNA
• The anti-codon on the TRNA binds to the mRNA codon in an anti-parallel and complimentary manner
• TRNA recognizes the codon on the MRNA and brings in the proper amino acid
• TRNAs are approximately 88 nucleotides long
• TRNA base pairs with itself in regions, forming double helical regions
• The three prime end of TRNA is where the amino acid gets attached
• The anti-codon of TRNA binds to the MRNA anti-parallel and complementary
• Modified bases occur in TRNAs after transcription, such as dihydro iDine and pseudo iDine
• There is redundancy in the genetic code, with multiple options for most amino acids
• Two strategies manage genetic code redundancy:

  • More than one TRNA for many amino acids
  • Some TRNAs can recognize and base pair with more than one codon
• The wobble position in TRNA allows flexibility in base pairing, with bacteria showing more flexibility than eukaryotes
• Aminoacyl TRNA synthetases recognize TRNA and put the proper amino acid on it, ensuring accuracy in protein synthesis
• In most organisms, there are 20 Aminoacyl TRNA synthetases, one for each amino acid
• Aminoacyl TRNA synthetases have error correction by hydrolytic editing to ensure accuracy in protein synthesis
• Ribosomes have a large and small subunit, with the large subunit containing the peptidyl transferase center for peptide bond formation
• Ribosome structure:

  • Large subunit and small subunit
  • Large subunit has 49 proteins, composed of many proteins and many ribosomal RNAs (rRNAs)
  • Small subunit has 33 different proteins and one rRNA
• Ribosome sites:

  • A site (aminoacyl site)
  • P site (peptidyl site)
  • E site (exit site)
• Ribosome function:

  • Peptide bond formation catalyzed by peptidyl transferase activity of the rRNA in the large subunit
  • Ribosome is a ribozyme, RNA molecules with catalytic activity
• Elongation factors:

  • EF-Tu (EF1 in eukaryotes, checks aminoacyl tRNA)
  • EF-G (EF2 in eukaryotes, helps ribosome move mRNA forward by one codon)
• Elongation factors in protein synthesis:

  • Aminoacyl tRNA bound to elongation Factor Tu (EFT) enters the free A site on the ribosome
  • If the anticodon of the charged tRNA does not match the codon in the mRNA, the tRNA is rejected
  • Trial and error process repeats until the correct tRNA is identified
  • Elongation Factor Tu hydrolyzes its bound GTP and dissociates if the tRNA is correctly matched and remains bound for a sufficient time
• Elongation Factor G binds to the ribosome, hydrolyzes GTP, and switches the ribosome back to a state where it can accept the next incoming tRNA
• Elongation factors improve speed and efficiency in protein synthesis and have an error-checking function mediated by GTP hydrolysis and release of EFTu and EFG
• In bacteria, mRNA structure includes:

  • 5' untranslated region (UTR)
  • Coding sequence
  • 3' UTR
  • Multiple proteins potentially encoded by one bacterial mRNA, making it polycistronic
• In eukaryotic mRNA, the structure includes:

  • 5' cap
  • 5' UTR
  • Coding sequence
  • 3' UTR
  • Each mRNA typically codes for one type of protein
• Initiation of translation in prokaryotes:

  • Shine-Dalgarno sequence on mRNA base pairs with ribosomal RNA
  • Small ribosomal subunit binds first, followed by initiation factors, tRNA, and then the large subunit
• Termination of translation:

  • A protein release factor recognizes the stop codon
  • The release factor triggers termination by hydrolyzing the bond between the final tRNA and the completed protein
• Translation initiation is crucial for determining the reading frame by finding the 5' most AUG codon
• Initiation of translation does not involve binding of initiation factors to the large ribosomal subunit before the small subunit binds to mRNA
• Shine-Dalgarno sequence is specific to prokaryotic mRNA and allows for multiple translation initiation sites
• The start codon (AUG) codes for methionine in translation
• The delaro sequence allows for multiple translation initiation sites on a UK carotic mRNA
• UK carotic mRNAs cannot code for methionine at any other position