Textbook Notes

• In the process of translation, the ribosome uses an mRNA template and aminoacyl-tRNA to synthesize a polypeptide.
• mRNA is read in a 5' to 3' direction and the polypeptide is synthesized from the N terminus to the C terminus.
• In an overview of translation, aminoacyl-tRNA binds to the ribosome, one by one, matching their anticodons to the codons on the message. The growing peptide chain is transferred from the first aminoacyl-tRNA to the incoming aminoacyl-tRNA. The first tRNA is released, and the ribosome move one codon length along the message, allowing the next tRNA to come into place. The ribosome eventually encounters a stop codon, at which point the polypeptide chain is released.
• The hydrolysis of ATP into AMP and PPi is used by aminoacyl-tRNA synthetase to attach an amino acid to the 3' CCA cup of tRNA.
• The anticodon loop contains a trinucleotide sequence called the anticodon that is complementary to the appropriate trinucleotide codon in the mRNA.
• In experiments with polyC and polyA nucleotides, only proline and arginine were produced respectively.
• The nature of the peptide product is determined not only by the composition of the mRNA, but also the reading frame, which is determined by the trinucleotide selected for the first amino acid incorporation.
• The AUG start codon encodes for N-formylmethionine in prokaryotes and methionine in eukaryotes.
• Sometimes bacteria will uses UUG, AUU, or GUG as a start codon, but it uses AUG the most.
• The three stop, or nonsense, codons are UGA, UAA, UAG. They do not code for an amino acid.
• Some organelles and organisms deviate from the standard genetic code encoding 20 standard amino acids.
• Recently the 21st and 22nd amino acids were discovered. They are selenocysteine and pyrrolysine, respectively.
• If guanine is at the 5' position of the anticodon, it can pair with cytosine or uracil on the codon.
• If uracil is in the 5' position of the anticodon, it pairs with adenine or guanine at the 3' position of the codon.
• If inosine is at the 5' end of the anticodon, it pairs with adenine, uracil, or cytosine on the 3' end of the codon.
• The genetic code is redundant, as 20 amino acids are encoded by 64 codons.
• Several codons often correspond to a single amino acid via the wobble effect in the 5' anticodon position, corresponding to the 3' codon position.
• Open reading frames (Orfs) are mRNA sequences bounded by start and stop codons that can be translated.
• The Shine-Dalgarno sequences help align mRNA on the ribosome so translation begins at the appropriate position.
• In prokaryotes, the pattern in mRNA is a Shine Dalgarno sequence (rich in purines), followed by a start codon, followed by an open reading frame, followed by a stop codon.
• Unusual base pairings found in tRNAs are pseudouridine, ribothymidine, and dihydrouridine.
• Pseudouridine.

  
• Ribothymidine

  
• Dihydrouridine

  
• The first step in protein synthesis is the formation of aminoacyl-tRNA.
• Aminoacyl-tRNAs are formed by the enzyme aminoacyl-tRNA synthetase (aaRS) in two steps. First, the amino acid is activated by ATP to form aminoacyl adenylate. Then, the activated amino acid is couples to the tRNA and AMP is released.
• Class I transfer is when the amino acid residue attaches to the 2'-hydroxyl of the 3' CCA cup in tRNA.
• Class II transfer is when the amino acid residue attaches to the 3'-hydroxyl of the 3' CCA cup in tRNA.
• Aminoacyl-tRNA synthetase (aaRS) identification of the correct tRNA is complex. Some aaRSs use the anticodon loop, but other aaRSs recognize different regions of the tRNA.
• The initiation factors in bacteria are IF1, IF2, and IF3.
• The elongation factors in bacteria are EF-Tu, EF-Ts, EF-G, and EF-P.
• The termination factors in bacteria are RF1, RF2, and RF3.
• The initiation factors in eukaryotes are eIF1, eIF1A, eIF2, eIF2b, eIF3, eIF4C, eIF4A, eIF4B, eIF4F, eIF5, and eIF6.
• The elongation factors in eukaryotes are eEF1a, eEF1 beta gamma, eEF2, and a/eIF5A.
• The termination factor in eukaryotes is eRF.
• IF1, eIF1, and eIF1A promote dissociation of the preexisting 70S or 80S ribosome.
• IF2, eIF2, and eIF2B help attach initiator tRNA.
• IF3, eIF3, and eIF4C are similar to IF1. They prepare the mRNA for ribosome binding.
• eIF4A, eIF4B, and eIF4F are the same as eIF1 and eIF1A.
• eIF5 helps to dissociate eIF2, eIF3, and eIF4C.