codon

Examples of codon in the following topics:

• Size Variation and ORF Contents in Genomes

  • The transcription termination pause site is located after the ORF, beyond the translation stop codon, because if transcription were to cease before the stop codon, an incomplete protein would be made during translation.
  • Normally, inserts which interrupt the reading frame of a subsequent region after the start codon cause frameshift mutation of the sequence and dislocate the sequences for stop codons.
  • For example, in a randomly generated DNA sequence with an equal percentage of each nucleotide, a stop-codon would be expected once every 21 codons.
  • Possible stop codons in DNA are "TGA", "TAA", and "TAG".
  • Thus, the last reading frame in this example contains a stop codon (TAA), unlike the first two.

• Transcription in Prokaryotes

  • The genetic code is a degenerate, non-overlapping set of 64 codons that encodes for 21 amino acids and 3 stop codons.
  • The codons encoding one amino acid may differ in any of their three positions.
  • A codon is made of three nucleotides.
  • Consequently there are 43 (=64) different codons.
  • The 64 codons encode 22 different amino acids and three termination codons, also called stop codons.

• The Central Dogma: DNA Encodes RNA and RNA Encodes Protein

  • Sixty-one of the codons encode twenty different amino acids.
  • Most of these amino acids can be encoded by more than one codon.
  • These triplets are called stop codons.
  • The codon AUG, also has a special function.
  • The reading frame for translation is set by the AUG start codon.

• The Mechanism of Protein Synthesis

  • The nucleotides around the AUG indicate whether it is the correct start codon.
  • Once the appropriate AUG is identified, eIF2 hydrolyzes GTP to GDP and powers the delivery of the tRNAi-Met to the start codon, where the tRNAi anticodon basepairs to the AUG codon.
  • The aminoacyl-tRNA with an anticodon complementary to the A site codon lands in the A site.
  • The ribosome translocates once codon on the mRNA.
  • The A site moves over an empty codon, and the process repeats itself until a stop codon is reached.

• The Initiation Complex and Translation Rate

  • The start codon also establishes the reading frame for the mRNA strand, which is crucial to synthesizing the correct sequence of amino acids.
  • The anticodon on the tRNAi then binds to the start codon via basepairing.
  • Once bound to the mRNA's 5' m7G cap, the 43S complex starts travelling down the mRNA until it reaches the initiation AUG codon at the start of the mRNA's reading frame.
  • Sequences around the AUG may help ensure the correct AUG is used as the initiation codon in the mRNA.
  • The anticodon on tRNAi-Met basepairs with the AUG codon.

• Unsticking Stuck Ribosomes

  • This lack of a stop codon results a significant issue for cells.
  • Subsequently, the ribosome moves from the 3' end of the truncated messenger RNA onto the tmRNA where it translates the codons of the tmRNA until the tmRNA stop codon is encountered.
  • The tmRNP binds to the A-site, allowing the ribosome to switch templates from the broken message onto the open reading frame of the tmRNA via the resume codon (blue GCA).
  • Upon reaching the tmRNA stop codon (red UAA), a hybrid protein with a proteolysis tag (green beads) is released.

• RNA and Protein Synthesis

  • Methionine and tryptophan are uniquely represented by a single codon.
  • At the other extreme, leucine is represented by eight codons.
  • Also, there are three stop codons that terminate polypeptide synthesis.
  • The anti-codon consists of a nucleotide triplet that is the complement of the amino acid's codon(s).
  • When read from the top to the bottom, the anti-codons depicted here should complement a codon in the previous table.

• Amino Acid Synthesis

  • Selenocysteine is incorporated when the mRNA being translated includes a SECIS element, which causes the UGA codon to encode selenocysteine instead of a stop codon.
  • It is coded with the codon UAG, which is normally a stop codon in other organisms.
  • This UAG codon is followed by a PYLIS downstream sequence.

• The Protein Synthesis Machinery

  • Specific tRNAs bind to codons on the mRNA template and add the corresponding amino acid to the polypeptide chain.
  • Of the 61 non-termination codons, one codon (AUG) also encodes the initiation of translation.
  • Each tRNA has a sequence of three nucleotides located in a loop at one end of the molecule that can basepair with an mRNA codon.
  • When the tRNA anticodon basepairs with one of the mRNA codons, the tRNA will add an amino acid to a growing polypeptide chain or terminate translation, according to the genetic code.
  • The opposite end of the folded tRNA has the anticodon loop where the tRNA will basepair to the mRNA codon.

• Slipped-Strand Mispairing

  • Start (ATG) is the start codon in which the ribosome initiates translation of nucleotide sequence into amino acids, and (-10 -35) is the promoter which is the binding site for the RNAP to initiate transcription of DNA into RNA.