Kevin Wyllie Week 2

Journal Week 2

See my user page.

The given DNA sequence is written in the top strand, while its complementary strand is shown below it.

5'-cgtatgctaataccatgttccgcgtataacccagccgccagttccgctggcggcatttta- 3'
3'-gcatacgattatggtacaaggcgcatattgggtcggcggtcaaggcgaccgccgtaaaat- 5'

Reading frames:

• +1
  • Transcribed: 5'- cgu aug cua aua cca ugu ucc gcg uau aac cca gcc gcc agu ucc gct ggc ggc auu uua -3'
  • Translated: Nter-R-M-L-I-P-C-S-A-Y-N-P-A-A-S-S-A-G-G-I-L-Cter (This is an open reading frame.)
• +2
  • Transcribed: 5'- gua ugc uaa uac cat guu ccg cgu ata acc cag ccg cca guu ccg ctg gcg gca uuu -3'
  • Translated: Nter-V-C-Cter
• +3
  • Transcribed: 5'- uau gcu aau acc aug uuc cgc gua uaa ccc agc cgc cag uuc cgc ugg cgg cat uuu -3'
  • Translated: Nter-Y-A-N-T-M-F-R-V-Cter
• -1
  • Transcribed: 5'- uaa aau gcc gcc agc gga acu ggc ggc ugg guu aua cgc gga aca ugg uau uag cau acg -3'
  • Translated: The first codon in this reading frame is a STOP codon, so there is no polypeptide.
• -2
  • Transcribed: 5'- aaa aug ccg cca gcg gaa cug gcg gcu ggg uua uac gcg gaa cau ggu auu agc aua -3'
  • Translated: Nter-K-M-P-P-A-E-L-A-A-G-L-Y-A-E-H-G-I-S-I-Cter (This is an open reading frame.)
• -3
  • Transcribed: 5'- aaa ugc cgc cag cgg aac ugg cgg cug ggu uau acg cgg aac aug gua uua gca uac -3'
  • Translated: Nter-K-C-R-Q-R-N-W-R-L-G-Y-T-R-N-M-V-L-A-Y-Cter (This is an open reading frame.)

• User:Kwyllie

Protocol

1. First, using the given DNA strand, write out the sequence for the complementary strand. A's pair with T's, while C's pair with G's.
   • Remember that although you may have written the new strand from left to right, due to DNA's antiparallel characteristic, it will be read in the reverse direction, assuming you designated that this new strand was the "bottom strand." To remind yourself of this, add the 5' and 3' notation as done for the original strand, although remember that the sides for either will be reversed.
2. To avoid errors when using the amino acids translation chart (discussed below), you should write out the mRNA transcript for all six of the frames.
   1. Start by copy/pasting the original (or top) strand and grouping the nucleotides into groups of three (retaining their order, of course). This allows you to more easily visualize each codon. This first sequence is your "+1" frame.
   2. Again, copy/paste the top strand, and group into threes, but this time start by deleting the very first nucleotide in the sequence. You'll notice that you have two nucleotides left over at the end. These can also be deleted. This is your "+2" frame.
   3. For the "+3" frame, start by deleting the first two nucleotides and continue as normal.
   4. For the "-1" frame, you should start by re-writing the strand in the 5' to 3' direction (remember that it is currently in the 3' to 5' direction). This may be tedious, but it can get very confusing to read the strand in reverse. After that, as before, group the nucleotides into groups of three.
   5. Once the bottom strand has been re-written appropriately, repeat the steps used for the "+" frames to get your "-2" and "-3" frames.
3. Finally, translate each frame.
   • Use the amino acid translator chart to convert each codon into an amino acid. Here's an amino acids chart from ManyLabs.org
   • If a "stop codon" is reached, the amino acid chain is terminated. No need to write "STOP." Instead, indicate the beginning and end of the chain with the "Nter" and "Cter" notation.
     • "Nter," short for "N-terminus" denotes the beginning of the chain, while "C-ter" denotes the end.
   • If a frame does not contain a STOP codon, then it referred to as an "open reading frame."