Zrusso Biol 368 week 2

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BIOL368/F11:Week 2

Electronic Lab Notebook

  • So I have no clue how to operate this software so we'll see how this goes.
  • Loaded the sample DNA which folds into a white protein, now I just have to somehow change it into a green and red proteins?
  • randomly mutating bases to see what happens...
  • For some reason my version won't load the organisms so I'm working with Robert on his computer
  • For Green-2, the only differences between the two alleles are at positions 79, 80 where the blue seqence goes 'A,C' and the yellow sequence goes 'G,G'. We discovered this by clicking the 'compare' button and selecting 'upper vs lower'
  • changing base 68 from A to C turns the yellow pigment protein white after folding, however the overall color is still blue from the other protein
    • blue dominant to white
  • white seems to be completely nonfunctional pigment and is recessive to all other pigments
  • difference between blue and yellow pigments is Tyr vs Trp with the codons of TAC vs TGG at the 10th amino acid
  • red is coded for by TTC at 10th amino acid for Phe
  • changing bases other then 78-80 which controls the 10th amino acid can create the red pigments, as long as Phe is at codon 78-80 but it doesn't seem to follow any rhyme or reason and the introns will disappear making huge proteins compared to what we had before.
    • changing the 10th amino acid to Val keeps the introns where they are, but the pigment turns white.
  • couldn't figure out how to create a true breeding purple plant since red and purple are on different alleles, until I added the Phe codon right after the Tyr codon and the allele turned purple!
  • adding the yellow codon right after the previous two makes the allele pigment black
  • turns out Green can also act like purple in that you put blue and yellow codons next to each other next to each other and you get green, so the pigment is coded by two codons. ---Cys, with Cys being the placeholder that gets replaced in the complex colors like green and purple.

Specific Tasks

  1. Blue is TyrCys with TACTGT codon, yellow is TrpCys with TGGTGT codon, red is PheCys with TTCTGT codon, Green is TyrTrp with TACTGG codon, Orange is PheTrp with TTCTGG codon, Black is TyrTrpPhe with TACTGGTTC codon, purple is TyrPhe with TACTTC codon, and white is ValCys with GTCTGT codon, all at the 78th base and onward.
  2. The white alleles are any sequence but the ones for the pigments listed as far as I can tell, so no, the white alleles are a bunch of different DNA sequences.
  3. The DNA sequence is identical except for bases 78-83, which changes to create the 10th and 11th amino acids which bring color except for black where you have all three.
  4. to construct a pure breeding purple flower, genetically modify a blue flower by adding the Phe codon directly after the 80th base, which codes for the codon for the blue color, this makes the allele purple. after that self-pollinate and you have purple flowers forever!
  5. mutations change the DNA sequence of the alleles, which can either confer new functionality or grant additional functionality.


Robert and I attempted to determine the genetic code for the regions that created the different pigmentation proteins. After experimenting with the two green pigments we concluded that two codons were responsible for pigmentation, which were located at the 78-83 bases, or the 10th and 11th amino acids. Phe was responsible for red, Tyr was responsible for blue, and Trp was responsible for yellow. Those three amino acids followed by a Cys would create that color pigment. However, if instead of a Cys, there was another one of the three previous amino acids listed, a new color would be formed. Phe and Tyr would make purple, Phe and Trp would make orange, and Tyr and Trp would make green. Black would be created if you put all three into one sequence and white was found when Val or any other non-aromatic amino acid was placed in the first spot with Cys as the second. White could also be created with putting changes anywhere else in the genetic code except for the 78-83rd bases due to the fact that white is the absence of color instead of an actual pigment. While His is another amino acid that absorbs light, however its introduction anywhere in the range stated previously only created white pigment. I do not know why His does not work while the rest do. I initially thought it was because it has only one absorbance while the other all have multiple, but Cys only has one as well and doesn't even have a ring structure, and replacing Cys with His creates white pigment.

Links for Biol 368

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Zeb Russo's Homepage

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Assignment Pages

BIOL368/F11:Week 7

BIOL368/F11:Week 8

BIOL368/F11:Week 9

BIOL368/F11:Week 10

BIOL368/F11:Week 11

BIOL368/F11:Week 12

BIOL368/F11:Week 14