Knguye66 Week 2
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Contents
Electronic Lab Notebook
- The purpose: The purpose of this investigation is to determine biological mechanisms that result in the expression of color.
- Methods:
- In this experiment, I used the Aipotu software to answer questions in Part II: Biochemistry. I looked for patterns and hints for expression of color in amino acid sequences to determine links between colors and if particular amino acids correspond to color. I first started off with the "Specific Tasks" for this lab to grasp a better understanding of the software and likewise, produce better results. Then, I systematically went through the software step-by-step (starting with clicking on each individual Greenhouse color) to answer questions (found in the results section).
- Methods:
- Observations:
- I first observed patterns in the data.
- FFFFFFFRRRRRR produced the color red
- RRRFFFFFFFRRR produced the color red
- KKKKKKLLLLLLF produced the color red
- KKKKKKLLLLLLL produced the color white
- SLQLNITMEVDFW produced the color orange
- EEEWWWWWWWEEE produced the color yellow
- I first observed patterns in the data.
This is my first hint that adding Phe will produce the color red since each of the first three amino acid sequences included a Phe, the combination of Phe and Trp will produce Orange, and the combination of Trp and Tyr will produce Blue, while white is when none or neither of the three amino acids are in the combination. My initial hypothesis is as follows:
- Phe produces the color Red, Trp produces the color Yellow, and Tyr produces the color Blue. These are the "primary" colors that can combine to create secondary colors (orange, purple, green, and even black).
Results
A) Which proteins are found in each of the four starting organisms?
- Data in the table below:
| Starting Organisms | Upper Folding Window (Allele 1) | Lower Folding Window (Allele 2) |
|---|---|---|
| Green-1 | Met Ser Asn Arg His Ile Leu Leu Val Tyr Trp Arg Gln (Green) | Met Ser Asn Arg His Ile Leu Leu Val Tyr Trp Arg Gln (Green) |
| Green-2 | Met Ser Asn Arg His Ile Leu Leu Val Tyr Cys Arg Gln (Blue) | Met Ser Asn Arg His Ile Leu Leu Val Trp Cys Arg Gln (Yellow) |
| Green-Red | Met Ser Asn Arg His Ile Leu Leu Val Phe Cys Arg Gln (Red) | no amino acid sequence found |
| White | Met Ser Asn Arg His Ile Leu Leu Val Val Cys Arg Gln (White) | no amino acid sequence found |
B) Allele|Color|Amino Acid Sequence
- As we see from the table above, the differences in the amino acid sequence are most prevalent in Green-2 with the switch from Tyr to Trp. In Green-Red, with the addition of Phe amino acid, and in White which is the original "Load Sample Protein" amino acid sequence.
C) Which features of a protein make it colored?
- The bond structures of a protein make it colored. In the protein, we look for amino acids with altering ring structures, such as that of Phe, Tyr, and Trp. Alternating double and single bonds result in resonance which lowers the wavelength and gives the ability to absorb more pigment and gain more photons. This results in color.
D) What features of the amino acid sequence make a protein a particular color?
- As observed from the results of the experiment, depending on where the three different aromatic amino acids are placed, Phenylalanine (Phe), Tyrosine (Tyr), and Tryptophan (Trp) are placed or replace another amino acid in the sequence, it results in a different color. For example, to make the color blue, Tyr replaces Val in the "Load Sample Protein" amino acid sequence. To make yellow, Trp replaces Val in the sequence. To make red, Phe replaces Val. A pattern that I have noticed is that these specific amino acids will be strategically in front of Cys.
E) How do the colors combine to produce an overall color? How does this explain the genotype-phenotype rules you found in part (I)?
- Primary colors, red, blue, and yellow form by replacing Val in "Load Sample Protein" sequence before Cys (ie. Phe=red, Tyr=Blue, Trp=Yellow)
- By combining the primary colors, green, orange, and purple are created. (Green=BluexYellow, Orange=RedxYellow, Purple=BluexRed)
- This aligns with the genotypic and phenotypic rules that the secondary colors (green, orange, and purple) have incomplete dominance.
F) Show your TA that you have made a purple protein. For full credit, you need to explain to your TA why it is purple.
- After creating purple, using the combination found in BluexRed, we add the amino acid that the sequence was lacking. As all amino acids in the sequence were except for the difference in Phe (making it red) vs. Tyr (making it blue), we add the corresponding amino acid necessary to make the purple protein. To the Upper Panel which used to be red, I added a Tyr (Blue) to the amino acid sequence which resulted in creating a purple protein.
Scientific Conclusions
The main finding for this week's experiment is that co-dominance exists between alleles which associate for a particular protein and color.
- Amino acids associated with color:
- Tryptophan with Yellow
- Tyrosene with Blue
- Phenylalanine with Red
- The combinations of these primary colors results in Orange, Green, Purple, and Black:
- Orange (TrpxPhe) by combining the two amino acid sequences for Yellow and Red
- Green (TyrxTrp) by combining the two amino acid sequences for Blue and Yellow
- Purple (TyrxPhe) by combining the two amino acid sequences for Blue and Red, or adding in Tyr and Phe to one amino acid sequence
- Black (Tyr,Phe,Trp) by adding in amino acid Tyr, Phe, and Trp to one amino acid sequence slowly creates a pigment closer to black
- Since the presence of specific amino acids resulted in a particular color, it may be due to the increased conjugation of these aromatic structures that allows for absorption of ultraviolet light and for that reflection of color. The colors work best when placed in front of Cys in the amino acid sequence as it falls closer to the middle of the "bulb" in the structure.
Data and Files
Acknowledgements
- This week I worked with Michael Armas (User:Marmas) for the Aipotu II: Biochemistry assignment and to Professor Dahlquist (User:Kdahlquist) for helping me and my partner with setting up and finding conclusions to our experiment.
Except for what is noted above, this individual journal entry was completed by me and not copied from another source. Knguye66 (talk) 15:04, 10 September 2019 (PDT)
References
(n.d.). Aipotu. Retrieved from http://aipotu.umb.edu/
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