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Purpose

To understand how changing an amino acid sequence of a plant can cause a change in expression of a hypothetical flower color.

Methods/Results

a) What are the differences in the amino acid sequences of the proteins produced by the alleles you define in Part I? Hint: use the Compare menu to find the difference(s) between the amino acid sequences.

Method: All 4 of the given Greenhouse flower colors were compared among each other and identified the difference of the amino acid sequences by using the Compare option in the Aipotu program to dispay the differences between the Upper and Lower Folding Window.

Result: Green-1 contains both amino acid sequences that code for a green colored flower, whereas Green-2 is a mixture between Blue and Yellow amino acid sequences. The difference between the Blue and Yellow sequences is that the Blue amino acid sequence contains a "Tyr" whereas a Yellow amino acid sequence contains a "Trp" instead. The Red flower only contains a single Red amino acid sequence. Lastly, the White flower contains two identical White amino acid sequences.

b) What features of the amino acid sequence make a protein pigmented?

Method: The White flower amino acid sequence was compared to the other colored flowers, then found relations between the colored flowers and finding the common amino acid sequence to make a protein pigmented.

Result: In the white flower, there is a "Val" in the 10th position, whereas the other pigmented flowers do not contain a "Val" in the 10th position, but a different amino acid is in its place to make the protein pigmented. Although, the 11th position is switched from "Cys" to "Trp" in order to make an amino acid sequence for green plants.

c) What features of the amino acid sequence make a protein a particular color?

Method: In order to identify which amino acid makes a protein a particular color, the sequences of each color flower were compared.

Result: In order to get Green-1, the 11th position has to be "Trp" and the 10th position is "Tyr". To get Green-2, which is the mixture between Blue and Yellow flowers, is that the Blue sequence need a "Cys" in the 11th position and a "Tyr" in the 10th position. The Yellow sequence is the same as the Blue sequence, except that "Trp" is in the 10th position. To get a Red protein, the sequence is similar to the Blue sequence but "Phe" is placed in the 10th position instead. Lastly, to get a White protein, which also has a similar sequence to the Blue protein but "Val" is in the 10th position.

d) How do the colors combine to produce an overall color? How does this explain the genotype-phenotype rules you found in part (I)?

Method: The amino acid sequence of Green-1 was compared to the Green-2, which is a heterozygote of Blue and Yellow proteins.

Result: The amino acid that is different between both sequence proteins that are combined, will be inserted near the 10th position. As to say that the new overall color with have both amino acids in its sequence. For example, the "Tyr" from the Blue and the "Trp" of the Yellow are placed in the same sequence at the 10th position to combine into a Pure Green protein.

e) Which proteins are found in each of the four starting organisms?

Method: The Amino acid sequence of each of the four organisms were recorded.

Result:

Protein of Each Starting Organism

Color	Amino Acid Sequence
Green-1	MSNRHILLVYWRQ
Green-2	Mix Between Blue (MSNRHILLVYCRQ) and Yellow (MSNRHILLVWCRQ)
Red	MSNRHILLVFCRQ
White	MSNRHILLVVCRQ

f) Using this knowledge, construct a purple protein.

Method: We went on the Genetics tab and decided to cross Green-2 and Red from the Greenhouse to produce a purple flower. The Purple flower was saved in the Greenhouse and we then went back to the Biochemistry tab. When we clicked on the purple flower from the Greenhouse, and the Lower and Upper Folding Windows were compared. Once the different amino acids were identified, we placed the missing amino acid into the corresponding sequence in the 10th position. After folding the sequence, we received a purple protein.

Result: MSNRHILLVFYCRQ or MSNRHILLVYFCRQ

Screenshot of Purple flower using Aipotu program

Data and Files

Put your data in the tables below:

(a) Which proteins are found in each of the four starting organisms?

Protein of Each Starting Organism

Organism	Allele	Color	Amino Acid Sequence
Green-1	Cg Cg	Green	MSNRHILLVYWRQ
Green-2	Cb Cy	Green	MSNRHILLVYWCRQ
Red	Cr Cr	Red	MSNRHILLVFCRQ
White	Cw Cw	White	MSNRHILLVVCRQ

(c) What features of a protein make it colored?

The 10th position amino acid cannot be "Val" and has to be either a "Tyr", "Trp", or a "Phe".

(d) What features of the amino acid sequence make a protein a particular color?

Firstly, inserting the differentiating amino acid, belonging to a different colored plant, into another colored plant's sequence at the 10th position will result to a flower that has a color which is a mixture between the 2 colors that were combined. For example, to make a true breeding Purple colored plant, one has to insert the "Phe" amino acid, from the Red flower, and place it into the 10th position of the Blue sequence or vice versa, but with inserting "Tyr" into the 10th position of the Red amino acid sequence. This will then result to a purple flower.

The code starting at the 10th position:

• FCRQ will result to a red flower, and
• YWCRQ will result to a green flower

(e) How do the colors combine to produce an overall color? How does this explain the genotype-phenotype rules you found in part (I)?

Through experimentation, it was found that inserting the amino acid/s that is/are present in the Lower Folding Window but not present in the Upper Folding Window, is placed in the 10th or 11th position in the sequence, and the protein will encode for the color mixture of the 2 given colors.

Scientific Conclusion

The main findings of this experiment was that pure true breeding colors and combine with other true breeding color flowers, to produce either a dominant color, or an even color mixture of offspring. In another aspect, changing the amino acid sequence at a particular position will result to an absence or presence of pigmentation. Specific amino acids encode for proteins expressing a specific color, like how "Phe" is the amino acid that encodes for a red flower color.

Acknowledgements

• Worked on this assignment with Ivy-Quynh Macaraeg. We met face-to-face twice outside of class. We messaged each other to share the available hours to meet. We both worked on the Specific Tasks together, but our explanations were made in our own individual words. Dramir36 (talk) 16:37, 10 September 2019 (PDT)

• Received help in making a Table by using a Wikipedia Help:Table page. Dramir36 (talk) 16:37, 10 September 2019 (PDT)

• Received help in highlighting text and making subscripts by using Wikipedia Help:Using colours, and Wikipedia Subscript and superscript. Dramir36 (talk) 18:48, 11 September 2019 (PDT)

• Except for what is noted above, this individual journal entry was completed by me and not copied from another source. Dramir36 (talk) 21:06, 11 September 2019 (PDT)