Marmas Week 2
Contents
Purpose
- Identify the differences in amino acid sequences of alleles.
- Identify what features of amino acid sequences of a protein are associated with pigment and color.
- Explain how genotype-phenotype rules apply to how how colors combine to produce a new color.
- Identify what proteins are present in each of the four starting organisms.
- Construct a purple protein using the information gathered of the biochemistry of plant color.
Methods
- Compare the proteins in the starting strains and compare the differences in allele, color, and amino acid sequence.
- Adjust amino acid sequence in the folding window to accrue new proteins the "History List" panel. These will be used to view new color combinations by adding to upper or lower window.
- Use "Compare" tab to compare the amino acid side-by-side.
- Compare the particular colors' protein sequence to the "sample protein"
- Use the sample protein to compare to colors. Change single amino acids in the sample protein to find what colors are made with what sequence patterns.
- Discover patterns that are associated with different colors
- Use "Hint" section of protocol to analyze patterns. Certain amino acids are associated with colors.
- Form Hypothesis using gathered information
- Considering the color absorbance of proteins such as Green Fluorescent Protein (GFP), the ring structures seem to play an important role on the appearance of color. With this information, proteins associated with colors (rather than the lack of color, white) should have ring structures with resonating bonds near one another.
Results
a) Proteins Produced in each of the four starting organisms:
| Starting Organism | Protein Produced by Allele 1 | Protein Produced by Allele 2 |
|---|---|---|
| Green-1 | Green-Colored Protein | Green Colored Protein |
| Green-2 | Blue-Colored Protein | Yellow-Colored Protein |
| Red | Red-Colored Protein | None |
| White | White-Colored Protein | White Colored Protein |
b) Considering alleles, color, and amino acid sequence of each flower, there are many differences. An allele describes that part of the chromosome that will code for a specific protein. This protein will provide a color (for this experiment, the proteins are titled "____-Colored Protein"), where as if two of the same allele are present, the color associated with the proteins will be the color of the flower. However, if two different alleles are present, each coding for a different colored protein, then the resulting color of the flower is different. For example, when a Blue-Colored Protein and a Yellow-Colored Protein are present, the resulting flower color is green. The amino acid sequence refers to the amino acids that make up the protein. Depending on the configuration of the shape, polarity, and amino acid contents, the protein is associated with a different color.
c) The color associated with the protein produced is dependent on whether it contains an aromatic amino acid which has resonance, specifically tryptophan, phenylalanine, and tyrosine. Tyrosine is associated with blue, phenylalanine is associated with red, and tryptophan is associated with yellow. To make a protein associated with a secondary color, the amino acid sequence must contain the combination of the previously stated amino acids that would intuitively make the secondary color desired.
d) A caveat that must be considered about color association and the amino acid that is associated with that color is the position of the aromatic amino acid in the sequence. Particularly, adding a tyrosine into the sequence will not always result in a blue color association. For example, tyrosine must not be near a positively charged amino acid. When considering the sample protein, the tyrosine will only make a Blue-Colored Protein if it is placed before C11, before M1, or before V9. Once the tyrosine is in a viable spot, a phenylalanine or tryptophan (or both) can be placed before or after it to create a secondary color (or black)
e) Colors that are mixed to produce a new color follow somewhat basic rules of color combinations; when two primary-colored proteins are produced, the resulting phenotype is the corresponding secondary color (ex. blue and yellow make green, red and yellow make orange, etc.). However, when a secondary-colored protein is present with a primary-colored protein, such as a Green-Colored Protein and a Red-Colored Protein, the resulting phenotype is Black. These follows the possible color combinations shown when the plants are crossed in Part I (Genetics).
f) A purple protein was created by adding either a Tyrosine before the F10 in a Red-Colored Protein, or adding a Phenylalanine before the Y10 in a Blue-Colored Protein. This was deduced by adding the amino acid that differentiated the Blue-Colored Protein and the Red-Colored Protein and adding it before the 10th amino acid.
Scientific Conclusions
- If a there is only one allele present, the color associated with the protein that is coded by that allele is the resulting color of the flower
- If two alleles associated with primary colors are present, the resulting color of the flower is the secondary color produced by the two primary colors. This is an example of codominance
- If one allele is associated with a secondary color and one is associated with a primary color that is used to make that secondary color, the resulting color of the flower is the same as the secondary color associated with allele. The Secondary color allele is dominant to the the primary color allele that is used to make the secondary color
- If one allele is associated with a secondary color and one is associated with a primary color that is NOT used to make that secondary color, the resulting color of the flower is black. This is an example of codominance, assuming that black is a mixture of all colors and that mixing two secondary colors produces a color that is approaching black.
- If an allele associated with a color is present with an allele associated with white, the flower color will be the color associated with the allele that is NOT white. White is the most recessive color
- If the amino acid sequence does not follow the pattern of a colored protein, then the resulting protein is associated with white
- Amino acid associations with color:
- Tryptophan is associated with the color yellow
- Phenylalanine is associated with the color red
- Tyrosine is associated with the color blue
- Tyrosine is only associated with the color blue if it comes before a Methionine, Cysteine, Tryptophan, or Phenylalanine
- If the protein has a combination of the above ring-structured amino acids, the resulting color associated with the protein will be that of the intuitive secondary color that will be associated with that protein
- If the protein contains all three of the ring-structured amino acids (works best if near the center of the structure), the resulting color associated with the protein is black
Data and Files
Acknowledgements
I would like to acknowledge my homework partner, Kaitlyn Nguyen
I would like to acknowledge Dr. Dahlquist for helping me with understanding the amino-acid-color correspondence
Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
Marmas (talk) 15:04, 12 September 2019 (PDT)
References
(2017, May 24). Aipotu. Retrieved from http://aipotu.umb.edu/
(2019, September 9). Help:Table. Retrieved from https://en.wikipedia.org/wiki/Help:Table
