Marmas Week 2

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

1. 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.
2. 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.
3. Discover patterns that are associated with different colors
   • Use "Hint" section of protocol to analyze patterns. Certain folding patterns are somewhat associated with colors.

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 polarity and shape of the protein seem to have an influence of the color. Both Green-Colored proteins are more polar than the other colors of protein. When the folding configuration of protein is altered to something other than the configuration of the starting organisms, the protein defaults to White-Colored, even if the protein is polar.

d) The features of the amino acid sequence that specifically alter color are the 10th or 11th amino acid in the sequence. This is not necessarily due to polar or charged characteristics, as changing the polar-uncharged Y10 in the Green-1 organism to a Serine, for example, does not maintain the green color. By modifying either the 10th or 11th protein in the sequence, the color will change. However, if the amino acid sequence is modified in a way that the configuration of the protein is altered, the default color is white.

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