Marmas Week 2 - Revision history

Marmas: just realized I forgot to add my template to this page, I know its way past the due date im sorry!

2019-10-03T18:39:15Z

just realized I forgot to add my template to this page, I know its way past the due date im sorry!

Marmas: /* Acknowledgements */ Forgot to add the statement!

2019-09-12T22:04:05Z

‎Acknowledgements: Forgot to add the statement!

Marmas: changed name of category

2019-09-12T02:00:23Z

changed name of category

Marmas: Added Category

2019-09-12T01:43:20Z

Added Category

Marmas: /* References */ added references

2019-09-12T01:07:03Z

‎References: added references

Marmas: /* Methods */ edited methods

2019-09-11T22:04:04Z

‎Methods: edited methods

Marmas: Fixed c and d

2019-09-11T22:02:42Z

Fixed c and d

Marmas: /* Scientific Conclusions */ added caveat for tyrosine

2019-09-10T22:56:53Z

‎Scientific Conclusions: added caveat for tyrosine

Marmas: /* Acknowledgements */ added acknowledgements

2019-09-10T22:47:46Z

‎Acknowledgements: added acknowledgements

Marmas: /* Data and Files */ added table break

2019-09-10T22:34:47Z

‎Data and Files: added table break

← Older revision		Revision as of 18:39, 3 October 2019
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		+	{{marmas}}
	==Purpose==		==Purpose==
	[[Category:Journal Entry]]		[[Category:Journal Entry]]

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 I would like to acknowledge my homework partner, [[User:knguye66|Kaitlyn Nguyen]]<br>
 I would like to acknowledge [[User:kdahlquist|Dr. Dahlquist]] for helping me with understanding the amino-acid-color correspondence<br>
 ==References==

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 ==Purpose==
-[[Category:Individual Journals]]
+[[Category:Journal Entry]]
 *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.

@@ Line 1: / Line 1: @@
 ==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.

← Older revision		Revision as of 01:07, 12 September 2019
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	==References==		==References==
		+	(2017, May 24). Aipotu. Retrieved from http://aipotu.umb.edu/<br>
		+	(2019, September 9). Help:Table. Retrieved from https://en.wikipedia.org/wiki/Help:Table
		+
	==Reflection==		==Reflection==

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 #* 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 folding patterns are somewhat associated with 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.

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 '''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.<br><br>
+'''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.<br><br>
-'''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. <br><br>
+'''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) <br><br>
 '''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).<br><br>
 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.

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 ** Phenylalanine is associated with the color red
 ** Tyrosine is associated with the color blue
 ** 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

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 ==Acknowledgements==
 ==References==
 ==Reflection==

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 |[[File:Marmas_Yellow_Protein.png|200px|thumb|Example of Yellow-Colored Protein]]
 |[[File:Marmas_Blue_Protein.png|200px|thumb|Example of Blue-Colored Protein]]
 |[[File:Marmas_Orange_Protein.png|200px|thumb|Example of Orange-Colored Protein]]
 |[[File:Marmas_Green_Protein.png|200px|thumb|Example of Green-Colored Protein]]