Knguye66 Week 2 - Revision history

Knguye66: add photos

2019-09-12T04:01:02Z

add photos

Knguye66: /* Data and Files */

2019-09-12T03:50:42Z

‎Data and Files

Knguye66: add acknowledgements

2019-09-12T03:41:26Z

add acknowledgements

Knguye66: add references

2019-09-12T03:40:02Z

add references

Knguye66: add answers to sci conclusions

2019-09-12T03:37:32Z

add answers to sci conclusions

Knguye66 at 03:26, 12 September 2019

2019-09-12T03:26:48Z

Knguye66: add answers

2019-09-12T03:26:06Z

add answers

Knguye66: add observation

2019-09-12T03:19:18Z

add observation

Knguye66: add answers to questions

2019-09-12T02:58:48Z

add answers to questions

Knguye66: add font color

2019-09-12T02:42:40Z

add font color

@@ Line 74: / Line 74: @@
 == Data and Files ==
+{|
-[[File:Knguye66_White.png|200px|thumb|Example of White-Colored Protein]]
+|[[File:Knguye66_Green.png|200px|thumb|Example of Green-Colored Protein]]
 == Acknowledgements ==

← Older revision		Revision as of 03:50, 12 September 2019
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	== Data and Files ==		== Data and Files ==
		+
		+	[[File:Knguye66_White.png\|200px\|thumb\|Example of White-Colored Protein]]

	== Acknowledgements ==		== Acknowledgements ==

@@ Line 76: / Line 76: @@
 == Acknowledgements ==
-* This week I worked with Michael Armas ([[User:Marmas]]) for the Aipotu II: Biochemistry assignment.
+* 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.
 [[User:Knguye66|Knguye66]] ([[User talk:Knguye66|talk]]) 15:04, 10 September 2019 (PDT)

← Older revision		Revision as of 03:40, 12 September 2019
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	== References ==		== References ==
		+	(n.d.). Aipotu. Retrieved from http://aipotu.umb.edu/
		+
	{{knguye66}}		{{knguye66}}

← Older revision		Revision as of 03:37, 12 September 2019
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	== Scientific Conclusions ==		== 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 ==		== Data and Files ==

@@ Line 59: / Line 59: @@
 '''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.
 == Acknowledgements ==

@@ Line 43: / Line 43: @@
 |}
-'''B)'''
+'''B)''' Allele|Color|Amino Acid Sequence
 '''C)''' Which features of a protein make it colored?

@@ Line 1: / Line 1: @@
 == Electronic Lab Notebook ==
-#The purpose: what was the purpose of your investigations?
+*The purpose: The purpose of this investigation is to determine biological mechanisms that result in the expression of color.
-#* Your methods: what did you actually do? Give a step by step account.
+** Methods:
-There should be enough detail provided so that you or another person could re-do it based solely on your notebook.
+*** 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).
-You may copy protocol instructions on your page and modify them as to what you actually did, as long as you provide appropriate attribution. Take advantage of the electronic nature of the notebook by providing screenshots, links to web pages, links to data, etc.
-# Your results: the answers to the questions in the protocol, plus any other results you gathered. Usually it makes sense to embed your answers to the questions/results in the "methods" in the order in which you obtained them.
+*Observations:
-#*
+** I first observed patterns in the data.
-# A scientific conclusion: what was your main finding for today's project? Did you fulfill the purpose? Why or why not?
+*** FFFFFFFRRRRRR produced the color red
-#*
+*** RRRFFFFFFFRRR produced the color red
 == Results ==

@@ Line 24: / Line 24: @@
 |-
 | Green-2
-| Met Ser Asn Arg His Ile Leu Leu Val {{font color|blue|Tyr}} Cys Arg Gln (Blue)
+| 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)
 |-
@@ Line 45: / Line 45: @@
 '''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)
 == Acknowledgements ==