Dramir36 Week 2 - Revision history

Dramir36: /* Acknowledgements */ included more ack.

2019-09-12T04:06:33Z

‎Acknowledgements: included more ack.

Dramir36: /* Scientific Conclusion */ removed indent

2019-09-12T04:02:55Z

‎Scientific Conclusion: removed indent

Dramir36: /* Scientific Conclusion */ indent

2019-09-12T04:02:42Z

‎Scientific Conclusion: indent

Dramir36: Included Scientific Conclusion

2019-09-12T04:02:30Z

Included Scientific Conclusion

Dramir36: /* Data and Files */ indented

2019-09-12T03:57:13Z

‎Data and Files: indented

Dramir36: /* Data and Files */ answered the letter questions

2019-09-12T03:56:22Z

‎Data and Files: answered the letter questions

Dramir36: /* Data and Files */ deleted question b

2019-09-12T01:49:32Z

‎Data and Files: deleted question b

Dramir36: /* Acknowledgements */ added more acknowledgements

2019-09-12T01:48:42Z

‎Acknowledgements: added more acknowledgements

Dramir36: /* Data and Files */ highlighted differences in sequences

2019-09-12T01:45:20Z

‎Data and Files: highlighted differences in sequences

Dramir36: added table to Data set

2019-09-12T01:30:23Z

added table to Data set

@@ Line 112: / Line 112: @@
 ==Acknowledgements==
-*Worked on this assignment with [[User:Imacarae|Ivy-Quynh Macaraeg]]. [[User:Dramir36|Dramir36]] ([[User talk:Dramir36|talk]]) 16:37, 10 September 2019 (PDT)
+*Worked on this assignment with [[User:Imacarae|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. [[User:Dramir36|Dramir36]] ([[User talk:Dramir36|talk]]) 16:37, 10 September 2019 (PDT)
 *Received help in making a Table by using a Wikipedia Help:Table page. [[User:Dramir36|Dramir36]] ([[User talk: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. [[User:Dramir36|Dramir36]] ([[User talk:Dramir36|talk]]) 18:48, 11 September 2019 (PDT)

@@ Line 108: / Line 108: @@
 ==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.
+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==

@@ Line 108: / Line 108: @@
 ==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.
+: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==

← Older revision		Revision as of 04:02, 12 September 2019
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	: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.		: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==		==Acknowledgements==

@@ Line 93: / Line 93: @@
 (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.
+: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:
+:The code starting at the 10th position:
 :*FCRQ will result to a red flower, and
 :*YWCRQ will result to a green flower
@@ Line 103: / Line 103: @@
 (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.
+: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.
 ==Acknowledgements==

← Older revision		Revision as of 01:49, 12 September 2019
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	\| C<sub>w</sub> C<sub>w\|\| White \|\| MSNRHILLV<span style="color:blue">VC</span>RQ		\| C<sub>w</sub> C<sub>w\|\| White \|\| MSNRHILLV<span style="color:blue">VC</span>RQ
	\|}		\|}
−
−
−	~~(b) allele color amino acid sequence (highlight differences)~~

← Older revision		Revision as of 01:48, 12 September 2019
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	*Received help in making a Table by using a Wikipedia Help:Table page. [[User:Dramir36\|Dramir36]] ([[User talk:Dramir36\|talk]]) 16:37, 10 September 2019 (PDT)		*Received help in making a Table by using a Wikipedia Help:Table page. [[User:Dramir36\|Dramir36]] ([[User talk: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. [[User:Dramir36\|Dramir36]] ([[User talk:Dramir36\|talk]]) 18:48, 11 September 2019 (PDT)

@@ Line 73: / Line 73: @@
 |-
 ! scope="row" | Green-1
-| C<sub>g</sub> C<sub>g|| Green || MSNRHILLVYWRQ
+| C<sub>g</sub> C<sub>g|| Green || MSNRHILLV<span style="color:green">YW</span>RQ
 |-
 ! scope="row" | Green-2
-| C<sub>b</sub> C<sub>y|| Green || MSNRHILLVYWCRQ
+| C<sub>b</sub> C<sub>y|| Green || MSNRHILLV<span style="color:green">YWC</span>RQ
 |-
 ! scope="row" | Red
-| C<sub>r</sub> C<sub>r|| Red || MSNRHILLVFCRQ
+| C<sub>r</sub> C<sub>r|| Red || MSNRHILLV<span style="color:red">FC</span>RQ
 |-
 ! scope="row" | White
-| C<sub>w</sub> C<sub>w|| White || MSNRHILLVVCRQ
+| C<sub>w</sub> C<sub>w|| White || MSNRHILLV<span style="color:blue">VC</span>RQ
 |}
-−
 (b) allele color  amino acid sequence (highlight differences)
 (c) What features of a protein make it colored?

@@ Line 5: / Line 5: @@
 :To understand how changing an amino acid sequence of a plant can cause a change in expression of a hypothetical flower color.
-==Methods==
+==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.
@@ Line 11: / Line 11: @@
 ::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.
-::Answer: 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.
+::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?
@@ Line 17: / Line 17: @@
 ::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.
-::Answer: 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.
+::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?
@@ Line 23: / Line 23: @@
 ::Method: In order to identify which amino acid makes a protein a particular color, the sequences of each color flower were compared.
-::Answer: 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.
+::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)?
@@ Line 29: / Line 29: @@
 ::Method: The amino acid sequence of Green-1 was compared to the Green-2, which is a heterozygote of Blue and Yellow proteins.
-::Answer: 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.
+::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?
@@ Line 35: / Line 35: @@
 ::Method: The Amino acid sequence of each of the four organisms were recorded.
-::Answer:
+::Result:
 {| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
 |+ style="text-align: center;" |Protein of Each Starting Organism
@@ Line 56: / Line 56: @@
 :f) Using this knowledge, construct a purple protein.
-::Method:
+::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.
-::Answer:
+::Result: MSNRHILLVFYCRQ or MSNRHILLVYFCRQ
 [[File:Purple.png|500px|thumb|center|Screenshot of Purple flower using Aipotu program]]
-Hints:
+==Data and Files==
 Put your data in the tables below:
@@ Line 96: / Line 67: @@
 (a) Which proteins are found in each of the four starting organisms?
-::Green-1
+{| class="wikitable" style="margin-left: auto; margin-right: auto; border: none;"
+|+ style="text-align: center;" |Protein of Each Starting Organism
-::Green-2
+|-
+! scope="col" | Organism !! scope="col" | Allele !! scope="col" | Color !! scope="col" | Amino Acid Sequence
-::Red
+|-
+! scope="row" | Green-1
-::White
+| C<sub>g</sub> C<sub>g|| Green || MSNRHILLVYWRQ