MSymond1 Week 2 - Revision history

Msymond1: added more references

2024-01-25T22:06:44Z

added more references

Msymond1: /* =References */

2024-01-25T06:36:10Z

‎=References

Msymond1: added references

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added references

Msymond1: finished acknowledgements

2024-01-25T06:34:11Z

finished acknowledgements

Msymond1: continued acknowledgments section

2024-01-25T06:27:55Z

continued acknowledgments section

Msymond1: started acknowledgements

2024-01-25T06:24:23Z

started acknowledgements

Msymond1: /* =Scientific Conclusion */

2024-01-25T06:20:44Z

‎=Scientific Conclusion

Msymond1: added conclusion

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added conclusion

Msymond1 at 06:15, 25 January 2024

2024-01-25T06:15:27Z

Msymond1: added purpose

2024-01-25T06:05:05Z

added purpose

← Older revision		Revision as of 22:06, 25 January 2024
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	Aipotu. (2024). Retrieved January 24, 2024, from https://aipotu.umb.edu/		Aipotu. (2024). Retrieved January 24, 2024, from https://aipotu.umb.edu/
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		+	Brown, T.A. (2002) Genomes 2, Ch. 3.3.2: The link between the transcriptome and the proteome (freely available on NCBI Bookshelf)
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		+	Nirenberg, M. (2004) Deciphering the Genetic Code—a Personal Account.
		+	Trends in Biochemical Sciences 29: 46-54. DOI: 10.1016/j.tibs.2003.11.009 (also on Brightspace)
		+
		+	Kaji, A., Kaji, H. (2004) The history of deciphering the genetic code: setting the record straight.
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		+	Trends in Biochemical Sciences 29: 293. DOI: 10.1016/j.tibs.2004.04.005 (also on Brightspace)
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		+	Moody, G. (2004) Digital Code of Life, Chapter 1, Hoboken, New Jersey: John Wiley & Sons, pp. 1-9. (on Brightspace)
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		+	Hayes, B. (2004) Ode to the Code, American Scientist 92: 494-498. (on Brightspace)
	*{{Template:MSymond1}}		*{{Template:MSymond1}}

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 [[https://en.wikipedia.org/wiki/Help:Wikitext#:~:text=The%20markup%20language%20called%20wikitext,edit%2C%20see%20Help%3AEditing.| Click here]]
 Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Msymond1|Msymond1]] ([[User talk:Msymond1|talk]]) 22:34, 24 January 2024 (PST)
-=======References======
+======References======
 LMU BioDb 2024. (2024). Week 2. Retrieved January 24, 2024, from
 https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_2

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 [[https://en.wikipedia.org/wiki/Help:Wikitext#:~:text=The%20markup%20language%20called%20wikitext,edit%2C%20see%20Help%3AEditing.| Click here]]
 Except for what is noted above, this individual journal entry was completed by me and not copied from another source. [[User:Msymond1|Msymond1]] ([[User talk:Msymond1|talk]]) 22:34, 24 January 2024 (PST)
 *{{Template:MSymond1}}

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 This lab showed significant implications for the molecular underpinnings for the pigmentation of the flowers found in parts I and II of the lab. After determining all possible alleles for the flowers, and which proteins are found to be different in the different alleles, this part of the lab was able to create an organism of a new allele for the color purple. After it was determined that the only difference between the red and blue DNA sequences (the sequences that made the purple heterozygote flower) was on base 79, and that there was one difference in proteins between the sequences, a sequence was created that had both of the proteins that set apart the DNA sequences.
 ======Acknowledgements======
 I worked with my homework partner Natalija Stojanovic. Although she was not present in class this week on Tuesday, we exchanged texts and called for 15 minutes. I helped clarify a few things about how to use the software to complete the assignment. I also consulted the homework partners who were working on the biochemistry section of the lab. I also consulted my professor Dr. Dahlquist during class, as she helped me determine the three aromatic amino acids.
 *{{Template:MSymond1}}

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 This lab showed significant implications for the molecular underpinnings for the pigmentation of the flowers found in parts I and II of the lab. After determining all possible alleles for the flowers, and which proteins are found to be different in the different alleles, this part of the lab was able to create an organism of a new allele for the color purple. After it was determined that the only difference between the red and blue DNA sequences (the sequences that made the purple heterozygote flower) was on base 79, and that there was one difference in proteins between the sequences, a sequence was created that had both of the proteins that set apart the DNA sequences.
 ======Acknowledgements======
-I worked with my homework partner Natalija Stojanovic. Although she was not present in class this week on Tuesday, we exchanged texts and called for 15 minutes. I helped clarify a few things about how to use the software to complete the assignment.
+I worked with my homework partner Natalija Stojanovic. Although she was not present in class this week on Tuesday, we exchanged texts and called for 15 minutes. I helped clarify a few things about how to use the software to complete the assignment. I also consulted the homework partners who were working on the biochemistry section of the lab. I also consulted my professor Dr. Dahlquist during class, as she helped me determine the three aromatic amino acids.
 *{{Template:MSymond1}}

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 F) The protein creates a purple pigmentation.
 *See figure 6
-======Scientific Conclusion=====
+=====Scientific Conclusion=====
 This lab showed significant implications for the molecular underpinnings for the pigmentation of the flowers found in parts I and II of the lab. After determining all possible alleles for the flowers, and which proteins are found to be different in the different alleles, this part of the lab was able to create an organism of a new allele for the color purple. After it was determined that the only difference between the red and blue DNA sequences (the sequences that made the purple heterozygote flower) was on base 79, and that there was one difference in proteins between the sequences, a sequence was created that had both of the proteins that set apart the DNA sequences.
 *{{Template:MSymond1}}

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-===Methods and Results===
+===Purpose===
 	The software Aipotu was used for this lab, using the molecular biology tab. The completion of the molecular biology section of this lab did require assistance from the group that completed the genetics portion and the biochemistry portion. They helped provide a list of all different alleles, as well as which alleles are true breeding. The molecular biology tab of this software displays the entire DNA and protein sequence of the alleles and what color pigment they make. The first DNA sequence edited in this experiment was the sequence from the red flower. The base that was edited was from the red sequence, and the base was base #20. It was changed from a G to a C. This led the protein sequence to not be folded, because it did not allow for methionine to be coded, therefore, no pigmented protein could be created, making it a white flower. This led to the discovery that there are multiple ways to create a white flower, because any DNA sequence that does not create a functional pigmented protein will create a white flower (figure 1). Using the knowledge of the different alleles, provided by the genetics group, as well as the biochemistry of a purple allele from the biochemistry group, a purple allele for flowers was created using the molecular biology of the organisms to create a true breeding purple organism (figure 2). The three aromatic amino acids that are responsible for color are phenylalanine, tyrosine, and tryptophan. The red sequence from a purple heterozygote had phenylalanine, and the blue sequence had tyrosine. So an amino acid sequence was created that had both of those amino acids. This was done by changing base 82 of a blue sequence to a U, giving it a phenylalanine.
 [[File:modifiedred.png|200px|thumb|right|Figure 1]]
 [[File:purpleorganism.png|200px|thumb|right|Figure 2]]
-====Specific Tasks====
+=====Specific Tasks=====
 A) There are no differences in the Green DNA sequences in the Green-1 flower. The differences between blue and yellow sequences in Green-2 were at positions 79, and 80. The differences between the red and white sequences in the red flower are at position 7. There were no differences between the white sequences in the white flower. Between every available allele of the colored (non-white) flowers, all of the differences in the DNA sequences fell in bases 79 and 80
 *See figure 3