Jnimmers Week 2 Individual Journal - Revision history

Jnimmers: /* Week 2 Individual Journal Assignment */

2019-09-12T06:11:08Z

‎Week 2 Individual Journal Assignment

Jnimmers: /* Acknowledgements */

2019-09-12T04:20:41Z

‎Acknowledgements

Jnimmers: /* Data and Files */

2019-09-12T04:19:39Z

‎Data and Files

Jnimmers: Added Data and Files section

2019-09-12T04:18:49Z

Added Data and Files section

Jnimmers at 04:10, 12 September 2019

2019-09-12T04:10:06Z

Jnimmers: Picture addition

2019-09-12T04:08:17Z

Picture addition

Jnimmers: Picture Descs

2019-09-12T04:06:25Z

Picture Descs

Jnimmers: Add pictures

2019-09-12T04:04:43Z

Add pictures

Jnimmers: more sections

2019-09-12T04:00:21Z

more sections

Jnimmers at 03:59, 12 September 2019

2019-09-12T03:59:41Z

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 =Week 2 Individual Journal Assignment=
 ==Electronic Lab Notebook==
+[[User:Jnimmers| John Nimmers-Minor]]
 ===Purpose===
 The purpose of these investigations were to gain a better understanding of DNA sequence coding, amino acids and their effect on allele function, and refresh my knowledge of molecular biology, genetics, and biochemistry, with an emphasis on molecular biology. By using the program, Aipotu, we will be working with and learning computation skills in the field of Biology that may be of use in the future.

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 * I would like to thank [[User:Kdahlquist| Dr. Kam Dahlquist]] for the introduction to the Apiotu program as well as information on how to operate it in order to complete the necessary tasks.
 * Thank you to my homework partner [[User:Msamdars| Mirhir Samdarshi]] for his assistance. We met in person and spoke over the phone in order to complete the Apiotu tasks and his Wiki syntax allowed for me to create my table that was utilized in this assignment
-*Thank you to [[User:Marmas| Mike Armas]] for his assistance in identifying the importance of the aromatic amino acids and their role in determining the color of each flower phenotype.
+*Thank you to [[User:Marmas| Mike Armas]] for his assistance in identifying the importance of the aromatic amino acids and their role in determining the color of each flower phenotype. Thank you to him for the assistance of my Wiki syntax in order to create a better, neater page layout.
 *Except for what is noted above, this journal entry was done by me and not copied from another source.

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-If you are interested in trying this project out yourself, please visit [[https://http://aipotu.umb.edu/  Apiotu's Website]] to download the program
+If you are interested in trying this project out yourself, please visit [[http://aipotu.umb.edu/  Apiotu's Website]] to download the program
 ===Acknowledgements===
 * I would like to thank [[User:Kdahlquist| Dr. Kam Dahlquist]] for the introduction to the Apiotu program as well as information on how to operate it in order to complete the necessary tasks.

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 The utilization of the Apiotu software gave me a small glimpse into the work of a Molecular Biologist, and while it was incredibly difficult to complete the asks using only knowledge on Molecular Biology, the utilization of different databases such as Genetics and Biocheistry made the tasks much similar. The purpose of this project was to help connect Biology principles with introductory level Computer Science learning, and it certainly succeeded in it's goal. This project helped bridge the gap between different specialities of Biology as well as help strengthen the mental connection I have between Biology and Computer Science by allowing Biological questions to be answered through computational means.
 ===Acknowledgements===
 * I would like to thank [[User:Kdahlquist| Dr. Kam Dahlquist]] for the introduction to the Apiotu program as well as information on how to operate it in order to complete the necessary tasks.

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 ====Task a)====
 *I first began by downloading and becoming accustomed to the Aipotu software with assistance from [[User:Kdahlquist| Dr. Kam Dalquist]] and my homework partner [[User:Msamdars | Mihir Sandarshi]]
-*Once accustomed, in order to obtain more pure breeding and hybrid alleles and corresponding phenotypes for the flowers being studied, each original color (Green-1, Green-2, Red, White, and Yellow) was cross and self breed, allowing for the finding of five new alleles (Blue, Black, Oramge, Purple and Yellow) using the Genetics tab (''See images on the left'') [[image:Before.PNG|thumb|Screenshot of Genetic tab before the cross breeding of species]][[image:After.PNG|thumb|Screenshot of Genetic tab after the cross breeding of species]]
+*Once accustomed, in order to obtain more pure breeding and hybrid alleles and corresponding phenotypes for the flowers being studied, each original color (Green-1, Green-2, Red, White, and Yellow) was cross and self breed, allowing for the finding of five new alleles (Blue, Black, Oramge, Purple and Yellow) using the Genetics tab (''See images on the right'') [[image:Before.PNG|thumb|Screenshot of Genetic tab before the cross breeding of species]][[image:After.PNG|thumb|Screenshot of Genetic tab after the cross breeding of species]]
 *With the new alleles discovered, Each pure-breeding allele had their DNA sequenece compared against the White allele (which was an arbitraty, recessive, and pure-breeding allele) to find where each DNA sequence differed.
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 *It was clear that the letters that made up the protein "LVKEIAMYRFATHER" corresponded to the abbreviation form of amino acids that could be created.
-*By using the Biochemistry tab to find the abbreviation names of all amino acids, it was possible to build the protein through the assembling of into amino acid components. ((''See image to the left'')) [[image:Protein fold.PNG|thumb|Photo of final protein fold of MLVKEIAMYRFATHER]]
+*By using the Biochemistry tab to find the abbreviation names of all amino acids, it was possible to build the protein through the assembling of into amino acid components. ((''See lowest image to the right'')) [[image:Protein fold.PNG|thumb|Photo of final protein fold of MLVKEIAMYRFATHER]]
 ===Results===

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		+	====Observation and Findings====

	*Based on the findings obtained through the solving of the Molecular Biology specific tasks, it was found that the Aromatic ring-structured amino acids: Tyrosine, Tryptophan, and Phenylalanine were the primary factors in determining whether or not a flower would have a certain color. Additionally, any flower that did not contain at least one of those amino acids would be produced with the White allele, which lead me to the conclusion about the aromatic amino acids determining the flower's phenotype.		*Based on the findings obtained through the solving of the Molecular Biology specific tasks, it was found that the Aromatic ring-structured amino acids: Tyrosine, Tryptophan, and Phenylalanine were the primary factors in determining whether or not a flower would have a certain color. Additionally, any flower that did not contain at least one of those amino acids would be produced with the White allele, which lead me to the conclusion about the aromatic amino acids determining the flower's phenotype.

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 *Amino Acid Sequence: MLVKEIAMYRFATHER- Met,Leu, Val, Lys, Glu, Ile, Ala, Met, Tyr, Arg, Phe, Ala, Thr, His, Glu, Arg
+====Allele and Sequence Table====
 *''DNA bases that differ from the bases at the same poistion on in the White flower sequence are bolded''
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