Kristoffer Chin: Week 2

To understand Molecular Genetics Explorer through application of molecular biology

Molecular biology deals with the association of genes and proteins, the Central Dogma.
Molecular Genetics Explorer is a greenhouse simulation program that allowed manipulation of flowers through: Genetics, Biochemistry, Molecular Biology, and evolution
Using the instructions in the.pdf file, we completed the molecular biology section of the assignment. The molecular biology tab was pre-set with 4 flowers: Green-1, Green-2, Red, and White. Looking at the the different flowers using the molecular biology tab, the Amino acid sequence and the DNA sequence was analyzed to understand how the pigments in these flowers were formed. Some pigments share incomplete dominance allowing new colors to form, such as that with Green-2 having a Blue and Yellow Pigment to make green.
The main goal is to create a true breeding purple pigmented flower. In order to do that, the amino acid and DNA sequence must be altered in order to create purple. To create the color purple, the amino acids of phenyalanine and tyrosine must be found side by side in the exon of the flower. Using the enter new DNA button, tyrosine was added next to the phenylalanine. The protein was folded and then compared to the opposite pigment so that it may be altered into a purple pigment as well.

A true breeding purple flower was made through altering the pigments of the red flower. Adding the tyrosine to both sequences allowed a purple allele. That allows for true breeding of the purple pigment because all of its future generations, when self bred, would only allow purple to be passed.

What are the differences in allele sequences that you found in Part I?
1. The differences in allele sequences was found in DNA sequence 79 and 80. In the blue allele, 79 and 80 was an AC creating an amino acid of Tyr while in the yellow allele, 79 and 80 was a GG with Trp amino acid.
Do all white alleles have the same DNA sequences?
1. Not all of the white alleles have the same DNA sequences. Having a white allele does not mean that it has a specific sequence to make that color. In fact, white means that there is no pigment meaning the reason it is white is due to an error in the DNA sequence such as the white allele in the red flower. The reason why it is white is because its promotoer sequence was not correct causing no expression of pigment. The white flower had the a promoter and sequence, but instead came out to be white.
Which DNA sequences are found in the four starting organisms?
1. The DNA sequence that were found in the four starting organisms had the following amino acid sequence corresponding to the DNA sequence in the exon: Met-Ser-Asn-Arg-His-Ile-Leu-Leu-Val-***-Cys-Arg-Gln. The asterik indicates the only altered sequences throughout all the allele pigments. Changing this protein will change the pigment of the flower.

Molecular biology helps with the application of the central dogma of biology. Using this knowledge, we were able to create a true breeding purple flower. At first, we wanted to make a true red and true blue flower and cross breed, the G1 would be all purple, but all the following would be a mix of red, blue, and purple. In order to make a true breeding purple, we figured the only way was to make it through some kind of alterations in the Amino acid sequence. Being that all the colors seem to only have a difference in one DNA and amino acid sequence, we added a new protein. We saw the purple pigment be created through the alterations of DNA which in turn changes RNA, protein, and the overall structure. The exercise was helpful in application of molecular biology showing that a single change in DNA can alter the entire organism, despite being virtual. It would be nice to see how this can be applied in real life, but would probably take a long time which is why it is better to use this program.

BIOL398-01: Bioinformatics Lab