BIOL368/F11:Class Journal Week 2

Zeb Russo

1. The purpose of this assignment was to refamiliarize ourselves with the underlying knowledge and skills that we are going to be using in Bioinformatics while we create databases of interconnected genes. Knowing how mutation and the interaction between genes, proteins, and RNA will help us in the long run.
2. I witnessed first hand how changing genetic code will directly influence the introns and exons of an mRNA as well as the final product.
3. I did not learn how to really use Aipotu because mine woulnd't work so I just watched and suggested changes to Robert as he worked the program. Also I'm still not completely clear how the program knew where to cut the exons and introns and changing bases would sometimes randomly create introns.

Zeb Russo 18:01, 7 September 2011 (EDT)

Robert W. Arnold

1. This assignment allowed to become familiar and comfortable with the software we will be using throughout the semester along with brushing up on topics we may not have seen in great detail since genetics.
2. This assignment taught me how to manipulate DNA structures using Aipotu to determine the effects of certain mutations. It allowed me to mutate DNA structures to get the results I wanted.
3. I agree with Zeb. I was unsure on what exactly was going on with the introns, exons and how a base shift in an intro would cause that entire intron to not be spliced. Specifically, when the mutations around aa 10 and 11 were changed. At times a simple change from A to T would cause the entire sequence to go from a normal 14 aa long chain to an 18 or even 19 aa long chain, an entire exon would be removed from the sequence. The exon being taken out allowed for certain amino acid sequences to be coded that were not supposed to be.

Robert W Arnold 18:22, 7 September 2011 (EDT)

Nicolette S. Harmon

1. The purpose of this assignment was to introduce us to the software that we will be using in this class. This assignment also gave us the chance to reacquaint ourselves with various aspects of biology that we may or may not have practiced in a while.
2. This assignment taught me how to manipulate the software in different ways to find the results that I was trying to achieve. I worked on the Genetics portion of this assignment so I was trying to find different methods of creating a purple flower.
3. It did not take me long to figure how to use the Genetics tab and to interpret the results I was getting. If there is anything that I may not be sure of it is how to use the other portions of this software that I have not had the chance to use yet.

• Nicolette S. Harmon 19:20, 7 September 2011 (EDT):

Chris Rhodes

1. The purpose of this weeks assignment was to help us get into the swing of the scientific process by giving us the opportunity to design and conduct our own mock experiments, think critically about the data received, and draw our own conclusions and next steps based on that data.
2. I learned a bit more about the reality of the scientific process and how to effectively and sometimes ineffectively run a series of experiments to get to a conclusion.
3. Since I only got to work with the Genetics portion of the program I didn't get a chance to understand the full capabilities of the other sections.

Chris H. Rhodes 19:48, 7 September 2011 (EDT)

Samantha Hurndon

1. The purpose to this assignment was to re-enforce the skills we had learned with this software along with learning new skills. The assignment also helped us with remembering concepts that may have been forgotten (I.e. ideas from cell function, genetics etc, as well as methods in conduction and writing lab reports.)
2. I learned about the processes of evolution. How certain traits survive/ die with different scenarios (i.e. change in fitness).
3. I had some issues with the Hardy-Weinberg Equilibrium. It had been awhile since I have used the equation or ideas behind that, so I had to google more information with it. It still confuses me a little, but I will do more research on it.

Samantha M. Hurndon

Alex Cardenas

1. The purpose of this assignment was to not only work together on the biological aspect of the assignment but also to get our feel for what kind of experiments we will do this semester.
2. From this assignment, I learned how to find the different allele sequences for different colors of plants. I also learned how to look for these by looking at all of the amino acid sequences that make up a certain color, and then finding which amino acids were differing in each sequence.
3. Since I did not perform any of the other three sections, I still would like to know how those are carried out.

Alex A. Cardenas Alex A. Cardenas 19:10, 13 September 2011 (EDT)

Week 2 Assignment

Isaiah M. Castaneda

1. The purpose of this assignment was to investigate biological mechanisms of an imaginary plant species through the application of a scientific-type process. These mechanisms would be studied through the use of various biological areas such as evolution, biochemistry, genetics, and DNA sequencing.
2. I learned that although these areas may be different, they all compliment each other and can serve one another in tackling the same problem. One of the particularly interesting things that I learned was how certain amino acids (Tyr, Trp, & Phe) could be responsible for pigmentation due to their unique structures.
3. Having worked on the genetics of this plant in Genetics lab and the biochemistry in Bioinformatics lab, I feel that I have a decent understanding in these two parts. However, I look forward to reading about the findings of the DNA and Evolutionary aspects. The evolutionary process comes off as a more different approach than the other 3, so it should be a fun little piece to read.

Isaiah M. Castaneda 00:10, 14 September 2011 (EDT)