04/25/19

Rationale:

to learn to conduct individual research, from the process of making a research question, to designing the methods and concluding from the acquired results.

Procedure:

1. The individual research was worked on.
2. group members used jmol and raptor x to start structure analysis
3. the final abstract for the presentation was submitted
4. The group worked until the end of lab.

Results

based on the analysis of protein structures, there is a significant difference in the structure when the start codon is changed for the tape measure protein of phage cheesy, elsa and napoleon b.

example, AUG, GUG and UUG in order for phage Elsa

final abstract:

AUG, UUG and GUG are the three start codons that initiate gene translation in all bacteria. Different start codons produce different amino acids, which interact differently with other amino acids to form different structure. Genes in arthrobacter phage genomes were used to explore whether changing the start codon of the gene causes a significant difference in the structure of the product protein which could explain why the original start codon was preferred..The start codons for tape measure proteins, major tail proteins, and minor tail proteins in the annotated genome of known, sequenced arthrobacter phage were collected using the Phages DB Database and DNA Master. The gene length, genome length, cluster ,%GC, and direction of the genes were also recorded to determine possible factors that make one start codon preferable to another in the phage genome. Raptor X and Jmol were used to determine the most probable structure of the product protein based on the amino acid sequence and compare the structures. The protein structures were drastically different even though the gene length, pham, and preferred start codon were the same. Overall, many factors that were noted in the quantitative data for the AM Tape Measure were the same or very similar, while the qualitative data produced varying protein structures. Knowledge of how certain start codon may result in a more preferable protein structure may help future research for designing  phages to be more effective by simply changing the start codon.

Conclusion:

currently, from our qualitative data, all we can conclude is that the protein structure changes. quantitative data is still currently being analyzed.

Future steps

Look into primary literature and find information to understand the difference in structures.