04/17/19

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. the group members found the start codons for their assigned proteins using phages db for the fasta file and dna master for the sequence.
3. group made the project outline
4. The grouped worked until the end of lab.

Results

so far. no real results. a lot of  the data collection has been performed.

project outline:

Title:

Analysis of start codons and change in structure due to start codons in proteins from arthrobacter phages

Guiding Question:

Can a different start site affect the translation of the gene sequence? Will it change the structure of the product protein? If the structure does not change, is there a possible reason to prefer a certain start codon over another?

Abstract:

ATG, TTG and GTG are the three start codons that initiate gene translation. But there is no known correlation between the start codons and the genes. Is there a factor that makes one start site preferable to another?. To answer this question, the start codons for tape measure protein, major tail protein and minor tail proteins were collected to find possible correlations. To analyze the structure of the product protein, predicted models were produced for the same protein using different start codons to see if there was a significant change in structure due to the change in start codons.

List of tools used

Phages DB, DNA Master, raptor x and jmol

Introduction (Background Information)

The standard genetic code table has one start codon, ATG. Over the years, however, many studies have demonstrated that alternative start codons, such as GTG and TTG, could be utilized for translation initiation. In accord of ranking of the start codons, genes starting with ATG are, on average, expressed at significantly higher levels than genes that start with GTG, and the very few genes that contain the start TTG. This is generally the case for genes in other bacteria as well, with ATG being the predominant start codon.

The AUG starts are replaced by GUG and especially UUG significantly less frequently than expected under the neutral expectation derived from the frequencies of the respective nucleotide triplet substitutions in non-coding regions and in 4-fold degenerate sites. Thus, AUG is the optimal start start codon that is actively maintained sites

Types of Data Collected

All the start codons of sequenced and annotated phages

Predicted protein structure of tape measure proteins with different start codons

Results (to date)

All start codons have been determined for tape measure proteins and major tail proteins.

Structures are still to be modelled and collected.

Conclusions (if any have been drawn)

As data is still being collected, we do not have any conclusions as of now

Conclusion

this research will require a great deal of data collection as there are a little more than 200 sequenced arthrobacter phages. enough data can be collected for the research in the given time.

Future steps

do more research, look into primary literature and find more tools that can be used.