Vkuehn Week 5

UniProt Exercise

• Opened and read Bioinformatics For Dummies
• The location where Proteins end up and how they get there are unique

• The folding and domains are very important and help determine the 3D structure
• Searched for the protein P00533 it is an epidermal growth factor receptor
• Here are the results:

• As new information comes out, older accession numbers don't go away, they just get stored as secondary accession numbers, but the most up to date information is only displayed
• The comments section is very useful for gathering information about the protein such as: function, catalytic activity, tissue specificity
• The cross-reference section is very useful for gathering other information in new databases. For example, EMBL-EBI gives a visual overview of the base pairs and other details:

[[1]]

• Here is an example of a 3D database result for the epidermal protein:

[[2]]

Summary of Epidermal Growth Factor Receptor

EGFR is a growth factor protein which is a receptor tyrosine binding ligand that activates signals to help convert extracellular cues into corresponding cellular responses. It is found in the cell membrane of homo sapiens and other membranes in the cell [[3]] . It belongs to the protein kinase sub family. The mRNA sequence that corresponds to the protein is 5,532 base pairs in length and its 3D structure has a complex of 2 biomacromolecules. [[4]]

Questions

1. The purpose of this exercise was to familiarize ourselves with Uniprot and to get used to gathering information about one protein from other databases. It made it clear what some of the benefits are of certain databases over others.
2. I learned that certain databases can be more clear and helpful in terms of visuals, which helps me personally understand how proteins are shaped of their size and structure. I also learned that using these databases is not as intimidating as it seems and that is is pretty easy to navigate back and forth between them.
3. Some things I think I could work on is learning which information is most useful and what to focus on in these databases. There is so much information but I was not sure what was the most important amongst all of it.