Science Buddies: "Ask an Expert"

For my science fair this year, I'm using a science-buddies project as a template (basis) for my idea, which involves amino acids and proteins & functions between species.

(project link on sciencebuddies: https://www.sciencebuddies.org/science-f ... ml#summary)

This isn't my exact project, but it's similar - I'm going to be using the NCBI BLAST (and other) databases to compare proteins and their functions between species.

Under "step 5" in the procedure, it states, "Explore the function(s) of your proteins using a domain identification database (see online tools listed in bibliography). These tools typically require you to input your amino acid sequence in FASTA format. Learn a little about some of the domains that you identify -- particularly any that occur in the regions that you have shown to be conserved. Can you see how do the functions of these domains relate to the overall job of the protein? How do your results here relate to the results of your sequence alignment?"

The part I'm confused about is the domain. ( "Learn a little about some of the domains that you identify -- particularly any that occur in the regions that you have shown to be conserved. Can you see how do the functions of these domains relate to the overall job of the protein?" ). What exactly does this detail - learning more about the domain(s) identified?

Thanks for the help!

katnaseth

Hi katnaseth,

I am sorry it has taken so long for someone to get back to you! This is not my area of expertise, but I will give you some advice to get started, and hopefully another Expert can add more specific advice.

I think you are using the Computational Exploration of Protein Function project (https://www.sciencebuddies.org/science- ... ml#summary) as a template. (The link was broken in your original message.)

A protein domain is a certain sequence of the protein that usually has an important function in that protein. Because it's important for the function, the amino acid sequence of the domain is usually conserved (meaning it does not change much, even as other parts of the protein mutate and evolve). Here is the Wikipedia article regarding protein domains: http://en.wikipedia.org/wiki/Protein_domain

When you identify the domains, you can start to make hypotheses about the function of your protein, based on the functions of the domains that you identified.

I hope this helps you get started. Please post again (in this same thread) if you have more questions!

Heather