tiffanytpham
Posts: 3
Joined: Mon Dec 29, 2003 1:28 pm

need help on protein functions

Postby tiffanytpham » Mon Dec 29, 2003 1:41 pm

I'm working on a science project about exploring protein function on computers. This is one of the projects listed on the Cutting Edge link. I don't understand which protein to pick. For example, I typed in a protein in the NCBI website (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi). After doing this, I was very confused because it came up with A LOT of links. Which am I supposed to choose? How do I know which one I should explore? Please help me!
Tiffany

davidkallman2
Former Expert
Posts: 40
Joined: Sun Dec 21, 2003 11:48 pm

Postby davidkallman2 » Thu Jan 01, 2004 12:03 pm

Hi Tiffany,

Are you doing your project as part of Science Buddies?

Did you look at prerequisites and suggestions on this project, i.e. "Advanced High School" and have completed high school biology. Does this describe you?

I'm afraid as the person watching the bulletin board, I can only help on Science Buddies projects. Sorry.
Cheers!

Dave
Science Buddies Mentor

chanapalmer
Posts: 1
Joined: Fri Jan 02, 2004 1:18 pm

Help choosing proteins and getting their sequences

Postby chanapalmer » Fri Jan 02, 2004 2:18 pm

Hi Tiffany,

I'm impressed that you've taken on such a challenging project. As you've probably figured out, you're going to have to do some extra background work to make up for your lack of training in this topic.

I just looked over the project description online and see that we already have many tips posted that are relevant to your questions, but since I think your problems are probably very common, I will reiterate what I see as the most useful tips.

It seems to me that your main problems are:
1) Choosing the "right" proteins to study - finding one that is informative and has enough sequence data.
2) Finding the amino acid and mRNA sequence for your chosen protein hidden amongst the many "hits" that you get from Genbank.

With regards to choosing a protein, you need to choose a few proteins that together will give you an interesting story. To meet this goal you should choose proteins of multiple types. Try to choose one protein from an essential life process - one that all organisms must do. DNA replication, RNA transcription and translation would fit this bill, as well as cell division.
You should also think about choosing a protein that is present only in a subset of species. Can you think of a trait or a biological process that not all organisms perform? How about a gene involved in breathing, skin pigmentation, or perhaps in hair or nail formation... any feature or process specific to "higher" organisms. You may be surprised to find that many genes involved in processes that appear to be specific to mammals, (such as keratin being the substance of hair), are also found in many other organisms that don't have the trait (in this example, you will also find keratin in hairless organisms). This happens when the same gene has evolved to a new function in a specific class of organisms. Despite this complication, you will see that a given gene will generally be much more similar in its sequence amongst closely related organisms since its job - in that set of organisms - is the same.

Your next problem is one that biologists often have - finding the sequence that you want amongst the many "hits" that you get with genbank. Usually the different links are different versions of the protein in multiple organisms, or different groups of scientists entering their own version of the same protein (sometimes the same gene is sequenced independently by many groups).
The hit that you want is the one that says your protein name and homo sapiens. Ideally, your protein or mRNA sequence should be annotated as "full length" meaning that it is complete.
In order to achieve this, I recommend refining your search to include the protein name as well as the word "homo sapiens". You should also try using the "limits" option to force the search words to be in the title of the article.


Let me know which protiens you're trying and I can try doing the same search to help you out if you're still having problems.

Good Luck!

tiffanytpham
Posts: 3
Joined: Mon Dec 29, 2003 1:28 pm

Postby tiffanytpham » Fri Jan 02, 2004 3:10 pm

Thanks for your help! I will now find more "important" proteins. The four proteins that I chose before were basically random; they were the causes of different diseases. I understand now that I have to choose a variety of proteins, not only just causes of diseases. Thank you! Have you read my email? I will let you know if I need any help with the proteins! :D
Tiffany

davidkallman2
Former Expert
Posts: 40
Joined: Sun Dec 21, 2003 11:48 pm

Postby davidkallman2 » Fri Jan 02, 2004 3:51 pm

Hi Tiffany,

I apologize if in any way I curbed your enthusiasm. That was not my intent. Have at it!
Cheers!



Dave

Science Buddies Mentor

tiffanytpham
Posts: 3
Joined: Mon Dec 29, 2003 1:28 pm

Postby tiffanytpham » Fri Jan 02, 2004 4:47 pm

Hi David,

No, you did not curb my enthusiasm at all. I just didn't get around to thanking you for your response. You probably know that this project has got me occupied! :D Well, thanks for your reply. I'm glad that people are reading my question. This forum is really useful.
Tiffany

davidkallman2
Former Expert
Posts: 40
Joined: Sun Dec 21, 2003 11:48 pm

Postby davidkallman2 » Fri Jan 02, 2004 6:11 pm

Hi Tiffany,

You're welcome! I was apprehensive that I had done something wrong. Thursday was my first day monitoring the bulletin board, and I'm glad to hear everything is OK by you.
Cheers!



Dave

Science Buddies Mentor


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