AP Research Goals:
Structure Meets Function:
Goal #1: Find a picture of your protein at the molecular level.
 Usually a ribbon structure is helpful.
 Identify secondary structure: o Are their a certain # of alpha helices? Beta pleated sheets?
 Identify tertiary structure: (you may be able to see it in the picture; you may have to go to the research to explain) o What are some of the important areas of your protein?
 Ex. Active site, binding site, place where your protein interacts with another molecule.
 Can you identify some amino acids that are important in these areas.
 Identify quarternary structure: (remember you may not have this) o Often separate polypeptides are different colors…but not always! o How many polypeptides? What makes them stick together?
Goal #2: Identify parts of your protein that are important for its function and explain why they are important for its function.
 Usually this is tertiary structure, but not always.
 Do specific amino acids cause interaction with another molecule?
 Are there any other types of atoms or molecules or ions that interact?
 Why is a certain shape or interaction important?
 Remember…need to tie to what the protein does!
Goal #3: Find the primary structure of your protein (BLAST is good for this).
 Know if your polypeptide is relatively short or long?
 Know if your polypeptide has regular patterns of amino acids…(some proteins only contain 2-3 types of amino acids; others are very diverse)
 Know if there is a certain region that is highly variable or highly conserved.
 Often there is a certain part of the sequence that is important. You may want to highlight this part if you find this information.
Goal #4: Can you identify how your protein interacts with other molecules or plays a role in the organism that its found in.
 Here you are really summarizing all levels of structure to show how the protein interacts.
 Some proteins interact with the cell membrane, others work in complexes with many proteins, others bind receptors…can you show the role at this level?
 Look at some of the model posters…students in the past have done a nice job finding ways to model the function at the molecular level.
Goal #5: How will your organize your presentation of structure?
 You both will present your structure and should show a complete analysis of structure. o Are their comparisons between the proteins that you want to highlight? o Are their major differences that you want to show? o Think about whether you present each structure separately or whether you bounce back and forth. o Think of this as a duel…which of the two proteins you are presenting gets the bucks?!?

Evolution:
Goal #1: Know if your protein is a general example or a specific example
 Most of you will find that you choose a particular example of your protein: Ex. There are many types of actin, you might choose actin a1 and find it has a specific role in the cell.
 It is ok if you focus your evolution discussion on a specific example but your structure meets function is more on the general structure.
Goal #2: Find out if the structure of your protein is conserved between organisms or if it is quite varied.
 Some proteins (like those in the mitochondria or those related to protein synthesis) are highly conserved between organisms. You may find they only differ if you are looking across kingdoms or domains. Other proteins (like a specific toxin) are very unique. Link the evolutionary nature of your protein to its function.
 See if you can support this with evidence from your BLAST search!
Goal #3: Find out if the function of your protein is the same in other organisms or if it does a different job in another organism.
 Our class example was thyroid hormone. Controls metabolism in humans and metamorphosis in frogs.
 One angle to take would be do scientists use the role of this protein in another organism to study its function. Often, scientists will alter the gene sequence of a protein in an organism where it does something very different (ex. Frog) and see the effects of the mutation. Some good model organisms are yeast, C. elegans, Drosophila, Sea Urchin.
Goal #4: Demonstrate an understanding of the evolutionary history of your protein.
 For some proteins, mutations have been selected for…(example sickle cell)
 Some proteins have helped us understand relationships between organisms (think back to
Cladistics)
 Is your protein useful for evolutionary comparisons, or is there a reason that a certain version of your protein is around?
Overall Goal: Ask a question to answer on your poster showing an understanding of the evolution of your protein.
 Look at #1-#4. What interesting evolutionary information have your found about your protein?
What question would engage a reader…or a research funding source to learn more about your protein or provide further $ to study your protein.
 Its not just about knowing information…its about presenting a case for why knowing this information is relevant!