You have recently identified a novel protein and obtained its sequence. How could you use this sequence to predict the function of the protein?

Question

A.  By using the sequence to make antibodies against the protein.
B.  By determining the secondary structure of the protein.
C.  By determining the DNA sequence that could encode the protein.
D.  By looking for conserved domains.

Clarify Question
· What is the key concept addressed by the question?
· What type of thinking is required?
· What key words does the question contain and what do they mean?

Gather Content
· What do you know about protein function? How does it relate to the question?

Consider Possibilities  
· What other information is related to the question? Which information is most useful?

Choose Answer
· Given what you now know, what information and/or problem solving approach is most likely to produce the correct answer?

Reflect on Process
· Did your problem-solving process lead you to the correct answer? If not, where did the process break down or lead you astray? How can you revise your approach to produce a more desirable result?

Answer 1

D.  By looking for conserved domains.

Clarify Question
· What is the key concept addressed by the question?
        o The question asks about domains of a protein.
· What type of thinking is required?
        o You are being asked to apply your knowledge of domains to explain that they determine the function of a protein.
· What key words does the question contain and what do they mean?
        o Protein sequence – this is the primary structure of a protein.
        o Function – this refers to specific activities of a protein.

Gather Content
· What do you know about protein function? How does it relate to the question?
        o The function of a protein is determined by its tertiary or three dimensional structure.

Consider Possibilities  
· What other information is related to the question? Which information is most useful?
        o The primary structure or amino acid sequence contains information that allows proteins to fold into specific secondary structures (alpha helix or beta sheet). This information is typically obtained by determining the DNA sequence of the gene encoding the protein and then translating it on the computer.
        o The secondary structure of a protein is important in determining the final tertiary structure of a protein, but do not always have specific activities.

Choose Answer
· Given what you now know, what information and/or problem solving approach is most likely to produce the correct answer?
        o The tertiary structure, or three-dimensional shape, of a protein determines its function. This structure can be broken into smaller conserved domains that fold into three-dimensional structures with distinct activities. By looking for these conserved domains in a sequence you can make predictions about the function of the complete protein.

Reflect on Process
· Did your problem-solving process lead you to the correct answer? If not, where did the process break down or lead you astray? How can you revise your approach to produce a more desirable result?
        o This question asked you to apply your knowledge of the different levels of protein structure to explain which would determine the function of a protein. If you got the correct answer, great job! If you got an incorrect answer, where did the process break down? Did you understand that the DNA sequence would give you the same sequence you already had? Did you think that the secondary structure of a protein determined the function of a protein? Did you realize that domains are three-dimensional structures that have specific functions?