You recently identified a novel protein that contains several membrane-spanning domains. You would predict that the amino acids embedded in the membrane would have ____ side groups.

Question

A.  nonpolar
B.  negatively charged
C.  polar uncharged
D.  positively charged

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 amino acid side groups? 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

A.  nonpolar

Clarify Question
· What is the key concept addressed by the question?
        o The question asks about membrane spanning domains of a protein.
· What type of thinking is required?
        o You are being asked to apply your knowledge of membrane-spanning domains to predict the properties of amino acids in these domains.
· What key words does the question contain and what do they mean?
        o Membrane – this is a lipid bilayer that has polar head groups interacting with water and long non-polar fatty tails that point into the membrane away from water.
        o Membrane-spanning domains – these are segments of a protein that cross a lipid bilayer.  

Gather Content
· What do you know about amino acid side groups? How does it relate to the question?
        o There are 20 common amino acid side groups with different functional groups.  Some are charged or polar which will interact positively with water.  Other side groups are non-polar and hydrophobic and will be repelled by water.

Consider Possibilities  
· What other information is related to the question? Which information is most useful?
        o The center of a membrane is a non-polar or hydrophobic environment.  In order for a protein to cross a membrane the side chains would need to be soluble in this lipid environment. Charged and polar side groups will be soluble in water and would not be soluble in a membrane.

Choose Answer
· Given what you now know, what information and/or problem solving approach is most likely to produce the correct answer?
        o Non-polar side chains on a protein would be most soluble in a membrane.

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 the properties of a membrane to predict which amino acid side chains would be found in a membrane-spanning domain. If you got the correct answer, great job! If you got an incorrect answer, where did the process break down? Did you understand that a membrane would be a non-polar and hydrophobic environment?  Did you recall that polar and charged amino acid side chains are hydrophilic and would not dissolve well in hydrophobic membranes.