2.5: End-of-Chapter Material

Chapter Summary

In this chapter, we’ve explored the structure and function of membranes. To do this, we first needed to explore some of the characteristics of the lipids and proteins that the membrane is made of. We identified four major characteristics of membranes:

1. The membrane is a bilayer made up of lipids and proteins.
2. The membrane is selectively permeable.
3. The membrane is organized but fluid.
4. The membrane is asymmetric.

We also learned that the fluidity of the membrane is dependent on its lipid composition—namely, the length and degree of unsaturation of the phospholipid tails and the cholesterol content. After that we discussed the difference between integral and peripheral proteins and how the secondary structure of membrane proteins contributes to its ability to span the entire membrane, including the hydrophobic portion of the membrane. We rounded out our discussion of membranes by briefly exploring the plasma membrane, which is a unique membrane in the cell, as it is in contact with the external environment. Outside of the plasma membrane is an additional structure known as the extracellular matrix in animal cells and the cell wall in plants and fungi. While these two have some similar roles, they are not the same.

Finally, we explored several experimental techniques throughout this chapter that can help us learn about membranes: fluorescence recovery after photobleaching (FRAP) helps us measure the movement of membrane components; hydropathy plots are a bioinformatic tool that predicts membrane-spanning alpha helices from the primary sequence of a protein, and SDS-PAGE and other kinds of gel electrophoresis can be used to learn more about DNA, RNA, and protein.

Review Questions

Note on usage of these questions: Some of these questions are designed to help you tease out important information within the text. Others are there to help you go beyond the text and begin to practice important skills that are required to be a successful cell biologist. We recommend using them as part of your study routine. We have found them to be especially useful as talking points to work through in group study sessions.

Topic 2.1: The Chemical Features of Biological Membranes

1. For the following molecules (phosphatidylcholine, cholesterol, generic glycolipid, sodium dodecyl sulfate [SDS]), examine the molecular structures and label the regions specified below. Note that each region may or may not be present in each molecule:
   1. the polar region (differentiate between charged and uncharged molecules of the polar region) and the nonpolar region
   2. a region that would be stiff and inflexible
   3. a glycerol residue (Some molecules have a serine residue instead; does yours?)
   4. a region that could easily have C=C bonds added (How would that affect the structure of that region?)
2. Identify which of these lipids (phosphatidylcholine, cholesterol, generic glycolipid, sodium dodecyl sulfate [SDS]) would be able to form lipid bilayers on their own. Use the details of the structures that you drew to explain why or why not.
3. Explain how thermodynamics, amphipathicity, and shape of lipids allow for the spontaneous assembly of lipids into phospholipid bilayers.
4. Which types of molecules are able to cross a membrane bilayer. Can you tell based on the chemical properties of the bilayer compared to the molecules attempting to cross? Explain.
5. For each of the four features of the cell membrane, explain how proteins and lipids generally contribute to those features. Where do carbohydrates fit in?
6. Explain why it is rare that lipids are able to flip between leaflets in a lipid bilayer.
7. What is meant by the term membrane asymmetry and how is this feature created and maintained?
8. What are the major differences between a synthetic phospholipid bilayer and a biological membrane?

Topic 2.2: Maintaining Fluidity in the Membrane

1. How do cells adjust their membrane composition to maintain fluidity of their lipid bilayers in varying conditions?
2. Despite appearances, cholesterol cannot form bilayers on its own. Use the structure of the molecule to explain why.
3. Explain how the structure of phospholipids is the basis of the major properties of the bilayers that they form: physical form of the bilayer, self-sealing property, selective permeability, and fluidity of the bilayer.
4. Describe how fluorescence recovery after photobleaching (FRAP) works and list the types of scientific questions that can be answered using this technique.
5. Describe the composition of lipid rafts and their role in cells.
6. Explain how reduced temperature can result in gel phase membranes. Why is this disastrous for living membranes?
7. Exposing living membranes to temperatures that are higher than what they are adapted for can also be disastrous… What’s the impact of higher temperatures on membrane fluidity, and why might that be detrimental?

Topic 2.3: Structure and Function of Membrane Proteins

1. Find images of all 20 amino acids (don’t memorize them!) online. Critically assess the structures and identify the following:
   1. The portion of the amino acid that is common to all of them.
   2. The portion that is unique to each amino acid, known as the R group or side chain.
   3. The functional groups that will form the peptide bond. Will anything be lost/gained during that reaction? How do these parts relate to the “N” and “C” terminus of a protein?
   4. The next questions are specifically for the R groups. Based solely on their structure, identify the following:
      • Any R groups that you would expect to have acidic properties. Will they gain or lose a proton during that reaction?
      • Any R groups that you would expect to have basic properties. Will they gain or lose a proton during that reaction?
      • Any R groups that would not be able to form H-bonds with water.
      • R groups that would form H-bonds but would not be acidic or basic.
      • R groups that could interact ionically with their neighbors.
      • Any R groups you would consider to be “big” or “small” relative to the others.
2. Define the four levels of protein folding and explain how each one is stabilized.
3. Are disulfide bridges covalent or noncovalent interactions? How do they form? Why are they considered to be uncommon in the cytosol?
4. Describe the functional roles of the following examples of membrane proteins:
   1. Integral proteins
   2. Peripheral proteins
   3. Glycoproteins
5. What is the difference between integral and peripheral membrane proteins? Discuss and compare the different strategies for association of proteins with membranes.
6. What is a domain in a protein? How does it relate to structure and/or function?
7. Compare the hydrophobic forces that hold a membrane protein in the lipid bilayer to those that help proteins fold into a unique three-dimensional structure.
8. How do cells restrict the movement of membrane proteins? Outline the different strategies and provide brief examples.
9. What feature of a membrane’s structure allows it to have separate identities and functions on each side?

Topic 2.4: Experimental Techniques in Membrane Biology

1. What is a hydropathy plot, and how does it help predict transmembrane regions?
2. Explain why hydropathy plots can only make predictions about transmembrane alpha helices and not beta barrels.
3. Explain why experimental techniques are needed to verify predictions from hydropathy plots.
4. Why is SDS needed for sample preparation in SDS-PAGE experiments?
5. What types of questions can be answered using SDS-PAGE?
6. How is DNA gel electrophoresis different from SDS-PAGE on proteins?