Need-To-Know Guide, Chapters 10-11 Chapter 10. Lipids Be able to name fatty acids according to convention: number of carbons: number of double bonds: Dposition of double bond. (Counting from the carboxyl carbon). Why do fatty acids usually have an even number of carbons? What are saturated and unsaturated fatty acids? How do the structures of these differ? How does this influence their fluidity? Understand that fatty acids are not lipids. We also need a headgroup to make a lipid. The simplest storage lipid, triacylglycerol, is three fatty acids, each in an ester linkage with a glycerol. Look at the structure of glycerol, and make sure you understand why triacylglycerol has three fatty acids. Once you understand the glycerol backbone, you will understand how glycerophospholipids and galactolipids are constructed. Now do the same thing with sphingosine. Note the amide linkage to the (single) fatty acid (why just one fatty acid?). Note the headgroup. Get very familiar with figure 10.6 (you do not need to know about archaeal membrane lipids, however). What is the backbone? What is the headgroup? How is the headgroup attached (phosphodiester or glycosidic linkage?). I am not asking that you draw the headgroups, but I would like you to know that ethanolamine and choline are positively charged (for a net neutral glycerophospholipid – remember the phosphate), and that serine and glycerol are neutral (for a net negative glycerophospholipid – because of the phosphate). You will also need to know (but not draw) the headgroups for ceramide, sphingomyelin, cerebrosides, globosides, and gangliosides. Be able to describe each of the lipids in the following table (number of fatty acid chains, head group, backbone). If you look at a structure, you should be able to classify a molecule as a sterol, or an eicosanoid. You should also be able to give a couple examples of structural and storage lipids. PIP2 is a special lipid that is important in signaling, which we will talk about in the upcoming chapters. You should understand the cleavage events that are catalyzed by phospholipases, and understand that these products can go on to participate in signaling cascades. Chapter 11. Biological Membranes and Transport backbone headgroupMembranes constructed as lipid bilayers. What does this mean? Understand what the transition temperature of a membrane is. It is right at the point where the membrane changes from a liquid-ordered state (like a buttery solid) to a liquid disordered state (like an oil). Below the transition temperature, the bilayer is liquid-ordered. Above the transition temperature, the bilayer is liquid-disordered. Cells change their lipid composition so that the transition temperature of the membrane matches the temperature that they live at (37 C for our cells, but might change extensively for cold-blooded creatures, bacteria, etc.). Revisit saturated and unsaturated lipids from Ch. 10 in order to understand how lipid composition can tune transition temperature. The most important take-home of the biological membrane section is that biological membranes are very dynamic, and their composition is very controlled. Examples include: (1) Lipid composition changes when temperature changes so that the biological membrane can remain near the transition temperature. (2) Different organelles and cell types have different lipid compositions. (3) Different lipid compositions of inner and outer leaflets (Phosphotidylserine is a very important inner leaflet lipid, and when it is trafficked to the outer leaflet, and visible to macrophages, the macrophages use this as a signal to engulf the damaged cell.) Cells control lipid composition on the inner and outer leaflets using the actions of flippases, floppases, and scramblases. What is the difference between the functions of these proteins? You should understand why a protein catalyst is required to flip a lipid from leaflet to leaflet. But lateral lipid movement is fast! We know this because of FRAP experiments, and because researchers have fluorescently labeled single lipids and watched them diffuse throughout the bilayer. (4) Microdomains and rafts. Recognize cholesterol and cytoskeletal proteins as important components of microdomain formation. Know that different proteins prefer different microdomains. (5) Curvature. This often leads to vesicle budding. Be able to name a few biological processes that involve vesicle fusion or budding (Figure 11-21 in your book). Proteins are often used to induce curvature, including caveolin and BAR domains. SNARES are used to induce fusion. Membrane proteins. You should be able to define peripheral vs. integral vs. amphitropic, transmembrane vs. monotopic. Do we usually see a-helical or b-strand based membrane proteins? How many residues is a membrane-spanning helix? You need to be able to read a hydropathy plot. Be able to give some examples of amino acids you would find in the bilayer, at the bilayer/aqueous interface, and on aqueous regions of the protein. Membrane transport. Understand the electrochemical potential. A metabolizing cell maintains a negative inside membrane potential. You should be able to tell whether a chemical gradient is thermodynamically uphill or downhill (this is easy!) and whether an electrical gradient leads to uphill or downhill movement of a charged solute. This is more conceptual. Draw a circle-cell with minuses inside and pluses outside like I showed you in class. Where does a charged solute want to go? (Assuming, of course, a transport protein provides a pathway across. Remember, opposite charges attract!). You will need to know how to calculate the electrochemical potential: the sum of thechemical and electric potentials. Ch. 11 has worked problems in the text, and the slides from class also have a worked example. You won’t see anything more difficult than these worked problems, and we will provide values for the gas constant and Faraday’s constant. Understand the analogy between transport proteins and enzymes: they lower the activation barrier for transport across a membrane (kinetics = rate), but do not change the equilibrium constant. Remember Michaelis-Menten kinetics, and what sign you expect for DG when transport is “uphill” or “downhill.” I went over illustrative examples of several passive transport mechanisms: facilitated diffusion (GLUT1), and simple diffusion/electrodiffusion (K+ channel,