Lipids
33. What is the function of the phosphotidylserine lipids?
33. What is the function of the phosphotidylserine lipids?
17. Given the structure of glycerol draw phosphatidate (diacylglycerol -3 phosphate). This is something you really should be able to do.
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18. Given the structures of glycerol and serine, draw phosphatidylserine. (See note above.)
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19. Given the structure of glycerol and choline, draw phosphatidylcholine. (Yup, this one too.)
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27. Using a pencil to sketch over the image provided, identify the two-isoprene units of limonene (shown below), a major component of citrus oil. You should trace the two isoprene units directly over the structure on this page. Remember that only the carbon positions are conserved in the assembly of isoprenes, not the double bonds or other substituents.
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3. Given the structure of gingerol, show the reverse aldol reaction that leads to zingerone.
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42. Calculate the energy cost (free energy change) of pumping an uncharged solute against a 1 X 104 concentration gradient at 25oC). (Hint: a concentration gradient is expressed as the ratio C2/C1).
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43. Calculate the energy cost (free energy change) of pumping Ca(II) from the cytosol, where the concentration is 1 X 10-7 M to the extracellular fluid where the concentration is 1 mM). Assume the temperature is 37o C and that the transmembrane potential is 50mV, negative inside.
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45. The Km of the glucose transporter GLUT2 is 40 mM. Calculate the effect on the rate of glucose flux into a hepatocyte of increasing the blood glucose concentration from 3 mM to 10 mM. Express your answer as the ratio of the rate between the two substrate concentrations.
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6. Draw 18:1 (9) cis-9-octadecanoic acid. (Note that on an exam you are not responsible for the common name or the complete chemical name. You are responsible for the use of the "" nomenclature.)
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7. Draw 20:5 ( 5,8,11,14,17) - eicosopentanoic acid. See note above. Are the alkene bonds cis or trans?
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34. What are the three major classes of transmembrane proteins? Why is it possible to have a single transmembrane helix but not a single transmembrane beta strand? Why is the only possible all-beta transmembrane protein is a beta barrel?
Alpha Helix, helical bundle, and beta barrel There is only one stable arrangement of b-strand sequences that forms an transmembrane protein: the beta barrel. Other beta sheet folds have exposed edges that leave hydrogen bond donors and acceptors exposed to the hydrophobic transmembrane, which is energetically unfavorable. In the beta barrel all the hydrogen bond donors and acceptors are satisfied. For this reason, there can be no single beta strand transmembrane protein, unlike the single span alpha helix. Many of the transporters of the outer membrane of gram negative bacteria are beta barrels.
10. What is anandamide? What are the two precursor molecules for the synthesis of anandamide? What are the biological effects of anandamide? What is the name of the class of proteins that mediate the effects of anandamide, and where are such proteins found in the cell? What is the name of the molecule found only in certain plants that mimics the effects of anandamide?
Another important naturally occuring derivative of arachidonic acid produced in the body is the lipid anandamide (from the Sanskrit ananda, joy or bliss). Anandamide is the ethanolamine derivative of arachadonic acid. It functions as both a neurotransmitter and an anti-inflammatory molecule. Anandamide is known as an endocannabinoid, acting in the nervous system to attenuate pain, enhance mood (producing a state of happiness and relaxation) and regulate appetite. Anandamide also acts on immune cells, suppressing the inflammatory response. Although anandamide is naturally produced in the body, it is also available in the diet; chocolate, for example, contains detectable amounts of anadamide. Cannabinoid compounds such as anandamide work by binding to proteins found on the surface of cells called cannabinoid receptors. These membrane proteins are widely expressed both in the nervous and immune systems. THC is found in plants like cannabis
5. What gives rise to the characteristic taste of Hershey'sTM chocolate? Does this knowledge impact your enjoyment of chocolate in any way?
Butyric acid which is found in vomit and sweat.
2. What subclass of lipid is the molecule canthaxanthin?
Canthaxanthin is an carontenoid lipid, part of the terpenoid family of lipids. It has potent antioxidant capacity.
39. What are caveolae and what is the function of the protein caveolin?
Caveolae are a distinct form of lipid raft, forming invaginations (or pits) in the plasma membrane due to the action of the membrane protein caveolin. Some signaling proteins are localized to caveoli. Endocytosis, twhich we discuss in the next section, is often associated with the "pits" formed by the action of caveolin. The caveolin proteins form hairpins in the membrane. Caveolae form when these hairpin proteins associate in the membrane.
29. What is the unique chemical step in the synthesis of the active hormone calcitrol ?
Cholecalciferol
32. Is diffusion of lipids perpendicular to the bilayer fast or slow? What types of enzymes catalyze the motion of lipids across the leaflets of the bilayer?
Diffusion of lipids is fast when in the plane of the bilayer such that within a bilayer, there may be a uniform distribution of lipids Flipasees and scramblases
23. What is the common structural property of the ether lipids? What is PAF, and why is PAF unusually soluble for a phospholipid?
Ether lipids are a distinct class of structural lipids, albeit similar to the glycerolphospholipids. Notice how, in the ether lipid one of the ester bonds (COOR) has been replaced by an ether bond (COR) Platelet activating factor is released from basophilis ( a type of leukocyte). It stimulates platelet aggregation, release of the vasoconstrictor serotonin and is generally important in the inflammatory and allergic response, particularly in asthma.
4. What is a fatty acid? What is the general (but not absolute) rule for the length of fatty acids, and what does this suggest about their biosynthesis? Are fatty acids (generally) branched or un-branched? Which parts of a fatty acid form the hydrocarbon tail? Which parts form the fatty acyl group?
Fatty acids are long unbranched hydrocarbons that terminate with a carboxylic acid. They are long (4-36 carbons, although most are at least 12 carbons in length), Most of them have an even number of carbons suggesting that they are synthesized in units of two carbons. Fatty acids are usually unbranched The hydrocarbon tail is just the carbon chain excluding the carbon that is connected to the oxygen. The fatty acyl group is the hydrocarbon chain including the carbon which is connected to the oxygen and the fatty acid is the hydro carbon with the carboxylic group.
40. What is the osmotic term of the free energy of transport equation? What is the chemical term of the free energy equation? (Note that on an exam you will be given the complete equation, but you must understand how to apply it and what each term represents).
Gibbs free energy
14. What is the function of serum albumin in the transport of free fatty acids?
In blood, free fatty acids circulate non-covalently bound to the carrier protein serum albumin. Most fatty acids, however, are not found in the free form but are instead found in esterified derivatives, that have much lower solubility.
41. What is the universal value of Go for all calculations of the free energy of transport across a bilayer?
It is always zero because because it is in equilibrium
11. Draw the structure of any chemically realistic wax. Name two functions for waxes.
Organisms use waxes as structural materials and water protectants. Waxes are used in the manufacture of candles, cosmetics, and polishes.
38. What are membrane rafts? What is the biological function of membrane rafts? What types of lipids are typically encountered in membrane rafts?
Other proteins are also relatively immobile, yet are not attached to the underlying cytoskeleton. This led to the concept of membrane rafts, local regions of membrane that are more gel phase due to their composition (particularly sphingolipids) and high cholesterol content. Some proteins (such as GPI linked proteins) prefer to locate to membrane rafts, others are excluded. As a result, some proteins become heavily co-localized within these domains. This is beneficial for membrane proteins that are functionally mutually interdependent. Membrane rafts can be thought of as icebergs floating in the phospholipid sea.
36. What is a peripheral membrane protein? What amino acids are modified with lipids in membrane proteins?
Peripheral proteins attach to integral membrane proteins or the lipid head groups. They may be permanently associated with one leaf of the membrane, or only temporally attached to the membrane, moving on and off the membrane. One ready way to experimentally distinguish peripheral from transmembrane proteins is that peripheral proteins can usually be easily removed from the membrane by changes in pH or ionic strength.
22. What are phospholipases? What is the specificity of each of the phospholipases? Why are phospholipases an important component of snake venoms? What is one role of phospholipases in ordinary physiology?
Phospholipases are enzymes that catalyze the selective breakdown of bonds in phospholipids. Phospholipases are found in all organisms and play important roles in the regulation of membrane physiology. However, they also are a major component of venoms, such as from rattlesnakes and vipers. These venoms contain Phospholipase A2. The phospholipases in venoms break down the lipid membranes in skin and other organs, causing extensive cellular damage. In addition, the released fatty acids can have other physiological effects.
21. What is the meaning of the term, prochiral? Why is glycerol a prochiral molecule? Is the phosphate group in the glycerol phospholipids at sn-1, sn-2 or sn-3? What does the s- in this nomenclature system refer to?
Prochiral molecules can convert achiral molecules to chiral molecules. Glycerol is a prochiral molecule because it is a chiral molecule however, by changing the terminal -OH group.
20. What types of fatty acids are normally found at the R1 position of a glycerolphospholipid? What types of fatty acid are normally found at the R2 position of a glycerolphospholipid?
R1 saturated R2 unsaturated
37. What is a lipid-anchored protein? What are the major classes of lipid anchored proteins, and to which amino acid in each is the lipid attached?
Some eukaryotic and viral membrane proteins (both peripheral and transmembrane) are covalently anchored to lipids, stabilizing their association with the membrane. Two frequently observed attachment moieties are through the attachment of a myristoyl group (a 14-carbon saturated fatty acid) to an N-terminal glycine of the protein, and the 16-carbon saturated palmitoyl group through a thioester to a cysteine residue in the protein. Specific enzymes add these lipids to the appropriate proteins.
31. What is the major biological function of Vitamin K? What is the Gla post-translational modification?
The body needs vitamin K to produce prothrombin, a protein and clotting factor that is important in blood clotting and bone metabolism. the oxidation of glutamic acid in select proteins to the modified amino acid gamma-carboxyglutamate, an amino acid with two COO- groups. Having a pair of COO- groups allows this amino acid to coordinate calcium ions. This is illustrated on the following slide.
1. What is the common chemical property of lipids? What are some of the functions of lipids? Are lipids more or less structurally diverse than other classes of biomolecules?
The common properties of lipids are that they are water insoluble molecules but they are highly soluble in organic solvents. Some of the functions of lipids are that it is used for energy storage, structural materials, cell membranes, and signaling molecules. In additions Lipids are the most structurally diverse of the biomolecules.
30. What is the significant function of the ubiquinones?
The free energy released by the spontaneous transfer of electrons from the NADH-Q reductase complex to ubiquinone is used for a very important purpose.
25. What are the gangliosides? What are the common structural features of the gangliosides?
The gangliosides have more complicated carbohydrate chains attached to the sphingosine unit. A common feature is the attachment of the NANA unit branched off the galactose unit.
8. What is the effect of fatty acid hydrocarbon chain length on the melting temperature of a lipid? What is the effect of unsaturation on the melting temperature of a lipid?
The longer the hydrocarbon chain the higher melting point because of the van-der-waals interactions. In addition, unsaturated lipids also have a lower melting point.
13. Draw a triacylglycerol that incorporates any three fatty acids. What is the major distinction between oils and solid fats?
The major distinction between oils and solid fats is that their melting points are different
28. What is the thermodynamic driving force for the synthesis of isoprenes from isopentyl pyrophosphate?
The negative charges on the oxygens
9. What are the eicosanoids? What lipid is a precursor to the eicosanoids? What drug blocks the formation of the prostaglandins? What is the enzyme that is inhibited by this drug, and what is its mode of inhibition? (Note: the answer for the second part of this question, can be found in the Enzyme Regulation PowerPoint.) How might the over-consumption of -6 fatty acids promote inflammation and disease?
The oxygenation of C20 polyunsaturated acids (such as arachadonic acid) gives rise to the eicosanoids, a class of hormone molecules that mediate a variety of biological effects. These include: Prostaglandin E2: constriction of blood vessels Prostacyclin: a vasodilator, also controlling blood clotting formation Thromboxane A2: formation of blood clots and Leukotriene B4: mediator of smooth muscle contraction and involved in airway constriction in asthma. NSAID's block the formation of the prostaglandins. Consumption of Too much omega 6 can raise your blood pressure, lead to blood clots that can cause heart attack and stroke, and cause your body to retain water.
12. Give two reasons why triacylglycerols are "preferable" to storage carbohydrates for the storage of biological energy.
The superior nature of triacylglycerols (as opposed to glycogen or starch) as an energy storage medium is due to the chemical properties of the two distinct classes of molecules. The fatty acids of triacylglycerols are more reduced than carbohydrates, leading to a greater amount of energy per molecule. In addition, triacylglycerols bind to significantly less water than storage carbohydrates and as such, a greater amount can be packed into a smaller volume.
15. What are ? What is Hormone Sensitive Lipase (HSL)? How is the catabolism of fatty acid droplets regulated?
Triacylglycerols are stored in adipocytes ("fat" cells) in the form of lipid droplets. The lipid droplets are coated with proteins called perilipins. They act as a shell to prevent the triacylglycerols from being degraded by lipases unless they are needed. The enzyme that breaks the triacylglycerols down into free fatty acids and glycerol is known as hormone sensitive lipase (HSL). The breakdown of triacylglycerols is carefully regulated in tune with the energy needs of the cell. When there is no need for the energy of free fatty acids, the perilipins act as a protective shell over the lipid droplet. But when the cell requires energy from free fatty acids HSL becomes phosphorylated which turns the enzyme on making the perilipins phosphorylated too. This causes them to change their conformation and "stand-up", exposing the surface of the lipid droplet to the now active HSL.
16. What is the structural distinction between a triacylglycerol and a glycerolphospholipid?
While triglycerides have glycerol and three fatty acids, phospholipids have glycerol, two fatty acids and a phosphate and alcohol
26. Name three general functions for steroids.
help control metabolism, inflammation, immune functions, salt and water balance
35. What is the fluid mosaic model? What is a membrane raft? What role do membrane rafts play in membrane biochemistry?
visualizes proteins floating in a sea of lipids, capable of diffusion throughout the plasma membrane. Phospholipids and proteins can diffuse in two dimensions but generally, not cross leaflets. local regions of membrane that are more gel phase due to their composition (particularly sphingolipids) and high cholesterol content.