Week two notes for Biochem
Week two notes for Biochem biology 305
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This 7 page Class Notes was uploaded by Kayla Notetaker on Wednesday April 13, 2016. The Class Notes belongs to biology 305 at Northwestern University taught by Professor Unger in Spring 2016. Since its upload, it has received 11 views. For similar materials see Biochemistry in Biology at Northwestern University.
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Date Created: 04/13/16
Week two Biochem Lipids and Membranes (Day 3) Lipid basic facts to memorize: Lipids are small The term refers to the monomer of the active class of molecules They are very structurally diverse ranging from simple to complex (sterols to conjugated gangliosides Defined by insolubility in water This sets them apart from other molecules that belong to distinct class of compounds Stereotype of being associated with membranes Lipids play other roles in biology Energy storage, hormones, precursors for signaling molecules, electron transfer, hydrophobic anchors for proteins, light absorbing pigments, and emulsifiers. A disruption of lipid homeostasis results in lethal diseases Not all lipids can be synthesized in the body Most complex lipids are amphiphiles which means they contain a hydrophobic and a hydrophilic regions This allows them to assemble non-covalent polymers With a few exceptions, the hydrophobic part of lipids are unbranched Formation of polymers is driven by the hydrophobic effect Isoprene A building block for isoprenoids Serve as membranous anchors for some proteins Scaffold for assembly of oligosaccharides Form the basis of many plant secondary metabolites and pigments Intermediates in the biosynthesis of pigments such as carotene (in carrots) Also serve as intermediates in the biosynthesis of cholesterol Cholesterol is an important building block for lipid hormones (aka steroids) Derivatives of isoprene polymers act as antioxidants (vitamin E) and blood clotting co-factors (vitamin K) This is due to the aromatic ring in vitamin E scavenges oxygen radicals to prevent oxidative damage to membranes Vitamin K undergoes an oxidation-reduction cycle during post- translational carboxylation of glutamate to carboxyglutamate which is needed in maturation of a few blood clotting factors Derivatives can also act as electron carriers in respiratory chain and photosynthesis Ubiquinone and plastoquinone are examples Fatty acids are hydrocarbon derivatives These are building blocks of most lipids Derived from hydrocarbons Have one terminal carboxyl group Water insoluble with exception of short chains Can be fully saturated (hard and waxy) or unsaturated (soft or liquidy) Bunches (aggregates) of fully saturated fatty acids have very high melting points Bunches (aggregates) of cis-unsaturated fatty acids have very low melting points because the double bond causes a kink which causes trouble when trying to pack fatty acids tightly together Many have multiple double bonds (always Cis configuration and never conjugated) Double bonds have a methylene group separating them Dienes are more stable but also more reactive and forms an allyl cation which is susceptible to modifications Don’t want spontaneous chemistry to occur Fatty acid nomenclature Systematic name Number 1 is Carbon on Carbon-oxygen double bond through the end of the carbon chain (in this example there is 18) Then a colon : Then the number of double bonds The position of the double bond (the number of the carbon it is on) should be in superscript above a triangle Example: Ѡ-system The 1 starts on the carbon farthest away from the carboxyl group and is designated Ѡ Position of first double bond is shown by counting back from Ѡ Example: Some polyunsaturated fatty acids cannot be produced by the body and must be consumed Arachidonic acid Precursor for eicosanoids which are paracrine modulators These act in the immediate environment in which they are formed (different from classical hormones) These can cause smooth muscle contractions, aid blood clotting, have roles in inflammation, fevers, wake-sleep cycles, and the tuning of tissue sensitivity to other hormones Have very short half lives Examples of drugs these are used in are ibuprofen or aspirin Fatty acids are the most important players Should know these names Myristic acid, palmitic acid, stearic acid, arachidic acid, palmitoleic acid, oleic acid, linoleic acid, a-linolenic acid, arachidonic acid. Triacylglycerols Known as storage fats Fats are stored in adipocytes Fat forms droplets inside the cell (about 80% of it’s mass) Lipases release free fatty acids from Triacylglycerols Fatty acids are transported (exported) from adipocyte and are bound to albumin while in transit to the site of utilization These are better for storage energy than polysaccharide glycogen because the oxidation of fatty acids yields much more ATP than oxidation of glucose Don’t need water to solvate because the emulsion/aggregation is not hydrated Meaning they weigh less Lipids and membranes-life and hydrophobic effect Cells use membranes as boundaries and to compartmentalize specific functions Membrane proteins serve as shuttles for food and waste to inform and transduce energy Membranes are flexible, self-sealing, and laterally responsive Self-sealing can be life-saving if torn apart Boundedness is as basic as heredity or metabolism, but is less understood Amphiphile properties Separation of water soluble and water insoluble regions in a molecule creates an amphiphile The hydrophilic heads will stay in the water while the hydrophobic tails will stick up into the air (if put in water) DAY 4 Micelle formation Amphiphilic molecules interact in solution The monomer covers surfaces, the monomer is solvated, aggregates form above the critical micelle concentration Micelle’s are basically when molecules create a bubble or circle (with hydrophobic parts inside and hydrophilic pieces outside) Upon dividing these two parts in water Hydrophobic effect will increase in size and reduces surface area Steric, solvation, and electrostatic effects tend to increase surface and reduce size Packing of hydrocarbon chains is ordered near the center and disordered near the outside Shape of micelles isn’t always spherical Bilayer forming amphiphiles- phospholipids, glycolipids, and ether lipids Triacylglycerols form emulsions but not membranes because they are not amphiphilic! Replacement of one fatty acid with a hydrophilic component creates very powerful amphiphiles with very low CMC’s Phospolipids Know general design of phospholipids, what types of headgroups exist, and what their properties are Insert a table maybe? Naturally occurring usually have a saturated fatty acid on C1 and an unsaturated acyl chain on C2 Roles of phospholipids Primary components of biological membranes Play important roles in cellular signal transduction Serve as apoptotic (cell death) signal Can modulate function of membrane embedded proteins Sphingolipids Sphingosine (a phospholipid) and fatty acids Plays important roles in myelination of nerve fibers Glycolipids are mostly found on cell surface Determine blood group Play important but not well understood role in molecular recognition (characterized by presence of sialic acid) Examples of diseases associated with sphingolipid metabolism Generalized gangliosidosis, Tay-sachs disease, Sandhoff’s disease, Fabry’s disease, etc Day 5 Macromolecular inventory Lipids and membranes pt 2 Single lipids to biological layers Hydrophobic effect dictates that diacylglycerols and sphingolipids form bilayered structures/membranes because hydrophobic part is too large to allow micelle formation Bilayers are a complex mixture of different types of lipids Several hundred different lipid species with a large variety of shapes Local enrichment or pooling of one type of lipid or another will Induce curvature Cause demixing (when lipids find similar lipids) Affect physical properties of the bilayer Differences in lipid shape will allow specific accommodation of different proteins that are imbedded in the bilayers From lipid to bilayers the shape matters Small headgroups reduce head repulsion and induce curvature toward headgroup (curvature like a smiley face) Large headgroups/single chain lipids increase head repulsion and induce curvature away from the headgroup (curvature like a frowny face) Some lipids are balance so no curvature is induced (like a straight line) The hydrophobic effect also dictates that planar bilayers fold back on themselves to form closed vesicular structures because you cannot have the hydrophobic core exposed to water Bilayers are very “schizophrenic” and violent Pressures inside the bilayer are fighting each other at pressures of over 100 atm Later pressure of 100 atm is equivalent to 1000 m depth in ocean In addition, cholesterol molecules rotate about long axis at about 100,000 rpm Each membrane has its own compositional “fingerprint” aka each membrane is specific (specificity) Each membrane does not synthesize its own lipids, lipids are synthesized in the smooth ER and inner mitochondrial membrane Each organ has a specific distribution of composition for each type of phospholipid Bilayers are asymmetric and lipids with different headgroups are found in the inner or outer leaflets of the bilayer Examples would be to find inositols inside and sphingomyelin outside On inner surface many proteins that are needed at membrane stick through electrostatic interactions which makes sense to have negative charge there How is asymmetry maintained? Lipids can’t easily exchange between leaflets A catalysis is needed to drag lipids from leaflet to leaflet Flippase, Floppase, and scramblase do this The function of these enzymes is essential because lipids are synthesized on either inner OR outer leaflet in ER and without this the size would be imbalanced Lipid Rafts Rafts are regions rich in sphingolipids and cholesterol The hydroxyl group on cholesterol can h-bond with the amide nitrogen in the sphingolipid backbone Some membrane proteins like to be in these environments and become hotspots for some biological processes Membrane remodeling Processes that require remodeling Vesicle transport, Exocytosis, Endocytosis, Cell migration, Cell division, Viral entry and exit Membranes need to bend which is common in all of these processes Accomplished by F-BAR which absorb onto flat membranes
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