Test 3 Study Guide
Test 3 Study Guide CHEM 351
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This 11 page Study Guide was uploaded by Kayli Antos on Sunday November 29, 2015. The Study Guide belongs to CHEM 351 at Towson University taught by Ana Soto in Summer 2015. Since its upload, it has received 16 views. For similar materials see Biochemistry in Chemistry at Towson University.
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Date Created: 11/29/15
Biochem Test 3 o Lipids And Membranes Lipids Can be used for: o energy storage o membrane structure o enzyme cofactors o electron carriers o hydrophobic protein anchors o digestive tract emulsifiers o hormones o intracellular messengers They are not considered macromolecules. Storage Lipids Derivatives of fatty acids and are used for energy storage. Their oxidation is exergonic and produces CO and 2 O. 2 Fatty acids are carboxylic acids with carbon chains that range from four to thirty 6 carbons in length. The simplified nomenclature is the chain length, colon, number of double bonds, and a delta with the double bond positions as a superscript (20:2Δ 9,1). The double bonds do not exhibit resonance. The double bonds cause the chain to change direction. Can name the fatty acid with an ω followed by the number of the first double bond from the end of the chain. Physical Properties Of Fatty Acids The hydrocarbon chain is nonpolar which makes the molecule insoluble in water. A short chain will result in the molecule being slightly soluble since the fatty acid is overall more polar. The chain length and degree of unsaturation affect the physical properties. Saturated fatty acids can pack closest together and exhibit stronger van der Waals interactions. Triacylglycerols Three fatty acids esterified on the same glycol. They’re nonpolar and hydrophobic. Will form oily droplets in cytosol. Stored in large amounts in adipocytes which contain enzymes that catalyze their hydrolysis. The fatty acids are linked to the glycerol via a deprotonated oxygen. Will release more energy upon oxidation due to the methylene groups being more reduced than the alcohol groups of carbohydrates. Triacylglycerols Store Energy Energy stored as fat has the following advantages: o Has more energy. o Are unhydrated less water weight for an organism to carry. o Can serve as insulation. o Not reactive, so can be stored in large quantities without side reactions occurring. Carbohydrates may have less energy than fat but it’s “quicker energy”. Structural Lipids Membrane lipids are amphipathic and pack into membrane bilayers. Types include: o glycerophospholipids o galactolipids and sulfolipids o archeal tetraether lipids o sphingolipids o sterols Glycerophospholipids The first and second carbons of a glycerol have fatty acids. The third has a polar molecule connect through a phosphodiester linkage. The polar group can be charged or uncharged. Typically one chain is short and the other has double bonds. Galactolipids And Sulfolipids Galactolipids: the first two carbons of the glycerol have attached fatty acids. The third has one or two galactose residues. Sulfolipids: the third carbon contains a sulfonated glucose residue. Sphingolipids No glycerol. Polar head and two nonpolar tails. One tail is a sphingosine (long chain amino alcohol) and the other is a long fatty acid. There are three subclasses: o Sphingomyelins: the polar head is phosphocholine o Glycosphingolipids: the ceramide moiety has one or more sugars attached o Gangliosides: have oligosaccharides containing at least one N- acetylneuramic acid residue Found in great numbers on plasma membranes thought to be recognition sites. The carbohydrate moiety of certain sphingolipids defines blood groups. Gangliosides are highly concentrated on the outside of cells and act as recognition points for extracellular molecules or neighboring cells. Sterols Found in most eukaryotic cell membranes. Steroid nucleus of four fused rings. This is planar and rigid. Cholesterol is the main sterol in animal tissues. Its polar head is an alcohol group. Can act as precursors for molecules with specific biological activities. Cell Membranes Flexible, self-sealing, selectively permeable. Contain proteins which catalyze cellular processes. Contain polar lipids and carbohydrates. Membrane Architecture Proteins are integrated in the lipid bilayer and are held in place by hydrophobic interactions. Since the interactions are noncovalent, the molecules can move laterally and this is called a fluid mosaic. Membrane Proteins Integral proteins are held in place by hydrophobic interactions between the membrane lipids and the proteins hydrophilic domains. Peripheral proteins are held in place by electrostatic interactions and hydrogen bonding with hydrophilic domains of integral proteins and polar heads of membrane lipids. Some proteins can also be covalently bonded to lipids. Integral Proteins Are specifically oriented in the lipid bilayer. Spans the bilayer with an α helix 20-25 residues long. If 20 or more hydrophobic residues are together, one can assume it forms an integral protein. Transmembrane Domains Have at least one hydrophibic domain. Form α helices or β sheets to maximize hydrogen bonding. Tyr and Trp are usually found in the interface of the lipid and water. Positively charged membranes are commonly found inside the membrane. Topology Of Integral Membrane Proteins β sheets don’t maximize hydrogen bonding but β barrels do. At least twenty transmembrane segments form β sheets that form a cylinder. Every other amino acid will be nonpolar. To remove from a membrane, add a detergent that will replace the lipid bilayer on the sides of the protein (like SDS). Lipids Anchor Some Membrane Proteins Some proteins have one or more lipids covalently bonded to them. This acts are a hydrophobic anchor in the lipid bilayer to keep the protein at the surface. Can also be anchored by interactions between positive residues and negatively charged lipid heads. Can also be removed via detergent. Peripheral Membrane Proteins Secured to membrane via electrostatic interactions. Can be removed via addition of a salt which has charges or changing the pH to denature the protein. Biological Membranes Can change shape without losing integrity due to noncovalent lipid-lipid interactions which leads to their mobility. At low temperatures, form a semi-solid liquid where motion is restricted. At high temperatures, fatty acids are in constant motion in a disordered state. Sterols disrupt membranes by inserting between lipids in the bilayer and decreasing lipid-lipid interactions. Also forces lipids closer together, increasing lipid-lipid interactions. Transmembrane Movement Some proteins facilitate “flip flop” diffusion by providing a more energetically favorable pathway. Lateral lipid movement occurs quickly and randomly. Membrane Protein Diffusion Some proteins associate with each other to form aggregates where they do not move relative to each other. Protein movement can also be restricted by proteins being anchored to internal structures. Immobile proteins form “fences” which restrict lipid movement. Membrane Rafts Long chains of sphingolipids can form stable associations with cholesterol. These microdomains are thicker and more ordered than neighboring domains. These segregations of proteins may increase protein collisions. Electrochemical Gradient Forms when oppositely charged ions are separated by a membrane. The membrane potential is V . m The movement of charged solutes is dependent on an electrical gradient and a chemical gradient. Transporters And Channels There are two categories of proteins involved in movement. o Transporters: bind to substrate with high specificity. Can be saturated. Also called carriers. o Channels: substrate moves faster than with transporter. Less specificity. Cannot be saturated. Movement dependent on electrochemical gradient. Also called pores. Two types of transporters. o Passive: facilitate diffusion down concentration gradient. o Active: move substrate against a concentration gradient. Energy used comes from a chemical reaction or the transport of a different substance down its concentration gradient. The Glucose Transporter Glucose enters RBCs via facilitated diffusion. Transporter is GLUT1 and is an integral protein. The channel is lined with hydrophilic residues which can form hydrogen bonds with glucose to aid in its travel through the channel. Transport into the cell is reversible and not against concentration gradient. Chloride-Bicarbonate Exchanger CO r2leased as waste from tissues to blood. Enters RBCs and is concerted to bicarbonate which is more soluble in blood so it reenters blood plasma and is transported to the lungs. In the lungs, the bicarbonate reenters the RBCs and is concerted back to CO w2ich is exhaled. Chloride-bicarbonate exchanger moves bicarbonate and chloride ions in opposite directions. The change is electroneutral since the ions have the same charge. They move in different directions so it’s antiport. Transport can also be symport or uniport. Active Transport Thermodynamically unfavorable so it must be coupled with a favorable reaction. Primary active transport is where an unfavorable reaction is directly coupled with an exergonic chemical reaction. Secondary active transport is where an unfavorable transport is coupled with a favorable transport of another solute which was initially transported against its electrochemical gradient via primary active transport. + + Na K ATPase In animal cells, the concentration of sodium ions is higher outside the cell and the concentration of potassium ions is higher inside the cell. Na K ATPase maintains this. When ATP is dephosphorylated, two potassium ions move into the cell and three sodium ions move out. The protein undergoes a conformational change due to the phosphorylation/dephosphorylation of an Asp residue. The movement of these ions changes the electrical potential of a cell. Secondary Active Transport E. coli produces a proton gradient and charge across its membrane. The lactose transporter provides proton reentry and also lactose entry via symport. In intestinal cells, glucose is accumulated by symport with sodium ions. G-Protein Coupled Receptors 3 components: receptor on membrane, G-protein, effector enzyme. The effector enzyme releases a second messenger which affects other targets. β-Adrenergic Receptor Integral proteins. Epinephrine binds conformational change G-protein release α subunit binds GTP activates adenylyl cyclase catalyzes synthesis of cAMP from ATP cAMP allosterically activated protein kinase A PKA catalyzes phosphorylation of specific proteins. Amplification One hormone binding to one receptor can release multiple G- proteins. Each activated adenylyl cyclase can produce several cAMP molecules. Each PKA can catalyze the phosphorylation of multiple molecules. Signal Termination When the epinephrine concentration drops, the hormone dissociates from the receptor. Hydrolysis of GTP by G faαors the conformation where G binds α Gβγ Here, the G-protein doesn’t activate adenylyl cyclase. o Bioenergetics Autotrophs And Heterotrophs Autotrophs- build biomolecules from CO and s2n energy. May produce O and H O as waste. 2 2 Heterotrophs- get energy and carbon from autotrophs. Produce CO 2s a waste product. May consume O and conv2rt it to H O. 2 Metabolism The sum of all chemical reactions in a cell or organism. Metabolic pathways are a series of enzyme catalyzed reactions. Catabolism- degradative metabolism, releases energy. Anabolism- synthetic metabolism, requires energy. Metabolic Pathways May be linear, branched, or cyclic. Catabolic pathways typically converge while anabolic pathways usually diverge. Catabolic an anabolic pathways are carefully regulated, one will be active while the other is suppressed. Equilibrium ΔG’° concentrations: [H O]255.5 M, [H ] 10+ -7M, [Mg ] 10 -3 M. ATP Hydrolysis Hydrolytic cleavage of the end Pi reduces electrostatic repulsion and the long Pi is resonance stabilized. ADP and Pi can be more solvated than ATP and are therefore is more stable. Any phosphate can be nucleophilically attacked and each position will yield a different type of product. Attack of the α Pi displaces it and transfers AMP. This is adenylylation and it releases a lot of energy. Flow Of Electrons The electromotive force is the force driving electron flow through a circuit and is proportional to the difference in electron affinity. Reduction Potentials A larger positive E° correlates to a higher electron affinity. o Glycolysis Glucose Can be: o Synthesized to complex polysaccharides o Stored o Oxidized to pyruvate to yield ATP o Oxidized to yield robose-5-phosphate for nucleic acid synthesis and NADH. Glycolysis glucose + 2 ADP + 2 NAD + 2 Pi 2 pyruvate + 2 ATP + 2 + NADH + 2 H + 2 H O 2 Step 1: Phosphorylation Of Glucose C6 gets phosphorylated to glucose 6-phosphate. The Pi comes from ATP. Catalyzed by hexokinase which undergoes an induced fit. Brings the ATP and glucose closer to each other and blocks the access of water. Step 2: Conversation Of Glucose 6-Pi To Fructose 6-Pi Isomerization catalyzed by phosphohexose isomerase. Reversible. Carbonyl and hydroxyl rearrangement at C1 and C2. Step 3: Phosphorylation Of Fruc 6-Pi To Fruc 1,6-BiPi Transfer of Pi from ATP to fructose 6-phosphate to yield fructose 1,6-bisphosphate catalyzed by phosphofructokinase (PFK-1). Irreversible and solidifies the path of glycolysis. PFK-1 is activated when ATP is low and inhibited when concentrations are high. Step 4: Cleavage Of Fructose 1,6-Bisphosphate Reversible aldol condensation catalyzed by fructose 1,6- bisphosphate aldose (or just aldose). Fructose 1,6-bisphosphate is cleaved to yield glyceraldehyde 3- phosphate and dihydroacetone phosphate. Step 5: Interconversion Of Triose Phosphates Dihydroxyacetone phosphate is reversibly converted to glyceraldehyde 3-phsphate by triose phosphate isomerase. C1, C2, and C3 are chemically indistinguishable from C6, C2, and C4 respectively. Step 6: Oxidation Of Glyceraldehyde 3-Pi To 1,3- Bisphosphoglycerate Glyceraldehyde 3-phosphate is oxidized to 1,3- bisphosphoglycerate by glyceraldehyde 3-phosphate dehydrogenase. The aldehyde is oxidized to a carboxylic acid anhydride with phosphoric acid. Mechanism NAD is reduced when a hydride ion transfers from the glyceraldehyde 3-Pi aldehyde to the nicotinamide ring of the + NAD . A sulfur on the enzyme bonds to the aldehyde carbon which causes the bond to oxygen to become a single bond and the oxygen has a negative charge. The NAD removed the H and the carbonyl reforms. The inorganic phosphate group then attacks the carbonyl carbon and the carbon detached from the sulfur of the enzyme. Step 7: Phosphoryl Transfer From 1,3-Bisphosphoglycerate To ADP Catalyzed by phosphoglycerate kinase. A coupled process with step 6. Substrate level phosphorylation; when ATP is formed from a phosphoryl group transferred from a substrate. Step 8: Conversion Of 3-Phosphoglycerate To 2- Phosphoglycerate Phosphoryl group is reversibly shifted from C2 to C3 by phosphoglycerate mutase. The enzyme is phosphorylated at a His and donates this Pi to C2. It then removes the Pi from C3. Step 9: Dehydration Of 2-Phosphoglycerate To PEP A water molecule is reversibly removed from 2-phosphoglycerate by enolase to form phosphoenolpyruvate. Very large Gibbs energy difference between reactant and products. Step 10: Transfer Of A Phosphoryl Group From PEP To ADP Catalyzed by pyruvate kinase. Pyruvate is in enol form and then tautomerized to keto form. Half of the energy from hydrolysis is conserved in ATP and the other half is used to make the ATP. Irreversible. Hexokinase Four different isozymes. I and II in muscle, allosterically inhibited by glucose 6-phosphate which is their product. The enzymes K is M lot smaller than the concertation of glucose in the blood, therefore these enzymes always work at top speed. IV is in the liver and has a larger K M Its rate will vary with the glucose available. Liver enzyme is inhibited by a regulatory protein. In the presence of fructose 6-phosphate, the protein binds hexokinase tightly but in the presence of glucose it is released. Hexokinase then leaves the nucleus and works in the cytosol. Phosphofructokinase I Catalyzes the reaction that commits glucose to glycolysis. Inhibited by high concentrations of ATP. ADP and AMP allosterically relieve the inhibition of ATP. Gluconeogenesis Converts pyruvate to glucose. Occurs in the liver, kidneys, and intestines. Shares several steps with glycolysis, but not all. Fructose 1,6-Bisphosphatase-1 Inhibited by AMP. PFK-I is its corresponding glycolytic enzyme. Insulin And Glucagon Glucagon signals the liver to produce more glucose. Fructose 2,6-Bisphosphate stimulated PFK-1/glycolysis. F26BP is formed when fructose 6-phosphate is phosphorylated by PFK-II and is broken down by F26BP-II. Pancreatic hormones. ???????????? − 1 Fructose 6-Pi ↔ fructose 1,6-BiPi ???????????? − 1 ???????????? − 2 Fructose 6-Pi ↔ F26BP ???????????? − 2 F26BP activates PFK-I and inhibits FBP-I. Pyruvate Kinase Allosterically inhibited by ATP, acetyl-CoA, and long chain fatty acids. Liver enzyme regulated by phosphorylation when glucose is low. Epinephrine activated glycogen breakdown and glycolysis in muscle. Other Hexoses Enter Glycolysis Ways fructose can enter glycolysis: o fructokinase catalyzes the phosphorylation of fructose o fructose 1-phos[hate can be cleaved to DHAP and glyceraldehyde o triose kinase catalyzed the phosphorylation of glyceraldehyde to form glyceraldehyde 3-phosphate Fates Of Pyruvate Metabolized one of three ways: o Aerobic: oxidized to acetyl-CoA which is oxidized to CO in 2 + citric acid cycle. NADH is reoxidized to NAD and it gives its 2 electrons to O . The energy of the electron transfer drives the synthesis of ATP. o Lactic acid fermentation: hypoxic conditions. Reduced to lactate which takes electrons from NADH to regenerate NAD . + Catalyzed by lactate dehydrogenase. o Ethanol fermentation: anaerobic conditions. Converted to ethanol and CO . Ye2st/microorganisms. First step decarboxylation by pyruvate carboxylase. Second step aldehyde reduced to ethanol by alcohol dehydrogenase. o Equations To Know [????] ∆???? ????????????????????????????????????= ????????ln ???????? + ????????∆???? Ψ is the transmembrane potential [????]???????????? ???????????? ???? ???????????? ????????= ????????????[???????????????? ΔG = ΔH – TΔS ???? ????2????] [????−] ′ [????+] = [????????]= ???? ???? ′ ′ ???????? °= −RTln???? ???????? ???? ] ???? ] ∆???? = ∆????° + ????????ln ???? ] ???? ] ???????? [???????????????????????????????? ???????????????????????????????? Nernst equation ???? = ????° + ???????? ln [???????????????????????????????? ???????????????????? ′ ′ ′ ∆???? ° = ???? ° ????????????ℎ???????????? − ???? °???????????????????? ∆???? ° = −????????∆????′° o Constants F = 96485 J/Vmol
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