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Biochem Exam 4 Study Guide

by: America Seach

Biochem Exam 4 Study Guide 87222 - BCHM 3050 - 002

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These are all the notes from the power points in class for exam 4.
Essential Elements of Biochemistry
Srikripa Chandrasekaran
Study Guide
glycolysis, biochemistry, ATP, electron, transport, Chain, krebs cycle, NADH, FADH
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This 44 page Study Guide was uploaded by America Seach on Sunday April 17, 2016. The Study Guide belongs to 87222 - BCHM 3050 - 002 at Clemson University taught by Srikripa Chandrasekaran in Spring 2016. Since its upload, it has received 86 views. For similar materials see Essential Elements of Biochemistry in Biology at Clemson University.


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Date Created: 04/17/16
BIOCHEM EXAM 4 NOTES LECTURE 15: CARBOHYDRATES - Monosaccharides - - general formulas for the aldose and ketose forms of monosaccharides; glyceraldehyde is an aldotriose and dihydroxyacetone is a ketotriose - three carbons makes it a triose - Monosaccharide Stereoisomers o Two molecules are described as stereoisomers of each other if they are made of the same atoms connected in the same sequence, but the atoms are positioned differently in space. o All have same chemical formula but structured different o Cannot superimpose o They are mirror images - D-ribose and L-ribose are enantiomers; non- superimposible mirror images; the are exact mirror images; we will mainly be discussing D form - Diastereomers are stereoisomers that are not enantiomers o Not complete mirror images, functional groups only different on a few carbon atoms o d-ribose and d-arabinose - Diasteriomers that differ at a single chiral carbon are EPIMERS (e.g., D-glucose and D- galactose differ in position of –OH at C atom #4 and D-glucose and D-mannose differ in position of -OH group at C atom #2) - o must know and recognize glucose, mannose, and galactose - Monosaccharide structure: Hemiacetal formation o Furanose ring- 5 membered o Forms a ring by the oxygen on carbon 4 attacking carbon 1; so oxygen is then shared between carbon 1 and carbon 4 o Carbon 1 loses the double bond and gets an H added; loses the aldehyde o The two possible diasteriomers that form because of cyclization are called anomers (α or β) o o For a six carbon sugar, its between carbon-1 and the oxygen on carbon-5 o At carbon-1, the oxygen loses the double bond and gets an H added o If the OH is to the right, then it goes to the bottom of the ring o Carbon-5 does not have its own OH anymore o Mannose has an OH going up on carbon-2 o Galactose has an OH going up on carbon-4 - Sugars: o Fructose has 6 carbon atoms, but still makes a 5 member ring; still a hexose sugar even though it has a 5 membered ring; a ketose sugar o Bond between 2 and 5 carbons - Examples of Monosaccharides o Important monosaccharides o Glucose (D-Glucose)- originally called dextrose, it is found in large quantities throughout the natural world  The primary fuel for living cells  Preferred energy source for brain cells and cells without mitochondria (erythrocytes) o Fructose (D-Fructose)- is often referred to as fruit sugar, because of its high content in fruit  On a per-gram basis, it is twice as sweet as sucrose; therefore, it is often used as a sweetening agent in processed food; more abundant in nature (honey, fruit, nectar)  Sperm use fructose as an energy source  Not the preferred energy source; will be transformed into glucose after a certain point. o Galactose- is necessary to synthesize a variety of important biomolecules  Important biomolecules include lactose, glycolipids, phospholipids, proetoglycan, and glycoproteins  Galactosemia is a genetic disorder resulting from a missing enzyme in galactose metabolism  Not important for energy  Important role in cell-cell communication  Bacteria relies on it for capsule transporter  Not focused on - Chemical Reactions of Monosaccharides o Oxidation- monosaccharides may readily undergo several oxidation reactions in the presence of metal ions or certain enzymes  A lactone can be produced if the carbonyl groups of aldonic or uronic acids react with an OH group in the same molecule  Vitamin C, a lactone, is a powerful reducing agent that protects cells from reactive oxygen and nitrogen species  oxidation: when it gets oxidized, the aldehyde (H- C=O) group becomes an acid  reduction: when it gets reduced, the aldehyde becomes an alcohol  Alcohol oxidized to aldehyde oxidized to acids  Acids reduced to aldehyde reduced to alcohol  Some people lack enzyme to process aldehyde and can’t drink alcohol  Carbon 1--- Aldehyde replaced with carboxylic acid = aldonic acid  Carbon 6--- uronic acid  Both carbon 1 and carbon 6 are oxidized = aldaric acid o Reduction- Sugar alcohols (alditols) are produced by the reduction of aldehyde and ketone groups of monosaccharides  Sugar alcohols are used in commercial food processing and in pharmaceuticals (e.g., sorbitol can be used to prevent moisture loss)  Reduced- glucitol  Do not want to reduce glucose too much  Sorbitol used in food industry to prevent water loss; not good for consumption for long periods of time or in large amounts o Glycosidic Bond Formation:  Disaccharides  Two monosaccharides are linked by a glycosidic bond  Linkages are named by a- or b-conformation and by which carbons are connected (e.g., a(1,4) or b(1,4))  Alpha glucose on left; can attack any OH group and they lose a molecule of water  Name bond according to which carbons are in the bond; and base it off the first sugar on whether it is alpha or beta  1,4 linkages are most common because they are closest to each other  Lactose (milk sugar)- is the disaccharide found in milk  One molecule of galactose linked to one molecule of glucose (b(1,4) linkage)  It is common to have a deficiency in the enzyme that breaks down lactose (lactase)  Lactose is a reducing sugar  Know if it is a reducing sugar: in the second sugar at the first carbon, there is the ability to build the chain further or can get reduced  Know where its found and what it is involved in  Know what two sugars are involved  Maltose (malt sugar)- is an intermediate product of starch hydrolysis  a(1,4) linkage between two molecules of glucose  a-glucose because the OHs are pointed away from the oxygen  Maltose is two alpha glucose units together with a 1,4 bond  found in lots of kids drinks  A reducing sugar  Cellbiose- is a degradation product of cellulose  Cellobiose is composed of two molecules of glucose linked with a b(1,4) glycosidic bond  Does not exist freely in nature  Beta glucose on left and right; two beta  Reducing sugar  Sucrose- is common table sugar (cane or beet sugar) produced in the leaves and stems of plants  One molecule of glucose linked to one molecule of fructose, linked by an a1,2 glycosidic bond  Sucrose is a non-reducing sugar  Extremely sweet because it has fructose in it  Alpha glucose; beta fructose  1 is on the glucose, 2 is on the fructose (it is a 6 carbon sugar but only forms a 5 carbon ring)  Both carbon atoms are reducing atoms participating in the bond so nothing can be added to this; nonreducing sugar  Will name both alpha and beta {EX: alpha, beta (1, 2) } since we have to name the ones that are reducing atoms and they both are - Polysaccharides: o Building a chain of monosaccharides o Plant source: starch is a bunch of alpha glucoses attached in an Alpha (1,4) glycosidic linkages  Amylopectin: branched starch  Amylose: unbranched starch  At branch point is an alpha (1,6) linkage o Animal source: stored in the liver of animals; glycogen is chemically identical to starch (with alpha 1,4 linkage), EXCEPT plant sources don’t branch out as much as animal sources do; o Cellulose: beta glucose 1,4 glycosidic linkage; more structured for support for plants; hydrogen bonding between each of the cellulose sheets  The bonds of the oxygen are what needed to be followed to see which is beta or alpha o Based on beta 1,4 glycosidic linkages: o Chitin: used as structural support in cell walls of fungi and skeletons of plants/crustaceans o Peptidoglycan: structural support in bacterial cell walls; sugar is extremely modified and have chain of amino acids to form a peptide bond; serve as antigens in some bacteria - Lectins: proteins which bind to carbohydrates on cell surface o Lectin poisoning can cause:  Anaemia  GI distress  Allergic reactions ( vary from mild to severe)  Symptoms: nausea, vomiting, bloating, diarrhea o How to prevent lectin related damage?  Cooking seeds and grains in high heat or moist heat will destroy lectin toxocity. o Soaking seeds and grains for at least 1 hourprior to cooking and discarding the soaked water gets rid of some of the lectins. o Proteins can form association with carbohydrates o Interact mostly on the cell surface o Glucose generally doesn’t interact with proteins unless modified o Lectins: proteins that bind to carbohydrates; can cause allergic reactions, illness, etc; technically a poison o Easy to remove from grains/seeds by heating them - Ricin: an example of a lectin; found in castor seeds; also called RIP (ribosome inactivating protein) o Destroys the glycosidic bond between sugar and nitrogen base in rRNA ---- which prevents eukaryotic translation! = Certain Death o Used in the show breaking bad LECTURE 16: INTRODUCTION TO GLYCOLYSIS - All living forms need energy- which can be acquired from the environment in different ways - One way the energy is available for organisms is in the form of nutrients. o Question – how a cell can utilize the energy present in nutrients? o All use ATP as energy currency and we all get it from the same food sources which is broken down into glucose o Need proteins for structural support; and proteins and fat can be used as food source because it ends up in the same pathway as glucose - ATP (Adenosine Triphosphate)- an adenine, a ribose, and three phosphate groups o Energy is stored between each phosphate group. The bond- phosphoanhydride bond- is broken and energy is released - Glucose: The ultimate molecule that provides the energy that subsequently gets stored in the form of ATP o Prebiotic “soup” made and one of the first organic things was formaldehyde which can be converted into glucose o More reliable energy source - Overview of Cellular Respiration o How is glucose used to produce energy? You and me, we are aerobic organisms, and we carry out ‘aerobic respiration’. Glucose is initially converted to pyruvate by a process called Glycolysis. This occurs in the cytoplasm of the cell. Glycolysis does not require oxygen and occurs in an anaerobic environment. Pyruvate then enters the mitochondria where it gets converted to acetylCoA, which enters the Kreb’s cycle. As these reactions happen, NADH and FADH2 which are electron carries are produced. They transport electrons through an ETC, which finally transfer electrons to oxygen and facilitate production of ATP by a process called oxidative phosphorylation. o Mitochondria in the cell: has its own DNA, powerhouse of the cell; o Glucose travels into mitochondria to be converted into energy o Glycolysis: glucose converted into pyruvate which is taken to the cell and converted to ATP o Ten steps between glucose and pyruvate o Some ATP produced in glycolysis - Glycolysis: the most ancient known reaction – from times on earth when only anaerobic organisms were present (before the amount of oxygen was sufficient) o Present in virtually all organisms on earth o Break down food into glucose o Converted from 6 carbon compound into two 3 carbon compounds (pyruvate) o Two molecules of NADH created; will be used later during ETC to create more ATP o A series of 10 steps to convert one molecule of glucose into two pyruvate  First phase is the ATP investment phase or the preparatory phase (1-5)  Second phase is the energy generation phase (6-10) o Net yield of 2 ATP at the end (in the cytoplasm)- get out 4 ATP but initially two were invested so only have a net gain of 2 - Step 1: Energy investment; first priming reaction o One molecule of ATP using the enzyme HEXOKINASE; a single phosphate is added to the glucose molecule and ATP is converted to ADP; negative charge traps glucose in the cell o Trapping glucose in the cell by means of converting it to glucose 6-phosphate – once glucose enters the cell – there are no transporters to transport glucose 6-phosphate so it stays in cell. o One direction – delta G has high negative value—makes it irreversible o -Hexokinase is used to take the H+ off the glucose molecule and split ATP into P and ADP– P added to the glucose molecule o Irreversible reaction– glucose will never be remade; know this because delta G is NEGATIVE; other factors either inhibit or activate the enzyme solely because it is a one way process; its own product will inhibit it (glucose-6- phosphate) o Glucose-6-phosphate can be taken down several different pathways o Converted into glycogen (alpha glucoses) - Step 2: o Glucose-6-phos converted into an isomer of itself- fructose g-phosphate o The enzyme is also called phosphohexoseisomerase, the carbonyl oxygen in G6P is shifted from Carbon 1 to Carbon 2, an aldose to a ketose isomerization. o Not inhibited or activated; positive delta G- reversible - Step 3: Called second priming reaction (second investment of ATP) o PFK1 very important enzyme in terms of regulation - the most regulated enzyme in glycolysis o Just like hexokinase commits the cell into internalizing glucose, PFK1 commits the cell to metabolizing glucose rather than converting into another sugar or storing it. o Meaning of the term bis-phosphate as oppose to using the term di-phosphate (bis means phosphate groups are on different carbon) o One direction; irreversible o Another ATP is being invested o Another phosphate group is added carbon-1 o Uses bisphosphate because they are attached to completely different carbon atoms o Phosphofructokinase is inhibited by ATP binding to the enzyme at its regulatory site - Step 4: o This step is why the process is called glycolysis because of the lysis (splitting) of the F1,6- bisphosphate. o Splitting catalyzed by aldolase o Six carbons until this - Step 5: End of the investment phase o Conversion of DHAP to G3P by the Triose phosphate isomerase – a very efficient enzyme (kinetically perfect enzyme – intermediate for this reaction is very unstable) and very fast reaction o This is the end of the investment phase – the end result of this phase is two molecules of G3P o Two molecules of glyceraldehyde 3-phosphate are produced so after step 5, everything is doubled! - Step 6: o From this stage always two reactions are happening per initial one molecule of glucose o Oxidation –G3P loses hydrogen (this is the only oxidation reaction in glycolysis) + phosphorylation o Oxidation reaction is providing energy to add phosphate in the form of the inorganic phosphate o NAD+ is absolutely needed for this step to occur (NAD+ is normally at low levels in the cell – cell have devised unique ways to regenerate the NAD+) o Everything that happens here is doubled o Where NADH is produced o Two things happening at the same time: oxidation (goes from H to OH) and phosphorylation (phosphate was also added) o Phosphorylation does not involve ATP so enzyme is not a transferase- it is an oxyoreductase o NAD+ gets reduced at the same time to NADH (two NADH produced) o Gain of electrons makes it have more potential and allows it to produce more energy o - Step 7: o 1,3-bisphosphoglycerate is a very high energy molecule o Substrate level phosphorylation o Here the ATP is made o 3 ways ATP can be formed in cells – substrate level, oxidative phosphorylation and photo phosphorylation (in plants) o Phospho glycerate kinase o Broken even – two ATP that was consumed has now being generated back. o Standard free energies of hydrolysis of some phosphorylated compounds o Reversible- no activators or inhibitors o Takes the product from step 6 and takes a phosphate off and adds it to ADP to form ATP o Enzyme involved in ATP production is phosphoglycerate kinase o Substrate Level Phosphorylation When ATP is generated while sitting on an enzyme like phosphoglycerate kinase, one group giving a phosphate to ADP and one releasing ATP o Two ATP are produced o Standard free energy of hydrolysis: High free energy of 1,3 bisphsophoglycerate (very negative value) o So extra energy from step 7 is released as heat o - Step 8: o 3 converted to 2 position – (seems like a simple move from carbon 3 to carbon 2) but it involves an intermediate (2, 3 bisphosphoglycerate) o Phosphoglycerate mutase is the enzyme o Product from the previous reaction is the substrate for the next reaction step o Mutase is an isomerase because the functional groups are just moved around - Step 9: Dehydration reaction o Losing water o enolase: lyase (NOT HYDROLASE); breaking large compound into smaller ones with water as one of the products o No inhibitors because its reversible o Can be inhibited by fluoride (obtained from an outside source) - Step 10: o PEP has a lot of energy (has a very negative Delta G) o A lot of heat energy is also released – reason for sweating while exercise? o Pyruvate kinase o deltaG is very negative o Very energetically favorable. o A disease – deficiency of pyruvate kinase – hemolytic anemia – erythrocytes are very sensitive because they solely depend on glycolysis to get ATP o Kinase= transfersase o Phosphate group in PEP is given to ADP to form ATP o Get back two molecules of ATP o Generated a total of four ATP but two were initially invested, so total gain of 2 ATP o Irreversible with inhibitors and activators o The activator is the product of step 3 o Pyruvate kinase is regulated by DIRECT COVALENT MODIFICATION  If you remove the phosphate- you activate it  If you add a phosphate- you shut it down  Keep phosphate group away- to keep ATP amounts high  Add a phosphate to stop ATP production  Secretion of insulin= keep phosphate group away and pyruvate kinase is more active  Secretion of glucagon= adds a phosphate and pyruvate kinase inactive  Pyruvate kinase is directly regulated through phosphorylation (Direct covalent modification) - Glucokinase is a molecular sensor of high glucose levels o The hormone insulin regulates the levels of Glucokinase o Send glucose to the liver o Lower the km, the higher the affinity o Extra glucose stored in the liver as glycogen o Lipogenesis: makes glucose into fat o Insulin helps glycolysis and synthesis of glycogen - Glycolysis occurs in two stages: o Stage 1:  Energy Investment or Priming stage.  Glucose is phosphorylated twice, and cleaved in half to form two glyceraldehyde-3P.  2 ATP are consumed. o Stage 2:  Energy Payoff (yielding) stage.  Glyceraldehyde-3P is oxidized to pyruvate.  4 ATP & 2 NADH are produced. o Net gain of two ATP - A Closer look at STAGE 1 of Glycolysis- Energy Investment o Glucose is phosphorylated twice, and cleaved in half to form two trioses. o 2 ATP are consumed. o Hexose is cleaved into 2 trioses. o Hexokinase rxn. Is referred to as a “gate rxn.” i.e. it helps “trap” hexoses within cell (imagine a bacterium) – the large negatively charged phosphate prevents hexose from crossing membrane back out of cell. o Phosphofructokinase is the “committing” step or reaction. Once past this point, metabolites (F-1,6-bP) are committed to pass through glycolysis. This will be a key point in regulation. o Phosphate groups are very “electrophilic”, i.e. the attract electrons from the rest of the molecule. o One phosphate group on each end of a hexose makes it very easy to break the c3-c4 covalent bond (i.e. via aldolase). - A Closer look at STAGE 2 of Glycolysis- Energy Payoff o Glucose is phosphorylated twice, and cleaved in half to form two trioses. o 2 ATP are consumed. o Hexose is cleaved into 2 trioses. o Substrate level phosphorylation occurs here - Regulation of Glycolysis o Higher km, lower affinity o Pyruvate kinase is the only one that gets covalently modified  Add phosphate inhibits it= glucagon  Removing phosphate activates it= insulin - Allosteric Regulation of Glycolysis o ATP is generally an inhibitor; where ATP inhibits, AMP and ADP activate o - Metabolic fate of Pyruvate o Aerobic: relies on oxygen for energy o Anaerobic: can live in environments without oxygen o All organism perform glycolysis o The carbon from pyruvate will be released as CO2; at the last step of aerobic respiration is where oxygen is used to make ATP o Anaerobic: per molecule of glucose, they get two ATP; pyruvate doesn’t enter the mitochondria- either gets converted to ethanol and CO2 (alcohol fermentation) or lactate o NADH will be oxidized to NAD+ as a way to recycle it and allow glycolysis to happen again o Humans go through homolactic fermentation when they work out but oxygen is not being delivered to the muscles fast enough- lactic acid will be produced and accumulated in the muscles which is why it hurts sometimes while/after working out o - Three possible fates for glycolytic pyruvate 1. Continue on to the TCA Cycle o Oxidized to produce more NADH and ATP 2. Lactic Acid Fermentation o Reduced to form lactic acid and NAD+ 3. Alcoholic Fermentation o Reduced to form ethanol and NAD+ o Only anaerobic respiration that releases CO2 - Question: Why must there be a “fate” for pyruvate produced in glycolysis? Why not just “discard” it? - ANSWERS: o Pyruvate is still somewhat reduced – i.e. still has some useful or “extractable” energy. Thus, for Aerobic Organisms that have TCA/Krebs, complete oxidation is best (to produce more NADH and eventually ATP via Resp. e transport). o Some organisms, however, may be aerobic, but oxygen may not be readily available. Without oxygen, glycolysis comes to a halt because it runs out of NAD . The remaining “fates” of pyruvate are “strategies” to help regenerate NAD in order to allow glycolysis to run for a while and produce nominal ATP.  Many microbes (e.g. Yeasts) will produce ethanol to accomplish this (as in brewing beer & wine).  Others (e.g. Lactobacillus) will produce lactic acid (as in yogurt). - Lactic Acid Fermentation o Lactate fermentation allows regeneration of NAD so that glycolysis can continue producing some ATP. o Especially important in “over-exercised” muscles. o Other acids can be produced (e.g. acetic, propionic, butyric by rumen microbes). o Lactate fermentation occurs in muscles when exercise has been so extensive that oxygen actually becomes limiting. This allows glycolysis to continue for a short while, until oxygen becomes more available (i.e. resting). Otherwise the pain & cramps associated with muscle fatigue follow. o Lactic acid and lactate are the same thing o Pyruvate is converted to lactate by the enzyme lactate dehydrogenase (oxyreductase)- oxidizes NADH to NAD+; pyruvate reduced to lactic acid o Need pyruvate processing so NADH can be recycled into NAD+ to be used in glycolysis - Alcohol Fermentation o Ethanol consumption stimulates NADH synthesis in the liver by the ADH reaction (reverse of above). o Excess NADH will inhibit glycolysis and fatty acid oxidation. o Acetaldehyde  Acetic Acid  Fatty acid synthesis. o Result is accumulation of fat in the liver (cirrhosis) and loss of function. o Pyruvate decarboxylate- gives you acetaldehyde by removing carbon dioxide o Acetaldehyde is reduced to ethanol; NADH is oxidized to NAD+ o Humans have evolved the ability to break down alcohol o - SUMMARY: o Irreversible reactions in glycolysis are regulated o Glycolysis happens in the absence of oxygen o Pyruvate can either participate in aerobic respiration or fermentation o Glycolysis is at the crossroads of other catabolic and anabolic processes LECTURE 17: AEROBIC RESPIRATION - TCA or Kreb cycle or Citric acid cycle - In mitochondria- pyruvate moves into the mitochondria (some energy it takes to move into mitochondria) - Gets converted into CoA - What to pay attention to how much NADH and FADH2 is produced (electron carriers) - NADH and FADH2 will go into specific area in mitochondria and will give the electrons into the electron transport chain and will get ATP - The Citric Acid Cycle o A series of reactions associated with the mitochondria where partly oxidized carbohydrate and lipid are completely oxidized to CO to2produce (some) ATP and (a lot of) reduced nucleotides. o Also known as the Tricarboxylic Acid (TCA) or the Krebs Cycle (after Sir Hans Krebs, 1937; Nobel Prize, 1953). - Review of Mitrochondrial Ultra Structure o Activities and Locations  TCA Cycle  Matrix  Succinate dehydrogenase  Cristae M.  Electron Transport  Cristae M.  PDH Complex  Inner M./matrix o Localization of PDH complex thought to be loosely associated with inner membrane/matrix interface. o Look at structure of mitochondria o Outer membrane (double layer) then gap then inner membrane (cristae membrane- pattern they make) (extensions of the same membrane) o Matrix has part of cytoplasm (Kreb’s cycle mostly happens here) o Inter membrane space between the outer and the inner membranes - Overview of TCA/Krebs/Citric Acid Cycle o Complete oxidation of pyruvate to CO . 2 o Reduction of nucleotide electron carriers. o Production of some ATP. o Regeneration of OAA. o Should be able to draw out cycle when finished with chapter o Constant supply of glucose = Kreb’s cycle continues o Every cycle starting from pyruvate (loss 3 CO2) (make 4 NADH every cycle) (one FADH2) (generate 1 ATP) (multiply by two cause everything happens twice) - Enzymes in the Kreb’s cycle 1. Pyruvate dehydrogenase 2. Citrate synthase 3. Aconitase 4. Isocitrate dehydrogenase 5. -Ketoglutarate dehydrogenase 6. Succinyl-CoA synthetase 7. Succinate dehydrogenase 8. Fumarase 9. Malate dehydrogenase o Pyruvate dehydrogenase [PDH]- substrate (2 pyruvate-3C), (releases 2 CO2) (reduces NAD+ to generate 2 NADH) (converts pyruvate to 2 acetyl-CoA (cofactor can easily be removed and has 2 carbon atoms)) (class of enzyme is oxioreductase) (part is sitting in the matrix and part is sitting in the inner membrane) o Citrate synthase (acetyl CoA (2C) joins oxzolo acetate (4C) to form citric acid)- class of enzyme (ligase) (attaches 2 compounds together) o Citrate isomerized to isocitrate (6C)- enzyme is aconitase (class is isomerase) o Isocitrate dehydrogenase (CO2 released and NADH produced) alpha ketoglucerate (produce) (5C) (only compound that has 5C) [isocitrate oxidized] (oxioreductase) o Alpha ketoglucerate dehydrogenase: enzyme (class- oxioreductase), loss CO2, gen NADH, product (succinyl CoA (4C)) o Succinyl-CoA synthetase: enzyme (class is ligase), takes away CoA from succinyl and makes it succinate (product) (4C): only enzyme which participates in substrate level phosphorylation (ATP generated) o Succinate dehydrogenase: only enzyme that generates FADH2 (oxioreductase), product is fumerate; converts succinate to fumerate and gives FADH2 o Fumarase- adds water molecule (ligase) forms malate o Malate dehydrogenase: oxaloacetate generated and NADH generated (oxioreductase) - A closer look at enzymes: 1. Pyruvate Dehydrogenase:  A complex of three separate enzymes.  Promotes entry of pyruvate into cycle via formation of acetyl-CoA.  Subjected to complex regulation.  Not one single enzyme; forms a complex of several enzymes; three enzymes doing individual activities; one removes co2, second oxidizes pyruvate and reduces NAD; third adds CoA  Two modes of Regulation:  Allosteric Regulation o Inhibitors: ATP, Acetyl- CoA, and NADH o Activators: AMP, CoASH, and NAD+  Covalent Modification o Phosphorylation of E1 (PDH)  inactivation o Modulate PDH protein kinase:  The activators & inhibitors of PDH are not acting via their inhibitory & activating effects on PDH Kinase. Each enzyme has its own binding sites for the same regulators.  ATP is universal inhibitor  Where ATP inhibits, AMP will activate  Where NADH inhibits, NAD+ activates  Have too much NADH/ATP, they will inhibit the processes  One enzyme is modified covalently by addition of a phosphate group (similar to enzyme- pyruvate kinase #10 of glycolysis); removing phosphate group activates it (pyruvate dehydrogenase), adding inhibits it - Regulatory Coordination between Glycolysis and TCA Cycle o A minus is an inhibitor o First two columns are from glycolysis o One more enzyme in glycolysis- hexokinase but isn’t a common one to TCA 2. Succinyl- CoA Thiokinase (Succinyl- CoA Synthetase) o High-energy CoA thioester is cleaved to form succinate. o Energy is conserved in Substrate Level Phosphorylation of GDP. o ATP is synthesized via Nucleoside diphosphate kinase. o Substrate level phosphorylation o Kinase because it stimulates phosphorylation of GTP o Not a transferase because the phosphate group does not come from another molecule; it is free floating o Classified as a ligase (adds a succinyl CoA); classified based on the reverse reaction o Every round you make one ATP o So far we have made 4 ATP (2 from glycolysis, 2 from krebs) 3. Succinate Dehydrogenase o SDH is part of complex II in respiratory electron transport. o Succinate is oxidized to fumarate, introducing a trans double bond. o Enzyme-bound FAD is reduced to FADH . 2 o FADH fe2ds electrons directly to Q in electron transport. o Regulation:  Succinate: activates.  ATP & Pi: activate.  OAA: inhibits o Only one to produce FADH2 as a reducing equivalent o Lives in inner mitochondrial membrane while all the others are in the matrix o Only enzyme that is stimulated by ATP o Participates in Krebs cycle but also part of the electron transport chain; dual function 4. Malate Dehydrogenase o The final (& anaplerotic) reaction of the TCA cycle. o Malate is oxidized to regenerate oxaloacetate; NAD is + reduced to NADH. o Forward reaction is not favorable (G = +29 kJ/mole) but pulled forward by depletion of OAA. o Generates oxaloacetate o This is the step that will deem whether kreb’s cycle will happen or not o Acetyl CoA is waiting for oxaloacetate for kreb’s cycle to occur o Anaplerotic reaction: any reaction that replenishes the intermediates of the krebs cycle; many, many of them; things outside of the cycle that can be converted to something used in the cycle; most reactions are from outside sources to produce an intermediate of the krebs cycle o One reaction in the cycle itself: last part catalyzed by malate dehydrogenase o Majority of anaplerotic reactions come from the outside; they fill in components of the cycle o Pyruvate carboxylate: can directly get converted to oxaloacetate; if there is a need for energy and there is not enough time to produce acetyl CoA, pyruvate will be converted directly to oxaloacetate o Body loses a molecule of ATP every time something is converted directly to oxaloacetate - Amphibolic Nature of TCA Cycle o Acetyl-CoA  fatty acids & sterols. o Glutamate  proteins & purines. o Succinyl-CoA  porphyrins (hemes, chlorophylls). o Oxaloacetate  gluconeo-genesis, aspartate (proteins), pyrimidines. o Oxaloacetate  TCA Cycle.  Malate deHydrogenase.  Pyruvate Carboxylase. o Pyruvate decarboxylase: in glycolysis- involved in ethanol (alcohol) fermenation o Pyruvate dehydrogenation: converts pyruvate to acetyl CoA o Pyruvate carboxylase: converts pyruvate directly to oxaloacetate - Cumulative Summary of Glycolysis and TCA Cycle o Glycolysis & TCA cycle involve multiple oxidation/reduction reactions. o Glucose has been completely oxidized to CO . 2 o A lot of reduced nucleotides (NADH & FADH ) an2 some ATP have been produced. o Both glycolysis & TCA cycle will stop unless oxidized nucleotides are regenerated. o Using the 10 NADH and 2 FADH to cr2ate more ATP LECTURE 18: RESPIRATORY ELECTRON TRANSPORT - 1 molecule of glucose--- glycolysis in CYTOPLASM produces 2 NADH and 2 ATP --- KREBS in MATRIX produces 2 FADH2, 8 NADH ---- ETC in INNER MEMBRANE has four complexes, and complex 4 accepts oxygen from the matrix and reduces oxygen to water - 8 NADH give to complex 1 - 2 FADH2 give to complex 2 - 2 NADH from glycolysis also go to complex 2 or complex 1 depending on what transporter brought it to the matrix - Enzyme at complex 2 is succinate dehyrdogenase which transfers fadh2 to fadh and sends it back into the cycle - Oxygen has the highest reduction potential - Glucose to pyruvate is common for aerobic and anaerobic - LEO says GER o When you gain an electron, you lose a positive charge o Positive charge represents a missing electron o Losing electrons is oxidation (so becomes more positive) o Gaining electrons is reduction (so becomes less positive) - Oxidation of Malate to form Oxaloacetate o NAD+ is reduced 0’ - Significance of Reduction Potential (E ) o Reduction potential: A measure of the affinity a substance has for electrons; the likelihood that something will get reduced o A “high (+)” E ’ means that a substance . . .  Has a high affinity for electrons.  Is not likely to be oxidized by other substances.  Is likely to be reduced by other substances.  Is likely to be a good oxidizing agent  The higher the reduction potential, the greater the ability for that compound to get reduced o When two different redox substances are mixed, electrons spontaneously “flow” from low E ’ to high E ’ substance. - Respiratory Electron Transport- The third stage of Aerobic Respiration o 1 Glucose à glycolysis à 2 NADH, 2ATP, 2 pyruvate; happens in cytoplasm o Have to get pyruvate and NADH into the mitochondria and that takes energy o Krebs cycle happening in the matrix o 2 pyruvate get converted to 2 acetyl CoA; two NADH produced; no ATP produced; NADH goes into krebs and produces 2ATP, 6 NADH, and 2 FADH2; o All travel to inner membrane where electron transport change occurs o The NADH from cytoplasm behaves differently than the NADH from krebs o One NADH produces 2.5 ATP o One FADH2 produces 1.5 ATP - Intro to ETC o Repiratory Electron Transport: A series of redox reactions associated with mitochondria where the electrons of reduced nucleotides produced in glycolysis and the TCA cycle are transferred through a series of electron carriers ultimately to oxygen to form H O. 2  Oxygen gets reduced to water  In the process, an electrochemical gradient is formed, which is used to drive ATP synthesis.  Respiratory electron transport occurs in the cristae membranes of mitochondria. o Complexes are found in the inner membrane o This happens in the folds of the membrane of the mitochondria - Positioning of Four Complexes in Cristae Membrane o Complexes: Mainly protein in nature o Separated, so need messengers to deliver from one complex to the next o Once they are embedded, they can’t move so they need transporters to move around the o Ubiquinone: lipid in nature so comfortable in lipid bilayer; can move; receives electrons from complex two and delivers it to complex 3 o Cytochrome C present in inter membrane space; takes electrons from complex 3 to complex 4 o Then 4 gives the electrons to oxygen o NADH is giving electrons to COMPLEX 1 to become NAD+ - Four Membrane Complexes: o Complex I – NADH dehydrogenase o Complex II – Succinate DH complex o Complex III – Cytochrome b/c com1lex o Complex IV – Cytochrome c oxidase o Complex 1: oxidizes NADH to NAD+; NADH hydrogenase takes the electrons o Complex 2: generates FADH2 o Complex 3 and 4: both have proteins that belong to the cytochrome family o Regenerating NAD and FAD: where they either go back glycolysis or krebs cycle - Four Complexes of Electron Transport o Complex I – NADH dehydrogenase  Entry point for NADH-bound electrons from glycolysis & TCA.  Transfers electrons from NADH to oxidized ubiquinone (a mobile lipophilic electron carrier dissolved in membrane). o Complex II – Succinate Dehydrogenase Complex  Transfers electrons from succinate (via bound FADH )2to oxidized ubiquinone. o Complex III – Cytochrome b/c c1mplex  Transfers electrons from reduced ubiquinone to oxidized cytochrome c o Complex IV – Cytochrome c oxidase  Transfers electrons from reduced cytochrome c to oxygen (the final e acceptor) to produce H 2. o Complex 1 and 2 do not interact with each other- they separately receive electrons o 1 à UBI à 2 à UBI à 3 à CYTOCHROME à 4 à oxygen - The four complexes are made up of four different types of proteins o Flavoproteins  Contain bound flavin nucleotides (FAD/FMN).  Cofactors  Proteins enriched in this o Fe-S Proteins  Non-heme proteins; contain 2 – 4 Fe atoms bound to protein via cysteine residues. o Cytochromes  Heme proteins – contain single Fe atoms bound to heme.  Donate a heme group o Ubiquinone (Coenzyme Q)  (Non-protein) Lipophilic molecule.  Nonprotein in nature; can move around the membrane - Each complex contains several electron carriers o Complex 1 and 2: Both contain members of the flavin family; no cytochrome o Complex 3 and 4: do not have any flavin; have cytochromes; o Complex 4 has copper in it and that’s what ultimately donates the electrons to oxygen o - Electron Transport in Relation to Reduction Potentials o Each transport complex (and the carriers therein) has their 0’ own characteristic reduction potential (E ). 0’ o Electrons flow from “less +” to “more +” E . o Oxygen has highest reduction potential o NADH has the lowest reduction potential because it is the first thing to donate an electron o Cyto C has higher than CoQ (ubiquinone) o Potential to get reduced- higher ability to accept electrons; at the end of the chain - Reduction potentials along ETC o The more positive, the higher the reduction potential--- so oxygen has a high positive number - Some “poisons” are inhibitors of Respiratory Electron Transport o Rotenone: broad spectrum insecticide produced by some leguminous plants (Lonchocarpus – derris root), also toxic to fish; kills by inhibiting respiratory e transport. o Amytal (amobarbitol)- a barbiturate drug that blocks electron transport from NADH to coenzyme Q at the same point as the insecticide rotenone. Sometimes used as a sedative or sleep-inducing agent (especially for animals). o Antimycin: Often used as an antibiotic for fungi; stops respiratory e transport between cyt b & c. Also approved as a “fishicide” to kill fish for manangement purposes. o Sodium Azide: Na-N=N=N. Azides very reactive, especially in light. o Cyanide toxicity = 50 – 200mg per individual (this is LD50). o Jonestown Massacre (1978) – cult members were forced to drink punch laced with KCN. o If you inhibit any of these, you will most likely die o Amytal, rotenone- complex 1 o Anitmycin- antifungal antibiotic; only for extreme cases; complex 3 o Carbon monoxide, cyanide, azide- blocks between complex 4 and oxygen o If you’re given the name of the poison, know what portion of ETC it inhibits - Other Electron Transport Processes o “Alternate Oxidase” in plants- known as “cyanide insensitive respiration”  Certain plants do not have complex 3 and 4 so they are insensitive to those poisons that inhibit it o Since they lack complexes, they do not produce as much ATP- so extra energy is released as heat; they grow best in warmer climates  “Skunk cabbage”, Voodoo Lily o Ubiquinone will deliver it to the alternate oxidase and go straight to oxygen - Functions of the Alternative Oxidase System o All respirations want to regenerate NAD and FAD o Alternate oxidase: produces less ATP - LECTURE 19: AEROBIC RESPIRATION- ATP SYNTHESIS ­ REVIEW: In most parts of our bodies, the NAD+ needs a transport system to get through the membrane. Takes the NADH from the cytoplasm to Complex 2; FADH2 is generated in complex 2, so FADH2 from mitochondria goes to complex 2 ­ Nothing was in the inter membrane space until now. The electrons get forced into it ­ ATP Synthesis Terminology o “loosely” referred to as phosphorylation of ADP o Three types of “phosphorylations” are recognized  Substrate Level Phosphorylation – ATP synthesis coupled to carbon metabolism.  Oxidative Phosphorylation – ATP synthesis coupled to oxidative processes of respiratory electron transport.  Photophosphorylation – ATP synthesis coupled to the light-driven reactions of photosynthesis. o During glycolysis- two enzymes participate in substrate level phosphorylation; krebs has one enzyme that does o What happens when ADP is sitting on an enzyme and accepts a phosphate from something sitting on the same enzyme - Three Sites in Electron Transport with Sufficient energy yield for ATP synthesis: o This illustration is inverted compared to previous illustrations. o Four complexes o Purple and blue is the inner membrane space o At the bottom is the matrix o At the top is the inter membrane space that up until now had nothing going on in it o Every time that NADH gives an electron to enzyme one sets off a domino effect that collects a lot of protons that are pushed into the inter membrane space o For every NADH in Complex ONE- 4 protons will be pumped into the inter membrane--- at the end there will be 10 protons in the inter membrane at the end of complex 4 o With complex 1 and 3- eight protons are in the inter membrane o Once protons have gone through a passage into the inter membrane, they cannot leave o 1 glucose produces 10 NADH (2 in the cytoplasm, 8 in the mitochondria) o If the NADH are sent to complex 2, and complex 2 sends them to complex 3 and complex 3 sends them to complex 4, only 6 protons are in the inter membrane instead of 10 (because complex one is completely skipped) o (8 total go to complex 1) Per NADH that goes through complex 1, you get 10 protons – so total 80 protons o (2 total go to complex 2) Per FADH2 goes to complex 2, you get 6 protons, so you get 12 in total o (2 total go to complex 2) Per NADH that goes to complex 2, you get 6 protons, so you get 12 protons in total o So 104 protons are in the inter membrane per molecule of glucose o Protons are unstable in the inter membrane, so they want to get back- go through a passage and produce 1 ATP per 4 protons that go through o For every 4 protons, there is one ATP produced- theoretically all of the 104 protons will produce 26 ATP in the mitochondria o Every NADH makes 2.5 ATP since every NADH makes 10 protons--- 4 protons make 1 ATP so 10/4 = 2.5 ATP o Make 30 (brain and muscles) -32 (liver) ATP per molecule of glucose o This is for the brain and muscles o The liver produces more ATP- because 2NADH go to complex 1 instead of complex 2; producing 112 protons--- produces 28 ATP + the four that are made through substrate level phosphorylation– so liver produces 32 total ATP o We don’t actually make 30 because we use some energy to move the NADH into the membrane- so net loss of about 1 ATP, but don’t normally include this - Stoichiometry of Respiratory Electron Transport o 4H from complex 1, 4H from complex 3, 2H from complex 4 o There will be 104 if it is in the brain/muscles and 112 if it is in the liver - Electron transport results in… o The creation of a transmembrane proton (pH) gradient. o Three instances where the E (and the associated G) are sufficient to drive ATP synthesis. o 1 NADH makes 2.5 ATP o 1 FADH2 makes 1.5 ATP o Light pink is the matrix- because of ETC pushing protons out of the matrix- so low concentration of H+ making the pH high (low acidity- so basic) o Dark pink is the inter membrane- protons are collected here- so high concentration of H+ making pH low (high acidity) o Transmembrane proton gradient is formed because not only are the concentrations opposite, the pH is too o Inter membrane is just an open space- between the inner and outer membrane; not a bilayer - Proton Gradient Represents Electrical and Chemical Free Energy o “electro-chemical potenial” o Electrical Potential  Refers to the charge differential across the membrane. o Chemical Potential  Refers to the concentration differential across the membrane. o Chemi-Osmotic Coupling Theory  Proposed by Peter Mitchell (1961).  Said that chemical reactions (ATP synthesis) could be coupled to osmotic gradients. o Electrochemical potential across the membrane (referred to as “proton motive force”) provided the energy for ATP synthesis o ATP synthesis is driven by the huge gradient o Only channel is the ATP synthase o ATP is made in the matrix - EXAMPLE EXAM PROBLEM: If you inject 1 pyruvate into an artificial mitochondria, everything is half of what it would be if glucose had produced 2 pyruvates because you can only go through the cycle once--- total 4 NADH (go to complex 1 to produce 40 protons), 1 FADH2 (go to complex 2 and make 6 protons), and 1 ATP ---- so total 46 H+ produced; divide 46/4 to get 11.5 ATP from protons then add the 1 ATP produced initially- so total 12.5 ATP could be produced with 1 pyruvate - Postulates of the Chemiosmotic Theory o Energy derived from electron transport is temporarily stored as a transmembrane difference in charge (electrical potential) and pH (chemical potential). o Protons can pass back through the inner membrane to the matrix only through specialized channels, i.e. the ATP synthase protein. o Return of protons back to matrix is coupled to ATP synthesis. o Every time you get 4 protons across, you get 1 ATP o Protons go back to the matrix by ATP synthase– 4 protons make 1 ATP - Evidence supporting the Chemiosmotic Theory o Actively respiring mitochondria secrete protons. o ATP synthesis stops when the inner membrane is disrupted (e.g. osmotic swelling, physical fragmentation). o Certain molecules that lower ATP synthesis do so by collapsing the proton gradient.  Uncouplers – hydrophobic compounds with a dissociable proton carry protons back across the membrane.  Ionophores – hydrophobic molecules that insert into membranes to form channels that allow the free passage of cations (including H ) back across membranes. o There appears to be “enough” electrochemical potential across the cristae membrane to drive ATP synthesis. o Secretion/leakage of protons is due to the fact that the outermembrane is a bit more permeable to protons than the inner membrane. o Uncouplers disrupt proton movement; organic compounds that can move across the membrane to the matrix- can carry protons with them to the matrix; competing with ATP synthase for protons- so these protons do not produce ATP - Examples of Uncouplers of ATP Synthesis o Dinitrophenol – toxic phenol; used as insecticide; human toxicity symptoms include marked fatigue, elevated body temperature, cyanosis. o Gramicidin – anitbiotic produced by Bacillus breva; used to treat local (topological) infections of gram+ bacteria. o Dinitrophenol was one of the first (and pretty effective) dieting aids. Essentially, you burn of CHO’s w/o ATP production. Side effects were “overheating” of body temperature (i.e. fevers). Death is quite possible due to induced fever. Banned by FDA in 1938 because it was a suspected carcinogen and no proof of safety for use in humans.; energy would be released as heat o Gramacidin has about 10 AA’s.; reduces ATP formation in gram positive bacteria o Ionophores form a channel so the protons can go through it; atp produced is much less - Heat Generation by Uncoupled Mitochondria o Important in hibernating & cold-adapted animals, newborn infants.  All have “brown fat” (i.e. adipose tissue enriched in mitochondria).  Electron transport is uncoupled by “uncoupling protein” (thermogenin).  Thermogenin is activated by fatty acids of adipose cells. o Brown fat forms uncouplers  Babies need to maintain a high body temp and they arent very active  Increases body temp and decreases ATP production  Lose baby fat, you lose uncouplers  Uncoupler does not directly interact with ATP synthesase; does not inhibit the function of ATP synthase- so not direct inhibitor - The ATP Synthase: o Total Mass  500,000kD o 22 different subunits o Two main complexes in one.  FoTransmembrane Stalk  F Sphere 1 o Functions of Subunits – Originally:  F1Sphere: Easily dislodged/separated during isolation; can still function as an ATPase when separated.  FoStalk: Embedded in and traverses inner membrane. o Now:  Rotor Assembly:  The C,, subunits – use the movement of protons back to matrix to turn the whole assembly.  Stator Assembly:  The A, B, , ,  subunits – together prevent rotation of the sphere while the rotor turns.   Subunits have active sites for ADP & Pi binding.   Subunits thought to have regulatory role/sites. o F1- beta subunit is the active portion; each beta is an active site with ATP is synthesized; o Moves because protons go through F0 subunit o Every time three protons go through, you make one ATP - Binding Change Mechanism for ATP Synthesis o ATP synthase ( subunits) has three conformationally distinct active sites: Open, Loose & Tight sites. o Proton transport drives rotation of the -subunit (dark blue) relative to the , 1 complex, inducing a change in reactant binding affinities. o ATP forms spontaneously from tightly bound ADP + Pi (& + 3H returned). o Beta is open- substrate can bind to it (ADP and phosphate o Once it binds, the proton comes in and it converts to the Loose beta o As the second proton comes in, ATP is synthesized = tight site where ATP is made o Third proton comes in and releases the ATP o Goes from open to loose to tight and ATP is released o Takes in 3 protons and spits out one ATP o Simultaneously, all three beta subunits can be in the different configurations- so beta 1 is in open, beta 2 is in loose, and beta 3 is in tight o At a time you can take in 9 protons and 3 ATP will be released - Reduced Nucleotides are not enough o Mitochondria require ADP and Pi o Phosphate Translocator  uses proton gradient to drive Pi uptake. o ADP/ATP Translocator  uses antiport to drive ADP uptake & exchange for ATP. o Why do you need 4 protons to form ATP?  It is needed to recruit an organic phosphate (h2po4-) through the transportor (phosphate translocase) o Three protons come in through ATP synthase, one proton comes in from phosphate translocase o ADP can only come in when ATP is kicked out through ADP- ATP translocator - External (glycolytic) NADH is not directly Accessible to Respiratory Electron Transport o Depending on which shuttle NADH takes, it will either get deposited in Complex 1 or complex 2 o Mitochondrial membranes are not permeable to NADH. o Two “shuttles” can transport NADH “equivalents”.  Glycerol-3-phosphate shuttle (brain & skeletal muscles).  Malate/Aspartate shuttle (liver). o Glycolysis is common in both anaerobic and aerobic o At the end of Krebs, 6 carbon dioxide (happens in the mitochondria) have been release by breathing out- but FADH2 and NADH have been produced o 104 protons in brain or muscle, 112 protons in live that produce ATP through oxidative phosphorylation - Glycerol-3-phosphate Shuttle: in Brain and Skeletal muscles o In brain or muscles--- complex 2 o Nadh is attacked by DHAP reductase which accepts the protons from NADH and oxidizes it to NAD+; and DHAP (dihydroxy acetone phosphate- is a ketone) will be reduced for glycerol-3 – phosphate (has an alcohol group so it can pass through the membrane of the mitochondria) o Goes through the outer membrane to the inner membrane to get reoxidized by glycerol 3 phosphate dehydrogenase o Aldehydes cannot get across the membrane, but ketones and alcohols can o ******glyceraldehyde 3 phosphate is very different- it is what produces NADH in step 6 of glycolysis******* - The Aspartate-Malate Shuttle o In the liver, goes to complex 1 o Malate from cytoplasm can enter into the matrix o Malate à oxaloacetate is formed in step 9 of the krebs by malate dehydrogenase (anaplerotic reaction- because it can come from something outside of the cycle itself- does not need to be made solely from fumerate) o When malate comes in, it takes electrons from NADH (oxidized to NAD+); when it is converted back to oxaloacetate, it gives back the protons to the NAD+ that is in the matrix and then NADH goes to complex 1 o Aspartate can move outside of the matrix o Do not need to know the alpha keto and glutamate portion - How much ATP is produced by the oxidation of a hexose? o What do we know for sure?  Glycolysis produces 2 NADH / hexose + 2 ATP (net).  Pyruvate deHase produces 2 NADH / hexose.  TCA cycle produces 6 NADH + 2 FADH / he2ose + 2 ATP.  Yield of ATP is related to the site where electrons feed into the transport chain. o The Glycerol-3P/DHAP shuttle results in NADH entry at complex II (in muscles) o The Malate/Aspartate shuttle allows entry of NADH at complex I (& thus is more efficient-ATP wise-than the G3P/DHAP shuttle. (in liver) - Best guess for overall summary reaction for aerobic respiration o


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