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Week 13 Notes

by: Jordana Baraad

Week 13 Notes BSC 450

Jordana Baraad
GPA 3.9
Fundamentals of Biochemistry
Dr. Ramonell

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Notes accompanying Powerpoints from lectures on Week 13 Tues 11/17 and Thurs 11/19.
Fundamentals of Biochemistry
Dr. Ramonell
Class Notes
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This 0 page Class Notes was uploaded by Jordana Baraad on Friday November 20, 2015. The Class Notes belongs to BSC 450 at University of Alabama - Tuscaloosa taught by Dr. Ramonell in Summer 2015. Since its upload, it has received 30 views. For similar materials see Fundamentals of Biochemistry in Biological Sciences at University of Alabama - Tuscaloosa.

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Date Created: 11/20/15
1117 Glycolysis Pa rt 1 Glycolysis includes the initial step in metabolizing glucose Metabolizing glucose catalysis Glycolysis 10 steps glucose l pyruvate Takes place in cytoplasm Citric Acid Cycle CAC in these notes and Oxidative Phosphorylation OP in mitochondria W oxygen I E 39 T 39 fa amicf39mlar matrix fa Poursscl waquot 39 Glycogen charides starch sucrose i syn 39lesis of ff 39 struct Y v V I V 0 2 s Ural 1 sf t Polymers storage AG 2 a 6 Z via 2 a m Ncsphate I 0 d A t Y a at s m Ziyfogag x Y Glycolysis is divided into two phases w 10 total rxns Prep phase 15 Glucose l 3C molecule no oxygen required Payoff phase 610 3C l pyruvate 2 NADH 4 ATP 2 ATP gained ancient pathway evolved in age wo much atmospheric 02 ATP and NADH formatin are coupled to glycolysis Small amount of energy in glycolysis Still LOTS remains in pyruvate Want oxygen around to complete oxidation Generate more ATP N 34 7 39139 2 gr quot y a r gaucoge 1 HAIL 1 c CW quotquot nW 69quot 9002 1 A610 quot xii l Importance of phosphorylated intermediates 1 no transporters for phosphorylated intermediates a want high concentration glucose outside low in cell b maintain concentration gradient i hexokinase adds phosphate to maintain this ii no exit from cell if phosphate attached charged 2 conserving chemical energy 3 phosphate group l increased biding interactions w enzyme a brings down activation energy b ATP acts as intermediate c allows conservation of potential energy Why do we use pyruvate Once reduced NAD must leave reactive site If can t leave can t l oxidative phosphorylation Keep NAD pool high in cell What problems will we encounter in glycolysis glucose l pyruvate prep phase 1 C6 l 2 C3 compounds G3P amp DHAP 2 G3P DHAP l 2 G3P a Conversion to avoid 2 pathways wasteful b isomerization rxn payoff 3 generate some ATP for cell a substratelevel phosphorylation b must generate highenergy molecules remember graph 4 G3P l pyruvate a Simplest steps possible to generate pyruvate amp highE molecules Problem 1 We Need 2 C3 units from a C6 skeleton Set up Conversion rS oriliu os e quot lsomerization rxn Use ATP to generate phosphate intermediates Step 1 Glucose is phosphorylated at the C6 position by hexokinase For exam KNOW rxns W enzymes 1 kinase bc need to add phosphate group keep glucose in the cell maintain concentration gradient will attach phosphates to fructose amp mannose as well Step 2 G6P lS ISOMERIZED TO F6P TO PHOSPHOGLUCOSE ISOMERASE Fig 145 Move carbonyl and hydroxyl groups Forms enediol intermediate Avoid negative buildup Linear form 1 binding opening ring a opening coordinated by His s in active site b active site base glutamate wn enzyme 2 proton abstraction a forms intermediate 3 generate AB catalysis l F6P 4 recyclizes l ring once leaves active site Step 3 F6P is phosphorylated by Phosphofructokinasel to form Fructose16Bisphosphate 1St committed step of glycolysis F16BP only goes into pathway that l pyruvate Phosphofructokinasel tightly regulated enzyme Retroaldol rxn splits F16BP Mg2 required to stabilize ATP Neutralization interactions w alpha and beta phosphates Acts like giant protonquot Step 4 F16BP is cleaved into 2 triose molecules by aldolase Not particularly favorable Two classes of aldolases 1 plants animals forms enolate intermediate amp Schiff base intermediate a required active site Lys b covalent catalysis 2 fungi bacteria Zn2 ion in active site to coordinate w carbonyl and stabilize enolate intermediate a metal ion assisted catalysis Formation of a Schiff base w the enzyme Dehydration rxn Figure 146 1 water molecule accommodated Glycolysis Pa rt 2 Problem 1 Solved Left w 2 C3 s from C6 Nxt need 2 C3 s to look the same Isomerase DHAP isomerized rapidly Low concentration pulls cleaving rxn forward 2 NADH l mitochondria donate to Complex l Problem 3 1 generate PEP 13BPG for substratelevel phosphorylation I ATP 2 2 NADH molecules a harvesting electrons wo stepwise oxidation made possible by electron acceptors everything converted to heat amp light excess gummy bear video Step 6 G3P l39l 13BPG Active site Cys As soon as BPG comes in attaches Pi can form interactions w active site 2 NADH formed leave 4repace phosphate if can t replace whole process stops must deprotonate Cys 5 nucleophilic substitution l 13BPT Step 7 Need kinase for substratelevel phosphorylation Phosphate coordinates ADP wn active site 2 ATP s formed amp 3PG 1119 Glycolysis Part Step 7 13BPG is converted to 3PGA by Phosphoglycerate kinase substratelevel phosphorylation 2 ATP 2 ATP from prep phase Problem 4 How do we get from 3PGA to Pyruvate 1 generate more atp Step 8 3PGA is coverted to 2PGA by phsophoglycerate mutase Enzyme already phosphorylated Covalent catalysis Mutases isomerization rxn involving transfer of functional group 2 active site His s 23BPG seen in hemoglobin Step 9 2PGA is converted to PEP by enolase Delta G not favorable but not MOST unfavorable 3 driving rxns 1 1st step catalyzed by hexokinase 2 committed step phosphofructokinasel 3 Step 10 pyruvate kinase 13 tightly regulated enzymes ensure that glycolysis irreversible Step 10 PEP is dephosphorylated to form pyruvate by pyruvate kinase metal ions coordinate charges in active site to add phosphate to ADP substratelevel phosphorylation metalassisted rxn Summary of Payoff Phase Fates of Pyruvate 1 reoxidizing NAD via fermentation under low oxygen concentration glycolysis runs constantly requires 15x more sugar burned wo oxidation cancers l tumors burn lots of sugar Warburg effect trackingtargeting tumors via sugar metabolism txt Box 141 HansKrebs developed Citric Acid TriCarboxylic Acid Krebs Cycle The Citric Acid Cycle The Citric Acid Cycle allta Krebs TriCarboxylic Glycolysis cytoplasm ALL hydrophilic enzymes Next phases mitochondria Move pyruvate amp 2 NADH s across mitochondrial membrane Some energy lost can t make as much ATP as NADH s generated in Krebs Cycle Only a small amount of energy available in glucose is captured in glycolysis Objective get as much energy out of pyruvate as possible Full oxidation rxn Citric acid cycle CAC 6 C02 comes from decarboxylation rxns generates NADH FADH2 GTP typically converted directly to ATP Cellular Respiration involves consumption of 02 and production of C02 Glu 602 6 C02 6 H20 1 Glu I C02 glycolysis CAC mitochondrial matrix generate C02 NADH FADH2 I electron transport chain ETC electons donated to 02 terminal electron acceptor forms H20 V C in itochondrial cistae Acetyl CoA has an activated acetate group Activated form bc thioester Must get rid of electrons to stick together Via dehydrogenase enzyme complex Passed btwn 3 enzymes V The biosynthesis of Acetyl CoA from pyruvate is accomplished by three enzymes Cofactors Pyruvate Rxns Dehydrogenase Complex TPP E1 Pyruvate Decarboxylation dehydrogenase CoA lipoamide E2 Dihydrolipoyl Acetyl CoA transacetylase FAD NADH E3 Dihydrolipoyl Transfer electrons to dehydrogenase NAD l NADH E2 Lipoyl cofactor swinging armquot Attached to Lys Reduc Acetyl CoA amp transfer some electrons to NAD l energy Swing btwn enzymes 1amp 3 E3 Must regenerate NADH on the spot As soon as reduced ALL THIS is entry rxn l Acetyl CoA for CAC Enzyme 1 Pyruvate Dehydrogenase TPP electron sink Delocalization of electrons to stabilize intermediate Pyruvate Dehydrogenate transfers the hydroxyethyl group to the 39 v aha 5 m 1 icing quotRCA alum Occurring in mitochondrial matrix 1 decarboxylation 2 Lipoamide arm 5 reduction a must be carried by NAD l ETC b oxidation of FAD resets The 40 structure of the enzyme complex is key to its function HUGE can be seen in electron microscope E2 60 subunits in complex CAC 2 NADH s 2 Acetyl CoA s Lipoamide arm blue Need cooperative binding in tetramer Don t work independently bc intermediates are so reactive Acetyl CoA feeds the CAC Step 1 Acetyl CoA oxaloacetate condensation l citrate Acceptor oxaloacetate 1St half steps 14 citrate C6 l succinate C4 NADH C02 s lost at Step 3 amp 4 2nOI half steps 59 regenerating succinate l oxaloacetate C4 FADH2


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