BIOL1024 Introduction to Cell Metabolism PART 2 PDF

BIOL1024 Declan A. Doyle Introduction to Cell Metabolism PART [email protected]. 2 uk Summary of first lecture Focus on glucose as the preferred energy source because it provides the greatest amount of energy and intermediates can be used in anabolic...

BIOL1024 Declan A. Doyle Introduction to Cell Metabolism PART [email protected]. 2 uk Summary of first lecture Focus on glucose as the preferred energy source because it provides the greatest amount of energy and intermediates can be used in anabolic metabolic pathways Gibbs free energy is an important indicator of whether or not a reaction is going to take place Exergonic/endergonic reactions and how biology can couple such reactions to drive the production of products Metabolic flux involves committed reactions that are far from equilibrium, compartmentalisation, enzyme isoforms, feedback inhibition, control of enzyme expression and multi-enzyme complexes. Learning outcomes for this lecture Learn 3 key structures and terminology. Understand the 3 irreversible steps of glycolysis. Examine the two steps that actually generate ATP. Learn about the NADH production step. Highlight a number of coupled reaction for endergonic/exergonic reactions as well as oxidation/reduction reactions. Learn about coenzymes. Learn how a number of these irreversible steps are overcome. Do I need to know the chemical structures? No but understanding metabolism and a few key structures leads to you knowing the structures Open chain and cyclic forms of glucose Glucose structure = hexose sugar with an aldehyde group at position 1. All of the hydroxyl groups are then on the right hand side apart from position 3 which is flipped to the left hand side.  Glycolysis: the 3 irreversible steps 1 Hexokina se Mg2+ ATP ADP D- GLUCOSE-6- GLUCOSE G°´ = -16.7 PHOSPHATE kJ/mol (G6P) (C6H12O6) G = -33.5 kJ/mol Glycolysis: the 3 irreversible steps Hexokina se Mg2+ ATP GADP= +33.5 D- GLUCOSE-6- GLUCOSE kJ/mol PHOSPHATE (G6P) This reaction does not happen using this enzyme, under these  Glycolysis: the 3 irreversible steps 2 Phosphofructokin ase ATP ADP FRUCTOSE-6- FRUCTOSE-1,6- PHOSPHATE G°´ = -14.2 BISPHOSPHATE (F6P) kJ/mol (FBP) G = -22.2 kJ/mol  AMP = Adenosine–P Key learning points ADP = Adenosine–P–P sequentially added ATP = Adenosine–P–P–P 1 2 3 4 5 6 FRUCTOSE-6- FRUCTOSE-1,6- GLUCO FRUCTOS PHOSPHATE BISPHOSPHATE E SE (F6P) (F1,6P) Bisphosphate means two added to different  Glycolysis: the 3 irreversible steps 3 Pyruvate kinase Carboxylate Carbonyl Methyl ADP PHOSPHOENOLPYRU ATP Learn this VATE G°´ = -31.4 PYRUVATEone CH3-CO-COO- (PEP) kJ/mol G = -16.7 kJ/mol Summary so far There are three irreversible steps in glycolysis Irreversible because of their large, negative G’s Learn the structures of glucose (open form) and pyruvate Even though these steps are irreversible, there are instances when it is desirable to reverse the metabolic flow of glycolysis e.g., bugs living on pyruvate  The role of coenzymes in metabolism A non-protein component of enzymes is called the cofactor. If the cofactor is organic, then it is called a coenzyme. Many of the coenzymes are derived from vitamins Vitamin Coenzyme Function nicotinamide adenine oxidation or hydrogen niacin dinucleotide (NAD+) transfer flavin adenine dinucleotide oxidation or hydrogen riboflavin (FAD) transfer pantothenic coenzyme A (CoA) Acetyl group carrier acid vitamin B-12 coenzyme B-12 Methyl group transfer Aldehyde group thiamin (B-1) thiaminpyrophosphate (TPP) transfer The role of coenzymes in metabolism A number are involved in catabolism of glucose – can be considered to be a co-substrate. Their role is to deliver chemical groups or atoms e.g., H+, phosphate, to/from the active site. The coenzyme nicotinamide adenine dinucleotide (NAD+) is involved in the transfer of protons. The coenzyme adenosine triphosphate (ATP) is involved in the transfer of phosphate groups.  NADH/NAD+ Nicotinamide Adenine ADP-Ribose- Nicotinamide Structure of the oxidised form NAD+ Oxidation and Reduction OXIDATION REDUCTION Loss of electrons Gain of electrons Gain of oxygen Loss of oxygen Loss of hydrogen Gain of hydrogen Results in many C-O bonds Results in many C-H bonds Results in compounds with lower Results in compounds with potential energy higher potential energy Remember OIL RIG OIL – Oxidation Is Loss (of electrons/hydrogen) RIG – Reduction Is Gain (of electrons/hydrogen) NADH/NAD+ (Released into solution) NADH/NADLet’s + see an example from metabolism CH3-CO-COO- + NADH + H+  CH3-CH(OH)- COO- + NAD+ Pyruvate Lactate More generally REDUCTIONS NADH + H+ NAD+ OXIDATIONS As the NADH is oxidised, the pyruvate is reduced. These coenzymes link oxidation and reduction reactions This reaction occurs in your muscles under low oxygen conditions.  NADH/NADLet’s + see an example from the glycolysis Glyceraldehyde P -3-phosphate dehydrogenase NAD+ NADH + H+ GLYCER glyceraldehyd 1,3- OL e- bisphosphoglycerat 3-phosphate G°´ = +6.3 e kJ/mol G = -1.7 kJ/mol ATP couples exergonic and endergonic reactions As well as being involved in the transfer of phosphate groups ATP/ADP + Pi play a key role in metabolism coupling together energy producing (exergonic) reactions with energy requiring (endergonic) reactions Remember the equilibrium of endergonic reactions lies in favour of substrate – but coupling it to an exergonic reaction can shift the equilibrium in favour of product. Coupling two reactions 1,3-bisphosphoglycerate + H2O 3-phosphoglycerate + Pi + H+ ΔG0’ = -50 kJ/mol ADP + Pi + H+ ATP + H2O ΔG0’ = +30 kJ/mol 1,3-bisphosphoglycerate + ADP 3-phosphoglycerate + ATP ΔG0’ = (-50 + 30) kJ/mol = -20 kJ/mol ΔG = +1.3 kJ/mol Coupling two reactions Phosphoglycerate kinase ADP 1,3- ATP 3-phosphoglycerate bisphosphoglycerat e Adenosine 5’-triphosphate - ATP is an energy transducer AdeninRibose- e- Guanosine 5’-triphosphate - GTP is an energy transducer GuaninRibose- e- Another high energy nucleotide ATP couples exergonic and endergonic reactions ENDERGONIC REACTIONS (biosynthesis, movement, maintaining ion gradients, etc.) ATP ADP + Pi EXERGONIC REACTIONS (glycolysis, TCA cycle, etc.)  ATP is an energy transducer It transfers energy between reactions It is not a store of energy It is produced on demand by the phosphorylation of ADP and Pi Fats, glycogen, glucose, etc., are a store of energy e phosphate groups are stabilized by resonance, and release a lot of energy up their hydrolysis. an liken phosphoester bonds on linked phosphate groups to magnets, where if you were to put t poled ends together they repel each other. When a phosphoester bond is cleaved, the energy in those bonds can be used to perform biochemical work, such as transferring a functional group one molecule to another.  Phosphorylation reactions are endergonic Hexokina se Mg2+ ATP= + ADP D- GLUCOSE-6- GLUCOSE G°´ = -16.7 PHOSPHATE kJ/mol (G6P) (C H O ) RVERSIBLE because to take G 6 12 6 = -33.5 and add it to ADP is highly endergon the phosphate kJ/mol  Phosphorylation reactions are endergonic Phosphorylation of glucose (or related hexose sugars) G°´ = x kJ/mol Hydrolysis of ATP to ADP + Pi G°´ = -30 kJ/mol Coupled reaction G°´ = -17 kJ/mol x + -30 = -17 Phosphorylation of glucose G°´ = -17 + 30 = +13 kJ/mol efore, phosphorylation needs to be coupled to a reaction that provides the energy the reaction happen.  Phosphorylation reactions are endergonic Coupled reaction Glucose + ATP  Glucose-6-P + ADP G°´ = -17 kJ/mol Remove the formation of ATP ADP + Pi  ATP G°´ = +30 kJ/mol Phosphorylation of glucose Glucose + Pi  Glucose-6-P G°´ = -17 + 30 = +13 kJ/mol fore, phosphorylation needs to be coupled to a reaction that provides the energy the reaction happen. Dephosphorylation reactions are exergonic If putting on a phosphate costs us +13 kJ/mol then taking it off provides 13 kJ/mol i.e., this reaction is spontaneous Glucose 6- The reason why the phosphata previous reaction is se irreversible is because we have coupled P it to ATP hydrolysis i.e., GLUCOSE-6- GLUCOSE we PHOSPHATE would have to remake (G6P)G°´ = -13 kJ/mol the ATP for it to be Coupling reactions P G3P dehydrogenase H NAD+ NADH + H+ G°´ = +6.3 kJ/mol 1,3- glyceraldehyd e- G = -1.7 kJ/mol bisphosphoglycerat 3-phosphate RERVERSIBLE e If phosphorylation is endergonic then it should be coupled to e.g., ATP hydrolysis. This reaction is coupled to the reduction of NAD+ requiring energy. Coupling reactions G is large and negative for the oxidation of an aldehyde to a carboxylate. This is coupled to the endergonic phosphorylation reaction and the NAD+ reduction. The energy of oxidation is initially trapped as a high-energy phosphate (1,3-bisphosphoglycerate) compound and then used to form ATP. Coupling reactions NAD+ NADH + H+ G3P dehydrogenase P A tricky reversal Carboxylate Pyruvate kinase | Carbonyl | Methyl ADP PHOSPHOENOLPYRU ATP PYRUVATE VATE G°´ = -31.4 (PEP) kJ/mol G = -16.7 kJ/mol Reversal is required for glucose formation (gluconeogenesis) IRRERVERSIBLE  A tricky reversal Pyruvate PEP carboxylase carboxykinase ATP, ADP GTP GDP + Pi + HCO-3 CO2 PHOSPHOENOLPYRU PYRUVAT OXALOACETA VATE E TE (PEP) Step Step 1: Carboxylation (ENDERGONIC) of 2: De-carboxylation (EXERGONIC) a he methyl group requires energy. the addition of a phosphate (ENDERGONIC) nowing the pyruvate structure allowsThe youphosphate donor and energy comes fro to work out oxaloacetate structure GTP not ATP. Oxidation reactions are exergonic NADH + ½O2 + H+  NAD+ + H2O ΔG0’ = -220 kJ/mol ADP + Pi = ATP ΔG0’ = +30 kJ/mol Energy from oxidation of NADH can be used to drive the formation of 3 ATPs There is a lot of energy trapped in NADH Summary – Structures to Learn Carboxylate Carbonyl Methyl or CH3-CO-COO- PYRUVATE GLYCER GLUCO OL SE Summary Coenzymes are required to transfer important groups such as phosphate and protons. Coupling reactions are important in driving forward metabolic pathways. Likewise reduction/oxidation coupling. Irreversible reactions can be reversed but require new pathways involving new enzymes.