Lecture 3 Topics. Review of ATP, enzymes and co-factors. Esssentials of enzyme regulation. Carbohydrate Catabolism. Brief carbohydrate review

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1 Lecture 3 Topics Review of ATP, enzymes and co-factors Esssentials of enzyme regulation arbohydrate atabolism Brief carbohydrate review First pathway

2 Electrostatic bond strain Ionization of ADP product Resonance stabilization of Pi (see Table 4) ATP

3 ompound (hydrolyzed to) Phosphoenolpyruvate (Pyruvate + Pi) ΔG o (kj/mol) Transfer Potential Type of ompound Enolic phosphate ause for ΔG o of ydrolysis Tautomerization of product (Pyr); Resonance stability of Pi Phosphoryl -group transfer potentials 1,3-Bisphosphoglycerate (3-PGA + Pi) Acyl phosphate Ionization of product (3-PGA); Resonance stability (Pi, 3-PGA) Phosphocreatine (reatine + Pi) Guanidine phosphate Resonance stability of product (creatine) Pyrophosphate (PPi) (Pi + Pi) Phosphoric acid anhydride Electrostatic bond strain in PPi substrate; Ionization and resonance stability of Pi group Receive P~group ATP (ADP + Pi) Same as PPi Same as PPi ADP (AMP + Pi) Same as PPi Same as PPi Acetyl-oA (and other thioesters) (Acetate + oa-s) Thioester No resonance stabilization of Acetyl-oA; Ionization and resonance stabilization of acetate Donate P~group Glucose-1-P (Glucose + Pi) Phosphate semiacetal Bonds in glucose-1-p not that strained Glucose-6-P (Glucose + Pi) Phosphate ester Bonds in glucose-6-p not strained AMP (Adenosine + Pi) Phosphate ester Phosphate (Pi) Phosphate Bonds in AMP not strained; Adenosine does not ionize Review p. 4

4 Enzymes (biological catalysts) E a E R P Enzyme catalyzed reaction reaction rates (flux) can be regulated provide specificity and couple reactions coordinate many reactions into metabolic networks (pathways) via shared intermediates

5 Enzyme lassification 1. xidoreductase 2. Transferase 3. ydrolase 4. Lyase 5. Isomerase 6. Ligase Transfer of electrons Transfer of functional groups Single bond cleavage (water) Bond cleavage by elimination Intramolecular rearrangement Bond formation (ATP dep.) p. 16

6 -FATRS (Non-protein moieties required for catalytic activity) 1. Metals Structural role (e.g., Mg 2+ ) atalytic role (e.g., Fe 2+ ) 2. o-enzymes rganic molecules (catalytic) o-substrates Prosthetic group - If transiently bound (e.g., ATP) - If covalently bound (e.g., FAD) Must be regenerated if altered in reaction (by same or different enzyme) Most water-soluble vitamins are precursors of co-enzymes see p. 14/15

7 Essentials of Enzyme Regulation 1. Total enzyme (protein) amount enzyme production (de novo synthesis) enzyme degradation (proteolysis) 2. Specific activity (at constant amount) allostery (effector binding to non-catalytic sites) covalent modification (reversible) What types of enzymes are usually regulated? Physiologically irreversible reactions ( ΔG < -20kJ) First irreversible reaction specific for a pathway (committed step) p. 17

8 Free Energy (G) Biochemical Pathway (16 reactions) ΔG = ΔG o + RTlnQ ΔG = ΔG o + RTlnQ

9 Allostery Allosteric Enzyme Reaction Velocity Michaelis-Menten Enzyme Substrate oncentration p. 17

10 + Activator Reaction Velocity No allosteric effector + Inhibitor Substrate oncentration p. 18

11 End product inhibition or Feed-back regulation A A A A x x x x B B B B x x D D E D E D E E p. 18

12 ovalent Modification Phosphorylation (Ser, Thr, Tyr,is, Asp) ENZ ATP ADP ENZ P - P Adenylylation (Tyr) ENZ ATP PPi ENZ P - Adenine p. 19

13 Uridylylation (Tyr) ENZ UTP PPi ENZ P - Uridine ADP-ribosylation (Arg, Glu, ys) ENZ NAD Nicotinamide ENZ 2 P - P - Adenine S-Adenosyl-methionine S-Adenosyl-homocysteine Methylation (Glu) ENZ ENZ 3 p. 19

14 Biologically Important Nucleophiles and Electrophiles Nucleophiles (electron rich) R R RS RS ydroxyl Sulfhydryl RN 3 + RN Amine N + R N N N R + + Imidazole R 2 R 1 R 1 R 3 R 3..+ El t hil ( l t d fi i t) R arbanion (stabilized by electron withdrawing group, e.g., R 1 is = or N) p. 20

15 Electrophiles (electron deficient) R 1 is or N) R 1 R 1 R 1 R 2 R R 2 arbocation R 3 R 2 arbonyl arbon - P - P R - - P is electrophilic in P- bonds R 1 N + R 2 is electronphilic in a cationic imine amine M n+ Metal cations + Proton p. 20

16 What pathways to study? Ready to go

17 onverging Theme of atabolism Numerous omplex Polymers (Food Matrix) Various Monomer Some Energy (ATP) Few ommon Intermediates Most Energy (ATP) Water arbon Dioxide

18 The Powertrain of uman Metabolism (The Big Picture ) ARBYDRATES PRTEINS LIPIDS Glucose Amino acids Fatty acids xaloacetate 2 Glycogen Glucose-6-P Pyruvate Acetyl-oA NAD ATP 2 2 Lactate Ketone bodies Ribose-5-P holesterol NADP NAD p. 21

19 arbohydrate atabolism

20 The Powertrain of uman Metabolism (verview) ARBYDRATES PRTEINS LIPIDS Glucose Amino acids Fatty acids xaloacetate 2 Glycogen Glucose-6-P Pyruvate Acetyl-oA NAD ATP 2 2 Lactate Ketone bodies Ribose-5-P holesterol NADP NAD p. 21

21 arbohydrates Empirical formula: [ 2 ] n Poly-, oligo-, di-, mono-saccharides polyhydroxylated aldehydes or ketones Most abundant organic molecules on earth Primary products of photosynthesis entral role in general metabolism (-skeletons) Basic component of food and feed

22 All Isomers onfigurational onstitutional Enantiomers (mirror images of each other) Diastereomers (NT mirror images of each other) Geometric isomers (on double bonds; E and Z configuration) Epimers (differ in configuration at only one chiral carbon) Stereoisomers or ptical Isomers

23 Important arbohydrate Structures 2 Aldose Ketose D-Glyceraldehyde (an aldotriose) L-Glyceraldehyde Dihydroxyacetone (a ketotriose) D-Fructose (a ketohexose) Enantiomers p. 22

24 2 D-Glyceraldehyde Epimers 2 D-Erythrose 2 D-Threose Epimers D-Ribose D-Arabinose D-Xylose D-Lyxose Epimers D-Allose D-Altrose D-Glucose D-Mannose D-Gulose D-Idose D-Galactose D-Talose p. 22

25 Reactions of Sugars Nucleophilic substitutions R R R' R' p. 23

26 2 2 2 α-d-glucopyranose (36.4%) 2 D-Glucose (0.003%) β-d-glucopyranose (63.6%) Anomers (special case of epimers) p. 23

27 ayworth Projections α-pyranose form β-pyranose form p. 23

28 Glucose Glucose John andy s Metabolism ne Step

29 Glucose (2 3 ) (2 2 ) (4 2 ) Glycolysis (22 ) 2 PD TA ycle NAD 2 ET Biological xidation ATP

30 There are two fundamentally different ways to generate ATP: 1. Substrate-level phosphorylation of ADP to ATP 2. Proton gradient-dependent dependent ATP synthesis

31 Substrate-level Phosphorylation (ATP) S red S ox + P i P~S ox ΔG +ΔG P~S ox + ADP S ox + ADP~P (ATP) i) P~S ox + 2 S ox + P i Example ΔG o = 49.6 ii) ADP + P i ATP + 2 ΔG o = P i = P 2-4 Σ ΔG o = 19.1

32 First Reaction in Glycolysis Glucose (Glc)? Glucose-6-phosphate (Glucose-6-P) (Glc-6-P) (G6P)