Lecture 3 Topics. Role of co-factors. Esssentials of enzyme regulation. Carbohydrate Catabolism. Brief carbohydrate review.

Transcription

1 Lecture 3 Topics Role of co-factors in catalysis Esssentials of enzyme regulation arbohydrate atabolism Brief carbohydrate review First pathway

2 ATP as universial carrier of chemical energy Role of enzymes Review

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

4 igh Energy Substrates ellular Macromolecules ATP + 2 G + G G + G ADP + Pi Intermediates of Metabolism Low Energy Products

5 ompound G o (kj/mol) Transfer Potential Type of ompound ause for G o of ydrolysis Table 4 Phosphoenolpyruvate (Pyruvate + Pi) 1,3-Bisphosphoglycerate (3-PGA + Pi) Enolic phosphate Acyl phosphate Tautomerization of product (Pyr); Resonance stability of Pi Ionization of product (3-PGA); Resonance stability (Pi, 3-PGA) Phosphoryl -group transfer potentials 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 Bonds in AMP not strained; Adenosine does not ionize Phosphate (Pi) Phosphate p. 4

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 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

8 Essentials of Enzyme Regulation 1. Total enzyme (protein) amount enzyme synthesis (de novo synthesis) enzyme degradation (proteolysis) 2. Specific activity (at constant amount) allostery (effector binding) covalent modification (reversible) 3. Strategic targets Physiologically irreversible reactions (large G) First irreversible reaction specific for a pathway (committed step) p. 17

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

10 Allostery Allosteric Enzyme (multi-subunit) Reaction Velocity Michaelis-Menten Enzyme Substrate oncentration p. 17

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

12 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

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

14 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

15 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

16 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 amine M n+ Metal cations + Proton p. 20

17 What pathways to study?

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 onverging Theme of atabolism omplex Polymers (Food Matrix) Various Monomer Some Energy (ATP) Few common intermediates Most Energy (ATP) Water arbon Dioxide

20 arbohydrate atabolism

21 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

22 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

23 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

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

25 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

26 R R R' R' p. 23

27 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

28 α-pyranose form β-pyranose form p. 23

29 Glucose Glucose John andy s Metabolism ne Step

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