1. Biochemistry Sixth Edition
Berg • Tymoczko • Stryer
Chapter 15:
Metabolism:
Basic Concepts and Design
Copyright © 2007 by W. H. Freeman and Company

2. Roadmap of Metabolic Pathways

3. Metabolism
Metabolism – reactions occurring in a living system that produce and consume the energy needed for the organism to exist.
Metabolic pathways.
Metabolic reactions.
High Energy bonds in compounds.
Thermodynamics of reactions.

4. Metabolism
Metabolism - the entire network of chemical reactions carried out by living cells
Metabolites - small molecule intermediates in the degradation and synthesis of biopolymers
Catabolic reactions - degrade biomolecules to create smaller molecules and energy
Anabolic reactions - synthesize biomolecules for cell maintenance, growth and reproduction

5. Catabolism and Anabolism
Catabolism Anabolism
degradative synthetic
oxidative reductive
energy producing energy requiring (exergonic) (endergonic)
makes pool molecules uses pool molecules
produces NADH & uses NADPH almost NADPH exclusively

6. Energy Overview Energy distribution
1/ / nutrients ----> pool molecules ----> CO2, H2O, NH3 
biomolecules

7. Pathways Metabolism includes all enzyme catalyzed reactions
Metabolism can be subdivided into various areas: hexose shunt, electron transport, etc.
The metabolism of the four major groups of biomolecules will be considered: Carbohydrates Lipids Amino Acids Nucleotides

8. Pathways
Multiple-step pathways permit control of energy input and output
Catabolic multi-step pathways provide energy in smaller stepwise amounts)
Each enzyme in a multi-step pathway usually catalyzes only one single step in the pathway
Control points occur in multistep pathways

9. Regulation
Metabolism is highly regulated to permit organisms to respond to changing conditions
Most pathways are irreversible
Flux - flow of material through a metabolic pathway which depends upon: (1) Supply of substrates (2) Removal of products (3) Pathway enzyme activities

10. Levels of Regulation
Direct regulation at the enzyme level (covalent or non-covalent).
Regulation via external communication (hormonal).
Regulation at the gene level (induction/repression).

11. Direct Regulation
Feedback Inhibition: The product of a pathway controls its own synthesis by inhibiting an earlier step (the first step or the “committed” step in the pathway) .
Feed-forward Activation: A metabolite early in the pathway activates an enzyme that appears later.
Interconvertible enzyme activity can be rapidly and reversibly altered by covalent modification. E.g. protein kinases and protein phosphatases.

12. Glucose Metabolism
Breakdown to small molecules and energy.

13. Metabolite Needed for formation of glycerol based phospholipids
and to run the
glycerol-P
shuttle.

14. Adenosine Nucleotides
Components of
an energy system.

15. ATP An energy carrier considered to be
common energy currency in a cell

16. Driving Forces behind the Energy of ATP Hydrolysis
Resonance energy of reactants vs products.
Charge repulsion of oxygens.
Number of charges on oxygens.
Solvation of reactants vs products.
Entropy – number of reactant vs product molecules.

17. Phosphate Resonance
pKas of phosphoric acid:
2.1, 6.9 and 12.3

18. Other High Energy Molecules

19. Go'of Hydrolysis

21. ATP
Use
Synthesis

22. Oxidation States Oxidation of triacylglycerols affords
more energy than do carbohydrates.

23. Sources of Energy

24. Biological Redox Energy
Electron Transport System (ETS) moves electrons from reduced coenzymes toward O2
This produces a proton gradient and a transmembrane potential
Oxidative Phosphorylation is the process by which the potential is coupled to the reaction: ADP + Pi ATP

25. NAD+ Oxidizes GAP
NADH carries electrons to the ETS.

26. Substrate Level Phosphorylation
Substrate Level Phophoryation occurs
When ATP is formed in a metabolic reaction.

27. Free Energy of Coupled Reactions
1,3-bisphosphoglycerate --- >
3-phosphoglycerate + Pi
Go' = kJ/mol
ADP + Pi --- >ATP
Go' = kJ/mol
1,3-bisphosphoglycerate + ADP ---- >
3-phosphoglycerate + ATP
Go' = kJ/mol

28. Aerobic Oxidation
Oxidative phosphorylation does not occur without electron transport.

29. Mitochondria Oxidation and electron transport
Oxidative phosphorylation

30. NAD+ A two electron transfer agent NicotinamideNucleotide
AMP = Adenine
Nucleotide
R = -PO3= for NADP+
AMP

31. Oxidation by NAD+
This side is the “A” face of the nicotinamide ring, the back side is the “B” face.

32. Oxidation by NAD+
A typically NAD+ oxidation is -OH to C=O

33. FAD A one electron transfer agent FMN = Flavin Mononucleotidein blue
Note that this is ribitol.
AMP in black

34. Oxidation by FAD
FAD and FMN also accept two electrons but these enter the isoalloxazine ring one at a time.

35. Oxidation by FAD
A typically FAD oxidation is -CH2-CH2- to -CH=CH-

36. Oxidized and Reduced Forms
This is an isoalloxazine ring system

37. Coenzyme A An acyl transfer agent (forms a thioester)
Note -PO3= on 3' of ribose
An acyl transfer agent (forms a thioester)

38. Thioesters

40. Carriers and Coenzymes

45. Review of G Equations For the reaction: A + B C + D
DG = DGo' + RT ln([C][D]/[A][B])
At standard state: All conc. are 1 M or 1 atm except [H+] and under these conditions:
DG = DGo'

46. Review of G Equations For the reaction: A + B C + D
At equilibrium: Keq = [C]eq[D]eq/[A]eq[B]eq and DG = 0, therefore:
DGo' = -RT ln Keq
For an oxidation-reduction reaction:
DGo' = -nDEo'F
(#e transferred)(cell potential)(Faraday’s const.)

47. Krebs Cycle Oxidations
Also, there are two oxidative decarboxylations in the Kreb’s Cycle (citric acid cycle).

48. Free Energy of a Redox Reaction
Oxidation Half-reaction: Half-Cell Potential
Malate > Oxaloacetate + 2 e + 2 H+ Eo' = v
Reduction Half-reaction:
NAD+ + 2 e + 2 H > NADH + H+ Eo' = v
Cell Reaction :
Malate + NAD > Oxaloacetate + NADH + H+
Cell Potential: Eo' = v
A cell reaction must contain an oxidation half-reaction
and a reduction half-reaction to equate electron flow.

49. Free Energy of a Redox Reaction
Go' = -nEo'F
= -(2)(-0.154)(96480)
= J/mol
= kJ/mol
The equilibrium of this redox reaction lies far to the left. Cellular concentrations of the metabolites must be such that the overall G is negative in order for the reaction to proceed as written on the previous slide. For a redox reaction to proceed spontaneously, the cell potential must be positive.

50. Free Energy of a Redox Reaction
Malate + NAD > Oxaloacetate + NADH + H+
Which reactant is oxidized ?
Which reactant is reduced ?
Which reactant is the oxidizing agent ?
Which reactant is the reducing agent ?
Malate
NAD+
NAD+
Malate

51. Reaction Types in Metabolism

52. Ligation with ATP

53. Isomerization

54. Group Transfer

55. Hydrolysis

56. Cleavage to form a Double Bond

57. Cleavage to form a Double Bond

58. Energy Charge of a Cell
ATP + ½ ADP Energy Charge = ATP + ADP + AMP
Limits are 0 and 1.0
If all is ATP, the energy charge = If all is AMP, the energy charge = 0
ATP can be regenerated using adenylate kinase
(this is a nucleoside monophosphate kinase):
2 ADP <===> ATP + AMP

59. Rate vs Energy Charge

60. Other ATP uses
ATP can also be used to make other NTPs with nominal energy exchange using a nucleoside diphosphate kinase.
ATP + NDP <===> ADP + NTP
Other involvement of ATP:
1. Phosphate transfer to make high energy bond: Glutamine synthesis uses P from ATP
Glu + ATP —> γ-PGlu + ADP, then NH3 displaces P to give Gln

61. Other ATP uses 2. PEP transfers P to make ATP:
Enol-P (PEP) + ADP —> Pyr + ATP
3. Nucleotide transfer to make high energy bond:
AMP from ATP combines with a fatty acid in making AcylSCoA catalyzed by acylSCoA synthetase (acyl thiokinase) during fatty acid activation.
FA + ATP —> acyl-AMP + PPi,
then CoASH displaces AMP to give acyl-SCoA

62. Effect of H+ on Keq pyruvate + NADH + H+ ----> lactate + NAD+
Keq' = Kapp =
[pyruvate][NADH]
so, Keq' = Keq (H+), where H+ is a reactant.
similarly, Keq' = Keq /(H+), where H+ is a product.

63. FAD vs FAD-flavoprotein
Electrons from succinate:
FADH2 + CoQ < === > FAD + CoQH2
Go' for free FAD in solution:
FAD H e- <===> FADH2 Eo' = v
CoQ H e- <===> CoQH Eo' = v
net FADH2 + CoQ <===> FAD + CoQH2 Eo' = +0.32v
Go' = -nEo'F = kJ/mol

64. FAD vs FAD-flavoprotein
CoQ + FADH2 < === > CoQH2 + FAD
Go' for FAD in a flavoprotein:
FAD H e- <===> FADH Eo' = v
CoQ H e- <===> CoQH Eo' = v
net FADH2 + CoQ <===> FAD + CoQH2 Eo' = v
Go' = -nEo'F = kJ/mol
This represents a difference in Go' of about 42 kJ/mol.

65. Table of Reduction Potentials

67. Biochemistry Sixth Edition
Berg • Tymoczko • Stryer
End of Chapter 15
Copyright © 2007 by W. H. Freeman and Company