Biochemistry

Sixth Edition

Berg • Tymoczko • Stryer

Chapter 15:
Metabolism:
Basic Concepts and Design

Copyright © 2007 by W. H. Freeman and Company

Roadmap
of
Metabolic
Pathways
 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.
 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
 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
 Energy Overview

Energy distribution

1/3 2/3
nutrients ----> pool molecules ----> CO2, H2O,
NH3

biomolecules
 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
 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
 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
 Levels of Regulation

1. Direct regulation at the enzyme level

(covalent or non-covalent).
2. Regulation via external communication
(hormonal).
3. Regulation at the gene level
(induction/repression).
 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.
 Glucose
Metabolism

Breakdown to
small molecules
and energy.
Metabolite

Needed for
formation of
glycerol based
phospholipids
and to run the
glycerol-P
shuttle.
Adenosine Nucleotides

Components of
an energy system.
 ATP
An energy carrier considered to be
common energy currency in a cell
 Driving Forces behind the
Energy of ATP Hydrolysis

1. Resonance energy of reactants vs

products.
2. Charge repulsion of oxygens.
3. Number of charges on oxygens.
4. Solvation of reactants vs products.
5. Entropy – number of reactant vs product
molecules.
Phosphate Resonance

pKas of phosphoric acid:

2.1, 6.9 and 12.3
Other High
Energy
Molecules
G of
o' Hydrolysis
 ATP

Use

Synthesis
 Oxidation States

Oxidation of triacylglycerols affords

more energy than do carbohydrates.
Sources of Energy
 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
 NAD+ Oxidizes GAP

NADH carries electrons to the ETS.

Substrate Level Phosphorylation

Substrate Level Phophoryation occurs

When ATP is formed in a metabolic reaction.
 Free Energy of Coupled Reactions

1,3-bisphosphoglycerate --- >

3-phosphoglycerate + Pi Go' = -49.4 kJ/mol

ADP + Pi --- >ATP Go' = +30.5 kJ/mol

1,3-bisphosphoglycerate + ADP ---- >

3-phosphoglycerate + ATP

Go' = -18.9 kJ/mol

 Aerobic
Oxidation

Oxidative
phosphorylation
does not occur
without electron
transport.
 Mitochondria
Oxidation
and
electron
transport

Oxidative
phosphorylation
NAD+ A two electron
transfer agent

Nicotinamide
Nucleotide

AMP = Adenine
Nucleotide

R = -PO3= for NADP+ AMP

 Oxidation by NAD+

This side is the “A” face of the nicotinamide

ring, the back side is the “B” face.
 Oxidation by NAD+

A typically NAD+ oxidation is -OH to C=O

 FAD A one electron
transfer agent

FMN = Flavin
Mononucleotide
in blue

Note that
this is
ribitol.

AMP in black
Oxidation by
FAD

FAD and FMN

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

A typically FAD oxidation is -CH2-CH2- to -CH=CH-

Oxidized and Reduced Forms

This is an isoalloxazine ring system

 Coenzyme A

Note -PO3= on 3' of ribose

An acyl transfer agent (forms a thioester)

Thioesters
Carriers and Coenzymes
 Review of G Equations
• For the reaction: A + B C+D

G = Go' + RT ln([C][D]/[A][B])

• At standard state: All conc. are 1 M or 1

atm except [H+] and under these conditions:

G = Go'
 Review of G Equations
• For the reaction: A + B C+D

• At equilibrium: Keq = [C]eq[D]eq/[A]eq[B]eq

and G = 0, therefore:

Go' = -RT ln Keq

• For an oxidation-reduction reaction:

Go' = -nEo'F
(#e transferred)(cell potential)(Faraday’s const.)
 Krebs Cycle Oxidations

Also, there are two oxidative decarboxylations

in the Kreb’s Cycle (citric acid cycle).
 Free Energy of a Redox Reaction

Oxidation Half-reaction: Half-Cell Potential

Malate ---- > Oxaloacetate + 2 e + 2 H+ Eo' = +0.166 v

Reduction Half-reaction:
NAD+ + 2 e + 2 H+ ---- > NADH + H+ Eo' = -0.32 v
Cell Reaction :
Malate + NAD+ ---- > Oxaloacetate + NADH + H+
Cell Potential: Eo' = -0.154 v
A cell reaction must contain an oxidation half-reaction
and a reduction half-reaction to equate electron flow.
Free Energy of a Redox Reaction
Go' = -nEo'F

= -(2)(-0.154)(96480)
= +29700 J/mol
= +29.7 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.
Free Energy of a Redox Reaction

Malate + NAD+ ---- > Oxaloacetate + NADH + H+

Which reactant is oxidized ? Malate

Which reactant is reduced ? NAD+

Which reactant is the oxidizing agent ? NAD+

Which reactant is the reducing agent ? Malate

Reaction Types in Metabolism
Ligation with ATP
Isomerization
Group Transfer
Hydrolysis
Cleavage to form a Double Bond
Cleavage to form a Double Bond
 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 = 1
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

Rate vs Energy Charge
 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
 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
 Effect of H+ on Keq
pyruvate + NADH + H+ ----> lactate + NAD+

[lactate][NAD+]
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.
 FAD vs FAD-flavoprotein

Electrons from succinate:

FADH2 + CoQ < === > FAD + CoQH2

Go' for free FAD in solution:

FAD + 2 H+ + 2 e- <===> FADH2 Eo' = -0.22v

CoQ + 2 H+ + 2 e- <===> CoQH2 Eo' = +0.10v

net FADH2 + CoQ <===> FAD + CoQH2 Eo' = +0.32v

Go' = -nEo'F = -61.7 kJ/mol

 FAD vs FAD-flavoprotein
CoQ + FADH2 < === > CoQH2 + FAD

Go' for FAD in a flavoprotein:

FAD + 2 H+ + 2 e- <===> FADH2 Eo' = 0.00v

CoQ + 2 H+ + 2 e- <===> CoQH2 Eo' = +0.10v

net FADH2 + CoQ <===> FAD + CoQH2 Eo' = +0.10v

Go' = -nEo'F = -19.3 kJ/mol

This represents a difference in Go' of about 42 kJ/mol.

Table of Reduction Potentials
 Biochemistry
Sixth Edition

Berg • Tymoczko • Stryer

End of Chapter 15

Copyright © 2007 by W. H. Freeman and Company