Transcript Ch15web.energy-meatbolism

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
(exergonic)
energy requiring
(endergonic)
makes pool molecules
uses pool molecules
produces NADH &
NADPH
uses NADPH almost
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
o'
G of
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
ADP + Pi --- >ATP
Go' = -49.4 kJ/mol
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+
Keq
[lactate][NAD+]
= ------------------------------[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
CoQ + 2 H+ + 2 e- <===> CoQH2
net
Eo' = 0.00v
Eo' = +0.10v
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