Transcript Lehninger Principles of Biochemistry

David L. Nelson and Michael M. Cox
LEHNINGER
PRINCIPLES OF BIOCHEMISTRY
Sixth Edition
CHAPTER 13
Bioenergetics and Biochemical
Reaction Types
© 2013 W. H. Freeman and Company
Plants
Humans
Catabolism extracts
energy from
nutrients.
Anabolism uses
energy to
synthesize
biomolecules.
Connection between catabolic and anabolic pathways
Features of Metabolism
1. Anabolic and catabolic pathways are reciprocally regulated.
example: fatty acid synthesis and degradation are not
both turned on simultaneously.
2. Catabolic and anabolic pathways that connect the same two
end points may use many of the same endpoints but
at least one step is catalyzed by different enzymes.
example: gluconeogenesis is the reverse of glycolysis
but several steps utilize different enzymes.
3. Paired catabolic and anabolic pathways often occur in
different cellular compartments.
example: fatty acid synthesis occurs in the cytosol,
while fatty acid degradation occurs in the mitochondria
Regulation of Metabolism
1. Substrate Availability
When an enzyme’s substrate concentration in a cell is
below Km, the enzyme operates at less than Vmax.
2. Allosteric Regulation
When a cell senses an enzyme should stop catalysis,
an effector molecule binds to an enzyme and inhibits it.
3. Hormonal Regulation
A cell responds to an external stimulus, such as a
hormone or growth factor, and alters the rate of
synthesis or degradation of an enzyme.
Catabolism
Extraction of energy from nutrients
Chapter 13 – Bioenergetics
Chapter 14 – Glycolysis & Gluconeogenesis
Chapter 15 – Glycogen Metabolism
Chapter 16 – Citric Acid Cycle
Chapter 17 – Fatty Acid Oxidation
Chapter 18 – Amino Acid Oxidation
Chapter 19 – Oxidative Phosphorylation
Thermodynamic Quantities
DG – Free energy change of a reaction. If DG is negative
the reaction releases energy and is exergonic. If DG
is positive the reaction results in the system
gaining free energy and is endergonic.
DH – change in enthalpy (heat) from the conversion of
reactants to products. If DH is negative the reaction
releases heat and is exothermic. If DH is positive
the reaction results in the system taking up heat from
the surroundings and is endothermic.
DS – change in entropy (disorder) that results from a reaction.
If the products of a reaction are more disordered than
the reactants DS has a positive value.
Relationship between DG, DH and DS
DG = DH - TDS
A reaction is favorable when DG is negative.
An increase in entropy (+DS) or a release of heat (-DH)
make DG more negative and are typical of
favorable reactions.
Consider the following reaction:
aA + bB  cC + dD
The equilibrium constant is given by:
Keq =
[C]c[D]d
[A]a[B]b
When the reaction is not at equilibrium there is a force
driving the reaction to equilibrium. This force is
represented by DG.
Biochemists’ Definitions
DGº - standard free energy change
DGº is the driving force toward equilibrium when reactants
and products are at 1 M concentrations at 298 K (25ºC).
DG’º - Biochemists’ standard free energy change
DG’º is the standard free energy change when pH = 7 and the
concentration of H2O is assumed to be constant
at 55.5 M.
See Page 507
Relationship between DG’º and K’eq
The standard free energy change for a reaction is dependent
on the equilibrium constant.
See Page 508
aA + bB  cC + dD
Keq =
[C]c[D]d
[A]a[B]b
DG’º = -RT lnK’eq
See Page 508
Example: An enzyme catalyzes the conversion of A to B.
At equilibrium there is 12 times more B than A.
What is the standard free energy change (DG’º )
for the conversion of A to B?
A  B
Keq =
[B]
[A]
DG’º = -RT lnK’eq
= -(8.315 J/mol*K)(298K)(ln12)
= -6157 J/mol = -6.16 kJ/mol
DG’º is negative so if we started with [A]=1M and [B]=1M
the reaction proceeds with a release of free energy.
See example on Page 508
= 12
Actual free energy changes depend on reactant and product
concentrations. During a reaction the reactant and product
concentrations may not be 1 M. The free energy change
will be dependent on the actual concentrations. The free
energy change is described by the following equation:
For the reaction A + B  C + D
See Pages 509-511
Standard free energy changes are additive
A  B  C
See Page 494
A thermodynamically unfavorable (endergonic) reaction can
be driven in the forward direction by coupling it to a
thermodynamically favorable (exergonic) reaction through
a common intermediate.
Glucose + Pi  glucose 6-phosphate
ATP  ADP + Pi
Sum:
DG’º = +13.8 kJ/mol
DG’º = -30.5 kJ/mol
ATP + glucose  ADP + glucose 6-phosphate
DG’º = +13.8 kJ/mol + (-30.5 kJ/mol) = -16.7 kJ/mol
Result: The overall reaction is exergonic (favorable)
Catabolism extracts
energy from
nutrients.
Anabolism uses
energy to
synthesize
biomolecules.
There is a large negative
free energy change
associated with ATP
hydrolysis
For most enzymes that utilize ATP,
the true substrate is MgATP2-
In a human erythrocyte, what is the actual free energy of
hydrolysis of ATP due to concentrations of ATP, ADP and Pi?
R = 8.315 J/mol*K
T = 298 K
From Table 13-5:
ATP  ADP + Pi
[ATP] = 2.25 mM
[ADP] = 0.25 mM
[Pi] = 1.65 mM
DG’º = -30.5 kJ/mol = 30,500 J/mol
DG = DG’º + RT ln [ADP][Pi] / [ATP]
DG = -30,500 J/mol + RT ln(0.25 x 10-3 M)(1.65 x 10-3 M)/(2.25 x 10-3 M)
DG = -30,500 J/mol + RT (-8.60)
DG = -30,500 J/mol + (-21320 J/mol)
DG = -51820 J/mol = -51.8 kJ/mol
Phosphoenolpyruvate has a high standard
free energy of hydrolysis
(hydrolysis of a phosphate ester bond)
1,3-bisphosphoglycerate has a high standard
free energy of hydrolysis
(hydrolysis of a phosphate ester bond)
Flow of phosphoryl groups is dependent on standard
free energies of hydrolysis
ATP can donate phosphoryl, pyrophosphoryl
and adenylyl groups
Transphosphorylations between nucleotides
Nucleoside diphosphate kinase catalyzes the reaction:
ATP + NDP  ADP + NTP
where NDP is any nucleoside diphosphate.
Adenylate kinase catalyzes the reaction:
2ADP  ATP + AMP
Phosphocreatine and creatine kinase
Phosphocreatine serves as a source of phosphoryl groups
for the synthesis of ATP.
ADP + phosphocreatine  ATP + creatine
Biological Oxidation - Reduction
Page 528
The flow of electrons in oxidation-reduction reactions
is the source of work done in a cell.
The source of electrons is the highly reduced molecules
in the food we eat. Example: glucose
Electrons are released by the oxidation of food molecules
and ultimately transferred to oxygen through
a series of electron carriers, releasing energy.
Common biological oxidation states of carbon
Four ways electrons are transferred in biological
oxidation-reduction reactions (see page 513-514)
1. Directly as electrons.
Fe2+ + Cu2+  Fe3+ + Cu+
2. As hydrogen atoms.
AH2  A + 2H (2H+ + 2e-)
3. As a hydride ion (:H-) which has two electrons.
NAD+ + H+ + 2e-  NADH
4. Through direct combination with oxygen.
R-CH3 + ½O2  R-CH2-OH
NADH and NADPH are soluble electron carriers
used by enzymes called dehydrogenases
Niacin is a vitamin that is a precursor to NADH and NADPH
NAD(H) versus NADP(H)
In a typical cell:
NAD+ / NADH ratio is high
NADP+ / NADPH ratio is low
This favors hydride transfer to NAD+ and
hydride transfer from NADPH.
In general, NAD+ is utilized as a hydride acceptor in
catabolic oxidation reactions and NADPH is
utilized as a hydride donor in anabolic
reduction reactions.
Enzymes that utilize NAD(P)(H) are oxidoreductases.
A common class of oxidoreductases is dehydrogenases.
Some enzymes use
flavin nucleotides for
oxidation-reduction