Transcript Principles of Metabolism - School of Biological Sciences

Principles of Metabolism
Some fundamental concepts
• Energy
– Potential vs kinetic
– Chemical vs electrical
• Work
– Moving material from place to place
– Creating order and structure
– Power – rate of doing work
Here comes the Law
• First Law – mass and energy are
conserved
• Second Law – seen as a whole, a system
always proceeds in the direction of more
disorder (entropy) and less ability to do
work (Gibbs free energy)
How is an organism different from a machine?
• A machine can maintain its structure even if it does no
work. Thus it is not coal, but the combustion of coal that
is what is needed to keep the steam engine operating.
• In an organism, oxidation goes on whether or not there is
food – if there is no food, the organism consumes itself.
If there is food, it provides both the energy to do work
and create order, and molecular building blocks which
become the substance of the organism.
Chemical equilibrium
• Specifically, systems approach
thermodynamic equilibrium by giving up
some of their potential to do work and
increasing their disorder. These facts
determine the direction in which a
chemical reaction will proceed
spontaneously, and the ratio of reactants
and products at equilibrium.
Cells are not systems at equilibrium
• In order to drive reactions that create and
maintain order and structure, cells must
couple these processes to energy-yielding
reactions. As a whole, a cell is far from
equilibrium and is operating as an open
system in steady state.
Role of enzymes in cellular
processes
• Increase the rate of spontaneous reactions
by lowering their activation energy.
• Couple energy yielding (exothermic)
reactions to energy requiring
(endothermic) reactions.
Lowering the activation energy of a spontaneous reaction
Coupling of reactions: a mechanical analogy
uncoupled
coupled
There are a number of important mediators of
energy coupling
• Carriers of phosphorylation potential (ATP, creatine
phosphate, GTP, UTP, etc.)
• Carriers of redox potential (NADH and FADH2 are
participants in catabolic processes, NADPH is involved
in anabolic processes like fatty acid synthesis)
• Gradients of electrical charge, which can apply electrical
driving force to ions (molecules or atoms that possess an
electrical charge)
• Gradients of chemical concentration, in which dissipation
of the gradient releases energy that is used to drive an
energy-requiring process
• Electrochemical gradients, in which the total energy
available is the sum of the electrical driving force and the
chemical driving force.
the different energy couplers are
interconvertible
• For example, as we will see in oxidative energy
metabolism, most of the potential energy of foodstuff is
captured first as reduced coenzyme (NADH, FADH2),
then converted to an electrochemical gradient of H+
across the mitochondrial inner membrane, and then
converted to ATP.
• Or in another example, the Na+ /K+ pump in the plasma
membrane is powered by ATP and creates an
electrochemical gradient of Na+ directed toward the cell
interior - diffusive leakage of Na+ back into the cell can
be coupled to energize uptake of glucose (some cell
types) or amino acids (almost all cell types).
Of all the couplers, ATP is the nearest thing to a
universal energy currency in cells

In ATP and ADP, a lot of free energy is stored in the electrostatic repulsion of the
adjacent O- , so these are sometimes called high-energy phosphate bonds.
ATP hydrolysis in cells

In the cell, the ΔG of the ATP hydrolysis can be even larger than the standard ΔG° of 7.3 kcal/mol
ΔG = ΔG° + RT ln ([ADP][Pi]/[ATP])
•
•
•
•
Standard conditions: [reactants] = 1 mol/l: ΔG = ΔG°
In cells the [ATP] is normally much higher than [ADP]; in muscle [ATP] = 4 mM;
[ADP]=0.013 mM
ΔG = ΔG° + RT ln ([ADP][Pi]/[ATP]) = -12 kcal/mol
Note: under these conditions in cells it also takes more energy to rephosphorylate
ADP! If you got more energy out, you had to also be putting more in.
If the system were in equilibrium (ΔG = 0), [ADP] would be over 105 times greater than
[ATP]
K is the equilibrium
ΔG0 = -RT ln K
constant
K= 10 –ΔG°/ 2.303 R T
K= 10-ΔG°´/ 5.70
K=2.2 x 105
ATP and its relatives

Apart of other nucleoside phosphates that are used in metabolism as energy carriers,
the structural motif of ATP returns in other important molecules:

NAD+/NADH + H+ and FAD/FADH2 serve as messengers/carriers for reduction
equialents (e- + H+)
• A + e- + H+----> AH,
• is a hydrogenation and is a reduction. The opposite is a dehydrogenation
reaction and is an oxidation.
ATP and its relatives

Apart from other nucleoside phosphates that are used in metabolism as energy
carriers, the structural motif of ATP returns in other important molecules:

Coenzyme A serves as a messenger/carrier of acetyl
groups
The cellular store of ATP is small and turns over
rapidly
• A 70 kg person might consume 2800 kcal/day
(=11,700kJ/day) of foodstuff
• If total energy metabolism operated at 50%
efficiency and none of the calories were stored
as fat or glycogen, and
• 1 mole of ATP yielded 50kJ of free energy
• About 117 moles or about 64 Kg of ATP would
be hydrolyzed per day, for a turnover rate of
1300/molecule/day
• Exertion would drive this value up substantially –
a 2 hour run could cost 60 moles of ATP.
To ensure that ATP can turn over rapidly, it should not have
to travel far – ideally, only a few microns at most!
This is an example showing the close placement of a mitochondrion to
the contractile machinery in a skeletal muscle cell
This is another example, in which mitochondria actually move to the site of the energy
demand. On the left is a cell of non-stimulated Malpighian tubule of the blood-feeding
bug Rhodnius. On the right is a portion of a cell from a stimulated tubule. Mitochondria
are entering the microvilli to be as close as possible to the apical membrane, the site of
an energy demanding ion transport process that is turned on when the bug is eliminating
the fluid and ions taken on in a blood meal.
Information and energy are
interconvertible
• Maxwell’s Demon – a simple example
• ATP and other phosphorylated molecules are
frequently information carriers as well as energy
carriers – for example, there is a large category
of G-proteins (GTP-binding proteins) that serve
as intracellular signals, and phosphorylating a
protein is a universal mechanism of controlling
that protein’s cellular function.
Metabolism consists of catabolism and
anabolism
• Foodstuffs and cellular energy reserves consist of
complex molecules rich in reducing power – the ability to
give up electrons and become oxidized.
• Catabolism (by mostly exergonic reactions) leads to the
creation of disorder in the cell - production of simpler,
energy-poor endproducts: carbon dioxide, water,
ammonia – sometimes with capture of free energy either
directly as ATP or as reduced coenzyme (NADH, FADH,
NADPH)
• Anabolism is biosynthesis – it involves creating
additional order in the cell - new covalent bonds are
formed – energy is provided by ATP and NADPH.
4 ways of stating the same energetic truth
• Irreversible reactions make metabolic pathways
directional – water that has fallen over a waterfall cannot
turn around and go back
• Every metabolic pathway has a first committed step –
early in the pathway, an exergonic reaction step commits
its product to continue in the pathway
• The same pathway usually cannot operate in either the
catabolic or anabolic direction – instead, there must be a
detour around each exergonic reaction step in the
pathway.
• Every pathway has a rate-limiting step – the choke-point
step in a reaction sequence is one at which reactants
and products are far from equilibrium with each other
and the enzyme is almost constantly saturated.
Control of metabolic pathways
• Allosteric control – substrates and/or products
of the pathway feed back on a rate-limiting
enzyme
• Covalent modification – the rate constants of
individual enzyme molecules may be changed
by phosphorylation, glycosylation,
binding/unbinding of a control protein, bonding
of Ca++, or subunit assembly/disassembly.
• Movement of enzymes between an active to an
inactive pool.
• Genetic control – induced synthesis of more or
less enzyme, or of an alternative enzyme.
A little review of redox
chemistry
Oxidation/reduction
• ‘Oxidation’ is not only the addition of
oxygen atoms
• Oxidation refers to the removal of
electrons
• Reduction is the addition of electrons
• Example: Fe2+ is oxidized if it loses an
electron to become Fe3+.
Oxidation/reduction
• This term also applies to shifts of electrons
between atoms linked by a covalent bond.
• When carbon is covalently bonded to an atom with
a strong affinity for e-, such as O, Cl, or S, it gives
up more than its equal share of electrons.
• It acquires a partial positive charge and is said to
be oxidized
Oxidation of methane (CH4)
• C atoms bonded to H have more than
their share of electrons and are thus
reduced
Oxidation of methane
• The C atom of CH4 can be
converted to CO2 through the
successive removal of its H
atoms.
• With each step, e- are shifted
away from C and C becomes
progressively more oxidized
Hydrogenation/dehydrogenation
• Often when a molecule picks up an e- it
also picks up a H+ at the same time.
• A + e- + H+----> AH
• This is a hydrogenation reaction and is a
reduction.
• The opposite is a dehydrogenation
reaction and is an oxidation.
“Life is nothing but an
electron looking for a
place to rest.”
Albert Szent-Gyorgi
Szent-Gyorgi received the
Nobel Prize for Physiology
and Medicine in 1937. He
was the first to isolate Vitamin
C. His discoveries provided
the basis for the discovery of
the “citric acid cycle”, the
substrate reactions of
oxidative metabolism.
An Overview of the 3 Stages of Energy Metabolism
 1st stage: Large molecules
in food are broken down
into smaller units. This is
a preparation stage
without capture of energy.
• Proteins -> amino
acids,
• Polysaccharides ->
monosaccharides
(glucose, ...)
• Fats -> glycerol,
fatty acids.
2nd stage:
Molecules are
degraded to simple
units that play a
central role in
metabolism. Most of
them are converted
into the acetyl unit of
acetyl CoA. Some
ATP is generated in
this anaerobic stage,
but amount is small
compared with 3rd
stage.
3rd stage: ATP is
produced from the
complete oxidation of the
acetyl unit of acetyl CoA.
Acetyl CoA brings acetyl
units into the citric acid
cycle, where they are
completely oxidized to
CO2. Four pairs of
electrons are transferred
(three pairs to NAD+ and
one pair to FAD) for each
acetyl group that is
oxidized. Then, a proton
gradient is generated as
electrons flow from the
reduced forms of these
carriers to O2, and this
gradient is used to
phosphorylate ADP to ATP.