Cellular physiology
ATP and Biological Energy
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The complexity of metabolism
This schematic diagram
traces only a few hundred of
the thousands of metabolic
reactions that occur in a cell.
The dots represent molecules,
and the lines represent the
chemical reactions that
transform them.
The reactions proceed in
stepwise sequences called
metabolic pathways, each
step catalyzed by a specific
enzyme.
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Metabolism, Energy and Life
The chemistry of life is organized into metabolic pathways
Metabolism - totality of an organism’s chemical processes
Metabolic reactions are organized into pathways that are
orderly series of enzymatically controlled reactions.
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Metabolism, Energy and Life
Metabolic pathways are generally of two types:
Catabolic pathways – release energy by breaking down complex
molecules to simpler compounds (cellular respiration which
degrades glucose to carbon dioxide and water; provides energy
for cellular work);
Anabolic pathways – consume energy to build complicated
molecules from simpler ones (photosynthesis which
synthesizes glucose from CO2 and H2O; any synthesis of a
macromolecule from its monomers).
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Organisms transform energy
Energy is a capacity to do work
Kinetic energy – energy in the process of doing work (energy of
motion).
Heat (thermal energy) is kinetic energy expressed in random
movement molecules.
Potential energy – energy that matter possesses because of its
location or arrangement.
In the earth’s gravitational field, an object on a hill or water
behind a dam have potential energy.
Chemical energy is potential energy stored in molecules
because of the arrangement of nuclei and electrons in its
atoms
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Organisms transform energy
Energy can be transformed from one form to another
Kinetic energy of sunlight can be transformed into the
potential energy of chemical bonds during photosynthesis.
Potential energy in the chemical bonds of gasoline can be
transformed into kinetic mechanical energy which pushes
the pistons of an engine
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The energy transformations of life are subject to
two laws of thermodynamics
Thermodynamics – study of energy transformations
First Law of Thermodynamics – energy can be transferred and
transformed, but it cannot be created or destroyed (energy of the
universe is constant)
Second Law of Thermodynamics – every energy transfer or
transformation makes the universe more disordered (every process
increases the entropy of the universe).
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The energy transformations of life are subject to
two laws of thermodynamics
Entropy – quantitative measure of disorder that is proportional to
randomness
Closed system – collection of matter under study which is isolated
from its surroundings
Open system – system in which energy can be transferred between
the system and its surroundings.
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The energy transformations of life are subject to
two laws of thermodynamics
The entropy of a system may decrease, but the entropy of the
system plus its surroundings must always increase.
Highly ordered living organisms do not violate the second law
because they are open systems.
For example, animals:
Maintain highly ordered structure at the expense of increased
entropy of their surroundings.
Take in complex high energy molecules as food and extract
chemical energy to create and maintain order.
Return to the surroundings simpler low energy molecules (CO2
and water) and heat.
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The complexity of metabolism
An unstable system is rich in free energy.
It has a tendency to change spontaneously to a more stable state.
(a) In this case, free energy is proportional to the girl's altitude.
(b) The free-energy concept also applies on the molecular
scale, in this case to the physical movement of molecules
known as diffusion.
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The complexity of metabolism
(c) Chemical reactions also involve free energy.
The sugar molecule on top is less stable than the simpler molecules
below.
When catabolic pathways break down complex organic molecules, a
cell can harness the free energy stored in the molecules to perform
work.
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Organisms live at the expense of free energy
Free energy: a criterion for spontaneous change
-It is the amount of energy that is available to do work.
Free energy (G) is related to the system’s total energy (H) and
its entropy (S) in the following way:
G= H – TS
Where
G = Gibbs free energy
H = enthalpy of total energy
T = temperature in K
S = entropy
Free energy (G) = Portion of a system’s energy available to do
work; is the difference between the total energy (enthalpy) and
the energy not available for doing work (TS).
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Organisms live at the expense of free energy
The maximum amount of usable energy that can be harvested from
a particular reaction is the system’s free energy change from the
initial to the final state.
This change in free energy (ΔG) is given by the Gibbs-Helmholtz
equation at constant temperature and pressure:
ΔG = ΔH – TΔS
Where:
ΔG = change in free energy
ΔH = change in total energy (enthalpy)
ΔS = change in entropy
T = absolute temperature in K (C+273)
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Free energy and equilibrium
There is a relationship between chemical equilibrium and the
free energy change (ΔG) of a reaction:
As a reaction approaches equilibrium, the free energy of
the system decreases (spontaneous and exergonic
reaction).
When a reaction is pushed away from equilibrium, the free
energy of system increases (non-spontaneous and
endergonic reaction).
When a reaction reaches equilibrium, ΔG = 0, because
there is no net change in the system.
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Free energy and metabolism
Reactions can be classified based upon their free energy
changes:
Exergonic reaction – a reaction that proceeds with a net
loss of free energy.
Endergonic reaction – an energy-requiring reaction that
proceeds with a net gain of free energy; a reaction
absorbs free energy from its surroundings.
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Free energy and metabolism
Exergonic reaction
Chemical products have
less free energy than the
reactant molecules.
Endergonic reaction
Products store more free
energy than reactants
Reaction is energetically
downhill.
Reaction is energetically uphill.
Spontaneous reaction.
ΔG is negative.
Non-spontaneous reaction
(requires energy input)
ΔG is positive.
-ΔG is the maximum
amount of work the reaction
can perform
+ΔG is the minimum amount of
work required to drive the
reaction.
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Free energy and metabolism
If a chemical process is exergonic, the reverse process
must be endergonic.
For example:
For each mole of glucose oxidized in the exergonic
process of cellular respiration, 2870 kJ are released (ΔG
= -2870 kJ/mol or -686 kcal/mol).
To produce a mole of glucose, the endergonic process of
photosynthesis requires an energy input of 2870 kJ (ΔG
= +2870 kJ/mol or +686 kcal/mol).
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How a free-energy gradient keeps metabolism
away from equilibrium: a hydraulic analogy.
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ATP (a) the structure of ATP and
(b) the hydrolysis of ATP to yield ADP and inorganic
phosphate.
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The Nature of ATP
ATP is the immediate source of energy that power cellular
work.
ATP powers three main kinds of work in a cell:
- mechanical work, cilia beating, the contraction of the
muscle cells, the movement of the chromosomes during
cellular reproduction;
- transport work, the pumping of substances across
membranes against the direction of spontaneous
movement;
- chemical work, the pushing of endergonic (absorbing
free energy from the surrounding) reactions that would
not occur spontaneously, such as the synthesis of
polymers from monomers.
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Energy coupling by phosphate transfer.
In this example, ATP
hydrolysis is used to drive
an endergonic reaction,
the conversion of the amino
acid glutamic acid (Glu)
to another amino acid,
glutamine (Glu--NH2).
(a) Without the help of ATP,
the conversion is nonspontaneous.
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Energy coupling by phosphate transfer.
(b) As it actually occurs in the
cell, the synthesis of glutamine
is a two-step reaction driven by
ATP.
The formation of a
phosphorylated intermediate
couples the two steps.
1. ATP phosphorylates
glutamic acid, making the
amino acid less stable.
2. Ammonia displaces the
phosphate group, forming
glutamine.
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Energy coupling by phosphate transfer.
(c) Adding the delta G for
the amino acid
conversion
to the delta G for the ATP
hydrolysis
gives the free-energy
change for the overall
reaction.
Because the overall
process is exergonic
(has a negative delta G),
it occurs spontaneously.
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ATP formation
We can write the chemical reaction for the formation of ATP
as:
a) in chemicalese: ADP + Pi + energy ----> ATP
b) in English: Adenosine diphosphate + inorganic Phosphate
+ energy produces Adenosine Triphosphate
The chemical formula for the expenditure/release of ATP
energy can be written as:
a) in chemicalese: ATP ----> ADP + energy + Pi
b) in English Adenosine Triphosphate produces Adenosine
diphosphate + energy + inorganic Phosphate
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How to Make ATP
Two processes convert ADP into ATP:
1) substrate-level phosphorylation; and
2) chemiosmosis.
Substrate-level phosphorylation occurs in the cytoplasm when
an enzyme attaches a third phosphate to the ADP (both ADP
and the phosphates are the substrates on which the enzyme
acts).
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Enzymes and the formation of NADH and ATP.
ATP regeneration
ATP is renewable and can be regenerated by the addition of
Exorgenic reaction –
phosphate to ADP
ATP
Energy
from
catabolism
ADP + P i
Endorgenic reaction
Requires G = +7.3 kcal/mol
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catabolic reaction
providing energy for ATP
making
Energy for
cellular
work
Enzymes
Catalyst – chemical agent that accelerate a reaction without
being permanently changed in the process.
Enzymes are catalytic proteins that change the rate of a
reaction without being consumed by the reaction.
The initial investment of energy for starting a reaction – the
energy required to break bonds in the reactant molecules –
is known as the free energy of activation, or activation
energy.
Transition state – unstable condition of reactant molecules
that have absorbed sufficient free energy to react.
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An energy profile of a reaction
The reactants AB and CD must absorb enough energy from
the surroundings to surmount the hill of activation energy
(EA) and reach the unstable transition state.
The bonds can then break,
and as the reaction
proceeds,
energy is released to the
surroundings during the
formation of new bonds.
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An energy profile of a reaction
This particular graph profiles the energy inputs and outputs
of an exergonic reaction, which has a negative ΔG; the
products have less free energy than the reactants.
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Enzymes lower the barrier of activation energy
Without affecting the free-energy change (delta G) for the
reaction, an enzyme speeds the reaction by reducing the
uphill climb to the transition state.
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Enzymes are substrate-specific
The reactant an enzyme acts on is referred to as the
enzyme’s substrate.
Substrate(s)
Enzyme
Product(s)
Glucose
Sucrose
+
H2O
Sucrase
Fructose
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Catalytic cycle
Active
site
Enzyme
(sucrase)
Substrate
(sucrose)
Fructose
Glucose
4
Products are
released
H2O
Enzyme and
1 substrate are
available
Enzymesubstrate
complex
3 Substrate is converted to products 2 Substrate binds to enzyme
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Environmental factors affecting enzymes
Optimal
temperature
for typical
human
enzyme
Optimal
temperature for
enzyme of
thermophilic (heattolerant) bacteria
20
40
60
80
100
Optimal
pH for
pepsin
Rate of reaction
Temperature (C)
0
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Optimal
pH for
trypsin
1
2
3
4 5
pH
6
7
8
9 10
Cofactors
Cofactors are nonprotein helpers for catalytic activity;
they are either bound tightly to the active site or bound
loosely and reversibly along with the substrate.
Cofactors may be either inorganic (Zn, Fe, Cu) or organic
(specifically called a coenzyme). Most vitamins are
coenzymes.
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Inhibitors
Active site
Substrate
(a) A substrate can
normally bind to the
active site of an enzyme
(b) A competitive
inhibitor mimics the
substrate and competes
for the active site
Competitive
inhibitor
(c) A noncompetitive inhibitor binds to
the enzyme at a location away from the
active site, but alters the conformation of
the enzyme so that the active site is no
longer fully functional
Noncompetitive inhibitor
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The control of metabolism
The molecules that naturally regulate enzyme activity in a
cell act like reversible noncompetitive inhibitors by binding to
an allosteric site.
Allosteric site
Active site
Active form
Inactive form
(a) Conformational changes in an allosteric enzyme
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The control of metabolism
Activator
Inhibitor
Active form stabilized by an Inactive form stabilized by an
allosteric activator molecule allosteric inhibitor molecule
(b) Allosteric regulation
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Feedback
Inhibition
Initial substrate
(threonine)
Enzyme 1 (threonine deaminase)
Intermediate A
Enzyme 2
Intermediate B
Enzyme 3
Intermediate C
Enzyme 4
Intermediate D
Enzyme 5
End-product
(isoleucine)
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Cooperativity
In an enzyme molecule with multiple subunits, the binding of one
substrate molecule to the active site of one subunit causes all the
subunits to assume their active conformation, via the mechanism
of induced fit.
Substrate
Active form stabilized by an
allosteric activator molecule
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Active form stabilized by a
substrate molecule
Enzymes localization
Each organelle contains certain number of enzymes that
carry out specific functions.
Some enzymes and enzyme complexes have fixed locations
within the cell as structural components of particular
membrane.
Others are in solution within specific membrane-enclosed
eukaryotic organelles.
For example, in eukaryotic cells the enzymes for cellular
respiration reside within mitochondria.
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Conclusions
1. ATP powers cellular work by coupling exergonic
reactions to endergonic reactions: it drives endergonic
reactions by transfer of the phosphate group to specific
reactants – cells can carry out work; cell respiration
(catabolic pathway) drives the regeneration of ATP from
ADP.
2. Enzymes speed up metabolic reactions by lowering
energy barriers (activation energy EA).
3. Enzymes are substrate-specific.
4. The active site is an enzyme’s catalytic center
5. A cell’s physical and chemical environment affects
enzyme activity.
6. Metabolic control often depends on allosteric regulation
7. The localization of enzymes within a cell helps order
metabolism
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Reading
Ch. 8 (142-161)
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