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21 views76 pages

11 Lecture

Uploaded by

pdhruvi785
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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10/5/2022

Cellular physiology

Metabolism, ATP and Biological Energy

Copyright © 2021 Pearson Education, Inc. All Rights Reserved


Key Concepts
• An organism’s metabolism transforms matter and energy,
subject to the laws of thermodynamics
• The free-energy change of a reaction tells us whether or
not the reaction occurs spontaneously
• ATP powers cellular work by coupling exergonic reactions
to endergonic reactions
• Enzymes speed up metabolic reactions by lowering energy
barriers
• Regulation of enzyme activity helps control metabolism

Copyright © 2021 Pearson Canada, Inc.


8-2
The Energy of Life
• A living cell is a miniature chemical factory where
thousands of reactions occur
• The cell extracts energy stored in sugars and other
energy-containing organic molecules, and applies energy
to perform work

Copyright © 2021 Pearson Canada, Inc.


8-3
An Organism’s Metabolism Transforms
Matter and Energy, Subject to the Laws of
Thermodynamics
• Metabolism is the totality of an organism’s chemical
reactions
• Metabolism is an emergent property of life arising from
interactions between molecules within cell

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8-4
10/5/2022

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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8-5
Organization of the Chemistry of Life
into Metabolic Pathways
• Metabolic pathways begin with a specific molecule
(substrate or reactant) and end with a product
• Each step is catalyzed by a specific enzyme

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8-6
Metabolic Pathways
• Catabolic pathways release energy by breaking down
complex molecules into simpler compounds
• Cellular respiration, the breakdown of glucose in the
presence of oxygen, is an example of catabolism

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8-7
Metabolic Pathways
• Anabolic pathways consume energy to build complex
molecules from simpler ones
• Synthesis of protein from amino acids is an example of
anabolism
• Bioenergetics is the study of how organisms manage
their energy resources

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8-8
10/5/2022

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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8-9
Forms of Energy
• Energy is the capacity to cause change
• Energy exists in various forms, some of which can perform
work
• Energy can be converted from one form to another

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8 - 10
Forms of Energy
• Kinetic energy is energy associated with motion
• Heat (thermal energy) is kinetic energy associated with
random movement of atoms or molecules
• Potential energy is energy that matter possesses
because of its location or structure
• Chemical energy is potential energy available for release
in a chemical reaction

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8 - 11
The Laws of Energy Transformation
• Thermodynamics is the study of energy transformations
• An isolated system is unable to exchange energy or
matter with its surroundings
– Example: liquid in a thermos
• In an open system, energy and matter can be transferred
between the system and its surroundings
• Organisms are open systems

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8 - 12
The First Law of Thermodynamics
• According to the first law of thermodynamics, the amount of
energy in the universe is constant
– Energy can be transferred and transformed, but it cannot be
created or destroyed
• The first law is also called principle of conservation of energy

Figure 8.3a The two laws of thermodynamics

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8 - 13
The Second Law of Thermodynamics
• During every energy transfer or transformation, some
energy is unusable, and often lost as heat
• Second law of thermodynamics
– Every energy transfer or transformation increases
entropy (disorder)of universe
Figure 8.3b The two laws of thermodynamics.

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8 - 14
The Laws of Energy Transformation
• Living cells unavoidably convert organized forms of energy
to heat
• Spontaneous processes occur without energy input
– they can happen quickly or slowly
• For a process to occur without energy input, it must
increase entropy of universe

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8 - 15
Biological Order and Disorder
• Cells create ordered structures from less ordered materials
– Requires the input of energy
• Organisms also replace ordered forms of matter and
energy with less ordered forms
• Energy flows into an ecosystem in form of light and exits in
form of heat

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8 - 16
Order as a Characteristic of Life
• Evolution of more complex organisms does not violate the
second law of thermodynamics
• Entropy (disorder) may decrease in an organism, but
universe’s total entropy increases

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8 - 17
The Free-Energy Change of a Reaction
Tells us Whether or not the Reaction
Occurs Spontaneously
• Biologists want to know which reactions occur
spontaneously and which require input of energy
• To do so, need to determine energy changes that occur in
chemical reactions

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8 - 18
The complexity of metabolism 10/5/2022

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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8 - 19
The complexity of metabolism 10/5/2022

(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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8 - 20
Organisms live at the expense of free energy 10/5/2022

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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8 - 21
10/5/2022

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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8 - 22
Free-Energy Change, G
• Living system’s free energy is energy that can do work
when temperature and pressure are uniform, as in a living
cell
• Change in free energy (∆G) is related to change in total
energy (also called enthalpy) (∆H), change in entropy (∆S),
and temperature in Kelvin (T):
∆G = ∆H – T∆S

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8 - 23
Free-Energy Change, G
• Only processes with a negative ∆G are spontaneous
• Spontaneous processes can be harnessed to perform
work
• During a spontaneous change, free energy decreases and
stability of a system increases

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8 - 24
Free Energy, Stability, and Equilibrium
• Free energy is a measure of a system’s instability, its
tendency to change to a more stable state
• Equilibrium is a state of maximum stability
• A process is spontaneous and can perform work only when
it is moving toward equilibrium

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8 - 25
The Relationship of free Energy to Stability,
Work Capacity, and Spontaneous Change
Figure 8.5 The relationship of free energy to stability, work
capacity, and spontaneous change.

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8 - 26
Free Energy and Metabolism
• The concept of free energy can be applied to the chemistry
of life’s processes
• Based on their free energy changes, all chemical
reactions, including metabolic processes can be classified
as exergonic or endergonic

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8 - 27
10/5/2022

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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8 - 28
10/5/2022

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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8 - 29
Free energy and metabolism 10/5/2022

Exergonic reaction Endergonic reaction


Chemical products have Products store more free
less free energy than the energy than reactants
reactant molecules.

Reaction is energetically Reaction is energetically uphill.


downhill.

Spontaneous reaction. Non-spontaneous reaction


(requires energy input)
ΔG is negative. ΔG is positive.

-ΔG is the maximum +ΔG is the minimum amount of


amount of work the reaction work required to drive the
can perform reaction.

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8 - 30
Exergonic and Endergonic Reactions
in Metabolism
• An exergonic reaction proceeds with a net release of free
energy and is spontaneous
Figure 8.6a Free energy changes (ΔG) in exergonic and
endergonic reactions.

• Exergonic reaction is spontaneous.


• Energy is released during the progress of
an exergonic reaction.
• The amount of energy released is delta G
less than zero.
• The progress of the reaction is the
difference between the higher free energy of
the reactants and the lower free energy of
the products.

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8 - 31
Exergonic and Endergonic Reactions
in Metabolism
• An endergonic reaction absorbs free energy from its
surroundings and is nonspontaneous
Figure 8.6b Free energy changes (ΔG) in exergonic and
endergonic reactions.
• Endergonic reaction is nonspontaneous.
• Energy is required during the progress of
an endergonic reaction.
• The amount of energy required is delta G
greater than zero.
• The progress of the reaction is the
difference between the lower free energy
of the reactants and the higher free energy
of the products.

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8 - 32
Equilibrium and Metabolism
• Reactions in a closed system eventually reach equilibrium
and then do no work
• Cells are not in equilibrium; they are open systems
experiencing a constant flow of energy and matter
• Defining feature of life is that metabolism is never at
equilibrium
• Catabolic pathway in a cell releases free energy in a series
of reactions

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8 - 33
10/5/2022

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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8 - 34
10/5/2022

How a free-energy gradient keeps metabolism


away from equilibrium: a hydraulic analogy.

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8 - 35
ATP Powers Cellular Work by Coupling
Exergonic Reactions to Endergonic Reactions
• Three kinds of cellular work
– Chemical
– Transport
– Mechanical
• To do work, cells manage energy resources by energy
coupling,
– use of an exergonic process to drive an endergonic
one

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8 - 36
The Structure and Hydrolysis of ATP
• Most energy coupling in cells is mediated by ATP (adenosine
triphosphate)
• ATP is the cell’s energy shuttle
Figure 8.9a The structure and hydrolysis of adenosine triphosphate
(ATP).

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8 - 37
The Structure and Hydrolysis of ATP
• Bonds between the phosphate groups of ATP can be broken by
hydrolysis
– Energy is released with the terminal phosphate bond of ATP
broken
– The release of energy comes from the chemical change to a state
of lower energy, not from the phosphate bonds themselves

Figure 8.9b The structure and


hydrolysis of adenosine
triphosphate (ATP).

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8 - 38
The Nature of ATP 10/5/2022

ATP is the immediate source of energy that powers 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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8 - 39
The Structure and Hydrolysis of ATP
• ATP drives endergonic reactions by phosphorylation,
transferring a phosphate group to some other molecule,
such as a reactant
• The recipient molecule is now called a phosphorylated
intermediate

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8 - 40
10/5/2022

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 non-
spontaneous.

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8 - 41
10/5/2022

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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8 - 42
10/5/2022
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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8 - 43
How ATP Drives Transport and Mechanical
Work
Figure 8.11 How ATP drives transport and mechanical work.

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8 - 44
The Regeneration of ATP
• ATP is a renewable resource regenerated from adenosine
diphosphate (ADP)
• Energy to phosphorylate ADP comes from catabolic
reactions in the cell
Figure 8.12 The ATP cycle.

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8 - 45
10/5/2022

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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8 - 46
Enzymes Speed up Metabolic Reactions
by Lowering Energy Barriers

• A Catalyst is a chemical agent that speeds up a reaction


without being consumed
• An enzyme is a catalytic protein
• Hydrolysis of sucrose by sucrase is an example of an
enzyme-catalyzed reaction
Figure 8.Un02

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8 - 47
The Activation Energy Barrier
• Every chemical reaction between molecules involves bond
breaking and bond forming
• Initial energy needed to start a chemical reaction is called
free energy of activation, or activation energy (EA)
• Activation energy is often supplied in form of thermal
energy that reactant molecules absorb from their
surroundings

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8 - 48
An energy profile of a reaction 10/5/2022

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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8 - 49
An energy profile of a reaction 10/5/2022

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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8 - 50
How Enzymes Speed up Reactions
• Enzymes catalyze reactions by lowering EA barrier
• Enzymes do not affect change in free energy (∆G)
– Rather, enzymes speed up reactions that would occur
eventually

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8 - 51
How Enzymes Lower the EA Barrier
Figure 8.14 The effect of an enzyme on 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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8 - 52
Substrate Specificity of Enzymes
• The reactant that an enzyme acts on is called the
substrate
– An enzyme binds to its substrate to form an enzyme-
substrate complex
• The substrate than an enzyme binds to, and therefore the
reaction catalyzed by each enzyme, is very specific

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8 - 53
Induced Fit Between an Enzyme and
its Substrate
• The active site is the region on an enzyme where the
substrate binds
• Induced fit of a substrate brings chemical groups of active
site into positions that enhance their ability to catalyze
reaction

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8 - 54
Induced Fit Between an Enzyme and
its Substrate
Figure 8.15 Induced fit between an enzyme and its
substrate.

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8 - 55
Catalysis in the Enzyme’s Active Site
• In an enzymatic reaction, the substrate binds to the active
site of the enzyme
• Active site can lower an EA barrier by
– Orienting substrates correctly
– Straining bonds in the substrate molecule
– Providing a favourable microenvironment
– Covalently bonding to the substrate

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8 - 56
The Active Site and Catalytic Cycle of
an Enzyme
Figure 8.16 The active site and catalytic cycle of an enzyme.

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8 - 57
The Active Site and Catalytic Cycle of
an Enzyme
Figure 8.16 The active site and catalytic cycle of an enzyme.

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8 - 58
The Active Site and Catalytic Cycle of
an Enzyme
Figure 8.16 The active site and catalytic cycle of an enzyme.

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8 - 59
Effects of Local Conditions on
Enzyme Activity
• An enzyme’s activity can be affected by
– General environmental factors, such as temperature
and pH
– Chemicals that specifically influence the enzyme
• Optimal conditions favour the most active conformation
(shape) for the enzyme

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8 - 60
Effects of Temperature and pH
• Each enzyme has an optimal pH at which it can function
Figure 8.17a Environmental factors affecting enzyme
activity.

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8 - 61
Effects of Temperature and pH
• Each enzyme has an optimal pH at which it can function
Figure 8.17b Environmental factors affecting enzyme
activity.

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8 - 62
Cofactors
• Cofactors are nonprotein enzyme helpers
• Cofactors may be inorganic (such as a metal in ionic form)
or organic
• An organic cofactor is called a coenzyme
• Coenzymes include vitamins

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8 - 63
Enzyme Inhibitors
• Competitive inhibitors bind to the active site of an
enzyme, competing with substrate
Figure 8.18 Inhibition of enzyme activity.

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8 - 64
Enzyme Inhibitors
• Noncompetitive inhibitors bind to an enzyme at a
separate site from the active site, causing a conformational
change in the enzyme that makes the active site less
effective
• Examples of inhibitors include toxins, poisons, pesticides,
and antibiotics
Figure 8.18 Inhibition of enzyme activity.

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8 - 65
The Evolution of Enzymes
• Enzymes are proteins encoded by genes
• Changes (mutations) in genes lead to changes in
enzyme’s amino acids
• Altered amino acids may alter enzyme’s substrate
specificity (change activity)
• Under new environmental conditions a novel form of an
enzyme may be favoured

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8 - 66
Regulation of Enzyme Activity Helps
Control Metabolism
• Chemical chaos would result if a cell’s metabolic pathways
were not tightly regulated
• A cell regulates its metabolism by:
– switching on or off genes that encode specific enzymes
– regulating activity of enzymes

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8 - 67
Allosteric Regulation of Enzymes
• Allosteric regulation may either inhibit or stimulate an
enzyme’s activity
• Allosteric regulation occurs when a regulatory molecule
binds to a protein at one site and affects protein’s function
at another site

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8 - 68
Allosteric Activation and Inhibition
• Most allosterically regulated enzymes contain multiple
polypeptide subunits
• Each enzyme has active and inactive forms

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8 - 69
Allosteric Activation and Inhibition
• Binding of an activator
stabilizes the active form of
an enzyme
• Binding of an inhibitor
stabilizes the inactive form
of an enzyme

Figure 8.20a Allosteric


regulation of enzyme activity.

Source: Protein Data Bank ID 1MDYO: “Crystal Structure of MyoD bHLH Domain-DNA
Complex: Perspectives on DNA Recognition and Implications for Transcriptional Activation”
from Cell, May 1994, Volume 77(3).
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8 - 70
Allosteric Regulation
• Cooperativity is a form of allosteric regulation that can
amplify enzyme activity
Figure 8.20b Allosteric regulation of enzyme activity.

Source: Protein Data Bank ID 1MDYO: “Crystal Structure of MyoD bHLH Domain-DNA
Complex: Perspectives on DNA Recognition and Implications for Transcriptional Activation”
from Cell, May 1994, Volume 77(3).
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8 - 71
Feedback Inhibition
• In feedback inhibition, the end product of a metabolic
pathway shuts down pathway

Figure 8.21 Feedback inhibition


in isoleucine synthesis.

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8 - 72
Specific Localization of Enzymes
Within the Cell
• Structures within the cell help bring order to metabolic
pathways
• Some enzymes act as structural components of
membranes

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8 - 73
Specific Localization of Enzymes Within
the Cell
• In eukaryotic cells, some enzymes reside in specific
organelles; for example, enzymes for cellular respiration
are located in mitochondria
Figure 8.22 Organelles and structural order in metabolism.

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8 - 74
Conclusions 10/5/2022

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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8 - 75
76

Reading:
Chapter 8 – pages 155-176

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