Transcript Life: The Science of Biology, 10e

8
Energy, Enzymes, and
Metabolism
8 Energy, Enzymes, and Metabolism
8.1 What Physical Principles Underlie
Biological Energy
Transformations?
8.2 What Is the Role of ATP in
Biochemical Energetics?
8.3 What Are Enzymes?
8.4 How Do Enzymes Work?
8.5 How Are Enzyme Activities
Regulated?
8 Energy, Enzymes, and Metabolism
Many laundry aids have been
developed that include various
enzymes to hydrolyze proteins,
fats, and starches to remove a
variety of stains.
Opening Question:
How are enzymes used in other
industrial processes?
8.1 What Physical Principles Underlie Biological Energy
Transformations?
A chemical reaction occurs when
atoms have enough energy to
combine or change bonding partners.
sucrose + H2O → glucose + fructose
reactants
products
8.1 What Physical Principles Underlie Biological Energy
Transformations?
Metabolism: the sum total of all
chemical reactions occurring in a
biological system at a given time.
Metabolic reactions involve energy
changes.
8.1 What Physical Principles Underlie Biological Energy
Transformations?
Energy is the capacity to do work, or
the capacity for change.
In biochemical reactions, energy
changes are associated with changes
in the composition and properties of
molecules.
8.1 What Physical Principles Underlie Biological Energy
Transformations?
All forms of energy are either:
• Potential energy—energy stored as
chemical bonds, concentration
gradient, charge imbalance, etc.
• Kinetic energy—the energy of
movement.
Energy can be converted from one
form to another.
Figure 8.1 Energy Conversions and Work
Table 8.1
8.1 What Physical Principles Underlie Biological Energy
Transformations?
Two types of metabolism:
• Anabolic reactions: complex
molecules are made from simple
molecules, and energy input is
required.
• Catabolic reactions: complex
molecules are broken down to simpler
ones, and energy is released.
8.1 What Physical Principles Underlie Biological Energy
Transformations?
Catabolic and anabolic reactions are
often linked.
The energy released in catabolic
reactions is used to drive anabolic
reactions—to do biological work.
8.1 What Physical Principles Underlie Biological Energy
Transformations?
The laws of thermodynamics apply to
all matter and all energy
transformations in the universe.
They help us to understand how cells
harvest and transform energy to
sustain life.
8.1 What Physical Principles Underlie Biological Energy
Transformations?
First law of thermodynamics: energy is
neither created nor destroyed.
When energy is converted from one
form to another, the total energy
before and after the conversion is the
same.
8.1 What Physical Principles Underlie Biological Energy
Transformations?
Second law of thermodynamics: when
energy is converted from one form to
another, some of that energy
becomes unavailable to do work.
No energy transformation is 100
percent efficient; some energy is lost
to disorder.
Figure 8.2 The Laws of Thermodynamics
8.1 What Physical Principles Underlie Biological Energy
Transformations?
Entropy is a measure of the disorder in
a system.
It takes energy to impose order on a
system. Unless energy is applied to a
system, it will be randomly arranged
or disordered.
8.1 What Physical Principles Underlie Biological Energy
Transformations?
In any system:
Total energy = usable energy + unusable energy
H = G + TS
enthalpy (H) = free energy (G) + entropy (S)
G = H – TS
(T = absolute temperature)
8.1 What Physical Principles Underlie Biological Energy
Transformations?
Free energy (G) is the usable energy
that can do work.
Change in energy can be measured in
calories or joules.
Change in free energy (ΔG) in a
reaction is the difference in free
energy between the products and the
reactants.
8.1 What Physical Principles Underlie Biological Energy
Transformations?
ΔG = ΔH – TΔS
If ΔG is negative, free energy is
released.
If ΔG is positive, free energy is
required.
• If free energy is not available, the
reaction does not occur.
8.1 What Physical Principles Underlie Biological Energy
Transformations?
Magnitude of ΔG depends on:
• ΔH—total energy added (ΔH > 0) or
released (ΔH < 0).
• ΔS—change in entropy. Large
changes in entropy make ΔG more
negative.
8.1 What Physical Principles Underlie Biological Energy
Transformations?
If a chemical reaction increases
entropy, the products will be more
disordered.
Example: In hydrolysis of a protein into
its component amino acids, ΔS is
positive.
8.1 What Physical Principles Underlie Biological Energy
Transformations?
Second law of thermodynamics:
disorder tends to increase because of
energy transformations.
Living organisms must have a constant
supply of energy to maintain order.
8.1 What Physical Principles Underlie Biological Energy
Transformations?
Exergonic reactions release free
energy (–ΔG).
• Catabolism: complexity decreases
(generates disorder).
Figure 8.3 Exergonic and Endergonic Reactions (Part 1)
8.1 What Physical Principles Underlie Biological Energy
Transformations?
Endergonic reactions consume free
energy (+ΔG)
• Anabolism: complexity (order)
increases.
Figure 8.3 Exergonic and Endergonic Reactions (Part 2)
8.1 What Physical Principles Underlie Biological Energy
Transformations?
In principle, chemical reactions can run
in both directions.
• At chemical equilibrium, ΔG = 0
AB
The concentrations of A and B
determine which direction will be
favored.
8.1 What Physical Principles Underlie Biological Energy
Transformations?
Every reaction has a specific
equilibrium point.
ΔG is related to the point of equilibrium:
the further towards completion the
point of equilibrium is, the more free
energy is released.
ΔG values near zero are characteristic
of readily reversible reactions.
Figure 8.4 Chemical Reactions Run to Equilibrium
8.1 What Physical Principles Underlie Biological Energy
Transformations?
ΔG also depends on the beginning
concentrations of reactants and
products, temperature, pressure, and
pH.
ΔG is determined under standard
conditions: 25°C, one atmosphere
pressure, one molar (1M) solutions,
and pH 7.
8.2 What Is the Role of ATP in Biochemical Energetics?
ATP (adenosine triphosphate) captures
and transfers free energy.
ATP releases a large amount of energy
when hydrolyzed.
ATP can phosphorylate, or donate
phosphate groups, to other molecules.
8.2 What Is the Role of ATP in Biochemical Energetics?
Hydrolysis of ATP yields free energy:
ATP + H2O  ADP + Pi + free energy
ΔG = –7.3 to –14 kcal/mol
(exergonic)
Figure 8.5 ATP
8.2 What Is the Role of ATP in Biochemical Energetics?
Two characteristics of ATP account for
the free energy released:
• Phosphate groups have a negative
charge and repel each other—the
energy needed to get them close
enough to bond is stored in the P~O
bond.
• The free energy of the P~O bond is
much higher than the energy of the
O—H bond that forms after
hydrolysis.
8.2 What Is the Role of ATP in Biochemical Energetics?
Bioluminescence is an endergonic
reaction driven by ATP hydrolysis:
Figure 8.5 ATP
8.2 What Is the Role of ATP in Biochemical Energetics?
The formation of ATP is endergonic:
ADP + Pi + free energy  ATP + H2O
Formation and hydrolysis of ATP
couples exergonic and endergonic
reactions.
8.2 What Is the Role of ATP in Biochemical Energetics?
Coupling of exergonic and endergonic
reactions is very common in
metabolism.
Hydrolysis of ATP releases free energy
to drive an endergonic reaction.
Figure 8.7 Coupling of ATP Hydrolysis to an Endergonic Reaction
8.2 What Is the Role of ATP in Biochemical Energetics?
An active cell needs to produce millions
of molecules of ATP per second.
An ATP is typically consumed within a
second of its formation.
Each ATP molecule undergoes about
10,000 cycles of synthesis and
hydrolysis every day!
8.3 What Are Enzymes?
Catalysts speed up the rate of a
reaction.
The catalyst is not altered by the
reactions.
Most biological catalysts are enzymes
(proteins) that act as a framework in
which reactions can take place.
8.3 What Are Enzymes?
Some reactions are slow because of an
energy barrier—the amount of energy
required to start the reaction, called
activation energy (Ea).
Activation energy puts the reactants in
a reactive mode called the transition
state.
Figure 8.8 Activation Energy Initiates Reactions
8.3 What Are Enzymes?
Activation energy changes the reactants
into unstable forms with higher free
energy—transition state
intermediates.
Activation energy can come from
heating the system—the reactants
have more kinetic energy.
Enzymes and ribozymes lower the
energy barrier by bringing the reactants
together.
8.3 What Are Enzymes?
Enzymes and ribozymes are highly
specific.
Reactants are called substrates.
Substrate molecules bind to the active
site of the enzyme.
The three-dimensional shape of the
enzyme determines the specificity.
Figure 8.9 Enzyme and Substrate
8.3 What Are Enzymes?
The enzyme–substrate complex (ES)
is held together by hydrogen bonds,
electrical attraction, or covalent
bonds.
E + S  ES  E + P
The enzyme may change while bound
to the substrate but returns to its
original form.
8.3 What Are Enzymes?
The dissociation constant (KD) is a
measure of the affinity of two
molecules.
The lower the KD, the tighter the
binding.
For enzymes and their substrates, KD
values range from 10–5 to 10–6 M. This
favors the formation of ES.
8.3 What Are Enzymes?
Enzymes lower the energy barrier for
reactions.
The final equilibrium does not change,
and ΔG does not change.
Enzymes can increase reaction rates
by 1 million to 1017 times!
Figure 8.10 Enzymes Lower the Energy Barrier
8.4 How Do Enzymes Work?
In catalyzing a reaction, an enzyme
may use one or more mechanisms:
• Orienting substrates
• Inducing strain in substrates
• Temporarily adding chemical groups
Figure 8.11 Life at the Active Site (Part 1)
Enzymes orient substrate molecules,
bringing together the atoms that will bond.
Figure 8.11 Life at the Active Site (Part 2)
Enzymes can stretch the bonds in
substrate molecules, making them
unstable.
Figure 8.11 Life at the Active Site (Part 3)
Enzymes can temporarily add
chemical groups to substrates.
8.4 How Do Enzymes Work?
Acid–base catalysis: enzyme side
chains transfer H+ to or from the
substrate, causing a covalent bond to
break.
Covalent catalysis: a functional group
in a side chain bonds covalently with
the substrate.
Metal ion catalysis: metals on side
chains loose or gain electrons.
8.4 How Do Enzymes Work?
Enzymes are much larger than their
substrates and the active site is
usually small.
The shape of the active site allows a
specific substrate to fit precisely.
8.4 How Do Enzymes Work?
Substrates bind to active sites by
hydrogen bonds, attraction and
repulsion of electrically charged
groups, and hydrophobic interactions.
Induced fit: enzyme changes shape
when it binds the substrate, which
alters the shape of the active site.
Figure 8.12 Some Enzymes Change Shape When Substrate Binds to Them
8.4 How Do Enzymes Work?
Some enzymes require “partners”:
• Prosthetic groups: non-amino acid
groups bound to enzymes
• Inorganic cofactors: ions
permanently bound to enzyme
• Coenzymes: small carbon-containing
molecules; not permanently bound
Table 8.2
8.4 How Do Enzymes Work?
The rate of a catalyzed reaction
depends on substrate concentration.
Concentration of an enzyme is usually
much lower than concentration of a
substrate.
At saturation, all enzyme is bound to
substrate; it is working at maximum
rate.
Figure 8.13 Catalyzed Reactions Reach a Maximum Rate
8.4 How Do Enzymes Work?
Maximum rate is used to calculate
enzyme efficiency: Molecules of
substrate converted to product per
unit time (turnover number).
Turnover ranges from 1 to 40 million
molecules per second!
8.5 How Are Enzyme Activities Regulated?
The thousands of chemical reactions
occurring in cells are organized in
metabolic pathways. Each reaction is
catalyzed by a specific enzyme.
The pathways are interconnected.
Regulation of enzymes and thus
reaction rates helps maintain internal
homeostasis.
8.5 How Are Enzyme Activities Regulated?
Complicated metabolic pathways can
be modeled using computer
algorithms.
This new field is called systems
biology.
Figure 8.14 Metabolic Pathways
8.5 How Are Enzyme Activities Regulated?
Inhibitors regulate enzymes:
Molecules that bind to the enzyme
and slow reaction rates.
Naturally occurring inhibitors regulate
metabolism.
8.5 How Are Enzyme Activities Regulated?
Irreversible inhibition: inhibitor
covalently bonds to side chains in the
active site and permanently
inactivates the enzyme.
Example: DIPF or nerve gas
Figure 8.15 Irreversible Inhibition
8.5 How Are Enzyme Activities Regulated?
Reversible inhibition: inhibitor bonds
noncovalently to the active site and
prevents substrate from binding.
Competitive inhibitors compete with
the natural substrate for binding sites.
Degree of inhibition depends on
concentrations of substrate and
inhibitor.
Figure 8.16 Reversible Inhibition (Part 1)
8.5 How Are Enzyme Activities Regulated?
The cancer drug methotrexate is a
competitive inhibitor.
It binds to the enzyme that catalyzes
formation of a coenzyme for purine
formation.
(Purines are needed for DNA
replication and cell division.)
In-Text Art, Ch. 8, p. 158
8.5 How Are Enzyme Activities Regulated?
Uncompetitive inhibitors bind to the
enzyme–substrate complex,
preventing release of products.
Noncompetitive inhibitors bind to
enzyme at a different site (not the
active site).
The enzyme changes shape and
alters the active site.
Figure 8.16 Reversible Inhibition (Part 2)
8.5 How Are Enzyme Activities Regulated?
Allostery: enzymes have different
shapes.
Allosteric regulation: an effector
binds enzyme at a site different from
the active site, which changes its
shape.
Active form—can bind substrate.
Inactive form—cannot bind substrate
but can bind an inhibitor.
Figure 8.17 Allosteric Regulation of Enzymes
8.5 How Are Enzyme Activities Regulated?
Most allosteric enzymes are proteins
with quaternary structure.
The active site is on the catalytic
subunit.
Inhibitors and activators bind to other
polypeptides called regulatory
subunits.
8.5 How Are Enzyme Activities Regulated?
Some allosteric enzymes have multiple
subunits with active sites. Substrate
binding at one site can have allosteric
effects, and reaction rate increases.
8.5 How Are Enzyme Activities Regulated?
Reaction rates versus substrate
concentration are very different than
for nonallosteric enzymes.
In-Text Art, Ch. 8, p. 159 (1)
In-Text Art, Ch. 8, p. 159 (2)
8.5 How Are Enzyme Activities Regulated?
For allosteric enzymes, reaction rate is
very sensitive to substrate
concentration (over a certain range).
They are very sensitive to low
concentrations of inhibitors.
Thus they are important in regulating
metabolic pathways.
8.5 How Are Enzyme Activities Regulated?
Metabolic pathways:
• The first reaction is the commitment
step—other reactions then happen in
sequence.
• Feedback inhibition (end-product
inhibition): the final product acts as a
noncompetitive inhibitor of the first
enzyme, which shuts down the
pathway.
8 Working with Data: How Does an Herbicide Work?
The weed-killer glyphosate inhibits an
enzyme (EPSP synthase) in the
metabolic pathway used to synthesize
several amino acids.
Experiment: Measure rate of the
synthesis reaction in the presence of
different concentrations of glyphosate
and substrate (PEP).
Working with Data 8.1, Figure A
Working with Data 8.1: How Does an Herbicide Work?
Question 1:
At about what substrate concentration
does EPSP synthase become
saturated when no glyphosate is
present?
How much substrate is needed to
saturate EPSP synthase in the
presence of 18 μM glyphosate?
In each case, what is the reaction rate
at saturation?
Working with Data 8.1: How Does an Herbicide Work?
Question 2:
Looking at the curve for the reaction
rate without inhibitor, is EPSP
synthase a multi-subunit allosteric
enzyme?
Explain your answer.
Working with Data 8.1: How Does an Herbicide Work?
Question 3:
Based on these data, what is the most
likely mechanism for glyphosate
inhibition of EPSP synthase:
competitive, noncompetitive, or
uncompetitive?
Why?
Figure 8.18 Feedback Inhibition of Metabolic Pathways
8.5 How Are Enzyme Activities Regulated?
Many enzymes are regulated through
reversible phosphorylation.
Enzymes can be activated when
protein kinase adds a phosphate
group and deactivated by protein
phosphatase.
8.5 How Are Enzyme Activities Regulated?
Every enzyme is most active at a
particular pH.
pH influences the ionization of
functional groups.
Example: at low pH (high H+) —COO–
may react with H+ to form —COOH
which is no longer charged; this
affects folding and thus enzyme
function.
Figure 8.19 pH Affects Enzyme Activity
8.5 How Are Enzyme Activities Regulated?
Every enzyme has an optimal
temperature.
At high temperatures, noncovalent
bonds begin to break.
Enzymes can lose tertiary structure and
become denatured.
Figure 8.20 Temperature Affects Enzyme Activity
8.5 How Are Enzyme Activities Regulated?
Isozymes: enzymes that catalyze the
same reaction but have different
properties, such as optimal
temperature.
Organisms can use isozymes to adjust
to temperature changes.
Enzymes in humans have higher
optimal temperature than enzymes in
most bacteria—a fever can denature
the bacterial enzymes.
8 Answer to Opening Question
Commercial use of purified enzymes is
a multibillion-dollar industry.
Many come from bacteria and fungi—
they are easy to grow in large
quantities for industry, and the
enzymes are easy to extract.