08 Lecture Presentation

8
Energy and
Enzymes:
An Introduction
to Metabolism
Lecture Presentation by
Cindy S. Malone, PhD,
California State University Northridge
© 2017 Pearson Education, Ltd.

Energy in Chemical Reactions
• Two types of energy exist
• Kinetic energy is energy of motion

• Thermal energy: energy of molecules moving
• Potential energy is energy that is stored in position

or configuration
• Chemical energy: energy stored in chemical bonds
• Energy can be transformed from one type to another

Ep (top)
Ek
Ek Ek Ek
Mechanical Heat Sound
energy
Ep (bottom)
1. Potential energy 2. Kinetic energy 3. Other forms of energy
Conclusion: Energy is neither created nor destroyed; it simply changes form.

Chemical Reactions Involve Energy
Transformations
• The amount of chemical energy in a covalent bond
is based on
• Position of shared electrons
• Distance from positive charges in nuclei
• The potential energy of a molecule depends on the

configuration and position of its shared electrons
• Weaker bonds with equally shared electrons have
high potential energy
• Stronger bonds with unequally shared electrons have
low potential energy
Equal sharing Unequal sharing
(nonpolar) (polar)
Longest, weakest Shortest, strongest

bonds bonds
Decreasing potential energy

Transformations
• In chemical reactions, if products have shorter,
stronger covalent bonds than the reactants
• The potential energy in the bonds decreases
• Change in energy is transformed to thermal energy or
light

Transformations
• Energy is conserved
• Energy cannot be created or destroyed
• Energy can only be transferred and transformed
• Enthalpy (H) includes
• The potential energy of the molecule (heat content)
• Effect of the molecule on surrounding pressure and
volume
• Changes in enthalpy (ΔH) are primarily based on the
difference in potential energy
Transformations
• Exothermic reactions
• Release heat energy
• ΔH < 0
• Products have less potential energy than reactants
• Endothermic reactions
• Heat energy is taken up
• ΔH > 0
• Products have higher potential energy than reactants

Transformations
• Entropy (S) is the amount of disorder
• When the products of a chemical reaction become

less ordered than the reactant molecules
• Entropy increases
• ΔS > 0
• Second law of thermodynamics states that total

entropy always increases in a system

Transformations
• Gibbs free energy (G) determines whether a
reaction is spontaneous or requires added energy to
proceed
• Calculate the change in G (ΔG) during the reaction
• Standard free-energy change equation:
ΔG = ΔH – TΔS
• ΔH = change in enthalpy
• ΔS = change in entropy
• T = temperature in degrees Kelvin
Transformations
• ΔG < 0 = a spontaneous reaction
• These reactions are exergonic
• ΔG > 0 = a nonspontaneous reaction that requires

energy input to occur
• These reactions are endergonic
• ΔG = 0 = a reaction that is at equilibrium

Temperature and Concentration Affect
Reaction Rates
• For most reactions to proceed
• One or more chemical bonds have to break
• Others have to form
• Substances must collide in a specific orientation that

brings the electrons involved near each other
• Higher concentrations and higher temperature
increase the number of collisions
• Higher concentrations and higher temperature

therefore increase reaction rate
Do chemical reaction rates increase with increased temperature and concentration?
Chemical reaction rates increase with increased temperature. They also increase with
increased concentration of reactants.
Chemical reaction rates are not affected by increases in temperature or concentration of reactants.
Experimental reaction: 3 HSO3–(aq) + IO3–(aq) 3 HSO4–(aq) + I –(aq)
Reactant concentrations constant Reactant concentrations vary

Temperature increases Temperature constant
Almost Many
continuous replicates
variation in at each
temperature concentration
Concentration
0.167 0.167 0.167 0.167 0.333
of 3 HSO3– (M):
Concentration
0.167 0.167 0.167 0.333 0.333
of IO3– (M):
Temperature (ºC): –1 50 23 23 23
Reaction rate, measured as 1/(time for reaction to go to completion), will increase with increased concentrations
of reactants and increased temperature of reaction mix.
There will be no difference in reaction rates among treatments in each setup.

(1/time to completion)
(1/time to completion)
Treatment
3
Reaction rate
Reaction rate
Treatment
2
Treatment
1
Temperature (ºC) Concentration of reactants (M)
Chemical reaction rates increase with increased temperature or concentration.

Nonspontaneous Reactions May Be Driven
Using Chemical Energy
• Energetic coupling
• Between exergonic and endergonic reactions
• Allows chemical energy released from one reaction

• To drive another reaction

Exergonic reaction
(releases energy)
Energy
Higher energy Lower energy
reactants products
Lower energy Higher energy

reactants products
Energy
Endergonic reaction
(requires energy)
Redox Reactions Transfer Energy via Electrons
• Reduction–oxidation reactions (redox reactions)

• Are chemical reactions that involve electron transfer
• Oxidation: loss of an electron(s)
• Reduction: gain of an electron(s)
• Always occur together

• Represent energetic coupling of two half-reactions
• Oxidation is exergonic
• Reduction is endergonic

Web Activity: Redox Reactions

Redox Reactions Transfer Energy via Electrons
• During a redox reaction, electrons can

• Be transferred completely from one atom to another
• Simply shift their position in covalent bonds

Electrons Electrons
pulled further pulled closer
from C; to O;
C is oxidized O is reduced
Potential
energy decreases
6 O2 6 CO 2 6 H2 O Release of
Glucose (oxygen) (carbon dioxide) (water) energy

Another Approach to Understanding Redox
• Electrons can be transferred from an electron

donor to an electron acceptor
• Most electron acceptors gain potential energy as
they are reduced
• Electrons are usually accompanied by a proton (H+)
• Reduction often “adds Hs”
• Oxidation often “removes Hs”

Another Approach to Understanding Redox
• Flavin adenine dinucleotide (FAD) accepts two

electrons plus two protons to form FADH2
• Nicotinamide adenine dinucleotide (NAD+)
accepts two electrons plus one proton to form
NADH
• These electron carriers readily donate electrons to

other molecules

(a) Flavin adenine dinucleotide (b) Nicotinamide adenine dinucleotide
AH2 + FAD A + FADH2 BH2 + NAD+ B + NADH + H+
AH2 A BH2 B
2e – + 2H+ 2e – + 2H+
FAD FADH2 NAD+ NADH + H+
Oxidized Reduced Oxidized Reduced
Flavin
Nicotinamide

ATP Transfers Energy via Phosphate Groups
• Adenosine triphosphate (ATP) is the energy

currency for cells
• It provides the fuel for most cellular activities
• ATP forms bonds between three negatively charged

phosphate groups
• Negative charges repel each other
• High-energy bonds store a large amount of potential

energy

(a) ATP stores a large amount of potential energy.
Phosphate groups
Adenine
Clustered negative charges

raise the potential energy of
linked phosphate groups
Ribose

ATP Hydrolysis Releases Free Energy
• Hydrolysis of the bond between the two outermost

phosphate groups results
• In formation of ADP and Pi (inorganic phosphate,
H2PO4−)
• In a highly exergonic reaction

• Releases 7.3 kilocalories of energy per mole of ATP

(b) Energy is released when ATP is hydrolyzed.
Inorganic
ATP Water ADP phosphate Energy

How Does ATP Drive Endergonic Reactions?
• Energy released during ATP hydrolysis is

transferred to a substrate by phosphorylation
• Phosphorylation is adding a phosphate group
• Usually causes a change in the protein’s shape
• Exergonic phosphorylation reactions are coupled to

endergonic reactions

Coupled reaction
Free energy relative to A + B
ATP A B Activated
substrate
Energy released
ΔG –
to synthesize BP
(kcal/mol)
A BP
Energy released
Uncoupled reaction to synthesize AB
ΔG
AB
A B ΔG
Energy required
to synthesize AB
Reactants Progress of reaction Products

How Enzymes Work
• Most biological chemical reactions occur fast

enough only in the presence of an enzyme
• Enzymes are protein catalysts
• Bring reactants together in precise orientations
• Make reactions more likely
• Are specific for a single type of reaction

Enzymes Help Reactions Clear Two Hurdles
• Before a reaction can take place, reactants need to

1. Collide in a precise orientation
2. Have enough kinetic energy to overcome repulsion

between electrons that come into contact as a bond
forms

Enzymes Bring Substrates Together
• Enzymes bring substrates together
• Substrates bind to the enzyme’s active site

• Enzymes help them collide in a precise orientation
• Bonds break and form to generate products
• Many enzymes undergo a conformational change

• When the substrates are bound to the active site
• This change is called an induced fit

Substrate
(glucose)
Substrate When the ATP and

(ATP) glucose bind to the
active site, the
enzyme changes
shape. This “induced
Enzyme ﬁt” reorients the
(glucokinase) substrates and binds
them tighter to the
active site.

Enzymes Bring Substrates Together
• Substrates bind via hydrogen bonding or other

interactions with amino acid residues in the active
site
• An unstable intermediate condition called the

transition state is formed
• Activation energy (Ea) is required to strain

substrates’ bonds so they can reach the transition
state

Enzymes Lower the Activation Energy
• Reactions occur when

• Reactants have enough kinetic energy to reach the
transition state
• The kinetic energy of molecules is a function of their

temperature
• Thus, reaction rates depend on

• The kinetic energy of the reactants
• The activation energy of particular reaction (the free

energy of the transition state)

Transition state
Free energy
Ea Activation energy
Reactants
ΔG
Products
Progress of reaction

• Interactions between the enzyme and the substrate

• Stabilize the transition state
• Lower the activation energy required for the reaction

to proceed
• Enzymes are not consumed during the reaction

Transition state
Free energy
Activation energy
with enzyme
Ea
Reactants
ΔG
ΔG does
not change
Products
Progress of reaction

• Enzyme catalysis has three steps:
1. Initiation—substrates are precisely oriented as

they bind to the active site
2. Transition state facilitation—interactions

between the substrate and active site R-groups
lower the activation energy
3. Termination—reaction products are released
from the enzyme

Substrates Transition state Products
Enzyme Shape
changes
1. Initiation: Substrates bind 2. Transition state facilitation: 3. Termination: Products have

to the active site in a specific Interactions between enzyme lower affinity for active site
orientation, forming an and substrate lower the and are released. Enzyme is
enzyme-substrate complex. activation energy. unchanged after the reaction.

What Limits the Rate of Catalysis?
• The speed of an enzyme-catalyzed reaction

1. Increases linearly at low substrate concentrations
2. Slows as substrate concentration increases

3. Reaches maximum speed at high substrate
concentrations

Maximum speed of reaction
Rate of product formation
Catalyzed
reaction
Uncatalyzed
reaction

Substrate concentration
What Limits the Rate of Catalysis?
• All enzymes show this type of “saturation kinetics”

• Active sites cannot accept substrates any faster
• No matter how large the concentration of substrates

gets
• Reaction rates level off because all available enzyme

molecules are being used

Do Enzymes Work Alone?
• Many enzymes are regulated by molecules that are

not part of the enzyme itself:
1. Cofactors are inorganic ions, such as Zn2+, Mg2+,
and Fe2+, that reversibly interact with enzymes
2. Coenzymes are organic molecules, such as NADH

or FADH2, that interact with enzymes
3. Prosthetic groups are non-amino acid atoms or
molecules that are permanently attached to proteins

What Factors Affect Enzyme Function?
• An enzyme’s structure is critical to its function
• Protein structure is dependent on folding

• Enzyme function is dependent on certain conditions
• Temperature affects the folding and movement of the
enzyme and its substrates
• pH affects the enzyme’s shape and reactivity
• Each enzyme has optimal temperature and pH

(a) Enzymes from different organisms may function best (b) Enzymes from different organisms may function best
at different temperatures. at different pHs.
From bacteria From bacteria
Relative chitinase activity (%)

Relative chitinase activity (%)
that live in a that live in a

cool and neutral hot and acidic
environment environment
From bacteria
that live in a
hot and acidic From bacteria
environment that live in a
cool and neutral
environment
Temperature (ºC) pH

Most Enzymes Are Regulated
• Regulatory molecules may control when and where

an enzyme functions
• May change the enzyme’s structure
• Or its ability to bind its substrate
• May either activate or inactivate the enzyme’s
function

Regulating Enzymes via Noncovalent
Interactions
• Regulation via noncovalent interactions
• Does not permanently affect the enzyme structure
• Is referred to as “reversible”
• Competitive inhibition occurs when a molecule

competes with the substrate for the active site
• Allosteric regulation occurs when a molecule
binds at a location other than the active site
• Causes a change in enzyme shape
• Can activate or deactivate the enzyme
(a) Competitive inhibition
Substrates
Regulatory
molecule
Enzyme in absence The substrates cannot bind when

of regulation a regulatory molecule binds to the
enzyme’s active site.
(b) Allosteric regulation (activation)
Shape
changes
Regulatory
molecule
Enzyme in absence The active site becomes available
of regulation to the substrates when a regulatory
molecule binds to a different site on
the enzyme.
(c) Allosteric regulation (inhibition)
Shape
changes
Regulatory
molecule
Enzyme in absence The active site becomes unavailable
of regulation to the substrates when a regulatory
molecule binds to a different site on
the enzyme.
Regulating Enzymes via Covalent Modifications
• Regulation may involve covalent modifications

• Changes the enzyme’s primary structure
• Can be reversible or irreversible
• Irreversible changes often result from cleavage of

peptide bonds
• Most common reversible modification of enzymes is
the addition of phosphate groups (phosphorylation)
• Causes a change in shape
• May activate or inactivate the enzyme
Unphosphorylated form (inactive) Phosphorylated form (active)
Sites of phosphorylation Phosphate groups cause loop to move
Activation loop

Enzymes Can Work Together in Metabolic
Pathways
• Metabolic pathways
• A series of reactions
• Each catalyzed by a different enzyme

• To build biological molecules
enzyme 1 enzyme 2 enzyme 3

A ------------- B -------------- C ------------- D

Metabolic Pathways Are Regulated
• Feedback inhibition occurs

• When an enzyme in a pathway is inhibited
• By the final product of that pathway
• Pathway can shut down when

• Products are no longer needed by the cell

Low product (active) High product (inactive)
Substrate Substrate
Active site
Enzyme 1 Enzyme 1
Allosteric Allosteric binding

binding site results in feedback
inhibition;
Intermediate A
enzyme 1 cannot
bind substrate
Feedback inhibition
Enzyme 2 Enzyme 2
Intermediate B
Enzyme 3 Enzyme 3
Product
Metabolic Pathways Evolve
• Enzymes evolved to make building blocks of life
• If substrates decline, new enzymes evolve to make

more of the substrates
• Retro-evolution—repetition of backward process

produces multistep metabolic pathway
• Patchwork evolution—new enzymes are recruited to

new pathways
• Bioremediation—engineering new pathways to
clean up pollutants
1. Enzyme 1 evolves
to convert substrate 1 into
Substrate 1 Enzyme 1 Key molecule a key product involved in
(e.g., nucleotide)
chemical evolution.
Substrate 1
depleted
2. Substrate 1 is used up
and a new enzymatic
Substrate 2 Enzyme 2 Enzyme 1 activity evolves to produce
substrate 1 from another
Substrate 2 substrate.
depleted
3. The cycle repeats.
Additional steps are added
Substrate 3 Enzyme 3 Enzyme 2 Enzyme 1 to the series of reactions,
ultimately forming a full
Continued evolution of new steps in pathway metabolic pathway.

Metabolic Pathways Evolve
• Metabolic pathways are vital to all cells

• Catabolic pathways break down molecules
• Anabolic pathways synthesize molecules

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8

© 2017 Pearson Education, Ltd.

• Two types of energy exist

• Kinetic energy is energy of motion

• Potential energy is energy that is stored in position

• Energy can be transformed from one type to another

© 2017 Pearson Education, Ltd.

1. Potential energy 2. Kinetic energy 3. Other forms of energy

Conclusion: Energy is neither created nor destroyed; it simply changes form.

© 2017 Pearson Education, Ltd.

• The potential energy of a molecule depends on the

Longest, weakest Shortest, strongest

© 2017 Pearson Education, Ltd.

© 2017 Pearson Education, Ltd.

• Products have less potential energy than reactants

• Products have higher potential energy than reactants

• When the products of a chemical reaction become

• Second law of thermodynamics states that total

© 2017 Pearson Education, Ltd.

• ΔG > 0 = a nonspontaneous reaction that requires

• ΔG = 0 = a reaction that is at equilibrium

© 2017 Pearson Education, Ltd.

• Others have to form

• Substances must collide in a specific orientation that

• Higher concentrations and higher temperature

Experimental reaction: 3 HSO3–(aq) + IO3–(aq) 3 HSO4–(aq) + I –(aq)

Reactant concentrations constant Reactant concentrations vary

There will be no difference in reaction rates among treatments in each setup.

Temperature (ºC) Concentration of reactants (M)

Chemical reaction rates increase with increased temperature or concentration.

• Allows chemical energy released from one reaction

© 2017 Pearson Education, Ltd.

Lower energy Higher energy

• Reduction–oxidation reactions (redox reactions)

• Reduction: gain of an electron(s)

• Always occur together

© 2017 Pearson Education, Ltd.

© 2017 Pearson Education, Ltd.

• During a redox reaction, electrons can

• Simply shift their position in covalent bonds

© 2017 Pearson Education, Ltd.

© 2017 Pearson Education, Ltd.

• Electrons can be transferred from an electron

• Oxidation often “removes Hs”

© 2017 Pearson Education, Ltd.

• Flavin adenine dinucleotide (FAD) accepts two

• These electron carriers readily donate electrons to

© 2017 Pearson Education, Ltd.

FAD FADH2 NAD+ NADH + H+

Oxidized Reduced Oxidized Reduced

© 2017 Pearson Education, Ltd.

• Adenosine triphosphate (ATP) is the energy

• ATP forms bonds between three negatively charged

• High-energy bonds store a large amount of potential

© 2017 Pearson Education, Ltd.

Clustered negative charges

© 2017 Pearson Education, Ltd.

• Hydrolysis of the bond between the two outermost

• In a highly exergonic reaction

© 2017 Pearson Education, Ltd.

© 2017 Pearson Education, Ltd.

• Energy released during ATP hydrolysis is

• Exergonic phosphorylation reactions are coupled to

© 2017 Pearson Education, Ltd.

1. Initiation—substrates are precisely oriented as

2. Transition state facilitation—interactions

2. Coenzymes are organic molecules, such as NADH