Energy and Metabolism

The Energy of Life

The living cell generates thousands of different reactions Metabolism Is the totality of an organisms chemical reactions Arises from interactions between molecules An organisms metabolism transforms matter and energy, subject to the laws of thermodynamics
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Metabolic Pathways

Biochemical pathways are the organizational units of metabolism Metabolism is the total of all chemical reactions carried out by an organism A metabolic pathway has many steps that begin with a specific molecule and end with a product, each catalyzed by a specific enzyme Reactions that join small molecules together to form larger, more complex molecules are called anabolic. Reactions that break large molecules down into smaller subunits are called catabolic.

Enzyme 1 A Reaction 1 Starting molecule B

Enzyme 2 C Reaction 2

Enzyme 3 D Reaction 3 Product

Metabolic Pathway

A sequence of chemical reactions, where the product of one reaction serves as a substrate for the next, is called a metabolic pathway or biochemical pathway Most metabolic pathways take place in specific regions of the cell.

Bioenergetics

Bioenergetics is the study of how organisms manage their energy resources via metabolic pathways Catabolic pathways release energy by breaking down complex molecules into simpler compounds Anabolic pathways consume energy to build complex molecules from simpler ones

Energy

Energy is the capacity to do work or ability to cause change. Any change in the universe requires energy. Energy comes in 2 forms: Potential energy is stored energy. No change is currently taking place Kinetic energy is currently causing change. This always involves some type of motion.

Forms of Energy

Kinetic energy is the energy associated with motion Potential energy Is stored in the location of matter Includes chemical energy stored in molecular structure Energy can be converted from one form to another

On the platform, a diver has more potential energy.

Diving converts potential energy to kinetic energy.

Climbing up converts kinetic energy of muscle movement to potential energy.

In the water, a diver has less potential energy.

Laws of Energy Transformation

Thermodynamics is the study of energy changes. Two fundamental laws govern all energy changes in the universe. These 2 laws are simply called the first and second laws of thermodynamics:

The First Law of Thermodynamics

According to the first law of thermodynamics Energy cannot be created or destroyed Energy can be transferred and transformed

Chemical energy

For example, the chemical (potential) energy in food will be converted to the kinetic energy of the cheetahs movement

Second Law of Thermodynamics

The disorder (entropy) in the universe is continuously increasing. Energy transformations proceed spontaneously to convert matter from a more ordered, less stable form, to a less ordered, more stable form Spontaneous changes that do not require outside energy increase the entropy, or disorder, of the universe For a process to occur without energy input, it must increase the entropy of the universe

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Second Law of Thermodynamics

During each conversion, some of the energy dissipates into the environment as heat. During every energy transfer or transformation, some energy is unusable, often lost as heat Heat is defined as the measure of the random motion of molecules Living cells unavoidably convert organized forms of energy to heat According to the second law of thermodynamics, every energy transfer or transformation increases the entropy (disorder) of the universe

Heat

co2

+
H2O

For example, disorder is added to the cheetahssurroundings in the form of heat and the small molecules that are the by-products of metabolism.

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Biological Order and Disorder

Cells create ordered structures from less ordered materials Organisms also replace ordered forms of matter and energy with less ordered forms The evolution of more complex organisms does not violate the second law of thermodynamics Entropy (disorder) may decrease in an organism, but the universes total entropy increases
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Biological Order and Disorder

Living systems

Increase the entropy of the universe Use energy to maintain order A living systems free energy is energy that can do work under cellular conditions Organisms live at the expense of free energy
50m

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Free Energy

Free energy is the portion of a systems energy that is able to perform work when temperature and pressure is uniform throughout the system, as in a living cell Free energy also refers to the amount of energy actually available to break and subsequently form other chemical bonds Gibbs free energy (G) in a cell, the amount of energy contained in a molecules chemical bonds (T&P constant) Change in free energy - G Endergonic - any reaction that requires an input of energy Exergonic - any reaction that releases free energy

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Exergonic reactions

Reactants have more free energy than the products Involve a net release of energy and/or an increase in entropy Occur spontaneously (without a net input of energy)
Reactants

Free energy

Amount of energy released (G <0)

Energy

Products

Progress of the reaction (a) Exergonic reaction: energy released

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Endergonic Reactions

Reactants have less free energy than the products Involve a net input of energy and/or a decrease in entropy Do not occur spontaneously
Products

Free energy

Energy Reactants

Amount of energy released (G>0)

Progress of the reaction (b) Endergonic reaction: energy required

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Energy released Energy supplied

Product Energy must be supplied. Reactant Reactant Energy is released.

Product

Endergonic

Exergonic
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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 materials A catabolic pathway in a cell releases free energy in a series of reactions Closed and open hydroelectric systems can serve as analogies
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Equilibrium and Metabolism

Reactions in a closed system eventually reach equilibrium

G < 0 G = 0

(a) A closed hydroelectric system. Water flowing downhill turns a turbine that drives a generator providing electricity to a light bulb, but only until the system reaches equilibrium.

Cells in our body experience a constant flow of materials in and out, preventing metabolic pathways from reaching equilibrium
(b) An open hydroelectric system. Flowing water keeps driving the generator because intake and outflow of water keep the system from reaching equlibrium. G < 0

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An Analogy For Cellular Respiration Glucose Catabolism

G < 0 G < 0 G < 0

(c) A multistep open hydroelectric system. Cellular respiration is

analogous to this system: Glucoce is brocken down in a series of exergonic reactions that power the work of the cell. The product of each reaction becomes the reactant for the next, so no reaction reaches equilibrium.

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Energy Coupling

Living organisms have the ability to couple exergonic and endergonic reactions: Energy released by exergonic reactions is captured and used to make ATP from ADP and Pi ATP can be broken back down to ADP and Pi, releasing energy to power the cells endergonic reactions.

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The Structure and Hydrolysis of ATP

ATP (adenosine triphosphate) Is the cells energy shuttle Provides energy for cellular functions
Adenine
N O
O O O O O O HC C NH2 C N CH N

-O -

O
O

CH2

N O H H H OH OH

Phosphate groups

Ribose

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The Structure and Hydrolysis of ATP

Energy is released from ATP when the terminal phosphate

bond is broken

Adenosine triphosphate (ATP)

H2O

Energy

Inorganic phosphate

Adenosine diphosphate (ADP)

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Cellular Work

A cell does three main kinds of work Mechanical Transport Chemical Energy coupling is a key feature in the way cells manage their energy resources to do this work ATP powers cellular work by coupling exergonic reactions to endergonic reactions

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Energy Coupling - ATP / ADP Cycle

Releasing the third phosphate from ATP to make ADP generates energy (exergonic): Linking the phosphates together requires energy - so making ATP from ADP and a third phosphate requires energy (endergonic), Catabolic pathways drive the regeneration of ATP from ADP and phosphate
ATP synthesis from ADP + P i requires energy ATP hydrolysis to ADP + P i yields energy

ATP

Energy from catabolism (exergonic, energy yielding processes)

Energy for cellular work (endergonic, energyconsuming processes)

ADP + P

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How ATP Performs Work

ATP drives endergonic reactions by phosphorylation, transferring a phosphate group to some other molecule, such as a reactant The recipient molecule is now phosphorylated The three types of cellular work (mechanical, transport, and chemical) are powered by the hydrolysis of ATP

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How ATP Performs Work

ATP drives endergonic reactions by phosphorylation, transferring a phosphate to other molecules - hydrolysis of ATP

P P

Motor protein Protein moved (a) Mechanical work: ATP phosphorylates motor proteins Membrane protein

ADP

ATP
P P Solute transported
i

+
P
i

Solute

(b) Transport work: ATP phosphorylates transport proteins

Glu + NH3
Reactants: Glutamic acid and ammonia

NH2

Glu

Product (glutamine) made

(c) Chemical work: ATP phosphorylates key reactants

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Activation Energy

All reactions, both endergonic and exergonic, require an input of energy to get started. This energy is called activation energy The activation energy, EA

Is the initial amount of energy needed to start a chemical reaction Activation energy is needed to bring the reactants close together and weaken existing bonds to initiate a chemical reaction. Is often supplied in the form of heat from the surroundings in a system.
A B D

Transition state
A B D A C B

Free energy

EA

Reactants G < O
D

Products Progress of the reaction

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Reaction Rates

In most cases, molecules do not have enough kinetic energy to reach the transition state when they collide. Therefore, most collisions are non-productive, and the reaction proceeds very slowly if at all. What can be done to speed up these reactions?

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Increasing Reaction Rates

Add Energy (Heat) - molecules move faster so they collide more frequently and with greater force. Add a catalyst a catalyst reduces the energy needed to reach the activation state, without being changed itself. Proteins that function as catalysts are called enzymes.
Activation Energy and Catalysis
Energy supplied

Activation energy Activation energy Reactant Reactant

Energy released

Product

Product

Uncatalyzed
Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Catalyzed
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Enzymes Lower the EA Barrier

An enzyme catalyzes reactions by lowering the EA barrier

Course of reaction without enzyme

EA
without enzyme EA with enzyme is lower

Free energy

Reactants

Course of reaction with enzyme

G is unaffected by enzyme

Products
Progress of the reaction
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Enzymes Are Biological Catalysts

Enzymes are proteins that carry out most catalysis in living organisms. Unlike heat, enzymes are highly specific. Each enzyme typically speeds up only one or a few chemical reactions. Unique three-dimensional shape enables an enzyme to stabilize a temporary association between substrates. Because the enzyme itself is not changed or consumed in the reaction, only a small amount is needed, and can then be reused. Therefore, by controlling which enzymes are made, a cell can control which reactions take place in the cell.

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Substrate Specificity of Enzymes

Almost all enzymes are globular proteins with one or more active sites on their surface. The substrate is the reactant an enzyme acts on Reactants bind to the active site to form an enzyme-substrate complex. The 3-D shape of the active site and the substrates must match, like a lock and key Binding of the substrates causes the enzyme to adjust its shape slightly, leading to a better induced fit. Induced fit of a substrate brings chemical groups of the active site into positions that enhance their ability to catalyze the chemical reaction When this happens, the substrates are brought close together and existing bonds are stressed. This reduces the amount of energy needed to reach the transition state.
Substate

Active site

Enzyme

Enzyme- substrate complex

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The Catalytic Cycle Of An Enzyme

1 Substrates enter active site; enzyme changes shape so its active site embraces the substrates (induced fit). 2 Substrates held in active site by weak interactions, such as hydrogen bonds and ionic bonds. 3 Active site (and R groups of its amino acids) can lower EA and speed up a reaction by acting as a template for substrate orientation, stressing the substrate bonds and stabilizing the transition state, providing a favorable microenvironment, participating directly in the catalytic reaction.

Substrates

Enzyme-substrate complex

6 Active site Is available for two new substrate Mole. Enzyme

5 Products are Released.

Figure 8.17 Products

4 Substrates are Converted into Products.

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The Catalytic Cycle Of An Enzyme

1 The substrate, sucrose, consists of glucose and fructose bonded together. Glucose 2 The substrate binds to the enzyme, forming an enzyme-substrate complex. Bond H2O 4 Products are released, and the enzyme is free to bind other substrates.

Fructose

Active site

Enzyme

3 The binding of the substrate and enzyme places stress on the glucose-fructose bond, and the bond breaks.

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Factors Affecting Enzyme Activity

Temperature - rate of an enzyme-catalyzed reaction increases with temperature, but only up to an optimum temperature. pH - ionic interactions also hold enzymes together. Inhibitors and Activators

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Effects of Temperature and pH

Each enzyme has an optimal temperature in which it can function

Optimal temperature for typical human enzyme Optimal temperature for enzyme of thermophilic (heat-tolerant) bacteria

Rate of reaction

40 Temperature (C) (a) Optimal temperature for two enzymes

20

80

100

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Effects of Temperature and pH

Each enzyme has an optimal pH in which it can function

Optimal pH for pepsin (stomach enzyme) Rate of reaction Optimal pH for trypsin (intestinal enzyme)

3 4 0 2 1 (b) Optimal pH for two enzymes

Figure 8.18 38

Factors Affecting Enzyme Activity

Inhibitor - substance that binds to an enzyme and decreases its activity feedback Competitive inhibitors - compete with the substrate for the same active site Noncompetitive inhibitors - bind to the enzyme in a location other than the active site Allosteric sites - specific binding sites acting as on/off switches
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Enzyme Inhibitors

Competitive inhibitors bind to the active site of an enzyme,

competing with the substrate

A substrate can bind normally to the active site of an enzyme. Substrate Active site

Enzyme

(a) Normal binding

A competitive inhibitor mimics the substrate, competing for the active site.

Competitive inhibitor

(b) Competitive inhibition

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Enzyme Inhibitors

Noncompetitive inhibitors bind to another part of an enzyme, changing the function

A noncompetitive inhibitor binds to the enzyme away from the active site, altering the conformation of the enzyme so that its active site no longer functions. Noncompetitive inhibitor (c) Noncompetitive inhibition

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Regulation Of Enzyme Activity Helps Control Metabolism

Chemical chaos would result if a cells metabolic pathways were not tightly regulated To regulate metabolic pathways, the cell switches on or off the genes that encode specific enzymes Allosteric regulation is the term used to describe any case in which a proteins function at one site is affected by binding of a regulatory molecule at another site Enzymes change shape when regulatory molecules bind to specific sites, affecting function

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Allosteric Activation and Inhibition

Most allosterically regulated enzymes are made from polypeptide subunits Each enzyme has active and inactive forms The binding of an activator stabilizes the active form of the enzyme The binding of an inhibitor stabilizes the inactive form of the enzyme

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Allosteric Regulation of Enzymes

Allosteric regulation may either inhibit or stimulate an enzymes activity

Allosteric enyzme with four subunits Active site (one of four) Allosteric activater stabilizes active from

Regulatory site (one of four) Active form

Activator Stabilized active form Allosteric activater stabilizes inactive form

Oscillation

Nonfunctional active site

Inactive form

Inhibitor

Stabilized inactive form

(a) Allosteric activators and inhibitors. In the cell, activators and inhibitors dissociate when at low concentrations. The enzyme can then oscillate again.

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Cooperativity

Is a form of allosteric regulation that can amplify enzyme activity

Binding of one substrate molecule to active site of one subunit locks all subunits in active conformation.

Substrate

Inactive form

Stabilized active form

(b) Cooperativity: another type of allosteric activation. Note that the inactive form shown on the left oscillates back and forth with the active form when the active form is not stabilized by substrate.

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Factors Affecting Enzyme Activity

Activators - substances that bind to allosteric sites and keep the enzymes in their active configurations - increases enzyme activity Cofactors - chemical components that facilitate enzyme activity Coenzymes - organic molecules that function as cofactors

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Regulation of Biochemical Pathways

Biochemical pathways must be coordinated and regulated to operate efficiently. Advantageous for cell to temporarily shut down biochemical pathways when their products are not needed Feedback Inhibition

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Feedback Inhibition

In feedback inhibition the end product of a metabolic pathway shuts down the pathway When the cell produces increasing quantities of a particular product, it automatically inhibits its ability to produce more

Active site available

Initial substrate (threonine) Threonine in active site Enzyme 1 (threonine deaminase) Intermediate A

Isoleucine used up by cell Feedback inhibition

Active site of enzyme 1 no longer binds threonine; pathway is switched off

Enzyme 2 Intermediate B Enzyme 3 Intermediate C

Isoleucine binds to allosteric site

Enzyme 4 Intermediate D Enzyme 5

End product (isoleucine)

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