Chapter 8An Introduction to Metabolism

Overview: The Energy of Life• The living cell is a miniature chemical factory

where thousands of reactions occur• The cell extracts energy and applies energy to

perform work• Some organisms even convert energy to light,

as in bioluminescence• Metabolism is the totality of an organism’s

chemical reactions• Metabolism is an emergent property of life that

arises from interactions between molecules within the cell

Enzyme 1

A BReaction 1

Enzyme 2

CReaction 2

Enzyme 3

DReaction 3

ProductStartingmolecule

•A metabolic pathway begins with a specific molecule and ends with a product•Each step is catalyzed by a specific enzyme

•Catabolic pathways release energy by breaking down complex molecules into simpler compounds

Anabolic pathways consume energy to build complex molecules from simpler ones

Forms of Energy• Energy is the capacity to cause change• Energy exists in various forms, some of which

can perform work

• Bioenergetics is the study of how organisms manage their energy resources

• 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• Energy can be converted from one form to another• Solar energy

– Light energy can be converted to chemical energy by photosynthesis

On the platform,the diver hasmore potentialenergy.

Diving convertspotentialenergy to kinetic energy.

Climbing up convertskinetic energy ofmuscle movement topotential energy.

In the water, the diver has lesspotential energy.

Add solar, potential, & chemical energy for this

picture.

The Laws of Energy Transformation

• Thermodynamics is the study of energy transformations

• A closed system, such as that approximated by liquid in a thermos, is isolated from its surroundings

• In an open system, energy and matter can be transferred between the system and its surroundings

• Organisms are open systems

The First Law of Thermodynamics• According to the first law of thermodynamics, the energy of the

universe is constant– Energy can be transferred and transformed– Energy cannot be created or destroyed

• The first law is also called the principle of conservation of energy

The Second Law of Thermodynamics• During every energy transfer or transformation, some energy is

unusable, often lost as heat• According to the second law of thermodynamics, every energy

transfer or transformation increases the entropy (disorder) of the universe

Chemical energy

Heat CO2

First law of thermodynamics Second law of thermodynamics

H2O

•Living cells unavoidably convert organized forms of energy to heat•Spontaneous processes occur without energy input; they can happen quickly or slowly (very slowly in order to get over EA)•For a process to occur without energy input, it must increase the entropy of the universe

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 universe’s total entropy increases

• The change in free energy (∆G) during a process is related to the change in enthalpy, or change in total energy (∆H), and change in entropy (T∆S):

∆G = ∆H - T∆S• Energy in reactions with a negative G can be

harnessed to perform work

• A living system’s free energy is energy that can do work when temperature and pressure are uniform, as in a living cell

1. The oxidation of glucose to CO2 and H2O is highly exergonic: G 636 kcal/mole. This is possible, but why is it very slow?a. Few glucose and oxygen molecules have the

activation energy at room temperature.b. There is too much CO2 in the air.

c. CO2 has higher energy than glucose.

d. The formation of six CO2 molecules from one glucose molecule decreases entropy.

e. The water molecules quench the reaction.

1. The oxidation of glucose to CO2 and H2O is highly exergonic: G 636 kcal/mole. This is possible, but why is it very slow?

a. Few glucose and oxygen molecules have the activation energy at room temperature.

b. There is too much CO2 in the air.

c. CO2 has higher energy than glucose.

d. The formation of six CO2 molecules from one glucose molecule decreases entropy.

e. The water molecules quench the reaction.

LE 8-5

Gravitational motion Diffusion Chemical reaction

More free energy

Change in Free Energy

• Free energy of the products – free energy of reactants = negative, then products have a greater stability than reactants

• Products have less free energy; in open system, must include environment

• An exergonic reaction proceeds with a net release of free energy

• An endergonic reaction absorbs free energy from its surroundings and reactants are more stable than products

LE 8-6a

Reactants

EnergyProducts

Progress of the reaction

Amount ofenergy

released(G < 0)

Free

ene

rgy

Exergonic reaction: energy released

LE 8-6b

ReactantsEnergy

Products

Progress of the reaction

Amount ofenergy

required(G > 0)

Free

ene

rgy

Endergonic reaction: energy required

2. Firefly luciferase catalyzes the following reaction:luciferin ATP adenyl-luciferin pyrophosphate Then the next reaction occurs spontaneously:adenyl-luciferin O2 oxyluciferin H2O CO2 AMP light What is the role of luciferase?

a. Luciferase makes the G of the reaction more negative.

b. Luciferase produces a transition state with a lower free energy

c. Luciferase alters the equilibrium point of the reaction.

d. Luciferase makes the reaction irreversible.e. Luciferase creates a phosphorylated intermediate.

2. Firefly luciferase catalyzes the following reaction:luciferin ATP adenyl-luciferin pyrophosphate Then the next reaction occurs spontaneously:adenyl-luciferin O2 oxyluciferin H2O CO2 AMP light What is the role of luciferase?

a. Luciferase makes the G of the reaction more negative.

b. Luciferase produces a transition state with a lower free energy.

c. Luciferase alters the equilibrium point of the reaction.

d. Luciferase makes the reaction irreversible.e. Luciferase creates a phosphorylated intermediate.

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

LE 8-7a

G = 0

A closed hydroelectric system

G < 0

LE 8-7b

An open hydroelectric system

G < 0

LE 8-7c

A multistep open hydroelectric system

G < 0G < 0

G < 0

Concept 8.3: ATP powers cellular work by coupling exergonic

reactions to endergonic reactions

• A cell does three main kinds of work:– Mechanical– Transport– Chemical

• To do work, cells manage energy resources by energy coupling, the use of an exergonic process to drive an endergonic one

Phosphate groupsRibose

Adenine

ATP (adenosine triphosphate) is the cell’s energy shuttle

ATP provides energy for cellular functions

• The bonds between the phosphate groups of ATP’s tail can be broken by hydrolysis

• Energy is released from ATP when the terminal phosphate bond is broken

• This release of energy comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves

LE 8-9

Adenosine triphosphate (ATP)

Energy

P P P

PPP i

Adenosine diphosphate (ADP)Inorganic phosphate

H2O

+ +

• In the cell, the energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction

• Overall, the coupled reactions are exergonic

LE 8-10Endergonic reaction: G is positive, reactionRequires input of energy

Exergonic reaction: G is negative, products have less free energy than reactants

G = +3.4 kcal/mol

G = –7.3 kcal/mol

G = –3.9 kcal/mol

NH2

NH3Glu Glu

Glutamicacid

Coupled reactions: Overall G is negative;together, reactions give off heat

Ammonia Glutamine

ATP H2O ADP P i

+

+ +

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

LE 8-11

NH2

Glu

P i

P i

P i

P i

Glu NH3

P

P

P

ATPADP

Motor proteinMechanical work: ATP phosphorylates motor proteins

Protein moved

Membraneprotein

Solute

Transport work: ATP phosphorylates transport proteins

Solute transported

Chemical work: ATP phosphorylates key reactants

Reactants: Glutamic acidand ammonia

Product (glutamine)made

+ +

+

Pi

ADP

Energy for cellular work(endergonic, energy-consuming processes)

Energy from catabolism(energonic, energy-yielding processes)

ATP

+

The Regeneration of ATP•ATP is a renewable resource that is regenerated by addition of a phosphate group to ADP•The energy to phosphorylate ADP comes from catabolic reactions in the cell•The chemical potential energy temporarily stored in ATP drives most cellular work

Enzymes speed up metabolic reactions by providing an alternative

pathway with a lower EA

• A catalyst is a chemical agent that speeds up a reaction without being consumed by the reaction

• An enzyme is a catalytic protein or RNA• Hydrolysis of sucrose by the enzyme sucrase is

an example of an enzyme-catalyzed reaction

LE 8-13

SucroseC12H22O11

GlucoseC6H12O6

FructoseC6H12O6

The Activation Energy Barrier• Every chemical reaction between molecules

involves bond breaking and bond forming• The initial energy needed to start a chemical

reaction is called the free energy of activation, or activation energy (EA)

• Activation energy is often supplied in the form of heat from the surroundings

LE 8-14

Transition state

C D

A B

EA

Products

C D

A B

G < O

Progress of the reaction

Reactants

C D

A B

Free

ene

rgy

How Enzymes Lower the EA Barrier

• Enzymes catalyze reactions by lowering the EA barrier—provide an alternative transition state

• Enzymes do not affect the change in free-energy (∆G); instead, they hasten reactions that could occur eventually

3. In the energy diagram below, which of the energy changes would be the same in both the enzyme-catalyzed and uncatalyzed reactions?

ab cde

3. In the energy diagram below, which of the energy changes would be the same in both the enzyme-catalyzed and uncatalyzed reactions?

ab cde

LE 8-15

Course ofreactionwithoutenzyme

EA

without enzyme

G is unaffectedby enzyme

Progress of the reaction

Free

ene

rgy

EA withenzymeis lower

Course ofreactionwith enzyme

Reactants

Products

Substrate Specificity of Enzymes

• The reactant that an enzyme acts on is called the enzyme’s substrate

• The enzyme binds to its substrate, forming an enzyme-substrate complex

• The active site is the region on the enzyme where the substrate binds

• Induced fit of a substrate brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction

LE 8-16

Substrate

Active site

Enzyme Enzyme-substratecomplex

If reversible, what are the possible types of bonds utilized by enzymes in their active sites?

Catalysis in the Enzyme’s Active Site

• In an enzymatic reaction, the substrate binds to the active site

• The active site can lower an EA barrier by– Orienting substrates correctly– Straining substrate bonds– Providing a favorable microenvironment– Covalently bonding to the substrate

LE 8-17

Enzyme-substratecomplex

Substrates

Enzyme

Products

Substrates enter active site; enzymechanges shape so its active siteembraces the substrates (induced fit).

Substrates held inactive site by weakinteractions, such ashydrogen bonds andionic bonds.

Active site (and R groups ofits amino acids) can lower EA

and speed up a reaction by• acting as a template for substrate orientation,• stressing the substrates and stabilizing the transition state,• providing a favorable microenvironment,• participating directly in the catalytic reaction.

Substrates areconverted intoproducts.

Products arereleased.

Activesite is

availablefor two new

substratemolecules.

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• Each enzyme has an optimal temperature in

which it can function• Each enzyme has an optimal pH in which it

can functionWe can find these in lab the next few weeks!

LE 8-18

Optimal temperature fortypical human enzyme

Optimal temperature forenzyme of thermophilic (heat-tolerant bacteria)

Temperature (°C)Optimal temperature for two enzymes

0 20 40 60 80 100

Rat

e of

reac

t ion

Optimal pH for pepsin(stomach enzyme)

Optimal pHfor trypsin(intestinalenzyme)

pHOptimal pH for two enzymes

0

Rat

e of

reac

t ion

1 2 3 4 5 6 7 8 9 10

Explain what is happening at each

section of the curve.

Cofactors• Cofactors are nonprotein enzyme helpers• Coenzymes are organic cofactors

Enzyme Inhibitors• Competitive inhibitors bind to the active site of

an enzyme, competing with the substrate• Noncompetitive inhibitors bind to another part

of an enzyme, causing the enzyme to change shape and making the active site less effective

LE 8-19Substrate

Active site

Enzyme

Competitiveinhibitor

Normal binding

Competitive inhibition

Noncompetitive inhibitorNoncompetitive inhibition

A substrate canbind normally to the

active site of anenzyme.

A competitiveinhibitor mimics the

substrate, competingfor the active site.

A noncompetitiveinhibitor binds to the

enzyme away from theactive site, altering the

conformation of theenzyme so that its

active site no longerfunctions.

Concept 8.5: Regulation of enzyme activity helps control

metabolism

• Chemical chaos would result if a cell’s metabolic pathways were not tightly regulated

• To regulate metabolic pathways, the cell switches on or off the genes that encode specific enzymes

Allosteric Regulation of Enzymes

• Allosteric regulation is the term used to describe cases where a protein’s function at one site is affected by binding of a regulatory molecule at another site

• Allosteric regulation may either inhibit or stimulate an enzyme’s activity

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

LE 8-20a

Allosteric enzymewith four subunits

Regulatorysite (oneof four) Active form

ActivatorStabilized active form

Active site(one of four)

Allosteric activatorstabilizes active form.

Non-functionalactive site

Inactive form Inhibitor Stabilized inactive form

Allosteric inhibitorstabilizes inactive form.

Oscillation

Allosteric activators and inhibitors

• Cooperativity is a form of allosteric regulation that can amplify enzyme activity

• In cooperativity, binding by a substrate to one active site stabilizes favorable conformational changes at all other subunits

LE 8-20b

Substrate

Binding of one substrate molecule toactive site of one subunit locks allsubunits in active conformation.

Cooperativity another type of allosteric activationStabilized active formInactive form

Michaelis-Menton

                                            Lineweaver-Burk analysis is one method of linearizing substrate-velocity data so as to determine the kinetic constants Km and Vmax. One creates a secondary, reciprocal plot: 1/velocity vs. 1/[substrate]. When catalytic activity follows Michaelis-Menten kinetics over the range of substrate concentrations tested, the Lineweaver-Burk plot is a straight line with

Y intercept = 1/Vmax,X intercept = -1/Kmslope = Km/Vmax

4. Which choice best describes what the H ATPase does in terms of flow of energy in many cells?

a. It converts light energy into energy in a concentration gradient.

b. It converts matter into energy in the form of an electrochemical gradient.

c. It pumps protons up their pressure gradient.

d. It converts chemical energy to energy in an electrochemical gradient and heat.

e. It converts energy in a concentration gradient to energy in an electrical gradient.

4. Which choice best describes what the H ATPase does in terms of flow of energy in many cells?

a. It converts light energy into energy in a concentration gradient.

b. It converts matter into energy in the form of an electrochemical gradient.

c. It pumps protons up their pressure gradient.

d. It converts chemical energy to energy in an electrochemical gradient and heat.

e. It converts energy in a concentration gradient to energy in an electrical gradient.

Feedback Inhibition

• In feedback inhibition, the end product of a metabolic pathway shuts down the pathway

• Feedback inhibition prevents a cell from wasting chemical resources by synthesizing more product than is needed

LE 8-21

Active siteavailable

Initial substrate(threonine)

Threoninein active site

Enzyme 1(threoninedeaminase)

Enzyme 2

Intermediate A

Isoleucineused up bycell

Feedbackinhibition Active site of

enzyme 1 can’tbindtheoninepathway off

Isoleucinebinds toallostericsite

Enzyme 3

Intermediate B

Enzyme 4

Intermediate C

Enzyme 5

Intermediate D

End product(isoleucine)

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 (oxidative phosphorylation in Ch.9; photsynthetic phosphorylation in Ch.10)

• Some enzymes reside in specific organelles, such as enzymes for cellular respiration being located in mitochondria— next chapter

LE 8-22

Mitochondria,sites of cellular respiration

1 µm