5887255 AP Bio Chapter Six an Introduction to Metabolism

8/7/2019 5887255 AP Bio Chapter Six an Introduction to Metabolism

1/13

1UNIT ONE: THE CHEMISTRY OF LIFEChChChChapter Six: An Introduction To Metabolismapter Six: An Introduction To Metabolismapter Six: An Introduction To Metabolismapter Six: An Introduction To Metabolism(Text from Biology, 6th Edition, by Campbell and Reece)

METABOLISM, ENERGY, AND LIFE

MetabolismMetabolismMetabolismMetabolism is the sum total of all chemical reactions in an organism.

The Chemistry of Life is Organized Into Metabolic Pathways

The thousands of chemical reactions in the cell are arranged in

intricate metabolic pathways that alter molecules in a step-by-step

fashion. Metabolism manages the material and energy resources of

the cell. Catabol ic pathwaysCatabolic pathwaysCatabolic pathwaysCatabolic pathways release energy by breaking down

complex molecules to simpler compounds. An example of such

pathway is cellular respiration, in which glucose and other fuels are

broken down into carbon dioxide and water. Anabolic pathwaysAnabolic pathwaysAnabolic pathwaysAnabolic pathways

consume energy to build complicated molecules from simpler ones.

An example is the building of a protein from amino acids.

Catabolic and anabolic pathways transfer energy the energy

produced by catabolism is used to power anabolism. This transfer is

called energy coupling.

The concepts in this chapter are central to bioenergeticsbioenergeticsbioenergeticsbioenergetics, the study

of how organisms manage their energy resources.

Organisms Transform Energy

EnergyEnergyEnergyEnergy is the capacity to do work. Cells must be able to transform energy from one type into another.

Anything that moves has kinetic energykinetic energykinetic energykinetic energy, the energy of motion. Moving objects perform work through

imparting motion to other matter. Light is also a type of kinetic energy light can power

photosynthesis. Heat is kinetic energy that results from the random movement of molecules.

Resting objects have stored energy, or potential energypotential energypotential energypotential energy, the energy matter

possesses because of its location or structure. Chemical energyChemical energyChemical energyChemical energy is a form ofpotential energy stored in molecules because of the arrangement of atoms in those

molecules.

An example of potential energy being transformed into kinetic energy can be seen

by a ball being thrown into the air when the ball is highest, there is the most

potential energy. This becomes kinetic energy as the ball moves toward the

ground. When chemical reactions rearrange the atoms of molecules in such a way

that potential energy in the molecules is converted into kinetic, chemical energy


2/13


can be used. Cellular respiration and other catabolic pathways can release stored energy in molecules

and make it available to the cell.

The Energy Transformations of Life Are Subject To Two Laws of Thermodynamics

ThermodynamicsThermodynamicsThermodynamicsThermodynamics is the study of the energy transformations that occur in a collection of matter. The

term systemis used to refer to matter being studied, while everything outside the system is referred to

as surroundings. A closed systemis isolated from its surroundings. In an open system, energy and

matter can be transferred between the system and its surroundings. Organisms are considered open

systems, since they can absorb energy (light or chemical) and release waste products to the

surroundings. Two laws of thermodynamics are central in energy transformations in organisms as well

as all matter.

The First Law of Thermodynamics

The first law ofThe first law ofThe first law ofThe first law of thermodynamicsthermodynamicsthermodynamicsthermodynamics states that the energy of the universe is constant: energy can be

transferred and transformed, but it cannot be created or destroyed. This law is also known as the

principle of conservation of energy.

The Second Law of Thermodynamics

The main idea behind the second law of thermodynamicsthe second law of thermodynamicsthe second law of thermodynamicsthe second law of thermodynamics is that every

energy transfer or transformation makes the universe more disordered.

EntropyEntropyEntropyEntropy is a measure of disorder and randomness. The greater entropy a

collection of matter has, the more disorganized it is. Thus, the second law

can also be written as: every energy transfer increases the entropy of the

universe.

Increasing entropy can be easy to observe in cases of physical

disintegration think of an old building crumbling to the ground.

Increasing heat is also increasing entropy, since heat is the energy of

random molecular motion. In most energy transformations, ordered forms

of energy are at least partly converted into heat.

Although forms of energy have been converted to heat, the first law of thermodynamics is still upheld,

since heat is a form of energy. While the quantityof energy in the universe is constant, the qualityof

the energy is not. Heat can be put to work only when there is a temperature difference that results in

heat moving from a warmer location to a cooler one as a result, it can be seen as the lowest grade

of energy.

While cells created ordered structures from less organized starting materials, organisms also take in

organized forms of matter and break them down into less ordered forms. For example, animals take in

starch, proteins, and complex molecules, then break them down, releasing carbon dioxide and water.


3/13

UNIT ONE: THE CHEMISTRY OChChChChapter Six: An Introductionapter Six: An Introductionapter Six: An Introductionapter Six: An Introduction(Text from Biology, 6th Edition,

Energy flows into an ecosystem

entropy of their surroundings.

Additionally, while the entropy

universeincreases.

Organisms Live at the Expense

A spontaneous process is a cha

harnessed to perform work. For

generate power. Nonspontane

example, cells must expend en

The stability of a system increa

change in a way that they beco

than the same water at sea lev

reservoir wall is removed). A st

Free Energy: A Criterion for Spo

Free energyFree energyFree energyFree energy is the portion of a

throughout the system. It is te

LIFEo Metabolismo Metabolismo Metabolismo Metabolismy Campbell and Reece)

as light, and then leaves as heat. Living syste

of a particular system can decrease, the total e

f Free Energy

ge that can occur without outside assistance.

example, the downhill flow of water can be us

us processes will only occur if energy is added t

rgy to create a protein about amino acids.

es when a spontaneous process occurs. Unsta

e stable. For example, a body of water in a re

l. The water will fall in order move toward grea

ndard for spontaneous process is free energy.

taneous Chang

ystems energy that can perform work when te

med free because it is available for work.

G


4/13


5/13


Free Energy and Metabolism

Exergonic and EndExergonic and EndExergonic and EndExergonic and Endergonic Reactions in Metabolismergonic Reactions in Metabolismergonic Reactions in Metabolismergonic Reactions in Metabolism

Chemical reactions can be classified as either exergonic (energy outward) or endergonic (energy

inward). An exergonic reactionexergonic reactionexergonic reactionexergonic reaction proceeds with a net release of free energy. Since the mixture loses

free energy, G is negative. (Remember free energy (G) moves outoutoutout from the reactants, so G is

negative). Exergonic reactions are those that occur spontaneously. The magnitude ofG is the

maximum amount of work the

reaction can perform.

An endergonic reactionendergonic reactionendergonic reactionendergonic reaction is one

that absorbs free energy from its

surroundings. This takes free

energy from the surroundings and

stores it in molecules, which

makes G positive. (Free energy

(G) is moving intointointointo the products,

so there is a positive G). These

reactions are nonspontaneous,

and the magnitude ofG is the

quantity of energy required to

power the reaction.

Metabolic DisequilibriumMetabolic DisequilibriumMetabolic DisequilibriumMetabolic Disequilibrium

In a closed system, reactions will reach equilibrium and be unable to do work. A cell that reaches

metabolic disequilibrium is dead no work is being performed. Thus, metabolic disequilibrium is

extremely important for life.

Since a cell is an open system, it can maintain disequilibrium. The constant transfer of materials in and

out of the cell prevents the metabolic pathways from reaching equilibrium. A catabolic pathway in a

cell releases free energy in a serious of reactions. The product of one reaction never continually

accumulates: instead, it becomes the reactant in the next step. The overall sequence of reactions is

powered by the large free-energy difference between glucose and the carbon dioxide and water (waste

products) at the end.

Free energy is transmitted to an ecosystem through sunlight animals and nonphotosynthetic

organisms depend on free-energy transfusions in the form of the products of photosynthesis.

Remember that energy couplingenergy couplingenergy couplingenergy coupling is the use of an exergonic process to drive an endergonic one.


6/13

UNIT ONE: THE CHEMISTRY OChChChChapter Six: An Introductionapter Six: An Introductionapter Six: An Introductionapter Six: An Introduction(Text from Biology, 6th Edition,

ATP Powers Cellular Work by C

A cell does:

1. Mechanical work, such2. Transport work, pumpin

movement

3. Chemical work, the pusas synthesizing polymer

ATP is usually the source of ene

The Structure and Hydrolysis o

ATP (adenosine triphosphate)ATP (adenosine triphosphate)ATP (adenosine triphosphate)ATP (adenosine triphosphate)

to one type of nucleotide found

ATP has the nitrogenous base a

ribose. It is very similar to an a

in RNA.

The bonds between the phosph

can be broken by hydrolysis. W

phosphate bond is broken, a mo

phosphate leaves the ATP, whic

ADP (adenosine disphosphate).

exergonic reaction that release

per mole of ATP hydrolyzed.

However, that was the free-en

G is about -13 kcal/mole, whi

conditions. Since the hydrolysi

referred to as high-energy phos

bonds are unusually strong h

fact, the bonds are relatively wbroken. The ADP and phosphat

energy is being released to crea

Since the phosphate groups are

instability of the bonds. This is

LIFEo Metabolismo Metabolismo Metabolismo Metabolismy Campbell and Reece)

upling Exergonic Reactions to Endergonic Reac

as the contraction of muscle cells or the beatin

g substances across membranes against the dir

hing of endergonic reactions that would not occ

s from monomers

rgy powering cellular work.

ATP

is closely related

in nucleic acids.

denine bonded to

enine nucleotide

te groups in ATP

hen the end

lecule of inorganic

h now becomes

This is an

7.3 kcal of energy

rgy change measured in laboratory conditions.

h is 78% greater than the energy released in th

of the phosphate bonds release energy, the bo

hate bonds. Be careful to not see high-energ

igh-energy in this case means that the hydroly

ak and unstable, which allows for the energy ree are more stable than the ATP. Thus, the chan

e stability.

all negatively charged, being bonded together s

comparable to a loaded spring.

6

ions

of cilia

ction of spontaneous

ur spontaneously, such

In the cell, the actual

standard laboratory

ds are sometimes

and think that the

sis yields energy. In

leased when they aree is exergonic free

o closely results in


7/13


8/13


atoms of molecules, existing bonds must be broken and new bonds of the product must be formed.

The reactant molecules absorb energy from their surroundings (free energy) to break, and then release

the energy when the new bonds of the product molecules are formed.

The energy required to start a reaction (break the bonds) is the free energy of activationfree energy of activationfree energy of activationfree energy of activation, also known

as activation energyactivation energyactivation energyactivation energy (EA). It is usually provided through heat the molecules absorb. When the

molecules absorb enough energy to become unstable, the bonds will break. Remember, systems rich in

free energy become unstable, and seek to become stable (breaking bonds). The speed of the reactant

molecules is increased as they absorb more heat, which makes the molecules collide more often and

more forcefully. When the molecules settle into a new, more stable

bonding arrangement, energy is released into the surroundings. If

the reaction was exergonic, EA will be repaid, since the formation ofthe new bonds will give off more energy than was invested in the

activation energy.

In the graph of a reaction, the free energy of activation is

represented as the energy needed to push the reactants over a hill,

where the downhill portion is where the reaction actually takes

place. The graph at right shows hypothetical molecules being

rearranged in a chemical reaction. This is an exergonic reaction,

since the products have less free energy than the reactants.

Enzymes and Activation Energy

Proteins, DNA, and other complex molecules are rich in free

energy and have the potential to break down spontaneously.

They exist only because only a few molecules have sufficient

activation energy at a cells temperature to break them apart.

Occasionally, the barrier for certain reactions must be lowered,

or else metabolism could not take place. While heat speeds a

reaction, too much heat will kill cells. Thus, organisms use

catalysts.

Through lowering the AE barrier, the transition stage is

accessible even at moderate temperatures. An enzyme does

not change the G for a reaction. It only speeds up reactions that would eventually occur. Since

enzymes are so selective about which reactions they catalyze, they determine which chemical

processes will be occurring in the cell.


9/13


Enzymes are Substrate Specific

The reactant an enzyme acts on is referred to as its substratesubstratesubstratesubstrate. The enzyme binds to its substrate (or

substrates). When the two are joined, the catalytic action of the enzyme changes the substrate to the

product of the reaction.

An enzyme can distinguish its substrate from even closely related compounds, such as isomers, so that

each type of enzyme catalyzes a particular reaction. For instance, sucrose will only accept sucrose.

Enzymes, as proteins, have a unique three-dimensional shape that allows them to recognize their

substrates.

A restricted region of the enzyme molecule binds to the substrate this region is the active siteactive siteactive siteactive site, and

is typically a pocket or groove on the surface of the protein. While the active site is formed by only a

few of the enzymes amino acids, the R groups play a large part in reinforcing the shape of the active

site. When the substrate enters the active site, it induces the enzyme to change in its shape slightly

so the active site fits even more snugly around the substrate. This induced f itinduced fitinduced fitinduced fit brings chemical groups

of the active site into positions that help the enzyme catalyze the chemical reaction.

The Active Site is the Enzymes Catalytic Center

In an enzymatic reaction, the substrate binds to

the active site to form an enzyme-substrate

complex. The substrate is usually held in the

active site with weak bonds, such as hydrogen or

ionic bonds. Side chains of a few of the aminoacids in the active site catalyze the conversion of

substrate to product, and the product departs

from the active site. The enzyme can then take

another substrate molecule into its active site.

The entire cycle happens quickly, and a single

enzyme molecule can act on a thousand

substrate molecules per second.


10/13


An enzyme can catalyze both the forward and reverse reactions of reversible metabolic reactions.

Enzymes catalyze in the direction of equilibrium: if there is more A than B, enzymes will transform B to

A and vice versa.

There are different ways enzymes can lower activation energy and speed up a reaction. In reactions

involving two or more reactants, the active site provides a template for the substrates to come

together in the proper position for a reaction to occur. As the active site folds around the substrates,

the enzyme may stress the substrate molecules in order to stretch and bend critical chemical bonds

that need to broken. EA involves the energy needed to break bonds, thus, distorting the substrate

reduces the amount of heat energy needed to reach the transition state.

The active site could also provide a small environment that is conducive to a particular type ofreaction. For example, if the active site has amino acids with acidic side chains, the active site could

be a pocket of low pH in an otherwise neutral cell. The active site could move H+ into the substrate as

a key step in catalyzing the reaction.

Another mechanism involves brief covalent bonding between the substrate and a side chain of an

amino acid of the enzyme. Of course, the reaction will always restore the side chains to their original

state in order to keep the active site the same as before.

The rate at which a certain amount of enzyme converts substrate to product is partly a function of the

initial concentration of the substrate. The more substrate molecules there are, the more frequently

they can access the active sites of enzyme molecules. However, at a certain point, all enzymes will bebusy converting substrates and adding more substrate will not speed up the reaction. The enzyme is

said to be saturated at the point when enzymes are constantly converting substrates. The rate of the

reaction can then be determined by the speed at which the active site can convert substrate to

product. When an enzyme population is saturated, the only way to increase productivity is to add

more enzymes.

A Cells Physical and Chemical Environment Affects Enzyme Activity

Effects of Temperature and pH

As a protein, an enzyme has conditions in which it worksoptimally, because that environment favors the most active

conformation for the enzyme molecule.

Up to a point, the velocity of an enzymatic reaction will increase

with increasing temperature, partly because substrates will

collide with active sites more frequently when moving quickly.

Beyond a certain point, the speed will drop sharply, since too

much heat will denature the enzyme, which after all, is a protein.


11/13


The temperature to the left of the optimal temperature-mark

(dotted line) is perfectly fine for the enzyme. Although it may be

too cold to catalyze a reaction, the enzyme will still be in its

original form. After the optimal temperature, right of the dotted

line, the enzyme will be denatured.

Just as an enzyme has an optimal temperature, it also has a pH

at which it is most active. Most enzymes work best from pH 6-

8, but there are exceptions. Unlike temperature, enzymes

cannot fall too far down either side, or they will denature. If they

become either too acidic or too basic, they denature. In the

diagram to the right, the area within the dotted line denotes theacceptable range for the hypothetical enzyme.

Cofactors

Many enzymes require nonprotein helpers for catalytic activity. These adjuncts, called cofactorscofactorscofactorscofactors, may

be bound tightly to the active site as permanent residents, or they could bind loosely and reversibly

along with the substrate. Some cofactors are inorganic, such as zinc, iron, and copper ions. If the

cofactor is an organic molecule, it is called a coenzymecoenzymecoenzymecoenzyme. Most vitamins are coenzymes or raw

materials from which coenzymes are made.

Enzyme Inhibitors

Certain chemicals selectively prevent the action of specific

enzymes. If the inhibitor attaches to the enzyme with covalent

bonds, inhibition is usually permanent. However, reversible

inhibition occurs when the inhibitor binds with weak bonds.

Some reversible inhibitors are competitive inhibitorscompetitive inhibitorscompetitive inhibitorscompetitive inhibitors,

resembling the normal substrate and competing for entrance

into the active site. They can reduce the productivity of

enzymes by physically blocking the substrate from entering the

active site. This kind of inhibition can be overcome by

increasing substrate content where more substrate molecules

than inhibitor molecules are available to enter the sites.

Noncompetitive inhibitorsNoncompetitive inhibitorsNoncompetitive inhibitorsNoncompetitive inhibitors do not directly compete with the

substrate. Instead, they bind to another part of the enzyme,

which causes the active site to change shape and either

become unreceptive to substrate or less effective at catalyzing

conversion of substrate to product.


12/13


THE CONTROL OF METABOLISM

All a cells metabolic pathways are not open at the same time. A cell carefully regulates when and

where various enzymes are active by either switching on and off the genes that encode specific

enzymes or regulating the activity of enzymes.

Metabolic Control Often Depends on Allosteric Regulation

In many cases, molecules that naturally regulate enzyme activity in the cell behave like reversible

noncompetitive inhibitors. They change an enzymes shape and function by binding weakly to an

Allosteric siteAllosteric siteAllosteric siteAllosteric site, a specific receptor site on some part of the enzyme molecule away from the active site.

It can either inhibit or stimulate the enzymes activity through binding to it.

Allosteric Regulation

Most allosterically regulated enzymes are constructed from

two or more polypeptide subunits. Each subunit has its own

active site, and allosteric sites are often located where two

subunits are joined. The entire complex switches between

the two conformational states, of which one is active and

one is inactive. The binding of an activator to an allosteric

site stabilizes the shape with a functional active site, while

the binding of an inhibitor stabilizes the inactive form of theenzyme. The areas of contact between the subunits of an

allosteric enzyme fit in such a way that a conformation

change in one subunit is transmitted to all others. Thus, a

single activator or inhibitor molecule binding to one allosteric

site will affect the active sites of all subunits.

Sometimes, an inhibitor and an activator are similar enough

in shape to compete for the same allosteric site. For

example, some enzymes of catabolic pathways may have an

allosteric site fitting both AMP (adenosine monophosphate) and ATP, being activated by AMP and

inhibited by ATP. This makes sense because a purpose of catabolism is to make ATP: if there are too

many AMP, it will stimulate key enzymes to speed up catabolism and make more ATP. If there is a

large supply of ATP, the ATP will compete for allosteric sites and slow down the catabolism.


13/13


Feedback Inhibition

Feedback inhibitionFeedback inhibitionFeedback inhibitionFeedback inhibition is the switching off of a

metabolic pathway by its end product, which acts as

an inhibitor of an enzyme within the pathway. Once

the end product accumulates in enough numbers, it

will allosterically inhibit the enzyme for the first step

of the pathway. This prevents the cell from wasting

chemical resources to synthesize more of a product

than necessary.

Cooperativity

Similar to allosteric activation, substrate molecules may

stimulate the catalytic powers of an enzyme. Recall that the

binding of a substrate to an enzyme can induce a favorable

change in the shape of the enzymes active site. If an

enzyme has two or more subunits, an interaction with one

substrate molecule can trigger the same conformational

change in all other subunits. Called cooperaticooperaticooperaticooperativityvityvityvity, this

mechanism amplifies the response of enzymes to substrates:

one substrate molecule primes an enzyme to accept

additional substrate molecules more readily.

The Localization of Enzymes Within a Cell Helps Order Metabolism

Structures within the cell help bring order to metabolic pathways. In some cases, enzymes for several

steps of a metabolic pathway are arranged together as a multienzyme complex. The arrangement helps

control the sequence of reactions. Some enzymes and enzyme complexes have fixed locations in the

cell as structural components. Others are in solution with specific membrane-enclosed eukaryotic

organelles, each with its own internal chemical environment. For example, enzymes used in cellular

respiration are kept within mitochondria.

5887255 AP Bio Chapter Six an Introduction to Metabolism

Documents

Transcript of 5887255 AP Bio Chapter Six an Introduction to Metabolism