AN ORGANISM’S METABOLISM

CHAPTER 8:AN INTRODUCTION TO METABOLISM

The living cell is a chemical factory in miniature

Examples are:Sugars can be converted to amino acidsAmino acids are linked together to make proteinsProteins are dismantled into amino acids that can be converted to sugarsSmall molecules are assembled into polymersPolymers may be hydrolyzed as needs of the cell changeFungus cells converting energy stored in organic molecules to light

AN ORGANISM’S METABOLISMThe totality of an organism’s chemical reactions is called metabolism

We can picture a cell’s metabolism as an elaborate road map of intersecting metabolic pathways

Each step of the pathway is catalyzed by a specific enzyme

Cells also have many mechanisms that regulate enzymes balance metabolic supply and demand, averting deficits or surpluses of important cellular molecules

Catabolic vs. AnabolicCatabolic pathways (breakdown pathways): release energy by breaking down complex molecules to simpler compounds

Ex: cellular respirationThe energy becomes available to do work in the cell

Anabolic pathways (biosynthetic pathways) consume energy to build complicated molecules

Ex: synthesis of a proteinRequires addition of energy (often from ATP)

Bioenergetics of the cell Study of how energy flows through living organisms

Energy is the capacity to cause change. Some forms of energy can be used to do work

Life depends on the ability of cells to transform energy form one type into another

The two main types of energy:Kinetic energyPotential energy

Kinetic energyAssociated with moving objects. Objects that move can perform work by imparting motion to other objects. Ex:

pool playerwater gushing over a dam turns turbinescontraction of leg muscle pushes bicycle pedal

Types of kinetic energy

HeatHeat (or thermal energythermal energy) it is energy associated with the random movement of atoms or molecules

LightLight is also a type of energy that can be harnessed to perform work, such as powering photosynthesis in green plants

Potential energyIt is energy that matter possesses because of its location or structure. Ex:

water behind a dam (why??)

Types of potential energyChemical energy is a term that refers to the potential energy available for release in a chemical reaction

Complex molecules, such as glucose, are high in chemical energy. Ex:

GasolineFood, oxygen

During what type of metabolic reaction will this energy be released?? (anabolic / catabolic)

What is the energy situation?

Laws of ThermodynamicsThermodynamics is the study of energy transformations

System: matter under study

Surroundings: as everything outside the system (rest of the universe)

An isolated system is unable to exchange either energy or matter with its surroundings

An open system can exchange energy and matter with its surroundings

Are organisms open or closed systems??

The First Law of ThermodynamicsThe principle of conservation of energy

“Energy can be transferred and transformed, but it cannot be created or destroyed”

= energy of the universe is constant

Question: do plants create energy??

Question: why can’t organisms simply recycle their energy over and over again?

The Second Law of ThermodynamicsDuring energy transfer or transformation, some energy becomes unavailable to do work. Usually, it is lost as heat.

Only a small fraction of the chemical energy from the food is transformed into the motion of the cheetah. Most is lost as heat (only ~ 10% is available for work at each trophic level)

Universal Disorder = EntropyThis ‘lost energy’ makes the universe more and more disordered

Entropy is a measure of the level of disorder or randomness

There is an unstoppable trend toward randomization of the universe as a whole. This is stated in the second law of thermodynamics

The Second Law of Thermodynamics

“Every energy transfer or transformation increases the entropy of the universe”

Spontaneous or nonspontaneous? A spontaneous process is one that can occur without an input of energy

Processes that occur spontaneously increase the entropy of the universe

Processes that cannot occur on their own are said to be nonspontaneous (energy must be added to the system in order for them to occur)

What about living systems?? Living systems increase the entropy of their surroundings

On a larger scale, energy flows into an ecosystem in the form of light and exits in the form of heat (refer to Fig 1.5)

The entropy of a particular system may actually decrease as long as the total entropy of the universe increases

Thus, organisms are islands of low entropy in an increasingly random universe

FREE ENERGY AND SPONTANEOUS REACTIONS

As biologists, we want to understand which reactions occur spontaneously and which ones require some input of energy from outside

Gibbs free energy is symbolized by the letter G. Free energy is the portion of a system’s energy that can perform work when temperature and pressure are uniform throughout the system, as in a living cell

Gibbs free energy

The change in free energy can be calculated with one of the following formulas:

∆G = ∆H – T ∆S

∆H is change in the system’s enthalpy (total energy)T is absolute temperature (in Kelvin units, K = ˚C + 273)∆S is change in the system’s entropy

∆G = Gfinal state - Ginitial state

A century of experiments has shown…∆G < 0 in all spontaneous processes (∆G is negative)

A process that is spontaneous will have more free energy at the beginning and less free energy at the end

This can be achieved by:-decreasing enthalpy (H) = losing total energy-by reducing order (increase in T∆S, increase in entropy)-or both

Spontaneous changes can be harnessed to perform work!!

Processes that have positive ∆G, or a ∆G = 0 are nonspontaneous

Two concepts related to free energy are stability and equilibrium

High Free Energy (G)Systems with high free energy are unstable, and tend to change in such a way that allows them to become more stable

A reaction is in equilibrium when the forward and backward reactions occur at the same rate. When a reaction proceeds toward equilibrium, the free energy decreases

While a reaction is moving toward equilibrium, it will be spontaneous and can perform work

Free energy increases when a reaction is somehow pushed away from equilibrium

Exergonic and Endergonic Reactions in Metabolism

Based on their free-energy changes, chemical reactions can be classified as either exergonic (energy outward) or endergonic (energy inward)

An exergonic reaction proceeds with a net release of free energy (∆G is negative). They occur spontaneously.

Ex: overall reaction for cellular respiration:

C6H12O6 + 6O2 6CO2 + 6H2O

∆G = - 686 kcal/mol

An endergonic reaction is one that absorbs free energy from its surroundings

The reaction will store free energy in molecules. ∆G is positive (non-spontaneous reaction)

The magnitude of ∆G is the quantity of energy required to drive the reaction

Ex: How much energy is needed to create glucose?

Where do plants get this energy from??

Equilibrium and Metabolism

An isolated system will eventually reach equilibrium, and then can’t do any work

Living cells (and most systems) are not in equilibrium.

A cell that has reached metabolic equilibrium is dead!

A catabolic pathway in a cell releases free energy in a series of reactions. An example is cellular respiration

Most of the reactions involved in respiration are reversible, but they are constantly ‘pulled’ in one direction, so they never reach equilibrium

The product of the reaction does not accumulate and becomes a reactant in the next step. Finally, waste products are expelled from the cell.

As long as cells have a steady supply of glucose or other fuels and oxygen, and are able to expel waste products to the surroundings, equilibrium is never reached and the work of life can continue

ATP POWERS CELLULAR WORKChemical work: driving endergonic reactions (non spontaneous), such as synthesis of polymers.

Transport work: pumping substances across membranes against the direction of spontaneous movement.

Mechanical work: such as the beating of cilia, contraction of muscle cells, movement of chromosomes

How? By coupling exergonic reactions to endergonic reactions

Structure and Hydrolysis of ATP

ATP (adenosine triphosphate) contains:Ribose (sugar)Adenine (nitrogenous base)A chain of three phosphate groups bonded to it

The bonds between the phosphate groups of ATP can be broken by hydrolysis

When the terminal phosphate bond is broken, a molecule of inorganic phosphate (HOPO3

2-) leaves the ATP, which becomes ADP

The reaction is exergonic and releases 7.3 kcal of energy per mol of hydrolyzed ATP (standard conditions)

ATP + H2O ADP + Pi

∆G = ?

The actual ∆G is about 13 kcal/mol (79% greater)

Cells manage their energy resources to do this work by doing energy coupling: the use of an exergonic process to drive and endergonic one

The reactants (ATP + H2O) have higher energy than the products. The release of energy during the hydrolysis of ATP comes from the chemical change to a state of lower free energy

The cell’s proteins harness the energy released during ATP hydrolysis in several ways to perform the three types of cellular work: chemical, transport and mechanical

Two reactions (endergonic + exergonic) can be coupled so that the overall reaction is exergonic

ATP and cell work

With the help of specific enzymes, the energy released by ATP hydrolysis is used to drive chemical reactions

The recipient of the phosphate group is then said to be phosphorylated

The phosphorylated intermediate is more reactive (less stable) than the original unphosphorylated molecule

Transport: powered by the hydrolysis of ATP

+ Pi = change in a protein’s shape = ability to bind another molecule

Sometimes this occurs via a phosphorylated intermediate

Mechanical work: powered by the hydrolysis of ATP

Mechanical work involves motor proteins moving along the cytoskeletal elements

ATP cycle

ATP = a renewable resource!

The free energy required to phosphorylate ADP comes from exergonic breakdown reactions (catabolism) in the cell

The ATP cycle couples the cell’s energy-yielding (exergonic processes) to the energy-consuming (endergonic) ones

Did you know??

In a working muscle cell, the whole ATP pool is recycled in less then a minute:

10 million molecules of ATP are consumed and regenerated per second per cell (600_million/minute)

ENZYMES SPEED UP METABOLIC RACTIONS

An enzyme is a macromolecule that acts as a catalyst: it speeds up a reaction without being consumed (we will focus on enzymes that are proteins)

Every chemical reaction between molecules involves both bond breaking and bond forming

Changing one molecule into another generally involves an intermediate step in which the molecule is highly unstable

In the instable state, bonds can be changed

In order to achieve the highly unstable state, the reactant molecules must absorb energy

This energy is called free energy of activation or activation energy

At the summit, the reactants are in an unstable condition known as the transition state

They are activated and their bonds can be broken

The bonds of the reactants break only when the molecules have absorbed enough energy to become unstable

As the atoms settle into their new, more stable bonding arrangements, energy is released to the surroundings

Activation energy provides a barrier that determines the rate of the reaction

For some reactions, the activation energy is modest enough that even at room temperature there is sufficient thermal energy for many of the reactants to reach the transition state in a short time. In most cases, however, it is very high

Enzymes Lower the Activation Energy Barrier

Proteins, DNA and complex molecules are rich in free energy and have the potential to decompose spontaneously.

Heat speeds a reaction by allowing reactants to attain the transition (unstable) state more often, but this solution would be inappropriate for biological systems:

1. High temp denatures proteins and kills cells

2. Heat would speed up all reactions

So the alternative is catalysis. An enzyme catalyzes a reaction by lowering the activation energy barrier

More on enzymes

An enzyme cannot change the ∆G for a reaction, and it cannot make an endergonic reaction exergonic

Enzymes can only hasten reactions that would occur eventually anyway

They also make it possible for the cell to have a dynamic metabolism

Substrate Specificity of EnzymesEnzymes act on another substance (substrate)

The enzyme binds to its substrate(s), forming an enzyme-substrate complex. The catalytic action of the enzyme converts the substrate to the product(s)

Enzyme + Enzyme- Enzyme +Substrate(s) > substrate > Product(s)

Complex

Ex: sucraseEnzymes = proteins

Proteins are macromolecules with a unique 3D configuration

The specificity of an enzyme results from its shape, which is a consequence of … ???

Only a small part of the enzyme actually binds to the substrate: active site

Active Site

It is typically a pocket or groove on the surface of the proteinwhere catalysis occurs

Specificity of an enzyme

Attributed to a compatible fit between the shape of its active site and the shape of the substrate

As the substrate enters the active site, interactions between its chemical groups and those on the R groups (side chains) of the amino acids from the active site cause the enzyme to change its shape slightly so that the active site fits even moresnugly around the substrate = induced fit

Catalysis in the Enzyme’s Active Site

The substrate is held in the active site by weak interactions.

R groups of a few amino acids catalyze the conversion of substrate to product, and the product departs from the active site

The enzyme is then free to take another substrate molecule into its active site

Very fast!!

A single enzyme molecule typically acts on about a thousand substrate molecules per second

Some enzymes are much faster

Very small amounts of enzyme can have a huge metabolic impact

Mechanisms by which enzymes lower activation energy 1. The active site provides a template on which the substrates

can come together in the proper orientation for the reaction to occur

2. As the active site or an enzyme clutches to the bound substrates, it may stress or bend critical chemical bonds that must be broken during the reaction. Distorting the substrate helps it approach the transition state and thus reduces the amount of free energy that must be absorbed to achieve that state

3. The active site may also provide a microenvironment that is more conductive to a particular type of reaction than the solution itself would be without the enzyme. Ex: the active site may be a pocket of low pH, so an acidic amino acid may facilitate H+ transfer to the substrate as a key step in catalyzing the reaction.

4. Direct participation of the active site in the chemical reaction by brief covalent bonding

Saturation of an enzymeThe rate at which an enzyme converts substrate to product partly depends on the initial concentration of the substrate

There is a limit at which the enzyme is said to be saturated: the rate of the reaction is determined by the speed at which the active site converts substrate to product.

At this point, what can you do to increase the rate of product formation ???

Effects of Local Conditions on Enzyme Activity

Each enzyme is going to have a set of optimal conditionsin which it has the most active shape

A. Effects of Temperature

B. Effects of pH

C. Cofactors

D. Enzyme Inhibitors

A. Effects of Temperature

The rate of an enzymatic reaction increases with increasing temperature, because substrates collide with active sites more frequently while moving rapidly

Above a certain temperature, the speed of enzymatic reaction drops sharply: the thermal agitation of the enzyme molecule disrupts the weak interactions

Most human enzymes have optimal temperatures of about 35-40 ˚C. Thermophilic bacteria that live in hot springs contain enzymes with optimal temperatures of 70 ˚C

B. Effects of pHEach enzyme also has an optimal pH, at which it is most active

For most enzymes, optimal pH is between 6-8, but there are exceptions:

Pepsin is a digestive enzyme in our stomach, it works best at ~pH 2Trypsin is a digestive enzyme present in the alkaline environment of the human intestine, and has an optimal pH of 8

C. Cofactors

Many enzymes require non-protein helpers, called cofactors, for catalytic activity:

Bind tightly (permanent)Loosely to the enzyme (with the substrate)

If the cofactor is an organic molecule, it is called a coenzyme.

Did you know??

Most vitamins are important in nutrition because they act as coenzymes or raw materials from which coenzymes are made

D. Enzyme Inhibitors

Certain chemicals inhibit the action of specific enzymes. It can be:

Reversible (weak interactions)Irreversible (covalent bonds)

Some reversible inhibitors resemble the normal substrate molecule and compete for admission into the active site

Competitive InhibitorsThey reduce the productivity of enzymes by blocking substrates from entering active sites. This kind of inhibition can be overcome by increasing the concentration of the substrate.

Non-competitive Inhibitors

They do not directly compete with the substrate, instead they impede enzymatic reactions by binding to another part of the enzyme.

Regulation: molecules naturally present in the cell often regulate enzyme activity by acting as inhibitors. Such selective inhibition is essential to the control of cellular metabolism

Toxins and Poisons

They are often irreversible enzyme inhibitors (Sarin: released in Tokyo subway 1995)

Many antibiotics are inhibitors of specific enzymes in bacteria (Penicillin: blocks synthesis of peptidoglycan used by many bacteria in their cell walls)

REGULATION OF ENZYME ACTIVITYIntrinsic to the process of life is a cell’s ability to tightly regulate its metabolic pathways by controlling when and where its various enzymes are active

Allosteric Regulation

They act as reversible non-competitive inhibitors

Via noncovalent interactions, they bind to the enzyme and change its shape and the functionality of the active sites

Allosteric Activation and Inhibition

Most enzymes that are regulated allosterically consist of two or more subunits, each composed of a polypeptide chain and having its own active site

The entire complex changes between two different shapes:Catalitically activeInactive

Case 1 (Allosteric Regulation)

An activating or inhibiting regulatory molecule binds to a regulatory site (allosteric site)

Activating molecule: stabilizes the shape that has functional active sites

Inhibiting molecule: stabilizes the inactive form of the enzyme

ATP and Allosteric Regulation

ATP plays a complex role in balancing the flow of traffic between anabolic and catabolic pathways by affecting key enzymes

ATP functions as an inhibitor: it binds to several catabolic enzymes allosterically, lowering their affinity for substrate

ADP functions as an activator of the same enzymes

WHY ???

A major function of catabolism is to regenerate ATP

When ATP production lags behind, ADP accumulates and activates the enzymes to speed up catabolism

If there is too much ATP, then catabolism slows down, as ATP inhibits the enzymes

Cooperativity = allosteric activation

The binding of one substrate molecule to one active site stimulates the catalitic powers of the enzyme by affecting the other active sites

When a substrate causes induced fit in one subunit can trigger the same change in the other sub units

This mechanism amplifies the response of enzymes to substrates The first substrate molecule primes the enzyme to accept

additional substrate molecules more readily

FEEDBACK INHIBITION

Occurs when a metabolic pathway is switched off by he inhibitory binding of its end product to an enzyme that acts early in the pathway

Example: as isoleucine accumulates, it slows down its own synthesis by allostarically inhibiting the enzyme in the first step of the pathway

Prevents the cell from wasting chemical resources

Location of Enzymes in the CellRemember that cells are not bags of chemicals

The cell is compartimentalized, and the cellular structures bring order to metabolic pathways

In some cases, enzymes required for a specific pathway are assembled into a multienzyme complex

Some enzymes and enzyme complexes have fixed locations within the cell and are structural components of particular membranes

Other enzymes are in solution within a specific organelle.

Example: enzymes for cellular respiration reside in specific locations within the mitochondria