Define energy related to work and heat and matter

01 Nov 2019

Chapter 7:

Energy and Metabolism

SOLOMON • MARTIN • MARTIN • BERG

BIOLOGY

tenth edition

Energy Conversion

Cells obtain energy in many forms, and have mechanisms that convert energy from one form to another

Radiant energy is the ultimate source of energy for life

Photosynthetic organisms capture about 0.02% of the sun’s energy that reaches Earth, and convert it to chemical energy in bonds of organic molecules

7.1 Biological Work

Matter: anything that has mass and takes up space

Energy: the capacity to do work (change in state or motion of matter)

Expressed in units of work (kilojoules, kJ) or units of heat energy (kilocalories, kcal)

1 kcal = 4.184 kJ

Potential Energy and Kinetic Energy

Potential energy: capacity to do work as a result of position or state

Kinetic energy: energy of motion is used, work is performed

POTENTIAL

Energy of position

KINETIC

Energy of motion

Figure 7-1 Potential versus kinetic energy

The potential chemical energy released by cellular respiration is converted to kinetic energy in the muscles, which do the work of drawing the bow. The potential energy stored in the drawn bow is transformed into kinetic energy as the bowstring pushes the arrow toward its target.

Organisms Carry Out Conversions Between Potential/Kinetic Energy

Most actions involve a series of energy transformations that occur as kinetic energy is converted to potential energy – or potential energy to kinetic energy

Chemical energy: potential energy stored in chemical bonds

Example: Chemical energy of food molecules is converted to mechanical energy in muscle cells

7.2 The Laws of Thermodynamics

Thermodynamics governs all activities of the universe, from cells to stars

Biological systems are open systems that exchange energy with their surroundings

Closed

system

Closed

system

Surroundings

Figure 7-2 Closed and open systems

A closed system does not exchange energy with its surroundings.

(b) An open system exchanges energy with its surroundings.

The First Law of Thermodynamics

Energy cannot be created or destroyed

Energy can be transferred or converted from one form to another, including conversions between matter and energy

The energy of any system plus its surroundings is constant

Organisms must capture energy from the environment and transform it to a form that can be used for biological work

The Second Law of Thermodynamics

When energy is converted from one form to another, some usable energy (energy available to do work) is converted into heat that disperses into the surroundings

As a result, the amount of usable energy available to do work in the universe decreases over time

Heat: the kinetic energy of randomly moving particles

Entropy

The measure of the disorder or randomness of energy

Organized, usable energy has a low entropy

Disorganized energy, such as heat, has a high entropy

No energy conversion is ever 100% efficient

The total entropy of the universe always increases over time

7.3 Energy And Metabolism

Metabolism: all chemical reactions taking place in an organism

Includes many intersecting chemical reactions

Two main types:

Anabolism: pathways in which complex molecules are synthesized from simpler substances

Catabolism: pathways in which larger molecules are broken down into smaller ones

Enthalpy is the Total Potential Energy of a System

Every specific type of chemical bond has a certain amount of bond energy: the energy required to break that bond

Enthalpy is equivalent to the total bond energy

Free Energy is Available to do Cell Work

Free energy: the amount of energy available to do work under the conditions of a biochemical reaction

Enthalpy (H), free energy (G), entropy (S); and absolute temperature (T) are related:

H = G + TS

As entropy increases, the amount of free energy decreases

Changes in Free Energy

Although the total free energy of a system (G) can’t be measured, changes in free energy can be measured

The rearranged equation can be used to predict whether a particular chemical reaction will release energy or require an input of energy:

Δ G = Δ H − T Δ S

Free Energy Decreases During an Exergonic Reaction

Exergonic reaction: releases energy and is a “downhill” reaction, from higher to lower free energy

ΔG is a negative number for exergonic reactions

A certain amount of activation energy is required to initiate every reaction, even a spontaneous one

Free Energy Increases During an Endergonic Reaction

Endergonic reaction: a reaction in which there is a gain of free energy

ΔG has a positive value: the free energy of the products is greater than the free energy of the reactants

Requires an input of energy from the environment

Figure 7-3 Exergonic and endergonic reactions

In an exergonic reaction, there is a net loss of free energy. The products have less free energy than was present in the reactants, and the reaction proceeds spontaneously.

(b) In an endergonic reaction, there is a net gain of free energy. The products have more free energy than was present in the reactants.

Diffusion is an Exergonic Process

Randomly moving particles diffuse down their own concentration gradient

Free energy decreases as entropy increases

Concentration gradient: an orderly state with a region of higher concentration and another region of lower concentration

A cell must expend energy to produce a concentration gradient

Free-Energy Changes and the Concentrations of Reactants/Products

Free-energy changes in a chemical reaction depend on the difference in bond energies between reactants and products

Also depends on concentrations of both reactants and products

A reaction that proceeds forward and in reverse at the same time eventually reaches dynamic equilibrium

Changes in Free Energy (cont’d.)

If the reactants have much greater free energy than the products, most of the reactants are converted to products and vice-versa

If the concentration of reactants is increased, the reaction will “shift to the right” and vice-versa

The reaction always shifts to reestablish equilibrium

Cells Drive Endergonic Reactions by Coupling Them

Endergonic reactions are coupled to exergonic reactions

Coupled reactions: thermodynamically favorable exergonic reaction provides energy required to drive a thermodynamically unfavorable endergonic reaction

In a living cell the exergonic reaction often involves the breakdown of ATP

Coupled Reactions (cont’d.)

Two reactions taken together are exergonic:

(1) A → B ΔG = +20.9 kJ/mol (+5 kcal/mol)

(2) C → D ΔG = −33.5 kJ/mol (−8 kcal/mol)

Overall ΔG = −12.6 kJ/mol (−3 kcal/mol)

Reactions are coupled if pathways are altered for a common intermediate link:

(3) A + C → I ΔG = −8.4 kJ/mol (−2 kcal/mol)

(4) I → B + D ΔG = −4.2 kJ/mol (−1 kcal/mol)

Overall ΔG = −12.6 kJ/mol (−3 kcal/mol)

7.4 ATP, Energy Currency of the Cell

Adenosine triphosphate (ATP): Nucleotide consisting of adenine, ribose, and three phosphate groups

The cell uses energy that is temporarily stored in ATP

Hydrolysis of ATP yields ADP and inorganic phosphate

ATP Donates Energy

Hydrolysis of ATP can be coupled to endergonic reactions in cells, such as the formation of sucrose

ATP + H2O → ADP + Pi

ΔG = −32 kJ/mol (or −7.6 kcal/mol)

glucose + fructose → sucrose + H2O

ΔG = +27 kJ/mol (or +6.5 kcal/mol)

glucose + fructose + ATP → sucrose + ADP + Pi

ΔG = −5 kJ/mol (−1.2 kcal/mol)

ATP Donates Energy (cont’d.)

The intermediate reaction in the formation of sucrose is a phosphorylation reaction: phosphate group is transferred to glucose to form glucose-P

glucose + ATP → glucose-P + ADP

glucose-P + fructose → sucrose + Pi

ATP Links Exergonic and Endergonic Reactions

Exergonic reactions

release energy

Energy released drives

endergonic reactions

Figure 7-6 ATP links exergonic and endergonic reactions

Exergonic reactions in catabolic pathways (top) supply energy to drive the endergonic formation of ATP from ADP. Conversely, the exergonic hydrolysis of ATP supplies energy to endergonic reactions in anabolic pathways (bottom).

The Cell Maintains a Very High Ratio of ATP to ADP

A typical cell contains more than 10 ATP molecules for every ADP molecule

High levels of ATP makes its hydrolysis reaction more strongly exergonic, and more able to drive coupled endergonic reactions

The cell cannot store large quantities of ATP

ATP is constantly used and replaced

7.5 Energy Transfer in Redox Reactions

Energy is transferred through the transfer of electrons from one substance to another

Oxidation: substance loses electrons

Reduction: substance gains electrons

Redox reactions often occur in a series of electron transfers

For cellular respiration, photosynthesis, and many other chemical processes

Electron Carriers Transfer Hydrogen Atoms

Redox reactions in cells usually involve the transfer of a hydrogen atom

An electron, along with its energy, is transferred to an acceptor molecule such as nicotinamide adenine dinucleotide (NAD+), which is reduced to NADH

XH2 + NAD+ → X + NADH + H+

NAD+ (oxidized)

NADH (reduced)

Nicotinamide

Ribose

Adenine

Ribose

Phosphate

Figure 7-7 NAD+ and NADH

NAD+ consists of two nucleotides, one with adenine and one with nicotinamide, that are joined at their phosphate groups. The oxidized form of the nicotinamide ring in NAD+ (left) becomes the reduced form in NADH (right) by the transfer of 2 electrons and 1 proton from another organic compound (XH2), which becomes oxidized (to X) in the process.

Electron Carriers (cont’d.)

An electron progressively loses free energy as it is transferred from one acceptor to another

In cellular respiration, NADH transfers electrons to another molecule

Energy is then transferred through a series of reactions that result in formation of ATP

NADP+ is not involved in ATP synthesis

Electrons of NADPH are used to provide energy for photosynthesis

Other Important Electron Carriers

Flavin adenine dinucleotide (FAD): nucleotide that accepts hydrogen atoms and their electrons

Reduced form is FADH2

Cytochromes: proteins that contain iron

The iron component accepts electrons from hydrogen atoms, then transfers the electrons to some other compound

Cells regulate rates of chemical reactions with enzymes, which increase speed of a chemical reaction without being consumed by the reaction

Example: Catalase has the highest known catalytic rate; it protects cells by destroying hydrogen peroxide (H2O2)

Most enzymes are proteins, but some types of RNA molecules also have catalytic activity

7.6 Enzymes

All Reactions Have a Required Energy of Activation

Even a strongly exergonic reaction may be prevented from proceeding by the activation energy required to begin the reaction

Energy of activation (EA) or activation energy: the energy required to break existing bonds and begin a reaction

Figure 7-10 Activation energy and enzymes

An enzyme speeds up a reaction by lowering its activation energy (EA). In the presence of an enzyme, reacting molecules require less kinetic energy to complete

a reaction.

An Enzyme Works By Forming an Enzyme–Substrate Complex

An enzyme controls the reaction by forming an unstable intermediate complex with a substrate

When the ES complex breaks up, the product is released

Enzyme molecule is free to form a new ES complex:

enzyme + substrate(s) → ES complex

ES complex → enzyme + product(s)

Active Sites

Enzymes bind to active sites to position substrates close together to speed up the reaction

Induced fit: binding of substrate to enzyme causes a change in shape to enzyme

Distorts the chemical bonds of the substrate

Proximity and orientation of reactants, plus strains in their chemical bonds, facilitate the breakage/formation of products

Enzymes are Specific

Due to shape of active site and its relationship to the shape of the substrate

Some are specific only to a certain chemical bond

Example: lipase splits ester linkages in many fats

Scientists classify enzymes into six classes that catalyze similar reactions

Each class is divided into many subclasses

TABLE 7-1 Important Classes of Enzymes

Many Enzymes Require Cofactors

Some enzymes have two components: an apoenzyme and a cofactor

Neither alone has catalytic activity, enzyme functions only when the two combined

Cofactors may be a specific metal ion

Iron, copper, zinc, and manganese all function as cofactors

Coenzymes

Organic, nonpolypeptide compound that binds to the apoenzyme and serves as a cofactor

Most are carrier molecules:

NADH, NADPH, and FADH2 transfer electrons

ATP transfers phosphate groups

Coenzyme A transfers groups derived from organic acids

Most vitamins are coenzymes or components of coenzymes

Each Enzyme Has an Optimal Temperature

Figure 7-12 The effects of temperature on enzyme activity

(a) Generalized curves for the effect of temperature on enzyme activity. As temperature increases, enzyme activity increases until it reaches an optimal temperature.

Enzyme activity abruptly falls after it exceeds the optimal temperature because the enzyme, being a protein, denatures.

Heat-Tolerant Archaea

Certain archaea have enzymes that allow them to survive in extreme habitats

Figure 7-13 Grand Prismatic Spring in Yellowstone National Park

The world’s third-largest spring, about 61 m (200 ft) in diameter, the Grand Prismatic Spring teems with heat-tolerant archaea. The rings around the perimeter, where the water is slightly cooler, get their distinctive colors from the various kinds of archaea living there.

Each Enzyme has an Optimal pH

Optimal pH for most human enzymes is 6 to 8

Figure 7-12b The effects of pH on enzyme activity

(b) Enzyme activity is very sensitive to pH. Pepsin is a protein-digesting enzyme in the very acidic stomach juice. Trypsin, secreted by the pancreas into the slightly

basic small intestine, digests polypeptides.

Enzymes in Metabolic Pathways

Metabolic pathway: the product of one enzyme-controlled reaction serves as substrate for the next in series of reactions

Removal of intermediate and final products drives the sequence of reactions in a particular direction

Enzymes can bind to one another to form a multienzyme complex that transfers intermediates in the pathway from one active site to another

The Cell Regulates Enzymatic Activity

Gene control: a specific gene directs synthesis of each type of enzyme

Gene may be switched on by a signal from a hormone or other signal molecule

Amounts of enzymes influence overall cell reaction rate

Rate of a reaction can be limited by enzyme concentration or by substrate concentration

Figure 7-14 The effects of enzyme concentration and substrate concentration on the rate of a reaction.

In this example the rate of reaction is measured at different enzyme concentrations, with an excess of substrate present. (Temperature and pH are constant.) The rate of the reaction is directly proportional to the enzyme concentration.

(b) In this example the rate of the reaction is measured at different substrate concentrations, and enzyme concentration, temperature, and pH are constant. If the

substrate concentration is relatively low, the reaction rate is directly proportional to substrate concentration. However, higher substrate concentrations do not increase the reaction rate because the enzymes become saturated with substrate.

The Cell Regulates Enzymatic Activity (cont’d.)

The product of one enzymatic reaction may control activity of another enzyme in a sequence of enzymatic reactions

When concentration of a product is low, the sequence of reactions proceeds rapidly

When concentration of a product is high, reactions stop

The Cell Regulates Enzymatic Activity (cont’d.)

Feedback inhibition

Enzyme regulation in which the formation of a product inhibits an earlier reaction in the sequence

The Cell Regulates Enzymatic Activity (cont’d.)

Some enzymes have an allosteric site that modifies the enzyme’s activity when an allosteric regulator is bound to it

Allosteric inhibitors keep the enzyme in its inactive shape

Allosteric activators result in a functional active site

Example: cAMP-dependent protein kinase

Cyclic AMP

Active

site

Allosteric

site

Regulator

(inhibitor)

Substrates

Figure 7-16 An allosteric enzyme

(a) Inactive form of the enzyme. The enzyme protein kinase is inhibited by a regulatory protein that binds reversibly to its allosteric site. When the enzyme is in this

inactive form, the shape of the active site is modifed so that the substrate cannot combine with it.

(b) Active form of the enzyme. Cyclic AMP removes the allosteric inhibitor and activates the enzyme.

Enzymes Are Inhibited by Certain Chemical Agents

Substrates

Active site

Active site not suitable

for reception of substrates

Enzyme

Inhibitor

Enzyme

Substrate

Inhibitor

Inhibitor binds to

active site

Figure 7-17 Competitive and noncompetitive inhibition (Reversible inhibition)

Competitive inhibition. The inhibitor competes with the normal substrate for the active site of the enzyme. A competitive inhibitor occupies the active site only temporarily.

(b) Noncompetitive inhibition. The inhibitor binds with the enzyme at a site other than the active site, altering the shape of the enzyme and thereby inactivating it.

Enzyme Inhibition (cont’d.)

Irreversible inhibition: inhibitor permanently inactivates or destroys an enzyme when the inhibitor combines with one of the enzyme’s functional groups, either at the active site or elsewhere

Many poisons are irreversible enzyme inhibitors, such as mercury and lead, nerve gases, cyanide

Some Drugs are Enzyme Inhibitors

Some drugs used to treat bacterial infections directly or indirectly inhibit bacterial enzyme activity

Example: sulfa drugs compete with PABA for the active site of the bacterial enzyme

Example: penicillin and related antibiotics irreversibly inhibit the bacterial enzyme transpeptidase

Drug resistance is a growing problem

Assignment

1. Define energy related to work and heat and matter

2. Use some examples to contrast potential energy and kinetic energy and differentiate with chemical energy

3. Define the concept of thermodynamic

4. Briefly give me your concept of entropy and importance in the Universe

5. Distinguish between exergonic and endergonic reaction

6. Discuss the central role of ATP in the overall energy metabolism of the cell

7. Explain how an enzyme lowers the required energy of activation for a reaction

8. Name 4 important classes of enzymes

9. Importance of pH in the function of enzymes

10. Briefly explain how antibiotics inhibit bacterial enzymes

Define energy related to work and heat and matter

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