Chapter 8

A. 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

B. An Organism’s Metabolism Transforms Matter and Energy, Subject to the Laws of Thermodynamics

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

1. Organization of the Chemistry of Life into Metabolic Pathways

A metabolic pathway begins with a specific molecule and ends with a product

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

Cellular respiration, the breakdown of glucose in the presence of oxygen, is an example of a pathway of catabolism

Anabolic pathways consume energy to build complex molecules from simpler ones

The synthesis of protein from amino acids is an example of anabolism

Bioenergetics is the study of how organisms manage their energy resources

2. Forms of Energy

Energy is the capacity to cause change

Energy exists in various forms, some of which can perform work

• Kinetic energy is energy associated with motion

• Heat 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

3. The Laws of Energy Transformation

Thermodynamics is the study of energy transformations

A closed system 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

1. 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, but it cannot be created or destroyed

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

2. The Second Law of Thermodynamics

   During every energy transfer or transformation, some energy is unusable, and is often lost as entropy (disorder) of the universe

   Living cells unavoidably convert organized forms of energy to heat

   Spontaneous processes occur without energy input; they can happen quickly or slowly

   For a process to occur without energy input, it must increase the entropy of the universe

4. 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

Energy flows into an ecosystem in the form of light and exits in the form of heat

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

C. The Free-energy Change of a Reaction Tells Us Whether or Not the Reaction Occurs Spontaneously

Biologists want to know which reactions occur spontaneously and which require input of energy

To do so, they need to determine energy changes that occur in a chemical reaction

1. Free-Energy Change, DG

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

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

(T): ∆G = ∆H – T∆S

Only processes with a negative ∆G are spontaneous

Spontaneous processes can be harnessed to perform work

2. Free Energy, Stability, and Equilibrium

Free energy is a measure of a system’s instability, its tendency to change to a more stable state

During a spontaneous change, free energy decreases and the stability of a system increases

Equilibrium is a state of maximum stability

A process is spontaneous and can perform work only when it is moving toward equilibrium

3. Exergonic and Endergonic Reactions in Metabolism

An exergonic reaction proceeds with a net release of free energy and is spontaneous

An endergonic reaction absorbs free energy from its surroundings and is nonspontaneous

4. 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 defining feature of life is that metabolism is never at equilibrium

A catabolic pathway in a cell releases free energy in a series of reactions

D. ATP Powers Cellular Work by Coupling Exergonic Reactions to Endergonic Reactions

A cell does three main kinds of work:

• Chemical

• Transport

• Mechanical

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

Most energy coupling in cells is mediated by ATP

1. The Structure and Hydrolysis of ATP

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

ATP is composed of ribose (a sugar), adenine (a nitrogenous base), and three phosphate groups

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

1. The Structure and Hydrolysis of ATP

The three types of cellular work (mechanical, transport, and chemical) are powered by the hydrolysis of ATP

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

ATP drives endergonic reactions by phosphorylation, transferring a phosphate group to some other molecule, such as a reactant

The recipient molecule is now phosphorylated

3. The Regeneration of ATP

ATP is a renewable resource that is regenerated by addition of a phosphate group to adenosine diphosphate (ADP)

The energy to phosphorylate ADP comes from catabolic reactions in the cell

E. Enzymes Speed Up Metabolic Reactions by Lowering Energy Barriers

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

An enzyme is a catalytic protein

Hydrolysis of sucrose by the enzyme sucrase is an example of an enzyme-catalyzed reaction

1. 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

2. How Enzymes Lower the EA Barrier

Enzymes catalyze reactions by lowering the EA barrier

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

3. 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

4. Catalysis in the Enzyme’s Active Site

In an enzymatic reaction, the substrate binds to the active site of the enzyme

The active site can lower an EA barrier by

• Orienting substrates correctly

• Straining substrate bonds

• Providing a favorable microenvironment

• Covalently bonding to the substrate

5. Effects of Local Conditions on Enzyme Activity

An enzyme’s activity can be affected by":

• Chemicals that specifically influence the enzyme

• General environmental factors, such as temperature and pH

Temperature and pH

Each enzyme has an optimal temperature in which it can function

Each enzyme has an optimal pH in which it can function

Cofactors

Cofactors are nonprotein enzyme helpers

Cofactors may be inorganic (such as a metal in ionic form) or organic

An organic cofactor is called a coenzyme

Coenzymes include vitamins

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

Examples of inhibitors include toxins, poisons, pesticides, and antibiotics

F. Regulation of Enzyme Activity Helps Control Metabolism

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

A cell does this by switching on or off the genes that encode specific enzymes or by regulating the activity of enzymes

1. Allosteric Regulation of Enzymes

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

Allosteric regulation occurs when a regulatory molecule binds to a protein at one site and affects the protein’s function at another site

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

Activators 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

2. Identification of Allosteric Regulators

Allosteric regulators are attractive drug candidates for enzyme regulation

Inhibition of proteolytic enzymes called caspases may help the management of inappropriate inflammatory responses

3. 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