Molecular and Cellular Biology: Enzymes

energy of activation

needed energy to initiate chemical reaction The activation energy needed to spark an exergonic or endergonic reaction can be heat energy or chemical energy. Reactions that require activation energy can also proceed in the presence of biological catalysts.

Adenosine diphosphate

Adenosine diphosphate and the phosphate ion can be reconstituted to form ATP, much like a battery can be recharged. To accomplish this, synthesis energy must be available. This energy can be made available in the cell through two extremely important processes: photosynthesis, and cellular respiration. These processes depend on the activities of a special group of coenzymes. Three important coenzymes are nicotinamide adenine dinucleotide (NAD), nicotinamide adenine dinucleotide phosphate (NADP), and flavin adenine dinucleotide (FAD)

denatured

An enzyme altered by heat

exergonic reaction

Any chemical reaction in which energy is released the products end up with less energy than the reactants.

The Laws of Thermodynamics

Energy has been expressed in terms of reliable observations known as the laws of thermodynamics.There are two such laws: 1."energy can neither be created nor destroyed." This law implies that the total amount of energy in a closed system (for example, the universe) remains constant. Energy neither enters nor leaves a closed system. Within a closed system, energy can change, however. For instance, the chemical energy in gasoline is released when the fuel combines with oxygen and a spark ignites the mixture within a car's engine. The gasoline's chemical energy is changed into heat energy, sound energy, and the energy of motion. 2. "that the amount of available energy in a closed system is decreasing constantly." Energy becomes unavailable for use by living things because of entropy,which is the degree of disorder or randomness of a system. The entropy of any closed system is constantly increasing. In essence, any closed system tends toward disorganization. Unfortunately, the transfers of energy in living systems are never completely efficient. Every body movement, every thought, and every chemical reaction in the cells involves a shift of energy and a measurable decrease of energy available to do work in the process. For this reason, considerably more energy must be taken into the system than is necessary to carry out the actions of life.

cofactors

Many enzymes are assisted by chemical substances called cofactors. Cofactors may be ions or molecules associated with an enzyme and are required in order for a chemical reaction to take place. Ions that might operate as cofactors include those of iron, manganese, and zinc. Organic molecules acting as cofactors are referred to as coenzymes

coenzymes

Organic molecules acting as cofactors are referred to as coenzymes. Examples of coenzymes are NAD and FAD (see the "ATP Production" section later in this chapter).

energy

Physicists define energy as the ability to do work; in this case, the work is the continuation of life itself.

Enzymes

The chemical reactions in all cells of living things operate in the presence of biological catalysts called enzymes. Because a particular enzyme catalyzes only one reaction, there are thousands of different enzymes in a cell catalyzing thousands of different chemical reactions. All enzymes are composed of proteins. When an enzyme functions, a key portion of the enzyme, called the active site,interacts with the substrate.

Adenosine Triphosphate (ATP)

The chemical substance that serves as the currency of energy in a cell is adenosine triphosphate (ATP). ATP is referred to as currency because it can be "spent" in order to make chemical reactions occur. The more energy required for a chemical reaction, the more ATP molecules must be spent. Virtually all forms of life use ATP, a nearly universal molecule of energy transfer. The energy released during catabolic reactions is stored in ATP molecules. In addition, the energy trapped in anabolic reactions (such as photosynthesis) is trapped in ATP molecules.

oxidation

The removal of electrons or protons from a coenzyme

chemical reaction

To initiate a chemical reaction, a type of "spark," referred to as the energy of activation,is needed. For example, hydrogen and oxygen can combine to form water at room temperature, but the reaction requires activation energy.

active site

When an enzyme functions, a key portion of the enzyme, called the active site,interacts with the substrate closely matches the molecular configuration of the substrate. After this interaction has taken place, a change in shape in the active site places a physical stress on the substrate. This physical stress aids the alteration of the substrate and produces the end products

Chemiosmosis

a complex process required for the actual formation of ATP molecules. Chemiosmosis involves the creation of a steep proton (hydrogen ion) gradient. This gradient occurs between the membrane-bound compartments of the mitochondria of all cells and the chloroplasts of plant cells. A gradient is formed when large numbers of protons (hydrogen ions) are pumped into the membrane-bound compartments of the mitochondria. The protons build up dramatically within the compartment, finally reaching an enormous number. The energy released from the electrons during the electron transport system pumps the protons. After large numbers of protons have gathered within the compartments of mitochondria and chloroplasts, they suddenly reverse their directions and escape back across the membranes and out of the compartments. The escaping protons release their energy in this motion. This energy is used by enzymes to unite ADP with phosphate ions to form ATP. The energy is trapped in the high-energy bond of ATP by this process, and the ATP molecules are made available to perform cell work. The movement of protons is chemiosmosis because it is a movement of chemicals (in this case, protons) across a semipermeable membrane. Because chemiosmosis occurs in mitochondria and chloroplasts, these organelles play an essential role in the cell's energy metabolism.

Adenosine triphosphatase

accomplishes the breakdown of an ATP molecule. The products of ATP breakdown are adenosine diphosphate (ADP) and a phosphate ion.

NAD and NADP

are structurally similar to ATP. Both molecules have a nitrogen-containing ring called nicotinic acid, which is the chemically active part of the coenzymes.

Catalysts

are substances that speed up chemical reactions but remain unchanged themselves. Catalysts work by lowering the required amount of activation energy for the chemical reaction. For example, hydrogen and oxygen combine with one another in the presence of platinum. In this case, platinum is the catalyst. In biological systems, the most common catalysts are protein molecules called enzymes. Enzymes are absolutely essential if chemical reactions are to occur in cells.

ATP Molecule

consists of three parts: 1.One part is a double ring of carbon and nitrogen atoms called adenine 2.Attached to the adenine molecule is a small five-carbon carbohydrate called ribose. 3.Attached to the ribose molecule are three phosphate units linked together by covalent bonds. The covalent bonds that unite the phosphate units in ATP are high-energy bonds. When an ATP molecule is broken down by an enzyme, the third (terminal) phosphate unit is released as a phosphate group, which is an ion. When this happens, approximately 7.3 kilocalories of energy are released. (A kilocalorie equals 1,000 calories.) This energy is made available to do the work of the cell.

endergonic reactions

energy is obtained and trapped from the environment. The products of endergonic reactions have more energy than the reactants taking part in the chemical reaction. For example, plants carry out the process of photosynthesis, in which they trap energy from the sun to form carbohydrates

Catabolic pathways

involve the breakdown or digestion of large, complex molecules. The general term for this process is catabolism The energy released during catabolic reactions is stored in ATP molecules

Anabolic pathways

involve the synthesis of large molecules, generally by joining smaller molecules together. The general term for this process is anabolism. the energy trapped in anabolic reactions (such as photosynthesis) is trapped in ATP molecules.

metabolic pathway

is a sequence of chemical reactions occurring in a cell. A single enzyme-catalyzed reaction may be one of multiple reactions in a metabolic pathway. Metabolic pathways may be of two general types: catabolic and anabolic.

Enzyme-catalyzed reactions

occur extremely fast. They happen about a million times faster than uncatalyzed reactions. With some exceptions, the names of enzymes end in "-ase." For example, the enzyme that breaks down hydrogen peroxide to water and hydrogen is catalase. Other enzymes include amylase, hydrolase, peptidase, and kinase. The rate of an enzyme-catalyzed reaction depends on a number of factors, such as the concentration of the substrate, the acidity and temperature of the environment, and the presence of other chemicals. At higher temperatures, enzyme reactions occur more rapidly, but only up to a point. Because enzymes are proteins, excessive amounts of heat can change their structures, rendering them inactive

cytochromes

participate in oxidation reduction reactions; Together with the coenzymes, cytochromes accept and release electrons in a system called the electron transport system. The passage of energy-rich electrons among cytochromes and coenzymes drains the energy from the electrons to form ATP from ADP and phosphate ions.

oxidation-reduction reactions

the chemical reactions performed by coenzymes The oxidation-reduction reactions performed by the coenzymes and other molecules are essential to the energy metabolism of the cell. During the chemical reactions of metabolism, coenzymes accept electrons and pass them on to other coenzymes or other molecules.

FAD

the chemically active portion is the flavin group. The vitamin riboflavin is used in the body to produce this flavin group.

enzyme-substrate complex

the time the active site is associated with the substrate, the combination is referred to as the enzyme-substrate complex.

reduction

The addition of electrons to a molecule

end products

The products of a chemical reaction catalyzed by an enzyme

substrate

The substance changed or acted on by an enzyme