Microbiology

Microbial life can exist only where molecules and cells remain organized, and energy is needed by all microorganisms to maintain organization.

Every activity taking place in microbial cells involves both a shift of energy and a measurable loss of energy. Although the second law of thermodynamics says that energy cannot be created or destroyed, but only transferred within a system, unfortunately, the transfers of energy in living systems are never completely efficient. For this reason, considerably more energy must be taken into the system than is necessary to simply carry out the actions of microbial life.

In microorganisms, most chemical compounds neither combine with one another automatically nor break apart automatically. A spark called the energy of activation is needed. The activation energy needed to spark an exergonic (energy-yielding) reaction or endergonic (energy-requiring) reaction can be heat energy or chemical energy. Reactions that require activation energy can also proceed in the presence of biological catalysts. Catalysts are substances that speed up chemical reactions but remain unchanged during the reactions. Catalysts work by lowering the required amount of activation energy for the chemical reaction. In microorganisms, the catalysts are enzymes.

Enzymes. Chemical reactions in microorganisms operate in the presence of enzymes.A particular enzyme catalyzes only one reaction, and thousands of different enzymes exist in a microbial cell to catalyze thousands of different chemical reactions. The substance acted on by an enzyme is called its substrate. The products of an enzyme-catalyzed chemical reaction are called end products.

All enzymes are composed of proteins. When an enzyme functions, a key portion of the enzyme called the active site interacts with the substrate. The active site closely matches the molecular configuration of the substrate, and after this interaction has taken place, a shape change at the active site places a physical stress on the substrate. This physical stress aids the alteration of the substrate and produces the end products. After the enzyme has performed its work, the product or products drift away. The enzyme is then free to function in the next chemical reaction. Enzyme-catalyzed reactions occur extremely fast.

With some exceptions, enzyme names end in “-ase.” For example, the microbial enzyme that breaks down hydrogen peroxide to water and hydrogen is called catalase. Other well-known enzymes are amylase, hydrolase, peptidase, and kinase.

The rate of an enzyme-catalyzed reaction depends on a number of factors, including the concentration of the substrate, the acidity of the environment, the presence of other chemicals, and the temperature of the environment. For example, at higher temperatures, enzyme reactions occur more rapidly. Since enzymes are proteins, however, excessive amounts of heat may cause the protein to change its structure and become inactive. An enzyme altered by heat is said to be denatured.

Enzymes work together in metabolic pathways. A metabolic pathway is a sequence of chemical reactions occurring in a cell. A single enzyme-catalyzed reaction may be one of multiple reactions in the metabolic pathway. Metabolic pathways may be of two general types: Some involve the breakdown or digestion of large, complex molecules in the process of catabolism. Others involve a synthesis, generally by joining smaller molecules in the process of anabolism.

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

Adenosine triphosphate (ATP). Adenosine triphosphate (ATP) is the chemical substance that serves as the currency of energy in the microbial cell. It is referred to as currency because it can be “spent” in order to make chemical reactions occur.

ATP, used by virtually all microorganisms, is a nearly universal molecule of energy transfer. The energy released during the reactions of catabolism is stored in ATP molecules. In addition, the energy trapped in anabolic reactions such as photosynthesis is also trapped in ATP.

An ATP molecule consists of three parts (Figure 1 ). One part is a double ring of carbon and nitrogen atoms called adenine. Attached to the adenine molecule is a small five-carbon carbohydrate called ribose. Attached to the ribose molecule are threephosphate groups, which are linked by covalent bonds. 

Figure 1

The adenosine triphosphate (ATP) molecule that serves as an immediate energy source in the cell.

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 a phosphate ion (Figure 1 ). With the release, approximately 7.3 kilocalories of energy (a kilocalorie is 1000 calories) are made available to do the work of the microorganism.

The breakdown of an ATP molecule is accomplished by an enzyme called adenosine triphosphatase. The products of ATP breakdown are adenosine diphosphate (ADP)and, as noted, a phosphate ion. Adenosine diphosphate and the phosphate ion can be reconstituted to form ATP, much as a battery can be recharged. To accomplish this ATP formation, energy necessary for the synthesis can be made available in the microorganism through two extremely important processes: photosynthesis and cellular respiration. A process called fermentation may also be involved.

ATP production. ATP is generated from ADP and phosphate ions by a complex set of processes occurring in the cell, processes that depend upon the activities of a special group of cofactors called coenzymes. Three important coenzymes are nicotinamide adenine di-nucleotide (NAD), nicotinamide adenine dinucleotide phosphate (NADP), and flavin adenine dinucleotide (FAD). All are structurally similar to ATP.

All coenzymes perform essentially the same work. During the chemical reactions of metabolism, coenzymes accept electrons and pass them on to other coenzymes or other molecules. The removal of electrons or protons from a coenzyme is calledoxidation. The addition of electrons or protons to a coenzyme is called reduction.Therefore, the chemical reactions performed by coenzymes are called oxidation-reduction reactions.

The oxidation-reduction reactions performed by the coenzymes and other molecules are essential to the energy metabolism of the cell. Other molecules participating in this energy reaction are called cytochromes. Together with the enzymes, cytochromes accept and release electrons in a system referred to as the electron transport system. The passage of energy-rich electrons among cytochromes and coenzymes drains the energy from the electrons. This is the energy used to form ATP from ADP and phosphate ions.

The actual formation of ATP molecules requires a complex process referred to aschemiosmosis. Chemiosmosis involves the creation of a steep proton gradient, which occurs between the membrane-bound areas. In prokaryotic cells (for example, bacteria), it is the area of the cell membrane; in eukaryotic cells, it is the membranes of the mitochondria. A gradient is formed when large numbers of protons (hydrogen ions) are pumped into membrane-bound compartments. The protons build up dramatically within the compartment, finally reaching an enormous number. The energy used to pump the protons is energy released from the electrons during the electron transport system.

After large numbers of protons have gathered at one side of the membrane, they suddenly reverse their directions and move back across the membranes. The protons release their energy in this motion, and the 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.