Ch_03

IntroductionEUCARYOTIC CELL

STRUCTURECell MembraneNucleusCytoplasmEndoplasmic ReticulumRibosomesGolgi ComplexLysosomes and PeroxisomesMitochondriaPlastidsCytoskeletonCell WallFlagella and Cilia

PROCARYOTIC CELLSTRUCTURE

Cell MembraneChromosomeCytoplasmCytoplasmic ParticlesBacterial Cell WallGlycocalyx (Slime Layers and

Capsules)FlagellaPili (Fimbriae)Spores (Endospores)RECAP OF STRUCTURAL

DIFFERENCES BETWEENPROCARYOTIC AND

EUCARYOTIC CELLSREPRODUCTION OF

ORGANISMS AND THEIRCELLS

Asexual Versus Sexual ReproductionLife CyclesEucaryotic Cell Reproduction

MitosisMeiosis

Procaryotic Cell ReproductionTAXONOMYMicrobial ClassificationDETERMINING RELATEDNESS

AMONG ORGANISMS

AFTER STUDYING THIS CHAPTER, YOU SHOULD

BE ABLE TO:

■ Explain what is meant by the cell theory■ State the contributions of Hooke, Schleiden &

Schwann, and Virchow to the study of cells■ Cite a function for each of the following parts of

a eucaryotic cell: cell membrane, nucleus, ribo-somes, Golgi complex, lysosomes, mitochondria,plastids, cytoskeleton, cell wall, flagella, and cilia

■ Cite a function for each of the following parts ofa bacterial cell: cell membrane, chromosome, cellwall, capsule, flagella, pili, and endospores

■ Compare and contrast plant, animal, and bacter-ial cells

■ Define the terms genus, specific epithet, andspecies

■ Describe the Five-Kingdom and Three-DomainSystems of classification

LEARNING OBJECTIVES

Cell Structure and Taxonomy

Introduction to MicroorganismsII

33

41

INTRODUCTION

In this chapter, you will learn about the structure of microorganisms. Becausethey are so small, very little detail concerning their structure can be determinedusing the compound light microscope. Our knowledge of the fine structure ofmicrobes has been gained through the use of electron microscopes. Such finedetail—detail that is beyond the resolving power of the compound light micro-scope—is referred to as the ultrastructure of the microorganisms. Also discussedin this chapter are the ways in which microorganisms and their cells reproduceand how microorganisms are classified.

42 CHAPTER 3

In biology, a cell is defined as the fundamental living unit of any organismbecause, like the total organism, the cell exhibits the basic characteristics of life.A cell obtains food (nutrients) from the environment to produce energy for me-tabolism and other activities. Metabolism refers to all of the chemical reactionsthat occur within a cell (see Chapter 7 for a detailed discussion of metabolismand metabolic reactions). Because of its metabolism, a cell can grow and repro-duce. It can respond to stimuli in its environment such as light, heat, cold, andthe presence of chemicals. A cell can mutate (change genetically) as a result ofaccidental changes in its genetic material—the deoxyribonucleic acid (DNA)that makes up the genes of its chromosomes—and, thus, can become better orless suited to its environment. As a result of these genetic changes, the mutantorganism may be better adapted for survival and development into a new species(pl. species) of organism.

In 1665, an English physicist named Robert Hooke published a book, entitledMicrographia, containing descriptions of objects he had observed using a compoundlight microscope that he had made. These objects included molds, rusts, fleas, lice,fossilized plants and animals, and sections of cork. Hooke referred to the smallempty chambers in the structure of cork as cells, probably because they remindedhim of the bare rooms (called cells) in a monastery. Hooke was the first person touse the term “cells” in this manner. Around 1838–1839, a German botanist namedMatthias Schleiden and a German zoologist named Theodor Schwann con-cluded that all plant and animal tissues were composed of cells; this later becameknown as the cell theory. Then in 1858, the German pathologist Rudolf Virchowproposed the theory of biogenesis—that life can only arise from preexisting life, and,therefore, that cells can only arise from preexisting cells. Biogenesis does not ad-dress the issue of the origin of life on earth, a complex topic about which much hasbeen written.

Cells

Considerable evidence exists to indicate that between 3.5 and 4 billion yearsago, the first bit of life to appear on earth was a very primitive cell similar to thesimple bacteria of today. Bacterial cells exhibit all the characteristics of life, al-though they do not have the complex system of membranes and organelles (tinyorgan-like structures) found in the more advanced single-celled organisms.These less complex cells, which include Bacteria and Archaea, are called pro-caryotes or procaryotic cells.a The more complex cells, containing a true nucleusand many membrane-bound organelles, are called eucaryotes or eucaryoticcells.a Eucaryotes include such organisms as algae, protozoa, fungi, plants, ani-mals, and humans. Some microorganisms are procaryotic, some are eucaryotic,and some are not cells at all (Fig. 3–1).

Viruses appear to be the result of regressive or reverse evolution, becausethey are composed of only a few genes protected by a protein coat, and some-times may contain one or a few enzymes. Viruses depend on the energy andmetabolic machinery of a host cell in order to reproduce. Because viruses areacellular (not composed of cells), they are usually placed in a completely sepa-rate category and are not classified with the simple procaryotic cells.

For those in the health professions, it is important to understand the struc-ture of different types of cells, not only to identify the various types of microor-ganisms, but also to understand differences in their structure and metabolism.These factors must be known before one can determine or explain how the drugsof modern chemotherapy can destroy pathogens but not healthy human cells.

Cytology, the study of the structure and function of cells, has developed dur-ing the past 60 years with the aid of the electron microscope and sophisticatedbiochemical research. Many books have been written about the details of thesetiny functional factories—cells—but only a brief discussion of their structure andactivities is presented here.

Cell Structure and Taxonomy 43

aAlternate spellings of procaryote and eucaryote are prokaryote and eukaryote.

Microorganisms

Acellular

VirusesPrionsViroids

Cellular

ProcaryotesArchaeaBacteriaCyanobacteria

EucaryotesAlgaeProtozoaFungi

Figure 3-1. Acellular and cellular microbes. Acellular microbes include viroids, prions, andviruses. Cellular microbes include the less complex procaryotes (archaeans and bacteria) andthe more complex eucaryotes (algae, protozoa, and fungi).

EUCARYOTIC CELL STRUCTURE

Eucaryotes (eu � true; caryo refers to a nut or nucleus) are so named because theyhave a true nucleus, in that their DNA is enclosed by a nuclear membrane. Mostanimal and plant cells are 10 to 30 �m in diameter, about 10 times larger than mostprocaryotic cells. Figure 3–2 illustrates a typical eucaryotic animal cell. This illus-tration is a composite of most of the structures that might be found in the varioustypes of human body cells. Figure 3–3 is a transmission electron micrograph(TEM) of an actual yeast cell. A discussion of the functional parts of eucaryoticcells can be better understood by keeping the illustrated structures in mind.

Cell Membrane

The cell is enclosed and held intact by the cell membrane, which is also referredto as the plasma, cytoplasmic, or cellular membrane. Structurally, it is a mosaiccomposed of large molecules of proteins and phospholipids (certain types offats). The cell membrane is like a “skin” around the cell, separating the contentsof the cell from the outside world. The cell membrane regulates the passage ofnutrients, waste products, and secretions into and out of the cell. Because thecell membrane has the property of selective permeability, only certain sub-stances may enter and leave the cell. The cell membrane is similar in structureand function to all of the other membranes that are found in eucaryotic cells.

44 CHAPTER 3

Figure 3-2. A typical eu-caryotic animal cell.(Cohen BJ, Wood DL:Memmler’s The HumanBody in Health andDisease, 9th ed.Philadelphia, LippincottWilliams & Wilkins, 2000.)

Nucleus

As previously mentioned, the primary difference between procaryotic and eu-caryotic cells is that eucaryotic cells possess a “true nucleus,” whereas procaryoticcells do not. The nucleus (pl. nuclei) unifies, controls, and integrates the functionsof the entire cell and can be thought of as the “command center” of the cell. Thenucleus has three components: nucleoplasm, chromosomes, and a nuclear mem-brane. Nucleoplasm is the gelatinous matrix or base material of the nucleus; likecytoplasm, nucleoplasm is a type of protoplasm. The chromosomes are embeddedor suspended in the nucleoplasm. The membrane that serves as a “skin” aroundthe nucleus is called the nuclear membrane; it contains holes (nuclear pores)through which large molecules can enter and exit the nucleus.

Eucaryotic chromosomes consist of linear DNA molecules and proteins (hi-stones and non-histone proteins). Genes are located along the DNA molecules.Although genes are sometimes described as “beads on a string,” each bead(gene) is actually a particular segment of the DNA molecule. Each gene containsthe genetic information that enables the cell to produce a gene product. Mostgene products are proteins, but some genes code for the production of two typesof ribonucleic acid (RNA): ribosomal ribonucleic acid (rRNA) and transferribonucleic acid (tRNA) molecules (discussed in Chapter 6). The organism’s


Figure 3-3. Cross-sectionthrough a yeast cell, showing thenucleus (N) with nuclear pores(P), mitochondrion (M), and vac-uole (V). The cytoplasm is sur-rounded by the cell membrane.The thick outer portion is the cellwall. (Lechavalier HA, Pramer D:The Microbes. Philadelphia, JBLippincott, 1970.)

complete collection of genes is referred to as that organism’s genotype (genome).To understand more about how genes control the activities of the entire organ-ism, refer to Chapters 6 and 7.

The number and composition of chromosomes and the number of genes on each chromosome are characteristic of the particular species of organism.Different species have different numbers and sizes of chromosomes. Humandiploid cells, for example, have 46 chromosomes (23 pairs), each consisting ofthousands of genes. It has been estimated that the human genome consists ofabout 30,000 genes.

When observed using a transmission electron microscope, a dark (electrondense) area can be seen in the nucleus. This area is called the nucleolus; it is herethat rRNA molecules are manufactured. The rRNA molecules then becomepart of the structure of ribosomes (discussed later).

Cytoplasm

Cytoplasm (a type of protoplasm) is a semifluid, gelatinous, nutrient matrix(also referred to as the cytosol). Within the cytoplasm are found insoluble stor-age granules and a variety of cytoplasmic organelles, including endoplasmicreticulum, ribosomes, Golgi complexes, mitochondria, centrioles, microtubules,lysosomes, and other membrane-bound vacuoles. Each of these organelles has ahighly specific function, and all of the functions are interrelated to maintain thecell and allow it to properly perform its activities. The cytoplasm is where mostof the cell’s metabolic reactions occur.

Endoplasmic Reticulum

The endoplasmic reticulum (ER) is a highly convoluted system of membranesthat are interconnected and arranged to form a transport network of tubules andflattened sacs within the cytoplasm. Much of the ER has a rough, granular ap-pearance when observed by transmission electron microscopy and is designatedas rough endoplasmic reticulum (RER). This rough appearance is due to themany ribosomes attached to the outer surface of the membranes. Endoplasmicreticulum to which ribosomes are not attached is called smooth endoplasmicreticulum (SER).

Ribosomes

Eucaryotic ribosomes are 18 to 22 nm in diameter. They consist mainly of ribo-somal RNA (rRNA) and protein and play an important part in the synthesis(manufacture) of essential proteins. Clusters of ribosomes (called polyribo-somes or polysomes) are sometimes observed, held together by a molecule ofmessenger RNA (mRNA).

Each eucaryotic ribosome is composed of two subunits—a large subunit (the60S subunit) and a small subunit (the 40S subunit)—that are produced in the nu-cleolus. The subunits are then transported to the cytoplasm where they remainseparate until such time as they join together with a messenger RNA (mRNA)

46 CHAPTER 3

molecule to initiate protein synthesis (Chapter 6). When united, the 40S and 60Ssubunits form an 80S ribosome. (The “S” refers to Svedberg units, and 40S, 60S,and 80S are sedimentation coefficients. A sedimentation coefficient expressesthe rate at which a particle or molecule moves in a centrifugal field; it is deter-mined by the size and shape of the particle or molecule.)

Most of the proteins released from the ER are not mature. They must un-dergo further processing in an organelle known as a Golgi complex before theyare able to perform their functions within or outside of the cell.

Golgi Complex

A Golgi complex, also known as a Golgi apparatus or Golgi body, connects orcommunicates with the ER. This stack of flattened, membranous sacs completesthe transformation of newly synthesized proteins into mature, functional onesand packages them into small, membrane-enclosed vesicles for storage withinthe cell or export outside the cell (exocytosis or secretion). Golgi complexes aresometimes referred to as “packaging plants.”

Lysosomes and Peroxisomes

Lysosomes are small (about 1 �m diameter) vesicles that originate at the Golgicomplex. They contain lysozyme and other digestive enzymes that break downforeign material taken into the cell by phagocytosis (the engulfing of large par-ticles by amebas and certain types of white blood cells called phagocytes). Theseenzymes also aid in breaking down worn out parts of the cell and may destroythe entire cell by a process called autolysis if the cell is damaged or deteriorat-ing. Lysosomes are found in all eucaryotic cells.

Peroxisomes are membrane-bound vesicles where hydrogen peroxide isboth generated and broken down. Peroxisomes contain the enzyme catalase,which catalyzes the breakdown of hydrogen peroxide into water and oxygen.Peroxisomes are found in most eucaryotic cells but are especially prominent inmammalian liver cells.

Mitochondria

The energy necessary for cellular function is provided by the formation of high-energy phosphate molecules such as adenosine triphosphate (ATP). The ATPmolecules are the major energy carrying or energy storing molecules within cells.Mitochondria (sing., mitochondrion) are referred to as the “power plants,”“powerhouses,” or “energy factories” of the eucaryotic cell, because this iswhere most of the ATP molecules are formed by cellular respiration. During thisprocess, energy is released from glucose molecules and other nutrients to driveother cellular functions (see Chapter 7). The number of mitochondria in a cellvaries greatly depending on the activities required of that cell. Mitochondria areabout 0.5 to 1 �m in diameter and up to 7 �m in length. Many scientists believethat mitochondria and chloroplasts arose from bacteria living within eucaryoticcells (see “Insight: The Origin of Mitochondria and Chloroplasts” on the web site).


Plastids

Plant cells contain both mitochondria and another type of energy-producing or-ganelle, called a plastid. Plastids are membrane-bound structures containing var-ious photosynthetic pigments; they are the sites of photosynthesis. Chloroplasts,one type of plastid, contain a green, photosynthetic pigment called chlorophyll.Chloroplasts are found in plant cells and algae. Photosynthesis is the process bywhich light energy is used to convert carbon dioxide and water into carbohy-drates and oxygen (Chapter 7). The chemical bonds in the carbohydrate mole-cules represent stored energy. Thus, photosynthesis is the conversion of light en-ergy into chemical energy.

Cytoskeleton

Running throughout the cytoplasm is a system of fibers, collectively known asthe cytoskeleton. The three types of cytoskeletal fibers are microtubules, micro-filaments (actin filaments), and intermediate filaments. All three types serve tostrengthen, support, and stiffen the cell as well as give the cell its shape. In addi-tion to their structural roles, microtubules and microfilaments are essential fora variety of activities, such as cell division, contraction, motility (see the sectionon flagella and cilia), and the movement of chromosomes within the cell.Microtubules are slender, hollow tubules composed of spherical protein sub-units called tubulins.

Cell Wall

Some eucaryotic cells contain cell walls—external structures that provide rigid-ity, shape, and protection (Fig. 3–4). Eucaryotic cell walls, which are much sim-pler in structure than procaryotic cell walls, may contain cellulose, pectin, lignin,chitin, and some mineral salts (usually found in algae). The cell walls of algaecontain a polysaccharide—cellulose—that is not found in the cell walls of anyother microorganisms. Cellulose is also found in the cell walls of plants. The cellwalls of fungi contain a polysaccharide—chitin—that is not found in the cellwalls of any other microorganisms. Chitin, which is similar in structure to cellu-lose, is also found in the exoskeletons of beetles and crabs.

48 CHAPTER 3

Cell walls

AbsentAnimalsProtozoaMycoplasma species

PresentPlantsAlgaeFungiMost bacteria

Figure 3-4. Presence or absenceof cell wall in various types ofcells.

Flagella and Cilia

Some eucaryotic cells (e.g., spermatozoa and certain types of protozoa and al-gae) possess relatively long, thin structures called flagella (singular, flagellum).Such cells are said to be flagellated or motile; flagellated protozoa are calledflagellates. The whipping motion of the flagella enables flagellated cells to“swim” through liquid environments. Thus, flagella are said to be organelles oflocomotion (cell movement). Flagellated cells may possess one flagellum or twoor more flagella. Cilia (singular, cilium) are also organelles of locomotion, butthey tend to be shorter (hairlike), thinner, and more numerous than flagella.Cilia can be found on some species of protozoa (called ciliates) and on certaintypes of cells in our bodies (e.g., the ciliated epithelial cells that line our respira-tory tract). Unlike flagella, cilia tend to beat with a coordinated, rhythmicmovement. Eucaryotic flagella and cilia, which contain an internal “9 � 2”arrangement of microtubules (Fig. 3–5), are structurally more complex than bac-terial flagella.

PROCARYOTIC CELL STRUCTURE

Procaryotic cells are about 10 times smaller than eucaryotic cells. A typicalEscherichia coli cell is about 1 �m wide and 2 to 3 �m long. Structurally,


Figure 3-5. Cilia. (A) TEM showing the cross-section of a tapeworm flame cell (an excretoryorgan) containing numerous cilia. (TEM by P. Engelkirk.) (B) Diagrammatic representation ofcilia in cross-section, illustrating the 9 � 2 arrangement of microtubules (see text). Individualcilia are round, but cilia in the flame cell are tightly squeezed together, resulting in their al-tered shape.

procaryotes are very simple cells when compared to eucaryotic cells, and yet theyare able to carry on the necessary processes of life. Reproduction of procaryoticcells is by binary fission—the simple division of one cell into two cells, follow-ing DNA replication (Chapter 6) and the formation of a separating membraneand cell wall. All bacteria are procaryotes, as are archaeans.

Within the cytoplasm of procaryotic cells are a chromosome, ribosomes, andother cytoplasmic particles (Fig. 3–6). Unlike eucaryotic cells, the cytoplasm ofprocaryotic cells is not filled with internal membranes. The cytoplasm is sur-rounded by a cell membrane, a cell wall (usually), and sometimes a capsule orslime layer. These latter three structures make up the bacterial cell envelope.Depending on the particular species of bacterium, flagella or pili (descriptionfollows) or both may be observed outside the cell envelope, and a spore maysometimes be seen within the cell.

Cell Membrane

Enclosing the cytoplasm of a procaryotic cell is the cell membrane (or plasma,cytoplasmic, or cellular membrane). This membrane is similar in structure and

50 CHAPTER 350 CHAPTER 3

Inclusion Cell wall

Ribosomes

Cytoplasm

Cell membrane

Chromosome

Plasmid

Flagella

Capsule

Capsule

Cell wallCellmembrane

Pili

Figure 3-6. Atypical procary-otic cell.

function to the eucaryotic cell membrane. Chemically, the plasma membraneconsists of proteins and phospholipids, which are discussed further in Chapter 6.Being selectively permeable, the membrane controls which substances may en-ter or leave the cell. It is flexible and so thin that it cannot be seen with a com-pound light microscope. However, it is frequently observed in transmission elec-tron micrographs of bacteria.

Many enzymes are attached to the cell membrane, and a variety of meta-bolic reactions take place there. Some scientists believe that inward foldings ofthe cell membranes—called mesosomes—are where cellular respiration takesplace in bacteria. This process is similar to that occurring in the mitochondria ofeucaryotic cells, in which nutrients are broken down to produce energy in theform of ATP molecules. On the other hand, some scientists think that meso-somes are nothing more than artifacts created during the processing of bacterialcells for electron microscopy.

In cyanobacteria and other photosynthetic bacteria (bacteria that convertlight energy into chemical energy), some internal membranes, which are infold-ings of the cell membrane, contain chlorophyll and other pigments that serve totrap light energy for photosynthesis. However, procaryotic cells do not havecomplex internal membrane systems similar to the endoplasmic reticulum andGolgi complex of eucaryotic cells. Procaryotic cells do not contain any membrane-bound organelles or vesicles.

Chromosome

The procaryotic chromosome usually consists of a single, long, supercoiled, cir-cular DNA molecule, which serves as the control center of the bacterial cell. It iscapable of duplicating itself, guiding cell division, and directing cellular activities.A procaryotic cell contains neither nucleoplasm nor a nuclear membrane. Thechromosome is suspended or embedded in the cytoplasm. The DNA-occupiedspace within a bacterial cell is sometimes referred to as the bacterial nucleoid.

The thin and tightly folded chromosome of E. coli is about 1.5 mm (1,500�m) long and only 2 nm wide. Since a typical E. coli cell is about 2 to 3 �m long,its chromosome is approximately 500 to 750 times longer than the cell itself—quite a packaging feat! Bacterial chromosomes contain between 850 and 6500genes, depending on the species. Thus, a bacterial chromosome contains suffi-cient genetic information to code for between 850 to 6500 gene products (en-zymes, other proteins, rRNA and tRNA molecules). In comparison, the chro-mosomes within a human cell contain about 30,000 genes (� 4000); enough tocode for approximately 30,000 gene products.

Small, circular molecules of double-stranded DNA that are not part of thechromosome (referred to as extrachromosomal DNA or plasmids) may also bepresent in the cytoplasm of procaryotic cells. A plasmid may contain anywherefrom fewer than 10 genes to several hundred genes. A bacterial cell may containone plasmid, multiple copies of the same plasmid, or more than one type of plas-mid (i.e., plasmids containing different genes). (Additional information about bac-terial plasmids is found in Chapter 7.) Plasmids have also been found in yeast cells.


Cytoplasm

The semiliquid cytoplasm of procaryotic cells consists of water, enzymes, dis-solved oxygen (in some cases), waste products, essential nutrients, proteins, car-bohydrates, and lipids—a complex mixture of all the materials required by thecell for its metabolic functions.

Cytoplasmic Particles

Within the bacterial cytoplasm, many tiny particles have been observed. Mostof these are ribosomes, often occurring in clusters called polyribosomes orpolysomes (poly meaning many). Procaryotic ribosomes are smaller than eu-caryotic ribosomes, but their function is the same—they are the sites of proteinsynthesis. A 70S procaryotic ribosome is composed of a 30S subunit and a 50Ssubunit. It has been estimated that there are about 15,000 ribosomes in the cy-toplasm of an E. coli cell.

Cytoplasmic granules occur in certain species of bacteria. These may bestained, by use of a suitable stain, and then identified microscopically. The gran-ules may consist of starch, lipids, sulfur, iron, or other stored substances.

Bacterial Cell Wall

The rigid exterior cell wall that defines the shape of bacterial cells is chemicallycomplex. Thus, the structure of bacterial cell walls is quite different from therelatively simple structure of eucaryotic cell walls, although they serve thesame functions—providing rigidity, strength, and protection. The main con-stituent of most bacterial cell walls is a complex macromolecular polymerknown as peptidoglycan (murein), consisting of many polysaccharide chainslinked together by small peptide (protein) chains. Peptidoglycan is only foundin bacteria. The thickness of the cell wall and its exact composition vary withthe species of bacteria. The cell walls of certain bacteria, called “Gram-positivebacteria” (to be explained in Chapter 4), have a thick layer of peptidoglycancombined with teichoic acid and lipoteichoic acid molecules. The cell walls of“Gram-negative bacteria” (also explained in Chapter 4) have a much thinnerlayer of peptidoglycan, but this layer is covered with a complex layer of lipidmacromolecules, usually referred to as the outer membrane, as shown inFigures 3–7 and 3–8. These macromolecules are discussed in Chapter 6.

52 CHAPTER 3

A plasmid is a small, circular molecule of double-stranded DNA. It is referred toas extrachromosomal DNA because it is not part of the chromosome. Plasmids arefound in most bacteria. A plastid is a cytoplasmic organelle, found only in certaineucaryotic cells (e.g., algae and plants). Plastids are the sites of photosynthesis.

Beware of Similar Sounding Words


Figure 3-7. Differences between Gram-negative and Gram-positive cell walls. The relativelythin Gram-negative cell wall contains a thin layer of peptidoglycan, an outer membrane, andlipopolysaccharide (LPS). The thicker Gram-positive cell wall contains a thick layer of pepti-doglycan and teichoic and lipoteichoic acids.

Figure 3-8. Bacterial cell walls. (A) A portion of the Gram-positive bacterium, Bacillus fastidi-ous; note the cell wall’s thick peptidoglycan layer, beneath which can be seen the cell mem-brane. (B) The Gram-negative bacterium, Enterobacter aerogenes; both the cell membrane andthe outer membrane are visible along some sections of the cell wall. (A: Volk WA, et al.:Essentials of Medical Microbiology, 5th ed. Philadelphia, Lippincott-Raven, 1996.)

Although most bacteria have cell walls, bacteria in the genus Mycoplasma donot. Archaeans (described later) have cell walls, but their cell walls do not con-tain peptidoglycan.

Glycocalyx (Slime Layers and Capsules)

Some bacteria have a thick layer of material (known as glycocalyx) located out-side their cell wall. Glycocalyx is a slimy, gelatinous material produced by thecell membrane and secreted outside of the cell wall. There are two types of gly-cocalyx. One type, called a slime layer, is not highly organized and is not firmlyattached to the cell wall. It easily detaches from the cell wall and drifts away.Bacteria in the genus Pseudomonas produce a slime layer, which sometimesplays a role in diseases caused by Pseudomonas species. Slime layers enable cer-tain bacteria to glide or slide along solid surfaces.

The other type of glycocalyx, called a capsule, is highly organized and firmlyattached to the cell wall. Capsules usually consist of polysaccharides, which maybe combined with lipids and proteins, depending on the bacterial species.Knowledge of the chemical composition of capsules is useful in differentiatingbetween different types of bacteria within a particular species; for example, dif-ferent strains of Haemophilus influenzae, a cause of meningitis and ear infec-tions in children, are identified by their capsular types. A vaccine, called Hibvaccine, is available for protection against disease caused by H. influenzae cap-sular type b. Other examples of encapsulated bacteria are Klebsiella pneumo-niae, Neisseria meningitidis, and Streptococcus pneumoniae.

Capsules can be detected using a negative stain, whereby the bacterial celland background become stained, but the capsule remains unstained (Fig. 3–9).Thus, the capsule appears as an unstained halo around the bacterial cell. Antigen-antibody tests (described in Chapter 16) may be used to identify specific strainsof bacteria possessing unique capsular molecules (antigens).

Encapsulated bacteria usually produce colonies on nutrient agar that aresmooth, mucoid, and glistening and referred to as S-colonies. Nonencapsulatedbacteria tend to grow as dry, rough colonies, called R-colonies. Capsules serve anantiphagocytic function, protecting the encapsulated bacteria from being phago-cytized (ingested) by phagocytic white blood cells. Thus, encapsulated bacteriaare able to survive longer in the human body than nonencapsulated bacteria.

Flagella

Flagella (sing., flagellum) are threadlike, protein appendages that enable bacte-ria to move. Flagellated bacteria are said to be motile, whereas nonflagellatedbacteria are usually nonmotile. Bacterial flagella are about 10 to 20 nm thick; toothin to be seen with the compound light microscope.

The number and arrangement of flagella possessed by a certain species of bac-terium are characteristic of that species and can, thus, be used for classification andidentification purposes (Fig. 3–10). Bacteria possessing flagella over their entiresurface (perimeter) are called peritrichous bacteria (Fig. 3–11). Bacteria with atuft of flagella at one end are described as being lophotrichous bacteria, whereasthose having one or more flagella at each end are said to be amphitrichous



Figure 3-9. Capsule stain. The capsule stain is an example of a negative staining technique.The bacterial cells and the background stain, but the capsules do not. The capsules are seenas unstained “halos” around the bacterial cells.

Peritrichous bacterium

Lophotrichous bacterium

Amphitrichous bacterium

Monotrichous bacterium

Figure 3-10. Flagellar arrangement. The four basic types of flagellar arrangement on bacteria:peritrichous � flagella all over the surface; lophotrichous � a tuft of flagella at one end; am-phitrichous � one or more flagella at each end; monotrichous � one flagellum.

bacteria. Bacteria possessing a single polar flagellum are described as monotri-chous bacteria. In the laboratory, the number of flagella that a cell possesses andtheir locations on the cell can be determined using what is known as a flagellastain. The stain adheres to the flagella, making them thick enough to be seen un-der the microscope.

Bacterial flagella consist of three, four, or more threads of protein (calledflagellin) twisted like a rope. Thus, the structures of bacterial flagella and eu-caryotic flagella are quite different. You will recall that eucaryotic flagella (andcilia) contain a complex arrangement of internal microtubules, which run thelength of the membrane-bound flagellum. Bacterial flagella do not contain mi-crotubules, and their flagella are not membrane-bound. Bacterial flagella arisefrom a basal body in the cell membrane and project outward through the cellwall and capsule (if present), as shown in Figure 3–6.

Some spirochetes (spiral-shaped bacteria) have two flagella-like fibrils calledaxial filaments, one attached to each end of the bacterium. These axial filamentsextend toward each other, wrap around the organism between the layers of thecell wall, and overlap in the midsection of the cell. As a result of its axial fila-ments, spirochetes can move in a spiral, helical, or inch-worm manner.

Pili (Fimbriae)

Pili (sing., pilus) or fimbriae (sing., fimbria) are hair-like structures, most oftenobserved on Gram-negative bacteria. They are composed of polymerized proteinmolecules called pilin. Pili are much thinner than flagella, have a rigid structure,and are not associated with motility. These tiny appendages arise from the cyto-plasm and extend through the plasma membrane, cell wall, and capsule (if pres-ent). There are two types of pili: one type enables bacteria to adhere or attachto surfaces; the other type (called a sex pilus) enables transfer of genetic mate-rial from one bacterial cell to another.

56 CHAPTER 3

Figure 3-11. A peritrichous Salmonella cell. (Volk WA, et al.: Essentials of MedicalMicrobiology, 5th ed. Philadelphia, Lippincott-Raven, 1996.)

The pili that enable bacteria to anchor themselves to surfaces (e.g., tissueswithin the human body) are usually quite numerous (Fig. 3–12). In some speciesof bacteria, piliated strains (those possessing pili) are able to cause diseases likeurethritis and cystitis, whereas nonpiliated strains (those not possessing pili) ofthe same organisms are unable to cause these diseases.

A bacterial cell possessing a sex pilus (called a donor cell)—and the cellonly possesses one—is able to attach to another bacterial cell (called a recipi-ent cell) by means of the sex pilus. Genetic material (usually in the form of aplasmid) is then transferred through the hollow sex pilus from the donor cell tothe recipient cell—a process known as conjugation (described more fully inChapter 7).

Spores (Endospores)

A few genera of bacteria (e.g., Bacillus and Clostridium) are capable of formingthick-walled spores as a means of survival when their moisture or nutrient sup-ply is low. Bacterial spores are referred to as endospores, and the process bywhich they are formed is called sporulation. During sporulation, a copy of thechromosome and some of the surrounding cytoplasm becomes enclosed in sev-eral thick protein coats. Spores are resistant to heat, cold, drying, and mostchemicals. Spores have been shown to survive for many years in soil or dust, and


Figure 3-12. Proteus vulgaris cell, possessing numerous short, straight pili and several longer,curved flagella; the cell is undergoing binary fission. (Volk WA, et al.: Essentials of MedicalMicrobiology, 5th ed. Philadelphia, Lippincott-Raven, 1996.)

some are quite resistant to disinfectants and boiling. When the dried spore landson a moist, nutrient-rich surface, it germinates, and a new vegetative bacterialcell (one capable of growing and dividing) emerges. Germination of a spore maybe compared with germination of a seed. However, in bacteria, spore formationis related to the survival of the bacterial cell, not to reproduction. Usually onlyone spore is produced in a bacterial cell and it germinates into only one vegeta-tive bacterium (Fig. 3–13). In the laboratory, endospores can be stained usingwhat is known as a spore stain. Once a particular bacterium’s endospores arestained, the technologist can determine whether the organism is producing ter-minal or subterminal spores. A terminal spore is produced at the very end of thebacterial cell, whereas a subterminal spore is produced elsewhere in the cell.Where a spore is being produced within the cell and whether or not it causes aswelling of the cell serve as clues to the identity of the organism.


Figure 3-13. A bacillus witha well-defined endospore (arrow). (Lechavalier HA,Pramer D: The Microbes.Philadelphia, JB Lippincott,1970.)

While performing spontaneous generation experiments in 1876 and 1877, a Britishphysicist named John Tyndall concluded that certain bacteria exist in two forms:a form which is readily killed by simple boiling (i.e., a heat labile form), and a formthat is not killed by simple boiling (i.e., a heat stable form). He developed a fractionalsterilization technique, known as tyndallization, which successfully killed both theheat labile and heat stable forms. Tyndallization involves boiling, followed by incu-bating, and then reboiling; these steps are repeated several times. The bacteria thatemerge from the spores during the incubation steps are subsequently killed duringthe boiling steps. In 1877, Ferdinand Cohn, a German botanist, described the mi-croscopic appearance of the two forms of the “hay bacillus,” which Cohn namedBacillus subtilis. He referred to small refractile bodies within the bacterial cells as“spores” and observed the conversion of spores into actively growing cells. Cohnalso concluded that when they were in the spore phase, the bacteria were heat re-sistant. Today, bacterial spores are known as endospores, whereas active, metabo-lizing, growing bacterial cells are referred to as vegetative cells. The experiments ofTyndall and Cohn supported Louis Pasteur’s conclusions regarding spontaneousgeneration and dealt the final death blow to that theory.

The Discovery of Endospores

RECAP OF STRUCTURAL DIFFERENCESBETWEEN PROCARYOTIC AND EUCARYOTICCELLS

Eucaryotic cells are divided into plant and animal types. Animal cells do nothave a cell wall, whereas plant cells have a simple cell wall, usually containingcellulose. Cellulose, a type of polysaccharide, is a rigid polymer of glucose (poly-mers and polysaccharides are described in Chapter 6). Procaryotic cells havecomplex cell walls consisting of proteins, lipids, and polysaccharides. Eucaryoticcells contain membranous structures (such as endoplasmic reticulum and Golgicomplexes) and many membrane-bound organelles (such as mitochondria andplastids). Procaryotic cells possess no membranes other than the cell membranethat encloses the cytoplasm. Eucaryotic ribosomes (referred to as 80S ribo-somes) are larger and more dense than those found in procaryotes (70S ribo-somes). The fact that 70S ribosomes are found in the mitochondria and chloro-plasts of eucaryotes may indicate that these structures were derived fromparasitic procaryotes during their evolutionary development. Other differencesbetween procaryotic and eucaryotic cells are listed in Table 3–1.

REPRODUCTION OF ORGANISMS AND THEIR CELLS

Reproduction (referring to the manner in which organisms reproduce) and cellreproduction (referring to the process by which individual cells reproduce) arecomplex topics, which can only be briefly discussed in a book of this size. It ishoped that students taking a microbiology course will have previously taken abiology course (in either high school or college) and will, therefore, have someprior knowledge of these topics.

Asexual Versus Sexual Reproduction

In asexual reproduction, a single organism is the sole parent. It passes copies ofall of its genes (i.e., its entire genome) to its offspring. Some single-celled eu-caryotic organisms can reproduce asexually by mitotic cell division (mitosis; de-scribed later), a process by which their chromosomes are copied and allocatedequally to two daughter cells. The genomes of the offspring are identical to theparent’s genome. Procaryotic organisms reproduce asexually by a processknown as binary fission (described later).

In sexual reproduction, two parents give rise to offspring that have uniquecombinations of genes inherited from both parents. The alternation of meiosis (de-scribed later) and fertilization is common to all organisms that reproduce sexually.In sexual reproduction, a zygote (fertilized egg) is formed by the fusion of gametes.

Most protists can reproduce asexually. Some protists are exclusively asex-ual, whereas others can also reproduce sexually (involving meiosis and the fu-sion of gametes). Fungi (other than yeasts) reproduce by releasing spores, whichare produced either sexually or asexually. Most yeasts reproduce asexually,either by simple cell division or by the process of budding. Budding, a type of


60 CHAPTER 3

mitosis, involves the formation of a small cell (called a bud), which then pinchesoff the parent cell. Some yeasts reproduce sexually.

Life Cycles

A life cycle can be defined as the generation-to-generation sequence of stagesthat occur in the reproductive history of an organism. The human life cycle(which is also the life cycle of most animals and some protists) involves produc-tion of haploid gametes by meiosis, fusion of gametes to produce a diploid zy-gote, and mitotic division of the zygote to produce a multicellular organism,

60 CHAPTER 1

Plant Type Animal Type Procaryotic Cells

Biological distribution All plants, fungi, and algae All animals and protozoa All bacteria

Nuclear membrane Present Present Absent

Membranous structures Present Present Generally absent except other than cell mesosomes and membranes photosynthetic membranes

Microtubules Present Present Absent

Cytoplasmic ribosomes 80S 80S 70S(density)

Chromosomes Composed of DNA Composed of DNA Composed of DNA aloneand proteins and proteins

Flagella or cilia When present, have a When present, have a Flagella, when present, complex structure complex structure have a simple twisted

protein structure; no cilia

Cell wall When present, of Absent Of complex chemical simple chemical constitution, containing constitution, usually peptidoglycancellulose

Photosynthesis Present Absent Present in cyanobacteria (chlorophyll) and some other bacteria

Eucaryotic Cells

T A B L E 3 - 1 Comparison Between Eucaryotic and Procaryotic Cells

composed of diploid cells. (Haploid cells contain only one set of chromosomes,whereas diploid cells contain two sets of chromosomes.)

Another type of life cycle that occurs in most fungi and some protists, in-cluding some algae, involves fusion of haploid gametes to form a diploid zygote,meiosis to produce haploid cells, and then division of the haploid cells by mito-sis to give rise to a multicellular adult organism that is composed of haploid cells.Gametes are then produced from the haploid organism by mitosis (rather thanby meiosis). Thus, the only diploid stage is the zygote.

A third type of life cycle that occurs in plants and some species of algae iscalled alternation of generations. In this type of life cycle, there are both diploidand haploid multicellular stages. The multicellular diploid stage is called thesporophyte. Meiosis in the sporophyte produces haploid cells called spores. Unlikea gamete, a spore gives rise to a multicellular organism without fusing with anothercell. A spore divides mitotically to generate a multicellular haploid stage called thegametophyte. The gametophyte makes gametes by mitosis. Fertilization results ina diploid zygote, which develops into the next sporophyte generation. Thus, thesporophyte and gametophyte generations take turns reproducing each other.

Eucaryotic Cell Reproduction

Eucaryotic cells may reproduce either by mitosis or meiosis. Mitosis results intwo cells (called daughter cells), which are identical to the original cell (the par-ent cell). Meiosis results in four cells, each of which contains half the number ofchromosomes as the parent cell.

MitosisThe word mitosis comes from the Greek word mito, meaning “thread.” Whencells are observed microscopically, thread-like structures can be seen during mi-tosis. Technically speaking, mitosis refers to nuclear division—the equal divisionof one nucleus into two genetically identical nuclei. Mitosis is preceded by repli-cation of chromosomes, which occurs during a part of the cell life cycle knownas interphase. During mitosis, the nuclear material of the parent cell shifts, re-organizes, and moves around, leading some people to refer to mitosis as “thedance of the chromosomes.” After mitosis occurs, the cytoplasm divides (aprocess known as cytokinesis), resulting in two daughter cells. Either haploid ordiploid cells can divide by mitosis.

MeiosisOnly diploid cells can undergo meiosis. As with mitosis, meiosis is preceded byreplication of chromosomes. In meiosis, diploid cells are changed into haploidcells. Human diploid cells, for example, contain 46 chromosomes, whereas hu-man haploid cells (sperm cells and ova) contain 23. Meiosis is the process bywhich gametes are produced. Many steps are involved in meiosis—too many todiscuss in detail here. Suffice it to say that meiosis involves two divisions (calledmeiosis I and meiosis II). The end result is four daughter cells, each of whichcontains only half as many chromosomes as the parent cell. Recall that mitosisproduces two daughter cells that are genetically identical to the parent cell.


Procaryotic Cell Reproduction

Procaryotic cell reproduction is quite simple when compared to eucaryotic celldivision. Procaryotic cells reproduce by a process known as binary fission, whereone cell (the parent cell) splits in half to become two daughter cells. Before aprocaryotic cell can divide in half, its chromosome must be duplicated (a processknown as DNA replication; discussed in Chapter 6), so that each daughter cellwill possess the same genetic information as the parent cell (Fig. 3–14).

The time it takes for binary fission to occur (i.e., the time it takes for oneprocaryotic cell to become two cells) is called the generation time. The genera-tion time varies from one bacterial species to another and also depends on thegrowth conditions (e.g., pH, temperature, availability of nutrients). In the labo-ratory (in vitro), under ideal conditions, E. coli has a generation time of about20 minutes—the number of cells will double every 20 minutes. Bacterial gener-ation times range from as short as 10 minutes to as long as 24 hours or evenlonger in some cases.

TAXONOMY

According to Bergey’s Manual of Systematic Bacteriology (described in Chapter4 and on the website for this book), taxonomy (the science of classification ofliving organisms) consists of three separate but interrelated areas: classification,nomenclature, and identification. Classification is the arrangement of organ-

62 CHAPTER 3

Parent cell

Two daughter cells

DNA replication

Figure 3-14. Binary fission. Note that DNAreplication must occur prior to the actualsplitting of the parent cell.

isms into taxonomic groups (known as taxa [sing., taxon]) on the basis of sim-ilarities or relationships. Taxa include kingdoms or domains, divisions or phyla,classes, orders, families, genera, and species. Closely related organisms (i.e., or-ganisms having similar characteristics) are placed into the same taxon.Nomenclature is the assignment of names to the various taxa according to in-ternational rules. Identification is the process of determining whether an isolatebelongs to one of the established, named taxa or represents a previouslyunidentified species.


A student at Central Texas College once told Dr. Engelkirk that the phrase “KingDavid Came Over For Good Spaghetti” helped her to remember the sequence oftaxa from Kingdom to Species. KDCOFGS. K for Kingdom, D for Division, C forClass, O for Order, F for Family, G for Genus, and S for Species. If you preferPhylum rather than Division, then substitute King Philip for King David. KPCOFGS.Or perhaps, you could come up with your own phrase to help you remember thesequence.

A Trick to Help You to Remember theSequence of Taxa From Kingdom to Species

When attempting to identify an organism that has been isolated from aclinical specimen, laboratory technologists are very much like detectives. Theygather “clues” (characteristics/attributes/properties/traits) about the organismuntil they have sufficient clues to identify (speciate) the organism. In most cases,the “clues” that have been gathered will match the characteristics of an estab-lished species. (Note: throughout this book, the term “to identify an organism”means to learn the organism’s species name—i.e., to speciate it.)

Microbial Classification

Since Aristotle’s time, naturalists have attempted to name and classify plants, an-imals, and microorganisms in a meaningful way, based on their appearance andbehavior. Thus, the science of taxonomy was established, based on the binomialsystem developed in the 18th century by the Swedish scientist, Carolus Linnaeus.In the binomial system, each organism is given two names (e.g., Homo sapiens forhumans). The first name is the genus (pl., genera), and the second name is the spe-cific epithet. The first and second names together are referred to as the species.

Because written reference is often made to genera and species, biologiststhroughout the world have adopted a standard method of expressing thesenames. To express the genus, capitalize the first letter of the word and underlineor italicize the whole word—for example, Escherichia. To express the species,capitalize the first letter of the genus name (the specific epithet is not capitalized)

and then underline or italicize the entire species name—for example,Escherichia coli. Frequently, the genus is designated by a single letter abbrevia-tion; in the example just given, E. coli indicates the species. In an essay or arti-cle about Escherichia coli, Escherichia would be spelled out the first time the or-ganism is mentioned; thereafter, the abbreviated form, E. coli, could be used.The abbreviation “sp.” is used to designate a single species, whereas the abbre-viation “spp.” is used to designate more than one species.

In addition to the proper scientific names for bacteria, acceptable terms likestaphylococci (for Staphylococcus spp.), streptococci (for Streptococcus spp.),clostridia (for Clostridium spp.), pseudomonads (for Pseudomonas spp.), my-coplasmas (for Mycoplasma spp.), rickettsias (for Rickettsia spp.), and chlamydias(for Chlamydia spp.) are commonly used. Nicknames and slang terms frequentlyused within hospitals are GC and gonococci (for Neisseria gonorrhoeae), meningo-cocci (for Neisseria meningitidis), pneumococci (for Streptococcus pneumoniae),staph (for Staphylococcus or staphylococcal), and strep (for Streptococcus orstreptococcal). It is common to hear healthcare workers using terms like meningo-coccal meningitis, pneumococcal pneumonia, staph infection, and strep throat.

Quite often, bacteria are named for the disease that they cause (see Table3–2 for examples). In a few cases, bacteria are misnamed. For example,Haemophilus influenzae does not cause influenza, which is a respiratory diseasecaused by influenza viruses.


Sometimes, bacteria and other microorganisms are named for the person who dis-covered the organism. An interesting example is the name of the plague bacillus. Thebacterium that causes plague was discovered in 1894 by Alexandre Emile JeanYersin (1863–1943), a French bacteriologist of Swiss decent, who worked for manyyears at various Pasteur Institutes in Vietnam. Yersin originally named the organismBacillus pestis, but in 1896 the name was changed to Pasteurella pestis, to honor LouisPasteur, with whom Yersin had studied. Then, many years later, taxonomistschanged the name to Yersinia pestis to honor the person who discovered the or-ganism. Other genera named for bacteriologists include Bordetella (Jules Bordet),Escherichia (Theodore Escherich), Neisseria (Albert Ludwig Neisser), and Salmonella(Daniel Elmer Salmon).

What’s in a Name?

Organisms are categorized into larger groups based on their similarities anddifferences. In 1969, Robert H. Whittaker proposed a Five-Kingdom System ofclassification, in which all organisms are placed into five kingdoms:

■ Bacteria and archaeans are in the Kingdom Procaryotae (or Monera)■ Algae and protozoa are in the Kingdom Protista (organisms in this king-

dom are referred to as protists)

■ Fungi are in the Kingdom Fungi■ Plants are in the Kingdom Plantae■ Animals are in the Kingdom Animalia (although humans are in the

Kingdom Animalia, in this book, the word “animals” refers to animalsother than humans)

Viruses are not included because they are not living cells; they are acellular.Note that four of the five kingdoms consist of eucaryotic organisms. Each king-dom consists of divisions or phyla which, in turn, are divided into classes, orders,families, genera, and species (Table 3–3). In some cases, species are subdividedinto subspecies, their names consisting of a genus, a specific epithet, and a sub-specific epithet (abbreviated “ssp.”); an example would be Haemophilus in-fluenzae ssp. aegyptius, the most common cause of “pink eye.” AlthoughWhittaker’s Five-Kingdom System has been the most popular classification sys-tem for the past 30 or so years, not all scientists agree with it; other taxonomicclassification schemes exist. For example, some scientists do not agree that algaeand protozoa should be placed into the same kingdom, and in some classificationschemes, protozoa are placed into a subkingdom of the Animal Kingdom.

In the late 1970s, Carl R. Woese (see Historical Note) devised a Three-Domain System of classification, which is gaining in popularity among scientists.In this Three-Domain System, there are two domains of procaryotes (Archaea and


Bacterium Disease

Bacillus anthracis AnthraxChlamydia pneumoniae PneumoniaChlamydia psittaci Psittacosis (“parrot fever”)Chlamydia trachomatis TrachomaClostridium botulinum BotulismClostridium tetani TetanusCorynebacterium diphtheriae DiphtheriaFrancisella tularensis Tularemia (“rabbit fever”)Klebsiella pneumoniae PneumoniaMycobacterium leprae Leprosy (Hansen’s disease)Mycobacterium tuberculosis TuberculosisMycoplasma pneumoniae PneumoniaNeisseria gonorrhoeae GonorrheaNeisseria meningitidis MeningitisStreptococcus pneumoniae PneumoniaVibrio cholerae Cholera

aIn some cases, these bacteria cause more than one disease.

T A B L E 3 - 2 Examples of Bacteria Named for the Diseases That They Causea

Bacteria) and one domain (Eucarya or Eukarya) which includes all eucaryotic or-ganisms. Archaea comes from archae, meaning “ancient.” Although members ofthe Domain Archaea have been referred to in the past as archaebacteria and ar-chaeobacteria (meaning “ancient” bacteria), these name have fallen out of favorbecause the archaeans are so different from bacteria. Similarly, organisms in theDomain Bacteria have, at times, been referred to as eubacteria, meaning “true”bacteria, but are now usually referred to as bacteria. Note that the domain namesare italicized. Domain Archaea contains 2 phyla and Domain Bacteria contains 23.The Three-Domain System is based on differences in the structure of certain ri-bosomal RNA (rRNA) molecules among organisms in the three domains.


During the 1970s, a molecular biologist named Carl Woese and his colleagues at theUniversity of Illinois shook up the scientific community by developing a system ofclassifying organisms that was based upon the sequences of nucleotide bases in theirribosomal RNA molecules. They demonstrated that procaryotic organisms can bedivided into two major groups (referred to as domains), based on differences intheir rRNA sequences, and that the rRNA from these two groups differed from therRNA of eucaryotic organisms. Although this system of classification was not widelyaccepted at first, Woese’s Three-Domain System has become the classification sys-tem most favored by microbiologists.

Carl R. Woese

DETERMINING RELATEDNESS AMONGORGANISMS

How do scientists determine how closely related one organism is to another?The most widely used technique for gauging diversity or relatedness is called ri-bosomal RNA (rRNA) sequencing. Ribosomes are made up of two subunits: asmall subunit and a large subunit. The small subunit contains only one RNAmolecule, which is referred to as the “small subunit rRNA” or SSUrRNA. TheSSUrRNA in procaryotic ribosomes is a 16S rRNA molecule, whereas theSSUrRNA in eucaryotes is an 18S rRNA molecule. (The “S” in 16S and 18Srefers to Svedberg units, which were discussed earlier.) The gene that codes forthe 16S rRNA molecule contains about 1500 DNA nucleotides, whereas thegene that codes for the 18S rRNA molecule contains about 2000 nucleotides.The sequence of nucleotides in the gene that codes for the 16S rRNA moleculeis called the 16s rDNA sequence. To determine “relatedness,” researchers com-pare the sequence of nucleotide base pairs in the gene, rather than comparingthe actual SSUrRNA molecules. If the 16S rDNA sequence of one procaryoticorganism is quite similar to the 16S rDNA sequence of another procaryotic or-ganism, then the organisms are closely related. The less similar the 16S rDNA

sequences in procaryotes (or the 18S rDNA sequences in eucaryotes), the lessrelated are the organisms. For example, the 18S rDNA sequence of a human ismuch more similar to the 18S rDNA sequence of a chimpanzee than to the 18SrDNA sequence of a fungus.

Perhaps taxonomists will someday combine the Three-Domain System andthe Five-Kingdom System, producing either a Six-Kingdom System (Bacteria,Archaea, Protista, Fungi, Plantae, and Animalia) or a Seven-Kingdom System(Bacteria, Archaea, Algae, Protozoa, Fungi, Plantae, and Animalia).


Escherichia coli Staphylococcus aureus(A Medically Important (A Medically Important

Human Being Gram-Negative Bacillus)a Gram-Positive Coccus)a

Kingdom (Domain) Animalia (Eucarya) Procaryotae (Bacteria) Procaryotae (Bacteria)

Phylum Chordata Proteobacteria Firmicutes

Class Mammalia Gammaproteobacteria Bacilli

Order Primates Enterobacteriales Bacillales

Family Hominidae Enterobacteriaceae Staphylococcaceae

Genus Homo Escherichia Staphylococcus

Species (a species Homo sapiens Escherichia coli Staphylococcus aureushas two names; the first name is the genus, and the second name is the specific epithet)

T A B L E 3 - 3 Comparison of Human and Bacterial Classification

aBased on Bergey’s Manual of Systematic Bacteriology, 2nd ed, vol. 1, 2001. Springer-Verlag, New York, NY.

68 CHAPTER 3

■ The cell is the fundamental unit of any livingorganism; it exhibits the basic characteristicsof life. All living organisms are composed ofone or more cells.

■ Complex eucaryotic cells contain membrane-bound organelles and a true nucleus, con-taining DNA. Procaryotic cells (archaeansand bacteria) exhibit all the characteristics oflife, but do not have a true nucleus or a com-plex system of membranes and membrane-bound organelles.

■ Some eucaryotic cells have cell walls toprovide rigidity, shape, and protection;these simple cell walls may contain cellu-lose, pectin, lignin, chitin, or mineral salts.Procaryotic bacterial cell walls are morecomplex, containing peptidoglycan and, insome cases, lipopolysaccharides.

■ In eucaryotic cells, energy is producedwithin mitochondria (“energy factories”).Energy-producing reactions occur at the cellmembranes of procaryotic cells.

■ External to the cell wall, some bacteria haveeither a capsule or a slime layer. Capsulesserve an antiphagocytic function and havebeen used in the production of certain vac-cines. Determining whether a bacterium pos-sesses a capsule is valuable when attemptingto identify the organism.

■ Many bacteria have flagella that enablemotility and some produce spores for sur-vival. Determining whether a bacteriumpossesses flagella is valuable when attempt-

ing to identify the organism, as are the num-ber and location of the flagella. Likewise,the presence or absence of spores is of valuewhen identifying bacteria.

■ Eucaryotic cells reproduce either by mitosisor meiosis, whereas procaryotic cells repro-duce by binary fission.

■ In the binomial system of nomenclature, thefirst name is the genus, the second name isthe specific epithet, and the two names to-gether represent the species.

■ Taxonomic classification of organisms sepa-rates them into kingdoms, divisions, orders,classes, families, genera, and species, basedon their characteristics, attributes, proper-ties, and traits.

■ In the Five-Kingdom System of classifica-tion, microorganisms are found in the firstthree kingdoms—Procaryotae (bacteria),Protista (algae and protozoa), and Fungi. Inthe Three-Domain System, microorganismsare found in all three domains—Archaea,Bacteria, and Eucarya.

■ The most widely used technique for deter-mining how closely one procaryotic organ-ism is related to another involves the genethat codes for the 16S rRNA molecule of ri-bosomes. The more similar the 16S se-quences, the more closely related are the or-ganisms. The less similar the 16S sequences,the less related are the organisms. For eu-caryotes, the 18s rRNA gene is used.

REVIEW OF KEY POINTS

ON THE WEB—h t t p : / / c o n n e c t i o n . l w w . c o m / g o / b u r t o n 7 e

■ Insight■ The Origin of Mitochondria and Chloroplasts

■ Increase Your Knowledge■ Critical Thinking■ Additional Self-Assessment Exercises


1. Molecules of extrachromosomalDNA are also known as:

a. Golgi bodies.b. lysosomes.c. plasmids.d. plastids.e. rough ER.

2. A bacterium possessing a tuft offlagella at one end of its cellwould be called what kind of bac-terium?

a. amphitrichousb. lophotrichousc. monotrichousd. peritrichouse. tufty

3. One way in which an archaeanwould differ from a bacterium isthat the archaean would possessno:

a. DNA in its chromosome.b. lipids in its cell membrane.c. peptidoglycan in its cell

walls.d. ribosomes in its cytoplasm.e. RNA in its ribosomes.

4. Some bacteria stain Gram-positive and others stain Gram-negative due to differences in thestructure of their:

a. capsule.b. cell membrane.c. cell wall.d. cytoplasm.e. ribosomes.

5. Of the following, which one is notfound in procaryotic cells?

a. cell membraneb. chromosomec. mitochondriad. plasmidse. ribosomes

6. The Three-Domain System ofclassification is based on differ-ences in which of the followingmolecules?

a. DNAb. mRNAc. peptidoglycand. rRNAe. tRNA

7. Which of the following is in thecorrect sequence?

a. Kingdom, Class, Division,Order, Family, Genus

b. Kingdom, Division, Class,Order, Family, Genus

c. Kingdom, Division, Order,Class, Family, Genus

d. Kingdom, Order, Class,Division, Family, Genus

e. Kingdom, Order, Division,Class, Family, Genus

8. Which one of the following isnever found in viruses?

a. capsidb. capsulec. DNA d. envelopee. RNA

SELF-ASSESSMENT EXERCISES

After you have read Chapter 3, answer the following multiple choice questions.

70 CHAPTER 3

9. The semipermeable structurecontrolling the transport of mate-rials between the cell and its ex-ternal environment is the:

a. cell membrane.b. cell wall.c. cytoplasm.d. nuclear membrane.e. protoplast.

10. In eucaryotic cells, what are thesites of photosynthesis?

a. Golgi bodiesb. mitochondriac. plasmidsd. plastidse. ribosomes

Ch_03

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