Microbiology Demystified By Belzy

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Chemical Elements and the Atom

Everything including you is composed of chemical elements. A chemical ele-

ment, sometimes simply referred to as an element, is a substance that cannot be

broken down into simpler substances by a chemical process. All matter is a com-

bination of chemical elements.

A chemical element is made up of atoms. An atom is the smallest particle of

an element; it cannot be further decomposed into smaller chemical substance

(Fig. 2-1). In the early 1800s, John Dalton developed the Atomic Theory, which

explains the relationship between an element and an atom. The Atomic Theory

CHAPTER 2 Chemical Elements of Microorganisms24

c02_betsy.qxd 5/11/05 2:24 PM Page 24

states that an element cannot be decomposed into two or more chemical sub-

stances because the element consists of one kind of atom. The atom is also the

smallest amount of matter that can enter into a chemical reaction. You’ll learn

about chemical reactions later in this chapter.

At the center of every atom is a nucleus. The nucleus does not change spon-

taneously unless it is unstable—making it radioactive—and does not participate

in a chemical reaction. It is for this reason that the nucleus for most atoms is con-

sidered stable.

Moving around the nucleus are electrons. An electron is a negatively charged

particle that follows a path called an orbital. Electrons are the parts of an atom

that enter into a chemical reaction.

The nucleus is made up of protons and neutrons. A proton is a positively

charged particle. A neutron is a particle that does not have a charge; it is called

neutral or uncharged. The number of protons in the nucleus equals the number

of electrons in an electrically stable atom. This makes the atom neutral because

the number of positively charged particles (protons) offsets the number of neg-

atively charged particles (electrons).

An element is identified by its atomic number. The atomic number is the num-

ber of protons in the nucleus of the atom. The atomic mass (also called the atomic

weight) is slightly less than the sum of the masses of an atom’s neutrons and pro-

tons. The standard for measuring atomic mass is called a dalton, named for John

Dalton. A dalton is also known as an atomic mass unit (amu). For example, a neu-

tron has an atomic mass of 1.088 daltons. A proton has an atomic mass of 1.077

daltons. An electron has an atomic mass of 0.0005 dalton.

Atoms that have the same atomic number are classified as the same chemical

element because these atoms behave the same way. Therefore, a chemical ele-

ment consists of one or more atoms that have the same atomic number.

CHAPTER 2 Chemical Elements of Microorganisms 25

Electron

Electron shells

Proton

Neutron

Orbital

Nucleus

Fig. 2-1. An atom is the smallest particle of an element.

c02_betsy.qxd 5/11/05 2:24 PM Page 25

Atoms of elements that have the same atomic number, but different mass

numbers are called isotopes. This difference is do to a difference in number of

neutrons.

Each chemical element is identified by a one or two-letter symbol that corre-

sponds to the first letter or the first two letters in its name. For example, the sym-

bol C is used for carbon. Some chemical elements have English names while

others have Latin names. It is for this reason that symbols for some chemical

elements seem strange at first glance. Take sodium, for example. You would

think its symbol should be S, but that’s the symbol for sulfur. The symbol for

sodium is Na—the first two letters of its Latin name, natrium.

There are 92 natural chemical elements and others that scientists synthesized

(created). All of these are organized into a table called the Periodic Table (see

“A Dinner Table of Elements: The Periodic Table”). The six most abundant

chemical elements in living things are carbon, oxygen, hydrogen, nitrogen,

phosphorus and calcium. The rest are also important (see Table 2-1) and are

found in trace amounts.

CHAPTER 2 Chemical Elements of Microorganisms26

Atomic Approximate

Element Symbol Number Atomic Weight

Calcium Ca 20 40

Carbon C 6 12

Chlorine Cl 17 35

Hydrogen H 1 1

Iodine I 53 127

Iron Fe 26 56

Magnesium Mg 12 24

Nitrogen N 7 14

Oxygen O 8 16

Phosphorus P 15 31

Potassium K 19 39

Sodium Na 11 23

Sulfur S 16 32

Table 2-1. Chemical Elements Commonly Found in All Living Things

c02_betsy.qxd 5/11/05 2:24 PM Page 26

A Dinner Table of Elements: The Periodic Table

As scientists continued to discover new chemical elements, it became appar-

ent that there needed to be a way to place chemical elements in some kind of

order. In this way, scientists can easily reference information about each chem-

ical element.

In the 1800s Russian chemist Dimitri Mendeleev organized chemical ele-

ments into a table by their atomic weight. Chemist H. G. J. Moseley reorganized

chemical elements using their atomic number rather than atomic weight.

Chemical elements were placed on the table in increasing atomic number. This

is referred to as the Law of Chemical Periodicity, and the table became known

as the Periodic Table (Fig. 2-2).

The Periodic Table consists of seven rows, each called a period. Chemical

elements that have the same number of electron shells are placed in the same

period. Rows are divided into columns, which are identified with the Roman

numerals IA through VIIIA or 1 through 18, depending on the author of the

Periodic Table. Chemical elements within the same column have the same chem-

ical properties. For example, chemical elements in column IA can easily be

joined with other chemical elements. In contrast, chemical elements in column

VIIIA will not join with other chemical elements.

Each chemical element is identified by its symbol on the Periodic Table and is

associated with two numbers. The number on top of the chemical symbol is the

atomic number. The number beneath the chemical symbol is the atomic weight.

The Glowing Tale of Isotopes

Scientists describe the decay of an isotope using half-life. The half-life of an iso-

tope is the time required for half the isotope’s radioactive atoms in a sample of the

isotope to decay into a more stable form. The rate at which the number of atoms

of an isotope disintegrates is called the isotope’s rate of decay, which can be a mat-

ter of seconds, minutes, hours, days, or years. Ernest Rutherford coined the term

half-life at the turn of the twentieth century. Rutherford discovered two kinds of

radiation that he called alpha and beta. Scientists acknowledged Rutherford’s

important contribution by naming an element for him: rutherfordium (Rf).

Around the same time, Marie Curie along with her husband Pierre Curie dis-

covered that atoms of the chemical element polonium (Po) and of the chemical

element radium (Ra) spontaneously decayed and gave off particles. She called

this process radioactivity.

CHAPTER 2 Chemical Elements of Microorganisms 27

c02_betsy.qxd 5/11/05 2:24 PM Page 27

1 H 1.

2 H

3 L

4 B

5 B 10

6 C 12

7 N 14

8 O 15

9 F 18

10 N

11 N

12 M

13 A

14 Si 28

15 P 30

16 S 32

17 C

18 A

19 K 39

20 C

21 Sc 44

22 T

23 V 50

24 C

25 M

26 F

27 C

28 N

29 C

30 Z

31 G

32 G

33 A

34 Se 78

35 B

36 K

37 R

38 Sr 87

39 Y 88

40 Z

41 N

42 M

43 T

44 R

45 R

46 P

47 A

48 C

49 In 11

50 Sn 11

51 Sb 12

52 T

53 I 12

54 X

55 C

56 B

57 L

72 H

73 T

74 W 18

75 R

76 O

77 Ir 19

78 P

79 A

80 H

81 T

82 P

83 B

84 P

)

85 A

)

86 R

)

87 F

)

88 R

89 A

)

58 C

59 P

60 N

61 P

)

62 Sm 15

63 E

64 G

65 T

66 D

67 H

68 E

69 T

70 Y

71 L

90 T

91 P

92 U 23

93 N

94 P

)

95 A

)

96 C

)

97 B

)

98 C

)

99 E

)

. 2

-2

c02_betsy.qxd 5/11/05 2:24 PM Page 28

A chemical element can have multiple isotopes. Each of those isotopes has

the same atomic number but different mass number. As you’ll recall from earlier

in this chapter, the mass number is the sum of protons and neutrons in the

nucleus. Each isotope of the same chemical element has a different number of

neutrons but the same number of protons.

Around They Go: Electronic Configuration

Previously in this chapter you learned that electrons of an atom move around the

atom’s nucleus in a pattern called an orbital. An orbital of an atom is organized

into one or more energy levels around the nucleus. The lowest energy level

orbital is closest to the nucleus. The highest energy level is in the outermost

orbital. The outermost orbital is called the valence shell. Each orbital holds a

maximum number of electrons.

An atom with completely filled shells is called an inert atom and is chemi-

cally stable. An inert atom tends not to react with other atoms. However, an atom

that has an incomplete set of electrons in its valence shell is chemically unstable

and tends to react with other atoms in an effort to become stable. Atoms want to

be stable, so they either empty or fill their valence shell.

If an atom’s valance shell is not filled, it is considered unstable. In order to

become stable the atom must undergo a chemical reaction to acquire one or more

electrons from another atom, give up one or more electrons to another atom, or

share one or more electrons with another atom.

A chemical reaction is a chemical change in which substances called reactants

change into substances called products by rearrangement, combination, or separa-

tion of elements. Chemical reactions occur naturally, sometimes taking a relatively

long time to complete. A catalyst can be used to speed up a chemical reaction.

Enzymes are chemical substances that act like catalysts to increase the rate of reac-

tion, without changing the products of the reaction or by being consumed in the

reaction. A catalyst remains unaffected by the chemical reaction and does not

affect the result of the reaction. It simply speeds up the reaction.

Before James There Was Bond . . . Chemical Bond

An atom stabilizes by bonding with another atom in order to fill out its outer set

of electrons in its valence shell. When two atoms of the same chemical element

CHAPTER 2 Chemical Elements of Microorganisms 29

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bond together they form a diatonic molecule. When two atoms of different chemi-

cal elements bond, they form a chemical compound.

Atoms are held together because there is an electrostatic attractive force

between the two atoms. Energy is required for the chemical reaction to bond

atoms. This energy becomes potential chemical energy that is stored in a mole-

cule or chemical compound.

For example, combining two atoms of hydrogen forms a hydrogen molecule,

H2 (Fig. 2-3). Combing a hydrogen molecule consisting of two atoms with one

oxygen atom forms the compound we know as water, H2O (Fig. 2-4).

Bonds are formed in two ways:

• Gain or lose an electron from the valence shell; called an ionic attraction.

• Share one or more electrons in the valence shell; called a covalent bond.

In reality, atoms bond together using a range of ionic and covalence bonds.

There are four kinds of chemical bonds:

• Ionic bond. Transfer electrons from one atom to another atom. An atom

becomes unbalanced when it gains or loses an electron. An atom that gains

an electron becomes negatively charged. An atom that loses an electron

CHAPTER 2 Chemical Elements of Microorganisms30

Fig. 2-4. Water is a compound consisting of two hydrogen atoms and one oxygen atom.

Fig. 2-3. Hydrogen becomes chemically stable by sharing a valence

electron with another hydrogen atom.

c02_betsy.qxd 5/11/05 2:24 PM Page 30

CHAPTER 2 Chemical Elements of Microorganisms 31

becomes positively charged. The atom is oxidized. An atom that is in-

volved in this exchange is called an ion. The atom that gives up an electron

is called a cation. A cation is positively charged. The atom that receives an

electron is called an anion, which is negatively charged. The reaction that

creates table salt from sodium and chlorine causes an ionic bond between

these atoms (Fig. 2-5).

• Covalent bond. Atoms share electrons in their valence shell (Fig. 2-5).

The shared electron orbits the nucleus of both atoms. A covalent bond is the

strongest bond and the most commonly found in organisms. There are three

kinds of covalent bonds: single, double, and triple. These names reflect

the number of electrons that are shared between the two atoms that form

the bond. Atoms that share electrons equally form nonpolar covalent

bond. Atoms that share electrons unequally form polar covalent bond.

• Coordinate covalent bond. A bond is formed when electrons of the shared

pair come from the same atom.

• Hydrogen bond. A hydrogen bond forms a weak (5% the strength of a

covalent bond), temporary bond that serves as a bridge between either dif-

ferent molecules or portions of the same molecule. For example, two water

molecules are physically combined using a hydrogen bond.

Decoding Chemical Shorthand

Over the years chemists have developed a way of describing atoms, chemical

elements, and reactions so they can convey ideas to each other. Table 2-2 shows

commonly used chemical notations that you’ll need to know when learning

about microbiology.

I Just Want to See Your Reaction

The process of bonding together atoms and separating atoms that are already

bonded together is called a chemical reaction. A chemical reaction causes a

change in the properties of atoms or to a collection of atoms, but the atoms

remain unchanged because of a change in the electron configuration. For example,

c02_betsy.qxd 5/11/05 2:24 PM Page 31

t v

tio

’s

l h

. C

e’

l h

rin

. 2

-5

c02_betsy.qxd 5/11/05 2:24 PM Page 32

a chemical reaction occurs when a sodium atom is combined with a chlorine

atom; the property of the resulting chemical compound is table salt. If the

sodium chloride (table salt) compound were broken down into its chemical ele-

ments, you would see that the atoms of sodium and chlorine remain unchanged.

Theoretically a chemical reaction can be reversed if the conditions are opti-

mal. A chemical reaction that is reversible is called a reversible reaction. (see

Fig. 2-6)

In practical use, same reactions can do this much easier than others. Some of

these reversible reactions occur due to the instability of the reactants and prod-

ucts, while others will only reverse under special conditions. Examples of spe-

cial conditions could be the presence of water or the application of heat.

CHAPTER 2 Chemical Elements of Microorganisms 33

Notation Description

Na+ The plus superscript indicates a positive ion.

Cl− The negative superscript indicates a negative ion.

Na+ + Cl−→ NaCl The plus sign indicates synthesizing (combining) two

particles. The right arrow indicates that a chemical

reaction occurs towards the product.

NaCl → Na+ + Cl− Decomposing (breaking up) a molecule or chemical

compound.

NaOH + HCl → NaCl + H2O Exchange reaction where a chemical compound is de-

composed into its chemical elements and those chemi-

cal elements are synthesized into a new compound.

Here, sodium hydroxide (NaOH) and hydrochloric acid

(HCl) form salt (NaCL) and water (H2O).

Na+ + Cl− →← NaCl Reversible reaction is noted with a right arrow over a

left arrow.

C – C Single covalent bond.

C = C Double covalent bond.

C ≡ C Triple covalent bond.

H2O A subscript following a chemical symbol indicates the

number of atoms (two hydrogen atoms). If no subscript

is used, then it is implied there is one atom (here, one

oxygen atom).

Table 2-2. Commonly Used Chemical Notations

c02_betsy.qxd 5/11/05 2:24 PM Page 33

The type of reaction that occurs can further describe a chemical reaction.

There are three types of chemical reactions:

• Synthesis reaction: Two or more atoms, ions, or molecules are bound to form

a larger molecule. A synthesis reaction combines substances called reactants

to form a new molecule, which is called a product. A reactant is a substance

that reacts in a reaction and the product is the result of a reaction. In Na+ +

Cl− → NaCl, sodium and chlorine are reactants and sodium chloride is the

product of this reaction. A synthesis reaction in a living organism is referred

to as an anabolic reaction or anabolism. These are metabolic pathways.

• Decomposition reaction: A reaction that breaks the bond between atoms in a

molecule or chemical compound. In NaCl → Na+ + Cl−, sodium chloride is

broken up into its chemical elements sodium and chlorine. A decomposition

reaction in a living organism is called a catabolic reaction or catabolism.

• Exchange reaction: A reaction that is both a synthesis reaction and a

decomposition reaction, where a chemical compound is decomposed into

its chemical elements and those chemical elements are synthesized into a

new chemical compound. In NaOH + HCl → NaCl + H2O, sodium hydrox-

ide (NaOH) and hydrochloric acid (HCl) enter into an exchange reaction

to form salt (NaCL) and water (H2O).

A chemical reaction theoretically can be reversed, but in practice some reac-

tions create an unstable chemical compound that might require special con-

ditions to exist for the reverse reaction to happen. Those special conditions

required to reverse a reaction appear below the arrow in the reaction notation.

Above the arrow appears any special condition that must exist for the synthe-

sized reaction to occur. In Fig. 2-6, a temperature of 250° C is the special con-

dition for the synthesized reaction to occur and absolute zero is necessary for the

decomposition reaction to occur.

A catalyst is a substance that speeds up the rate of a chemical reaction by

decreasing the energy needed to run the reaction without changing the reactants

or products. Enzymes are an example of a biological substance that acts as cat-

alysts to speed up a reactor rate.

CHAPTER 2 Chemical Elements of Microorganisms34

Fig. 2-6. In theory all chemical reactions are reversible. In

practice these are called reversible reactions.

X Y XY+

heat

water

c02_betsy.qxd 5/11/05 2:24 PM Page 34

• Velocity. A specific level of energy is required for a bond to occur. This energy

level is called activation energy and is different for each chemical reaction.

• Orientation. Two atoms, ions, or molecules must strike each other at a

position where bonding can occur.

• Reaction rate. Collisions must occur frequently at the proper orientation

and at the activation rate in order for bonding to happen. There are two

ways to increase the reaction rate. These are an increase in temperature and

an increase in pressure. Both cause atoms, ions, and molecules to move

faster and increase the probability of a collision.

• Size. The atomic weight of an element influences the speed of a chemical

reaction. An atom with a larger atomic weight than another atom requires

more energy to be expended to increase the speed of the chemical reaction

that binds the atom to another atom.

CATALYST: MAKING THINGS HAPPEN

Living organisms possess large molecules of proteins that are called enzymes.

These enzymes act as catalysts. A catalysts is a chemical substance that speeds-

up the rate of a chemical reaction. These catalysts do this without affecting the

end products of the reaction, nor permanently altering themselves.

In order for an enzyme to be effective it must interact with a chemical called

a substrate. The enzyme attaches itself to the substrate in an area that will most

likely increase its ability to react. This enzyme-substrate complex lowers the

activation energy of the reaction and enables the collision of chemicals involved

in the reaction to be more effective.

An important factor of enzymes is that they can reduce the reaction time with-

out the need to increase temperature. This is very important in living organisms

because high temperatures can break apart the proteins that make up the cell.

CHEMICAL COMPOUND:

MAKING SOMETHING USEFUL

As you learned previously in this chapter, a chemical element is a substance that

cannot be divided into other chemical substances. For example, you cannot fur-

ther divide hydrogen into anything because hydrogen is an element.

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In its simplest form, a chemical element is made up of one atom. In its more

complex form, a chemical element is made up of two or more atoms, which is

called a molecule of the chemical element. For example, binding together two

hydrogen atoms forms a hydrogen molecule.

H + H → H2

In order to make different things you need to combine different atoms and

molecules of different chemical elements. This combination is called a com-

pound. For example, combining two hydrogen molecules to an oxygen atom

results in the compound we know as water.

H2 + O → H2O

Molarity: Hey, There’s a Mole Amongst Us

It seems nearly impossible to measure a molecule’s mass or size. Fortunately,

there is Avagadro’s number, which is the number of particles in a mole of a sub-

stance. The number is 6.022 × 1023. Amadeo Avagadro was an Italian physicist

for whom the value was named.

Scientists can measure molecules using units called a mole. Abbreviated as

mol. One mole is equal to the atomic weight of an element expressed in grams.

A mole is the weight in grams of a substance that is equal

to the sum of the

atomic weights of the atoms in a molecule of the substance. This is referred to

as a gram molecular weight.

Let’s look at a water molecule to determine how many moles there are in a

liter of water.

• Find the atomic mass for each chemical element that makes up water.

Water has two chemical elements. These are hydrogen and oxygen.

• Look up the symbol for each element on the Periodic Table. These are H

and O for hydrogen and oxygen.

• Note the bottom number alongside the symbol. This is the atomic mass for

the chemical element. These are 1 for hydrogen and 16 for oxygen.

• Multiply the number of atoms of each chemical element in the molecule by

its atomic mass to determine the value for one mole for the chemical ele-

ment. For water, there are two hydrogen atoms so this will be 2 × 1g. One

CHAPTER 2 Chemical Elements of Microorganisms36

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mole of a hydrogen molecule H2 equals 2 g. Water has one oxygen atom.

Therefore, multiply 1 × 16 g. One mole of oxygen is 16 g.

• Sum the atomic mass of atoms that make up the molecule to determine one

mole of the molecule. For water this is 2 g ++ 16 g = 18 g. One mole of

water equals the atomic mass of 18 g.

• The weight of one mole is the atomic mass of a molecule expressed in

grams. Therefore, one mole of water weighs 18 grams.

• A liter of water has a mass of 1,000 grams. Calculate the number of moles

per liter by dividing the number of grams (1,000) by one mole of water (18

grams). The result is 55 moles/liter.

An Unlikely Pair: Inorganic and Organic

Chemical compounds are divided into two general categories of substances.

These are:

• Inorganic compound. A compound that does not contain the chemical ele-

ment carbon (C).

• Organic compound. A compound containing carbon atoms, the exception

is carbon dioxide (CO2). Carbon dioxide is inorganic.

• Inorganic compounds are further divided into three categories. These are:

• Acids. An acid is any compound that dissociates into one or more hydro-

gen ions (H+) and one or more negative ions (called anions) and is a pro-

ton donor.

• Bases. A base is any compound that dissociates into one or more positive

ions (called cations) and one or more negative hydroxide ions. The nega-

tive hydroxide ions (OH−) can either accept or share protons.

• Salts. A salt is an ionic compound that dissociates into one or more positive

or negative ions in water, although some salts are not soluble in water. The

positive and negative ions are neither hydrogen ions nor hydroxide ions.

Sodium and chlorine atoms break away from the salt lattice when water

molecules surround them. Water molecules become oriented so that the pos-

itive poles face the negatively charged chlorine ions and the negative poles

face the positively charged sodium ions. The water’s hydrogen shells react

with the sodium and chlorine ions, drawing the ions from the salt lattice.

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THE pH SCALE

There must be a balance between acids and bases in order to maintain life. An

imbalance disrupts homeostasis. The acid-base balance is measured using the

pH scale. The pH scale (Fig. 2-7) measures the acidity or alkalinity (base) of a

substance using a pH value from 0 to 14. Values on the pH scale are logarithmic

values. A pH value of 7 is neutral, which is the pH of pure water. A pH value

greater than 7 is a base or alkaline. A pH value less than 7 is an acid. A change

in one pH value is a large change because it is a logarithmic scale. For example

a pH of 1 has 10 times more hydrogen ions than a pH of 2 and 100 times more

hydrogen ions than a pH of 3 (pH = −log10[H+]).

Adding a substance that will increase or decrease the concentration of hydro-

gen ions can change the pH value of a substance. Increasing the concentration

of hydrogen ions makes the substance more acidic and decreasing the concen-

tration makes the substance more alkaline.

CHAPTER 2 Chemical Elements of Microorganisms38

Fig. 2-7. The pH scale is a logarithmic scale that measures

the acidity or alkalinity of a substance.

Distilled water

Oven cleaner

Stomach acid

Acidity

Alkalinity

(Base)

Lemon juice

Vinegar

Tomatoes

Black coffee

Urine

Bile

Baking soda

Milk of Magnesia

Household Bleach

Ammonia

Lime water

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The pH value of chemical compounds in living things naturally fluctuates

during metabolism. Metabolism is a collection of chemical reactions occurring

in a living organism. Sometimes the chemical compound is more acidic than

alkaline and vice versa. Any drastic sway in the acid-base balance could have a

devastating effect. A chemical compound called a buffer is used to prevent harm-

ful swings in the acid-base balance. A buffer releases hydrogen ions or binds

hydrogen ions to stabilize the pH. A weak acid or base does not easily separate

(ionization).

ORGANIC COMPOUNDS

An organic compound is a compound whose chemical elements include carbon.

Carbon plays an import role in living things because compounds that contain it

build many different organic compounds, each having different structures and

functions. The large size of most carbon-containing molecules and the fact that

they don’t dissolve easily in water makes them useful in building body structures.

Organic compounds also store energy required by an organism for metabolism.

Carbon can combine with other atoms because carbon has four electrons in

its outer shell. This leaves room for four additional electrons from other atoms

to bond to the carbon atom in a biological reaction (Fig. 2-8). Carbon also has

low electronegativity and lacks polarity when a bond is formed.

A carbon atom commonly combines with other carbon atoms to form a car-

bon chain. There are two forms of carbon chains. These are straight carbon

chains and ring carbon chains. Fig. 2-9 shows how this is used to illustrate fruc-

tose. Carbon chains are the basic form for many organic compounds.

Organic compounds come in many sizes—small to large. Many, but not all,

large organic compounds are called polymers. A polymer is made up of small

molecules called monomers. A monomer is another name for subunit. Monomers

are bonded together to form a polymer in a process called dehydration synthe-

sis, which removes water molecules from the compound.

CHAPTER 2 Chemical Elements of Microorganisms 39

Fig. 2-8. The lines indicate a single bond with other atoms.

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A large organic compound is called a macromolecule which in many cases is

a polymer. A macromolecule can be reduced to its monomer in a process called

hydrolysis, which adds water molecules to the polymer.

There are four types of organic compounds that are macromolecules. These are:

• Carbohydrates

• Lipids

• Proteins

• Nucleic acids

Carbohydrates

Carbohydrates store energy from an organism in the form of sugar, starches and

in the human body, glucogen. Cellulose is also a carbohydrate used as bulk to

move food and waste through the gastrointestinal tract. Carbohydrates are also

used as material in the cell wall. Carbohydrates are organized into three major

Carbohydrate groups. These are:

• Monosaccharides. Some of the important monosaccharides are: glucose, the

main energy source for an organism; fructose, acquired by eating fruit; galac-

tose, which is in milk; deoxyribose, DNA; and ribose, RNA. A monomer is

also a monosaccharide.

• Disaccharides. This is a combination of two monosaccharides bonded dur-

ing dehydration synthesis. Sucrose (table sugar) and lactose (milk sugar)

CHAPTER 2 Chemical Elements of Microorganisms40

H H

OH OH

CH2OH

HOCH2

Glucose

C6H12O6

Fructose

C6H12O6

Fig. 2-9. A carbon cain is used to show the compound fructose.

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are disaccharides. Sucrose contains glucose and fructose.

Lactose contains

glucose and galactose.

• Polysaccharides. A polysaccharide is comprised of many monosaccharides

and includes glycogen, starch, cellulose, and chitin, which is an amino sugar.

Lipids

Lipids are our fats and provide protection, insulation and can be used as an

energy reserve. They are important components to the cell membrane and store

pigments.

There are four kinds of lipids. These are:

• Triglycerides. Triglycerides protect and insulate the body from most lipids

and are a source of energy. Because lipids have few polar covalent bonds,

they are mostly insoluble (do not mix well) with polar solvents, like water.

• Phospholipids. Phospholipids are a major component in cell membranes.

• Steroids. Steroids are cholesterol and some hormones.

• Eicosanoids. Eicosanoids are divided into two kinds. These are prostaglan-

dins and leukotrienes. Prostaglandins are involved in various behaviors

such as dilating airways, regulating body temperature, and aiding in the

formation of blood clots. Leukotrienes are involved in inflammatory and

allergic responses.

Other kinds of lipids include fatty acids, lipoproteins and many plant pig-

ments including chlorophyll and beta-carotene and the fat soluble vitamins such

as A, D, E and K.

Proteins

Proteins comprise about 50% of a cell’s dry weight and make up material in the

cell wall. Proteins are peptidoglycans and help to transport chemicals into and

out of a cell. In addition, proteins are part of cell structures and cytoplasmic

components. Some proteins are antibodies that kill bacteria and play a role in

muscle contractions and provide movement of microorganisms. Proteins are

made up of polypeptides that bond together using peptide bonds. There are four

structural levels of proteins. These are:

• Primary. The primary structure is the sequence in which amino acids are

linked to form the polypeptide. Sequences are genetically determined and

even the slightest alteration within the sequence may have a dramatic effect

on the way the protein functions.

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• Secondary. The secondary structure is locally folded and is the repeated

twisting of the polypeptide chain that links together the amino acids. There

are two types of secondary structures. These are a helix and a pleated sheet.

The alpha-helix is a clockwise spiral structure. The pleated sheet forms the

parallel portion of the polypeptide chain.

• Tertiary. The tertiary structure is the three-dimensional active structure of

the polypeptide chain. Tertiary structure is the minimal level of structure

for biological activity.

• Quarternary. Is where the proteins, in order to be functional, contain sub-

units of polypeptide chains. An example would be DNA polymerase.

Proteins have many roles in a living organism. They are found in bone colla-

gen and connective tissue and provide protection in the form of immunoglobins,

which are antibodies. Some of the other important proteins are:

• Myosin. Muscle contraction.

• Actin. Muscle contraction.

• Hemoglobin transports oxygen (O2) and carbon dioxide (CO2) in blood.

• Enzymes. An enzyme that is a biological catalyst that increases the rate of

chemical reactions in cells by reducing the energy required to begin the

reaction. The reaction does not change the enzyme. The name of an

enzyme typically ends with “-ase.”

• Flagellin. Protein in flagella.

The Blueprint of Protein Synthesis

Proteins play a critical role in chemical reactions of microorganisms and other

kinds of organisms. Information needed to direct the synthesis of a protein is

contained in DNA (Deoxyribonucleic Acid). This information is transferred

through generations from parent to child microorganisms. Nucleotides also store

energy in high-energy bonds and form together to make nucleic acids.

There are three parts to a nucleotide:

• A nitrogen base, such as adenine.

• A five-carbon sugar, such as ribose.

• One or more phosphate groups.

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Nucleic acids form by the joining of nucleotides that have stored energy that

the microorganism needs for metabolism. Enzymes form to speed the rate of the

chemical reaction that breaks these high-energy bonds to release the energy

needed for cell metabolism.

Nucleic acids are long polymer chains that are found in the nucleus of cells

and contain all the genetic material of the cell. Genetic material determines the

activities of the cell and is passed on from generation to generation.

TYPES OF NUCLEIC ACIDS

There are two types of nucleic acids found in the cell:

• Deoxyribonucleic acid (DNA). DNA is a double strand of nucleotides that

is organized into segments. Each segment is called a gene. Genes deter-

mine the genetic markers that are inherited from previous generations of

the organism. A genetic marker is a specific genetic characteristic such as

CHAPTER 2 Chemical Elements of Microorganisms 43

Table 2-3. Scientists and Their Contributions

Year Scientist Contribution

1803 John Dalton Developed the Atomic Theory that explains the rela-

tionship between an element and an atom.

1860 Dimitri Mendeleev Organized chemical elements into a table according

to its atomic weight.

1800 H. G. J. Moseley Organized chemical elements into a table according

to their atomic numbers.The table was originally

know as the Law of Chemical Periodicity and has

since been called the Periodic Table.

1911 Ernest Rutherford Developed the Rutherford model of an atom and

developed the concept of half-life.

1903 Marie and Pierre Curie Discovered radioactivity.

1811 Amadeo Avagadro An Italian physicist after whom the value of the

number of molecules in a mole of a substance

was named.

1913 Niels Bohr Proposed that electrons occupy a cloud surrounding

the nucleus of an atom. This is called an orbital.

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the ability to synthesize proteins. Protein controls activities of the cell.

Some microorganisms, such as viruses contain either DNA or RNA but not

both. Think of DNA as a set of instructions.

• Ribonucleic acid (RNA). RNA is a single strand of nucleotides that relays

instructions from genes to ribosomes, guiding the chemical reactions in the

synthesis of amino acids into protein. Think of RNA as the person who car-

ries out the instructions of DNA.

The Power House: ATP

Energy is stored in adenosine triphosphate (ATP) molecules. ATP supplies power

necessary to:

• Move flagella in microorganisms.

• Move chromosomes in the cytoplasm.

• Transport substances in and out of the plasma membrane.

• Synthesis reactions.

ATP is synthesized from adenosine diphosphate (ADP) and a phosphate

group (P), the latter of which gets its energy from the decomposition reaction of

glucose and other substances. ATP releases energy in the form of ADP and P

when ATP is decomposed.

Quiz

1. What is a dalton?

(a) The equivalent of a nanometer

(b) The unit of measurement used to measure the structure of an atom

(d) The unit of measurement used to measure atomic weight

2. What is the name given to a chemical element whose atoms have a

different number of neutrons?

(a) Complex element

(b) Differential element

CHAPTER 2 Chemical Elements of Microorganisms44

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(d) Stable element

3. How is the valence shell used?

(a) The valence shell is used in bonding together two stable atoms.

(b) The valence shell is used in bonding together two inorganic, stable atoms.

(d) The valence shell is used in bonding together two unstable atoms.

4. What process is used for two atoms to bond together?

(a) Hydrogen synthesis

(b) Ionic synthesis

(d) Covalent synthesis

5. What is the difference between a molecule and a chemical compound?

(a) A molecule consists

of two or more atoms of different chemical

elements. A chemical compound consists of two or more atoms of

the same chemical element.

(b) A molecule consists of only two atoms of the same chemical ele-

ments. A chemical compound consists of more than two atoms of

different chemical elements.

element. A chemical compound consists of two or more atoms of

different chemical elements.

(d) A molecule consists of two or more atoms of organic chemical ele-

ment. A chemical compound consists of two or more atoms of inor-

ganic chemical elements.

6. What kind of bond shares electrons in the valence shell?

(a) Endergonic bond

(b) Covalent bond

(d) Ionic bond

7. What kind of reaction uses chemical energy to bond atoms together?

(a) Endergonic reaction

(b) Fusion reaction

(d) Exchange reaction

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8. What kind of reaction performs synthesis and decomposition?

(a) Endergonic reaction

(b) Fusion reaction

(d) Exchange reaction

9. What is the importance of orientation in a chemical reaction?

(a) Atoms must be in the ideal position when they collide in order to

have a high probability of bonding.

(b) All atoms must be in a polar orientation in order for a chemical reac-

tion to occur.

reaction to occur.

(d) Orientation is of no importance for a chemical reaction to occur.

10. How does an enzyme increase the likelihood that two atoms will bond?

(a) An enzyme temporarily moves other atoms away, so it is highly likely

that collision will occur.

(b) An enzyme temporarily changes the chemical environment, so it is

highly likely that collision will occur.

position where it is highly likely that it will collide and bond with

another atom.

(d) An enzyme temporarily changes the pH level, so it is highly likely

that collision will occur.

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CHAPTER

Observing

Microorganisms

Growing up you were probably forever being told to wash your hands so you

would not become infected by germs. You probably complied only to stay out

of trouble because no matter how well you focused on your hands, you never

saw a germ on them. Today you realize that a germ is a microorganism, one of

the many microorganisms that surround us. Microorganisms cannot be seen with

the naked eye, but you can see them with the aide of a microscope. In this chap-

ter, you’ll learn how to view microorganisms under a microscope.

Size Is a Matter of Metrics

We could describe the size of a microorganism in a variety of ways. A micro-

organism is small, tiny, and miniscule. It is smaller than a human hair. Millions

of them can fit on the head of a pin. All of these words give you an idea of how

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small a microorganism really is, but there’s a problem using them to describe

size. What is tiny? Are we talking about the diameter of a human hair or its

length? As for the head of a pin, how big is the pin?

Words that are normally used to describe size do so in relative terms rather

than provide a precise measurement. Relative terms compare one thing to

another thing without scientific precision. For example the statement, “millions

of them can fit on the head of a pin” isn’t precise and raises a lot of questions.

How many millions? What size is the head of the pin?

Speaking in relative terms is fine if you want to convey a general sense of

size. Saying that millions of microorganisms can fit on the head of a pin gives

someone a sense that a microorganism isn’t the size of a dog or cat, but is some-

thing much smaller. However, scientists need to precisely measure the size of a

microorganism in order to prevent diseases.

Let’s see how this works by examining a surgical mask commonly used by

medical professionals to control the flow of microorganisms. If you could zoom

in on a surgical mask you would see that the surgical mask is a weave of threads

that form a tiny web consisting of squareish holes. The size of each hole is deter-

mined by how close each strain of thread is to each other. Size is critical to

reduce the spread of disease carrying microorganisms. If the hole is smaller than

the microorganism, then the microorganism is unable to pass through the surgi-

cal mask. It becomes trapped or simply moves in a direction of less resistance.

However a microorganism can easily pass through a hole that is larger than the

microorganism.

Among other reasons, medical professionals choose surgical masks based on

the size of microorganisms that they want to control. In order to make this selec-

tion, they need to precisely measure the size of a microorganism and the size of

the holes created by the web of threads in the surgical mask.

NO FEET, PLEASE

Scientists measure the size of microorganisms—and practically everything

else—by using metric measurements, commonly called the metric system. A

system is a way of doing something, such as having a system to beat the odds in

Las Vegas. The metric system is a way of measuring things by using multiples

or fractions of ten, called factors of ten or the power of ten.

The metric system is the standard way of measuring things throughout the

world except in the United States where we use the U.S. customary system of

measurement, which includes inches, feet, and yards. The metric system is part

of the the Système International d’Unités (SI system).

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It is usually at this point in the study of microbiology when some students

begin a slow panic because they must learn a new measurement system. Don’t

panic! The metric system is very easy to learn—much easier to learn than the

U.S. measurement system.

THE PREFIX FIXES ALL YOUR PROBLEMS

The first trick to learning the metric system is to memorize the meaning of six

prefixes. In the metric system, each prefix means that a meter is either multiplied

or divided by a multiple of 10.

The second trick to learning the metric system is to learn how to multiply and

divide by 10. This is easy because all you need to do is move the decimal point.

The decimal point is moved to the right one place when multiplying by 10. The

decimal point is moved to the left one place when dividing by 10.

Let’s see how this works. First, multiply 1 meter by 10.

1 × 10 = 10

Now convert a meter to a decimeter. From the previous section, you know

that a decimeter is one-tenth of a meter, which means that you must divide

by 10.

1 ÷ 10 = 0.10

Table 3-1 shows the prefixes for the metric system and their equivalent in

meters.

CHAPTER 3 Observing Microorganisms 49

Prefix Value in Meters

Kilo (km) (kilo = 1,000) 1,000 m

Deci (dm) (deci = 1/10) 0.10 m

Centi (cm) (centi = 1/100) 0.01 m

Milli (mm) (milli = 1/1000) 0.001 m

Nano (nm) (nano = 1/1,000,000,000) 0.000000001 m

Pico (pm) (pico = 1/1,000,000,000,000) 0.000000000001 m

Table 3-1. Prefixes

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A meter is the standard for length in the metric system. A kilogram is the stan-

dard for mass in the metric system. A gram uses the same prefixes as a meter to

specify the number of grams that are represented by a value. For example, a kilo-

meter is 1,000 meters and a kilogram is 1,000 grams. This makes it a lot easier

to learn the metric system since the number of grams and meters are indicated

by the same set of prefixes.

Table 3-2 contains a list of various ways to express a gram. You’ll notice that

this table contains two prefixes that were not used in Table 3-1. These are deka-

and hecto-. The prefix deka- means 10 and the prefix hecto-

means 100. That’s

10 grams and 100 grams.

SIZING UP MICROORGANISMS

How small is a microorganism? You are probably asking yourself this question

after learning the metric system of measurement. The answer depends on the

kind of microorganism that you are measuring. As you’ll remember from

Chapter 1, there are two general categories of microorganisms. These are pro-

karyotes and eukaryotes. Fig. 3-1 illustrates the relative size of a microorganism

when compared to other things.

CHAPTER 3 Observing Microorganisms50

Prefix Value in Grams

Kilo (kg) 1,000 g

Hecto (hg) 100 g

Deka (dag) 10 g

Gram (g) 1 g

Deci (dg) 0.1 g

Centi (cg) 0.01 g

Milli (mg) 0.001 g

Micro (µg) 0.000001 g

Nano (ng) 0.000000001 g

Pico (pg) 0.000000000001 g

Table 3-2. Units of Mass in the Metric System

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Here’s Looking at You

The principal way a microbiologist studies microorganisms is by observing them

through a microscope. A microscope is a device that enlarges objects using a

process called magnification. The simplest form of a microscope is a magnify-

ing glass consisting of a single lens that is shaped in such a way as to make

things appear larger than they are to the naked eye. And the simplest magnify-

ing glass is the bottom of an empty glass. Some glasses are slightly bent at the

bottom, causing a magnifying effect if held at a certain height over an object.

This causes a change in the ray’s path.

The most complex microscope is an electron microscope, which uses elec-

trons to increase the apparent size of an object. Electron microscopes are capa-

ble of magnifying the organs of a microorganism called organelles, which you’ll

learn about later in this book. That is, an electron microscope is capable of show-

ing what is inside a bacterium and virus.

WAVELENGTH

You don’t really “see” anything. It sounds strange, but it is true. You see only the

reflection of light waves—or, in the case of an electron microscope, the reflec-

tion or absence of electrons. Electromagnetic radiation is generated by a variety

CHAPTER 3 Observing Microorganisms 51

10m 1m 0.1m 1cm 1mm 100 µm 10 µm 1µm 100nm 10nm 1nm 0.1nm

Electron Microscope

Light Microscope

Unaided Human Eye

Human Frog

Egg

Bacteria Viruses AtomProteins

Lipids

Chicken

Egg

Fig. 3-1. Comparative sizes of humans and microorganisms.

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of sources, such as the sun, a light bulb, or a radio transmitter. It takes the form

of a wave similar in shape to an ocean wave.

A wave has two characteristics. These are the wave height and the wave-

length. The wave height is the highest level above the surface traveled by

the wave. Let’s say that you’re traveling across a calm stretch of ocean. This

is the surface. Your boat is then pushed high above the surface by a swell—the

wave height—before returning to the surface. The wavelength is the distance

between the highest point of two waves. That is, the distance the boat trav-

els between the highest point of the first wave and the highest point of the

second wave.

Waves of electromagnetic radiation are in a continuous scale and are

clustered into groups called bands. They are given names based on their

wavelengths. Some are probably familiar to you, such as x-rays, visible light

waves, and radio waves. These groups are assembled into the electromagnetic

spectrum.

Waves such as light waves are generated from a source such as the sun and

strike an object such as your friend. Your friend absorbs some light waves and re-

flect other light waves. Your eyes detect only the reflected light waves.

It is this principle that enables you to observe a microorganism using a micro-

scope. Light waves from either a light bulb or room light are reflected on to the

microorganism. Reflected light waves are observed using the microscope. As

you’ll learn in Chapter 4, sometimes a microorganism reflects few light waves,

making it difficult to see under a microscope. A stain is used to cause the micro-

organism to reflect different light waves. Microorganisms are visible under an

electron microscope by directing waves of electrons onto the microorganism.

Some electron waves are absorbed and others are reflected. The reflected waves

are detected by an electronic circuit that displays an image of the microorganism

on a video screen.

What Big Eyes You Have: Magnification

Light reflected from a specimen travels in a straight line to your eyes, which

lets you see the specimen at its natural size. You can magnify the size of the

specimen by looking at the specimen through a concave lens. A convex lens (Fig.

3-2) is usually made out of glass or plastic; the back of the lens is bent inward

and the front is bent outward. It is like looking into a bubble. A magnifying

glass is a convex lens.

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The specimen is the focal point, which is the place where all the reflected

light originates. Light travels in a straight line from the focal point to the lens

where the light is bent in a process called refraction. The angle at which light

is bent is called the angle of refraction, which is measured in degrees from the

natural path of the light. The degree of angle of refraction is determined by

the curvature in the lens. The more the lens curves, the greater the angle of

refraction.

The image appears larger as the light reflected from the image is refracted.

Although the image appears magnified, curvature does distort the image. The

amount of distortion depends on the angle of refraction and the distance between

the lens and the specimen, which is called the focal length. The point at which

light rays meet is called the focal point (Fig. 3-3).

CHAPTER 3 Observing Microorganisms 53

Fig. 3-2. Convex lens.

Focal Point

Focal Length

Fig. 3-3. The focal point is where light rays meet.

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You probably saw a distorted image when using a magnifying glass and were

able to minimize the distorted effect by changing the distance between the mag-

nifying glass and the specimen.

The Microscope

A microscope is a complex magnifying glass. In the 1600s, during the time of

Antoni van Leeuwenhoek (see Chapter 1), microscopes consisted of one lens

that was shaped so that the refracted light magnified a specimen 100 times its

natural size. Other lenses were shaped to increase the magnification to 300 times.

However, van Leeuwenhoek realized that a single-lens microscope is difficult

to focus. Once Van Leeuwenhoek brought the specimen into focus, he kept his

hands behind his back to avoid touching the microscope for fear they would

bring the microscope out of focus. It was common in the 1600s for scientists to

make a new microscope for each specimen that wanted to study rather than try

to focus the microscope.

The single-lens magnifying lens or glass is a thing of the past. Scientists today

use a microscope that has two sets of lenses (objective and ocular), which is

called a compound light microscope. Fig. 3-4 shows parts of a compound light

microscope. A compound light microscope consists of:

CHAPTER 3 Observing Microorganisms54

Ocular

(eyepiece)

Body

Arm

Coarse focus

adjustment knob

Fine focus

adjustment knob

Stage adjustment knobs

Interpupillary adjustment

Nosepiece

Objective lens (4)

Mechanical stage

Substage condenser

Aperture diaphragm control

Base with light source

Field diaphragm lever

Light intensity control

Fig. 3-4. Parts of a compound light microscope.

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• Illuminator. This is the light source located below the specimen.

• Condenser. Focuses the light through the specimen.

• Stage. The platform that holds the specimen.

• Objective. The lens that is directly above the stage.

• Nosepiece. The portion of the body that holds the objectives over the stage.

• Field diaphragm. Controls the amount of light into the condenser.

• Base. Bottom of the microscope.

• Coarse focusing knob. Used

to make relatively wide focusing adjustments

to the microscope.

• Fine focusing knob. Used to make relatively small adjustments to the

microscope.

• Body. The microscope body.

• Ocular eyepiece. Lens on the top of the body tube. It has a magnification

of 10× normal vision.

MEASURING MAGNIFICATION

A compound microscope has two sets of lenses and uses light as the source of

illumination. The light source is called an illuminator and passes light through

a condenser and through the specimen. Reflected light from the specimen is

detected by the objective. The objective is designed to redirect the light waves,

resulting in the magnification of the specimen.

There are typically four objectives, each having a different magnification.

These are 4×, 10×, 40×, and 100×. The number indicates by how many times the

original size of a specimen is magnified, so the 4× objective magnifies the spec-

imen four times the specimen size. The eyepiece of the microscope is called the

ocular eyepiece and it, too, has a lens—called an ocular lens—that has a magni-

fication of 10×.

You determine the magnification used to observe a specimen under a micro-

scope by multiplying the magnification of the objective by the magnification of

the ocular lens. Suppose you use the 4× objective to view a specimen. The image

you see through the ocular is 40× because the magnification of the object is mul-

tiplied by the magnification of the ocular lens, which is 10×.

Many microscopes have several objectives connected to a revolving nose-

piece above the stage. You can change the objective by rotating the nosepiece

until the objective that you want to use is in line with the body of the micro-

scope. You’ll find the magnification marked on the objective. Sometimes the

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mark is color-coded and other times the magnification is etched into the side

of the objective.

RESOLUTION

The area that you see through the ocular eyepiece is called the field of view.

Depending on the total magnification and the size of the specimen, sometimes

the entire field of view is filled with the image of the specimen. Other times,

only a portion of the field of view contains the image of the specimen.

You probably noticed that the specimen becomes blurry as you increase mag-

nification. Here’s what happens. The size of the field of view decreases as mag-

nification increases, resulting in your seeing a smaller area of the specimen.

However, the resolution of the image remains unchanged, therefore you must

adjust the fine focus knob to bring the image into focus again.

Resolution is the ability of the lens to distinguish fine detail of the specimen

and is determined by the wavelength of light from the illuminator. At the begin-

ning of this chapter you learned about the wave cycle, which is the process of

the wave going up and then falling down time and again. A wavelength is the

distance between the peaks of two waves. As a general rule, shorter wavelengths

produce higher resolutions of the image seen through the microscope.

CONTRAST

The image of a specimen must contrast with other objects in the field of view or

with parts of the specimen itself to be visible in different degrees of brightness.

Suppose the specimen was a thin tissue layer of epidermis. The tissue must be a

different color than the field of view, otherwise the tissue and field of view

blend, making it impossible to differentiate between the two. That is, the tissue

and the field of view must contrast.

Previously in this chapter you learned that what you see is light reflected by

the specimen (or the transmitted light if the specimen doesn’t absorb light).

The illuminator shines white light onto the specimen. White light contains all

the light waves in the visible spectrum. The specimen absorbs some of the

light waves and reflects other light waves, giving the appearance of some color

other than white.

Light waves that are reflected by the specimen are measured by the refractive

index. The refractive index specifies the amount of light waves that is reflected

by an object. There is a low contrast between a specimen and the field of view if

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they have nearly the same refractive index. The further these refractive indexes

are from each other, the greater the contrast between the specimen and the field

of view.

Unfortunately, refractive indexes of the specimen and the field of view are

fixed. However, you can tweak the refractive index of the specimen by using a

stain. The stain adheres to all or part of the specimen, absorbing additional light

waves and increasing the difference between the refractive indexes of the speci-

men and the field of view. This results in an increase in the contrast between the

specimen and the field of view.

Oil Immersion

A challenge facing microbiologists is how to maintain good resolution at mag-

nifications of 100× and greater. In order to maintain good resolution, the lens

must be small and sufficient light must be reflected from both the specimen

and the stain used on the specimen. The problem is that too much light is lost;

air between the slide and the objective prevents some light waves from pass-

ing to the objective, causing the fuzzy appearance of the specimen in the ocu-

lar eyepiece.

The solution is to immerse the specimen in oil. The oil takes the place of air

and, since oil has the same refractive index as glass, the oil becomes part of the

optics of the microscope. Light that is usually lost because of the air is no longer

lost. The result is good resolution under high magnification.

TYPES OF LIGHT COMPOUND MICROSCOPES

There are five popular light compound microscopes used today (see Table 3-3).

Bright-Field Microscope

The bright-field microscope is the most commonly used microscope and consists

of two lenses. These are the ocular eyepiece and the objective. Light coming from

the illuminator passes through the specimen. The specimen absorbs some light

waves and passes along other light waves into the lens of the microscope, causing

a contrast between the specimen and other objects in the field of view. Specimens

that have pigments contrast with objects in the field of view and can be seen by

using the bright-field microscope. Specimens with few or no pigments have a low

contrast and cannot be seen with the bright-field microscope. Some bacteria have

low contrast.

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Dark Field Microscope

The dark-field microscope focuses the light from the illuminator onto the top of

the specimen rather than from behind the specimen. The specimen absorbs some

light waves and reflects other light waves into the lens of the microscope. The

field of view remains dark while the specimen is illuminated, providing a stark

contrast between the field of view and the specimen.

Phase-Contrast Microscope

The phase-contrast microscope bends light that passes through the specimen so

that it contrasts with the surrounding medium. Bending the light is called mov-

ing the light out of phase. Since the phase-contrast microscope compensates for

the refractive properties of the specimen, you don’t need to stain the specimen

to enhance the contrast of the specimen with the field of view. This microscope

is ideal for observing living microorganisms that are prepared in wet mounted

slides so you can study a living microorganism.

CHAPTER 3 Observing Microorganisms58

Type of

Microscope Features Best Used for

Bright-field

Dark-field

Phase-

contrast

Fluorescent

Transmission

electron

microscope

Scanning

electron

microscope

Uses visible light

Uses visible light with a that causes the

rays of light to reflect off the specimen

Uses a condenser that increases

differences in the refractive index of

structures within the specimen

Uses ultraviolet light to stimulate mole-

cules of the specimen to make it stand

out from its

background

Uses electron beams and electro-

magnetic lenses to view thin slices

of cells

Uses electron beams and electro-

magnetic lenses

Observing dead stained spe-

cimens and living organ-

isms with natural color

Observing living

organisms

Observing internal

structures of specimens

Observing specimens or anti-

bodies in clinical studies

Observing exterior surfaces

and internal structures

Giving a three-dimensional

view of exterior surfaces

of cells

Table 3-3. Quick Guide to Microscopy

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Fluorescent Microscope

Fluorescent microscopy uses ultraviolet light to illuminate specimens. Some

organism fluoresce naturally, that is, give off light of a certain color when

exposed to the light of different color. Organisms that don’t fluoresce naturally

can be stained with fluorochrome dyes. When these organisms are placed under

a fluorescent microscope with an ultraviolet light, they appear very bright in

front of a dark background.

Differential Interface Contrast Microscope (Nomanski)

The differential interface contrast microscope, commonly known as Nomanski,

works in a similar way to the phase-contrast microscope. However, unlike the

phase-contrast microscope (which produces a two-dimensional image of the

specimen), the differential interface contrast microscope shows the specimen in

three dimensions.

THE ELECTRON MICROSCOPE

A light compound microscope is a good tool for observing many kinds of

microorganisms. However, it isn’t capable of seeing the internal structure of a

microorganism nor can it be used to observe a virus. These are too small to effec-

tively reflect visible light sufficient to be seen under a light compound micro-

scope. In order to view internal structures of viruses and internal structures of

microorganisms, microbiologists use an electron microscope where specimens

are viewed in a vacuum.

Developed in the 1930s, the electron microscope uses beams of electrons and

magnetic lenses rather than light waves and optical lenses to view a specimen.

Very thin slices of the specimen are cut so that the internal structures can be

viewed. Microscopic photographs called micrographs are taken of the specimen

and viewed on a video screen. Specimens can be viewed up to 200,000 times

normal vision. However, living specimens cannot be viewed because the speci-

men must be sliced.

Transmission Electron Microscope

The transmission electron microscope (TEM) has a total magnification of up to

200,000× and a resolution as fine as seven nanometers. A nanometer is

1/1,000,000,000 of a meter. The transmission electron microscope generates an

image of the specimen two ways. First, the image is displayed on a screen sim-

ilar to that of a computer monitor. The image can also be displayed in the form

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of an electron micrograph, which is similar to a photograph. Specimens viewed

by the transmission electron microscope must be cut into very thin slices, other-

wise the microscope does not adequately depict the image.

Scanning Electron Microscope

The scanning electron microscope (SEM) is less refined than the transmission

electron microscope. It can provide total magnification up to 10,000× and a res-

olution as close as 20 nanometers. However, a scanning electron microscope

produces three-dimensional images of specimen. The specimen must be freeze-

dried and coated with a thin layer of gold, palladium, or other heavy metal.

Preparing Specimens

There are two ways to prepare a specimen to be observed under a light com-

pound microscope. These are a smear and a wet mount.

Smear

A smear is a preparation process where a specimen that is spread on a slide. You

prepare a smear using the heat fixation process:

1. Use a clean glass slide.

2. Take a loop of the culture.

3. Place the live microorganism on the glass slide.

4. The slice is air dried then passed over a Bunsen burner about three times.

5. The heat causes the microorganism to adhere to the glass slide. This is

known as fixing the microorganism to the glass slide.

6. Stain the microorganism with an appropriate stain (see “Staining a Speci-

men” later in this chapter).

Wet Mount

A wet mount is a preparation process where a live specimen in culture fluid is

placed on a concave glass side or a plain glass slide. The concave portion of the

glass slide forms a cup-like shape that is filled with a thick, syrupy substance,

such as carboxymethyl cellulose. The microorganism is free to move about

within the fluid, although the viscosity of the substance slows its movement.

This makes it easier for you to observe the microorganism. The specimen and

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the substance are protected from spillage and outside contaminates by a glass

cover that is placed over the concave portion of the slide.

STAINING A SPECIMEN

Not all specimens can be clearly seen under a microscope. Sometimes the spe-

cimen blends with other objects in the background because they absorb and

reflect approximately the same light waves. You can enhance the appearance of

a specimen by using a stain. A stain is used to contrast the specimen from the

background.

A stain is a chemical that adheres to structures of the microorganism and in

effect dyes the microorganism so the microorganism can be easily seen under a

microscope. Stains used in microbiology are either basic or acidic.

Basic stains are cationic and have positive charge. Common basic stains are

methylene blue, crystal violet, safranin, and malachite green. These are ideal for

staining chromosomes and the cell membranes of many bacteria.

Acid stains are anionic and have a negative charge. Common acidic stains are

eosin and picric acid. Acidic stains are used to stain cytoplasmic material and

organelles or inclusions.

Types of Stains

There are two types of Stains: simple and differential. See Table 3-4 for a sum-

mary of staining techniques.

Simple Stain

A simply stain has a single basic dye that is used to show shapes of cells and the

structures within a cell. Methylene blue, safranin, carbolfuchsin and crystal vio-

let are common simple stains that are found in most microbiology laboratories.

Differential Stain

A differential stain consists of two or more dyes and is used in the procedure to

identify bacteria. Two of the most commonly used differential stains are the

Gram stain and the Ziehl-Nielsen acid-fast stain.

In 1884 Hans Christian Gram, a Danish physician, developed the Gram stain.

Gram-stain is a method for the differential staining of bacteria. Gram-positive

microorganisms stain purple. Gram-negative microorganisms stain pink. Staphy-

lococcus aureus, a common bacterium that causes food poisoning, is gram-

positive. Escherichia coli is gram-negative.

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The Ziehl-Nielsen acid-fast stain, developed by Franz Ziehl and Friedrick

Nielsen, is a red dye that attaches to the waxy material in the cell walls of bac-

teria such as Mycobacterium tuberculosis, which is the bacterium that causes

tuberculosis, and Mycobacterium leprae, which is the bacterium that causes

leprosy. Microorganisms that retain the Ziehl-Nielsen acid-fast stain are called

acid-fast. Those that do not retain it turn blue because the microorganism

doesn’t absorb the Ziehl-Nielsen acid-fast stain.

Here’s how to Gram-stain a specimen (Fig. 3-5).

CHAPTER 3 Observing Microorganisms62

Apply Crystal Violet Stain Apply Iodine Alcohol wash Apply Safranin

Orange

Fig. 3-5. How to Gram-stain a specimen.

Type Number of Dyes Used Observations Examples

Simple stains Uses a single dye Size, shape, and Methylene blue

arrangement of cells Safranin

Crystal violet

Differential stains Uses two or more dyes Distinguish gram-positive Gram stain

to distinguish different or gram-negative Ziehl-Nielsen

types or different Distinguishes the members acid-fast stain

structures

of bacteria of mycobacteria and

nocardia from other

bacteria

Special stains These stains identify Exhibit the presence

specialized structures of flagellae Shaeffer-Fulton

Exhibits endospores spore staining

Table 3-4. Quick Guide for Staining Techniques

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1. Prepare the specimen using the heat fixation process (see “Smear” earlier

in this chapter).

2. Place a drop of crystal violet stain on the specimen.

3. Apply iodine on the specimen using an eyedropper. The iodine helps the

crystal violet stain adhere to the specimen. Iodine is a mordant, which is a

chemical that fixes the stain to the specimen.

4. Wash the specimen with ethanol or an alcohol-acetone solution, then wash

with water.

5. Wash the specimen to remove excess iodine. The specimen appears purple

in color.

6. Wash the specimen with an ethanol or alcohol-acetone decolorizing solution.

7. Wash the specimen with water to remove the dye.

8. Apply the safranin stain to the specimen using an eyedropper.

9. Wash the specimen.

10. Use a paper towel and blot the specimen until the specimen is dry.

11. The specimen is ready to be viewed under the microscope. Gram-positive

bacteria appear purple and gram-negative bacteria appear pink.

Here’s how to apply the Ziehl-Nielsen acid-fast stain to a specimen.

1. Prepared the specimen (see “Smear” earlier in this chapter).

2. Apply the red dye carbol-fuchsin stain generously using an eyedropper.

3. Let the specimen sit for a few minutes.

4. Warm the specimen over steaming water. The heat will cause the stain to

penetrate the cell wall.

5. Wash the specimen with an alcohol-acetone decolorizing solution con-

sisting of 3 percent hydrochloric acid and 95 percent ethanol. The hydro-

chloric acid will remove the color from non–acid-fast cells and the

background. Acid-fast cells will stay red because the acid cannot pene-

trate the cell wall.

6. Apply methylene blue stain on the specimen using an eyedropper.

Special Stains

Special stains are paired to dye specific structures of microorganisms such as

endospores, flagella, and gelatinous capsules. One stain in the pair is used as a

negative stain. A negative stain is used to stain the background of the micro-

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organism, causing the microorganism to appear clear. A second stain is used to

colorize specific structures within the microorganism. For example, nigrosin

and India ink are used as a negative stain and methylene blue is used as a posi-

tive stain.

The Schaeffer-Fulton endospore stain is a special flagellar stain that is

used to colorize the endospore. The endospore is a dormant part of the bac-

teria cell that protects the bacteria from the environment outside the cell.

Here’s how to apply the Schaeffer-Fulton endospore stain.

1. Prepare the specimen (see “Smear” earlier in this chapter).

2. Heat the malachite green stain over a Bunsen burner until it becomes fluid.

3. Apply the malachite green to the specimen using an eyedropper.

4. Wash the specimen for 30 seconds.

5. Apply the safranin stain using an eyedropper to the specimen to stain parts

of the cell other than the endospore.

6. Observe the specimen under the microscope.

Quiz

1. What is a nanometer?

(a) 1/1,000,000,000 of a meter

(b) 1/100,000 of a meter

(d) 1,000,000,000 meters

CHAPTER 3 Observing Microorganisms64

Year Scientists Contribution

1884 Hans Christian Gram Developed the Gram stain used to stain and identify

bacteria.

Franz Ziehl and Developed the Ziehl-Nielsen acid-fast stain used

Friedrick Nielsen to stain bacteria.

Table 3-5. Scientists and Their Contributions

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2. What magnification is used if you observe a microorganism with a

microscope whose object is 100× and whose ocular lens is 10×?

(a) 1000× magnification

(b) 100× magnification

(d) 10,000× magnification

3. What is the function of an illuminator?

(a) To control the temperature of the specimen

(b) To keep the specimen moist

a microscope

(d) To keep the specimen dry

4. What is the area seen through the ocular eyepiece called?

(a) The stage

(b) The objective

(d) The field of view

5. How do you maintain good resolution of a specimen at magnifications

greater than 100×?

(a) Display the specimen on a television monitor.

(b) Use a single ocular eyepiece.

(d) Avoid moving the specimen.

6. What is a micrograph?

(a) A microscopic photograph taken by an electron microscope

(b) A microscopic diagram of a specimen

(d) A growth diagram of a specimen

7. What is a smear?

(a) A smear is a preparation process in which a specimen is spread on a

slide.

(b) A smear is a preparation process in which a specimen is dyed.

scope.

(d) A smear is a process used to identify a specimen.

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8. What process is used to cause a specimen to adhere to a glass slide?

(a) The heat fixation process

(b) Wet mount

(d) Clear glue

9. Why is a specimen stained?

(a) A stain is used to label a specimen.

(b) A stain is used to determine the size of a specimen.

by the specimen into the microscope.

(d) A stain is used to determine the density of a specimen.

10. When would you use a wet mount?

(a) A wet mount is used to observe a dead specimen under a micro-

scope.

(b) A wet mount is used to observe a live specimen under a microscope.

microscope.

(d) A wet mount is the first step in preparing a specimen.

CHAPTER 3 Observing Microorganisms66

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CHAPTER

Prokaryotic Cells

and Eukaryotic Cells

What do you and Athletes Foot have in common? You’ll recall from Chapter 1

that Tinea pedis is the scientific name for athlete’s foot and that it is caused by

the Trichophyton fungus. Both of you are alive. Sometimes it’s hard to imagine

that microorganisms are alive because we can’t see them with our naked eye—

although they make their presence known to us in annoying ways.

Humans, Trichophyton, and all other living things are alive because they

carry on the six life processes, something non-living things do not do. The six life

processes require a living thing to:

• Metabolize. Breakdown nutrients for energy or extract energy from the

environment.

• Be responsive. React to internal and external environmental changes.

• Move. Whether it is the entire organism relocating within its environment,

cells within that organism or the organelles inside those cells.

• Grow. Increase the size or number of cells.

• Differentiate. The process where cells that are unspecialized become spe-

cialized. (An example would be a single fertilized human egg, developing

into an individual). Prokaryotic cells do not differentiate.

• Reproduce. Form new cells to create a new individual.

c04_betsy.qxd 5/11/05 2:29 PM Page 67

Have a cellular structure. Cells that metabolize, respond to changes, move,

grow, and reproduce.

For additional information, see Table 4-1.

In this chapter, you will learn about cellular structure by exploring two kinds of

cells. These are prokaryotic cells and eukaryotic cells. Bacteria are prokaryotic

organisms. Animals, plants, algae, fungi and protozoa are eukaryotic organisms. See

Table 4-2 for a summary of differences between prokaryotic and eukaryotic cells.

Prokaryotic Cells

A prokaryotic cell is a cell that does not have a true nucleus. The nuclear struc-

ture is called a nucleoid. The

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MICROBIOLOGY DEMYSTIFIED

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MICROBIOLOGY DEMYSTIFIED

TOM BETSY, D.C.

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McGRAW-HILL

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I would like to dedicate this book to my wife, Shelley,

and my two babies, Juliana and Thomas,

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and the continued joy they bring to my life.

Dr. Tom Betsy

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00 Betsy FM 5/11/05 2:20 PM Page v

Introduction xiii

Acknowledgments xix

CHAPTER 1 The World of the Microorganism 1

Types of Microorganisms 2

What Is a Microorganism? 4

What’s in a Name: Naming and Classifying 5

How

nucleoid contains most of the cell’s genetic mate-

CHAPTER 4 Prokaryotic and Eukaryotic Cells68

Eukaryotic Prokaryotic

Process Cells Cells Viruses

Metabolism: Sum of Yes Yes Uses their host’s cells for

all chemical reactions metabolism

Responsiveness: Yes Yes Some viruses react and multiply

Ability to react to once they enter a host cells

environmental stimuli

Movement: Motion of Yes Yes Virions (viruses outside of a host

individual organelles, cell) are nonmotile

a single cell, or entire Use Brownian movement

organism (random collision)

Growth: Increase in size Yes Yes No

Differentiate Yes No No

Reproduction: Yes Yes Inside host cells

Increase in number

Cellular structures Yes Yes No cytoplasmic membrane

No cell structure

Table 4-1. Basic Life Processes in Microorganisms

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rial and is usually a single circular molecule of DNA. Karyo- is Greek for “ker-

nel.” A prokaryotic organism, such as a bacterium, is a cell that lacks a mem-

brane-bound nucleus or membrane-bound organelles. The exterior of the cell

usually has glycocalyx, flagellum, fimbriae, and pili (Fig. 4-1).

CHAPTER 4 Prokaryotic and Eukaryotic Cells 69

Characteristics Prokaryotic Cells Eukaryotic Cells

Cell wall Include peptidoglycan Chemically simple

Chemically complex

Plasma membrane No carbohydrates Contain carbohydrates

No sterols Contain sterols

Glycocalyx Contain a capsule or Contained in cells that

a slime layer lack a cell wall

Flagella Protein building blocks Multiple microtubules

Cytoplasm No cytoplasmic streaming Contain cytoskeleton

Contain cytoplasmic streaming

Membrane-bound None Endoplasmic reticulum

organelles Golgi complex

Lysomes

Mitochondria

Chloroplasts

Ribosomes 70S 80S

Ribosomes located in

Organelles are 70S

Nucleus No nuclear membrane Have a nucleus

No nucleoli Have a nuclear membrane

0.2–2.0 mm in diameter Have a nucleoli

10–100 mm in diameter

Chromosomes Single circular chromosome Multiple linear chromosomes

No histones Have histones

Cell division Binary fission Mitosis

Sexual reproductions No meiosis Meiosis

DNA transferred in fragments

Table 4-2. Differences between Prokaryotic and Eukaryotic Cells

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PARTS OF PROKARYOTIC CELLS

Glycocalyx

Glycocalyx is a sticky, sugary envelope composed of polysaccharides and/or

polypeptides that surround the cell. Glycocalyx is found in one of two states. It can

be firmly attached to the cell’s surface, called capsule, or loosely attached, called

slime layer. A slime layer is water-soluble and is used by the prokaryotic cell to

adhere to surfaces external to the cell.

Glycocalyx is used by a prokaryotic cell to protect it against attack from the

body’s immune system. This is the case with Streptococcus mutans, which is a

bacterium that colonizes teeth and excretes acid that causes tooth decay. Normally

the body’s immune system would surround the bacterium and eventually kill it,

but that doesn’t happen with Streptococcus mutans. It has a glycocalyx capsule

state, which prevents the Streptococcus mutans from being recognized as a foreign

microorganism by the body’s immune system. This results in cavities.

Flagella

Flagella (Fig. 4-2) are made of protein and appear “whip-like.” They are used by

the prokaryotic cell for mobility. Flagella propel the microorganism away from

CHAPTER 4 Prokaryotic and Eukaryotic Cells70

RibosomesCapsule

Cell wall

Plasma

membrane

Chromosome

(DNA)

Nucleoid

Inclusion

body

FlagellumFimbriae

S-layer

Fig. 4-1. A prokaryotic cell.

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harm and towards food in a movement known as taxis. Movement also occurs in

response to a light or chemical stimulus. Movement caused by a light stimulus

is referred to as phototaxis and a chemical stimulus causes a chemotaxis move-

ment to occur.

Flagella can exist in the following forms:

• Monotrichous: One flagellum.

• Lophotrichus: A clump of flagella, called a tuft, at one end of the cell.

• Amphitrichous: Flagella at two ends of the cell.

• Peritrichous: Flagella covering the entire cell.

• Endoflagellum: A type of amphitrichous flagellum that is tightly wrapped

around spirochetes. A spirochete is a spiral-shaped bacterium that moves

in a corkscrew motion. Borrelia burgdorferi, which is the bacterium that

causes lyme disease, exhibits an endoflagellum.

Fimbriae

Fimbriae are proteinaceous, sticky, bristle-like projections used by cells to attach

to each other and to objects around them. Neisseria gonorrhoeae, the bacterium

that causes gonorrhea, uses fimbriae to adhere to the body and to cluster cells of

the bacteria.

Pili

Pili are tubules that are used to transfer DNA from one cell to another cell sim-

ilar to tubes used to fuel aircraft in flight. Some are also used to attach one cell

CHAPTER 4 Prokaryotic and Eukaryotic Cells 71

Fig. 4-2. A flagellum has a long tail that extends

from the cell.

c04_betsy.qxd 5/11/05 2:29 PM Page 71

to another cell. The tubules are made of protein and are shorter in length than

flagella and longer than fimbriae.

CELL WALL

The prokaryotic cell’s cell wall is located outside the plasma membrane and

gives the cell its shape and provides rigid structural support for the cell. The cell

wall also protects the cell from its environment.

Pressure within the cell builds as fluid containing nutrients enters the cell. It

is the job of the cell wall to resist this pressure the same way that the walls of a

balloon resist the build-up of pressure when it is inflated. If pressure inside the

cell becomes too great, the cell wall bursts, which is referred to as lysis.

The cell wall of many bacteria is composed of peptidoglycan, which covers

the entire surface of the cell. Peptidoglycan is made up of a combination of pep-

tide bonds and carbohydrates, either N-acetylmuramic acid, commonly referred

to as NAM, or N-acetylglucosamine, which is known as NAG.

The wall of a bacterium is classified in two ways:

• Gram-positive. A gram-positive cell wall (Fig. 4-3) has many layers of

peptidoglygan that retain the crystal of violet dye when the cell is stained.

This gives the cell a purple color when seen under a microscope.

CHAPTER 4 Prokaryotic and Eukaryotic Cells72

Periplasmic

space

Lipoteichoic acid Teichoic acid

Fig. 4-3. Gram-positive cell wall.

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• Gram-negative. A gram-negative cell wall (Fig. 4-4) is thin. The inside is

made of peptidoglycan. The outer membrane is composed of phospholipids

and lipopolysaccharides.

The cell wall does not retain the crystal of violet dye when the cell is stained.

The cell appears pink when viewed with a microscope.

CYTOPLASMIC MEMBRANE

The prokaryotic cell has a cell membrane called the cytoplasmic membrane that

forms the outer structure of the cell and separates the cell’s internal structure

from the environment. The cytoplasmic membrane is a membrane that provides

a selective barrier between the environment and the cell’s internal structures.

The cytoplasmic membrane (Fig. 4-5) provides a selective barrier, allowing

certain substances and chemicals to move into and out of the cell. The cyto-

plasmic membrane is a bilayer of phospholipids that has polar and nonpolar

parts, which is referred to as being amphipathic. The nonpolar parts share elec-

trons of atoms equally. The polar parts share electrons unequally. Each polar

part has a head that contains phosphate and is hydrophilic (“water-loving”).

Each nonpolar part has two tails composed of long fatty acids that are hydro-

phobic (“water-fearing”).

CHAPTER 4 Prokaryotic and Eukaryotic Cells 73

Phospholipid

Integral protein

Lipopolysaccharide

Peptidoglycan

O-specific

side chains

Porin

Braun’s

lipoprotein

Outer

membrane

Periplasmic

space and

peptidoglycan

Plasma

membrane

Fig. 4-4. Gram-negative cell wall.

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The heads always face a watery fluid such as the extracellular

fluid on the

outside of the cell and the intracellular fluid inside the cell. Tails align back to

back preventing the watery fluid from crossing the cytoplasmic membrane.

The Fluid Mosaic Model

In 1972, S. J. Singer and G. L. Nicolson developed the Fluid Mosaic Model,

which describes the structure of the cytoplasmic membrane. They called this a

mosaic because proteins within the cytoplasmic membrane are arranged like

tiles in a mosaic artwork. The term fluid is used to imply that membrane proteins

and lipids flow freely within the cytoplasmic membrane. There are two kinds of

proteins within the cytoplasmic membrane. These are:

• Integral proteins. An integral protein extends into the lipid bilayer.

Integral proteins are typically glycoproteins that act like a molecular sig-

nature that cells use to recognize each other. Glycoproteins have a carbo-

hydrate group attached to them. Two examples are:

• Transmembrane protein. A transport protein that regulates the move-

ment of molecules through the cytoplasmic membrane.

• Channel protein. A channel protein forms pores or channels in the

cytoplasmic membrane that permit the flow of molecules through the

cytoplasmic membrane.

CHAPTER 4 Prokaryotic and Eukaryotic Cells74

Integral

protein

Glycolipid Oligosaccharide

Hydrophobic

α helix

Integral

protein

Hopanoid

Phospholipid

Peripheral

protein

Fig. 4-5. The cytoplasmic membrane enables some substances to pass into and out

of the cell.

c04_betsy.qxd 5/11/05 2:29 PM Page 74

• Peripheral proteins. Peripheral proteins are on the inner and outer surface

of the cytoplasmic membrane and have the characteristics of a polar and

non-polar regions.

The Function of the Cytoplasmic Membrane

The cytoplasmic membrane regulates the flow of molecules (such as nutrients)

into the cell and removes waste from the cell by opening and closing passages

called channels. In photosynthetic prokaryotes, the cytoplasmic membrane func-

tions in energy production by collecting energy in the form of light.

The cytoplasmic membrane is selectively permeable because it permits the

transport of some substances and inhibits the transport of other substances. Two

types of transport mechanisms are used to move substances through the cyto-

plasmic membrane. These are passive transport and active transport.

Passive Transport

Passive transport moves substances into and out of the cell down a gradient

similar to how a rock rolls downhill, following the gradient. There are three

types of passive transport. These are:

• Simple diffusion. Simple diffusion is the movement of substances from a

higher-concentration region to a lower-concentration region (net move-

ment). Only small chemicals (oxygen and carbon dioxide) or lipid-soluble

chemicals (fatty acids) diffuse freely through the cytoplasmic membrane,

using simple diffusion. Large molecules (monosaccharide and glucose) are

too large to enter the cell.

• Facilitated diffusion. Facilitated diffusion is the movement of substances

from a higher-concentration region to a lower-concentration region (net

movement) with the assistance of an integral protein across a selectively

permeable membrane. The phospholipid bilayer prevents the movement of

large molecules across the membrane until a pathway is formed using

facilitated diffusion. The integral protein acts as a carrier by changing the

shape of large molecules so the protein can transport the large molecules

across the membrane.

• Osmosis. Osmosis is the net movement (diffusion) of a solvent (water in

living organisms) from a region of higher water concentration to a region

of lower concentration.

CHAPTER 4 Prokaryotic and Eukaryotic Cells 75

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Active Transport

Active transport is the movement of a substance across the cytoplasmic mem-

brane against the gradient by using energy provided by the cell. This is similar

to pumping water against gravity through a pipe. Energy must be spent in order

for the pump to work.

A cell makes energy available by removing a phosphate (P) from adenosine

triphosphate (ATP). ATP contains chemical potential energy that is released by

a chemical reaction within the cell. It is this energy that is used to change the

shape of the integral membrane protein-enabling substances inside the cell to be

pumped through the cytoplasmic membrane. For example, active transport is

used to pump sodium (Na+) from a cell.

Group Translocation

Group translocation is a diffusion process that immediately modifies a substance

once the substance passes through the cytoplasmic membrane. The cell must

expend energy during group translocation, which is supplied by high-energy

phosphate compounds such as phosphoenolpyruvic acid (PEP). Group trans-

location occurs in prokaryotic cells.

Endocytosis and Exocytosis

Endocytosis and exocytosis are processes used to move large substances or lots

of little ones into and out of a cell. Large substances enter the cell by endocyto-

CHAPTER 4 Prokaryotic and Eukaryotic Cells76

How Osmosis Works

• Isotonic solution. “Iso” means the same if a cell is placed in an isotonic solu-

tion. This means that there is the same concentration of solute and solvent

(water) inside and outside of the cell. There is an equal movement of sub-

stances into and out of the cell.

• Hypertonic solution. In a hypertonic solution, the cell is placed in an envi-

ronment where there is a higher concentration of solute. What happens is that

the water inside the cell will move out of the cell by osmosis causing it to

shrink. This shrinking of the cell is called crenation.

• Hypotonic solution. When a cell is placed in a hypotonic solution, there is

more water outside of the cell than inside. This means there is more solute con-

centration inside of the cell. The water outside will move into the cell by osmo-

sis causing the cell to swell and ultimately break apart. This is called lysis.

c04_betsy.qxd 5/11/05 2:29 PM Page 76

sis. There are two kinds of endocytosis. These are phagocytosis and pinocytosis.

Phagocytosis engulfs solid substances (large molecules) while pinocytosis

engulfs liquid substances (small molecules). Exocytosis is the process that cells

use to remove large substances, which is the way waste products and useful mate-

rial as hormones and neurotransmitters are expelled from a cell through vesicles.

Cytosol and Cytoplasm

The cytosol is the intracellular fluid of a prokaryotic cell that contains proteins,

lipids, enzymes, ions, waste, and small molecules dissolved in water, com-

monly referred to as semifluid. Substances dissolved in cytosol are involved in

cell metabolism.

The cytosol also contains a region called the nucleoid, which is where the

DNA of the cell is located. Unlike human cells, a prokaryotic microorganism has a

single chromosome that isn’t contained within a nuclear membrane or envelope.

Cytosol is located in the cytoplasm of the cell. Cytoplasm also contains the

cytoskeleton, ribosomes, and inclusions.

Ribosomes

A ribosome is an organelle within the cell that synthesizes polypeptide. There

are thousands of ribosomes in the cell. You’ll notice them as the grainy appear-

ance of the cell when viewing the cell with an electron microscope.

A ribosome is comprised of subunits consisting of protein and ribosomal

RNA, which is referred to as rRNA. Ribosomes and their subunits are identified

by their sedimentation rate. Sedimentation rate is the rate at which ribosomes

are drawn to the bottom of a test tube when spun in a centrifuge. Sedimentation

rate is expressed in Svedberg (S) units. A sedimentation rate reflects the mass,

size, and shape of a ribosome and its subunits. It is for this reason why the sed-

imentation rates of subunits of a ribosome do not add up to the ribosome’s

sedimentation rate.

Ribosomes in prokaryotic cells are uniquely identified by the number of pro-

teins and rRNA molecules contained in the ribosome and by sedimentation rate.

Prokaryotic ribosomes are relatively small and less dense than

ribosomes of

other microorganisms. For example, bacterial ribosomes have a sedimentation

rate of 70S compared to the 80S sedimentation rate of a eukaryotic ribosome,

which you’ll learn about later in this chapter.

Ribosomes and their subunits are targets for antibiotics that kill a bacterium

by inhibiting the bacterium’s protein synthesis. These antibiotics only kill cells

that have a specific ribosome sedimentation rate. Cells with a different ribosome

CHAPTER 4 Prokaryotic and Eukaryotic Cells 77

c04_betsy.qxd 5/11/05 2:29 PM Page 77

sedimentation rate are unaffected by the antibiotic. This enables the antibiotic to

kill bacterium and not the body that is infected by the bacterium.

For example, erythromycin and chloramphenicol, popular antibiotics, kill

bacteria whose subunits have a sedimentation rate of 50S. Streptomycin and

gentamycin affect bacteria whose subunits have a 30S sedimentation rate.

Inclusions

An inclusion is a storage area that serves as a reserve for lipids, nitrogen, phos-

phate, starch, and sulfur within the cytoplasm. Scientists use inclusions to iden-

tify types of bacteria. Inclusions are usually classified as granules.

• Granule inclusion. Membrane-free and densely packed, this type of inclu-

sion has many granules each containing specific substances. For example,

polyphosphate granules, also known by the names metachromatic gran-

ules and volutin, have granules of polyphosphate that are used to synthe-

size ATP and are involved in other metabolic processes. A polyphosphate

granule appears red under a microscope when stained with methylene blue.

• Vesicle inclusion. This is a protein membrane inclusion commonly found

in aquatic photosynthetic bacteria and cyanobacteria such as phytoplank-

ton, which suspends freely in water. These bacteria use vesicle inclusions

to store gas that give the cell buoyancy to float at a depth where light, car-

bon dioxide (CO2), and nutrients—all required for photosynthesis—are

available.

Eukaryotic Cells

A eukaryotic cell (Fig. 4-6) is larger and more complex than a prokaryotic cell

and found in animals, plants, algae, fungi, and protozoa. When you look at a

eukaryotic cell with a microscope you’ll notice a highly organized structure of

organelles that are bound by a membrane. Each organelle performs a specialized

function for the cell’s metabolism. Eukaryotic cells also contain a membrane-

bound nucleus where the cell’s DNA is organized into chromosomes.

Depending on the organism, a eukaryotic cell may contain external projec-

tions called flagella and cilia. These projections are used for moving substances

along the cell’s surface or for moving the entire cell. Flagella move the cell in a

wavelike motion within its environment. Cilia move substances along the cell’s

CHAPTER 4 Prokaryotic and Eukaryotic Cells78

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surface and also aid in movement of the cell. Flagella and cilia are comprised of

axoneme microtubules. An axoneme microtubule is a long, hollow tube made

of protein called a tubulin.

CELL WALL

Many eukaryotic cells have a cell wall. The composition of the cell wall differs

with each organism. For example, the cell walls of many fungi are composed of

chitin cellulose. Chitin is a polysaccharide, which is a polymer of N-acetylglu-

cosamine (NAG) units. The cell wall of other fungi is made of cellulose, which

is also a polysaccharide. Cellulose is also found in the cell wall of plants and

many algae. Yeast has a cell wall composed of glucan and mannan, which are

two polysaccharides.

In contrast, protozoa have no cell wall and instead have a pellicle. A pellicle

is a flexible, proteinaceous covering. Eukaryotic cells of other organisms (such

as animals) that lack a cell wall have an outer plasma membrane that serves as

an outside cover for the cell. The outer plasma membrane has a sticky carbo-

CHAPTER 4 Prokaryotic and Eukaryotic Cells 79

GASV

GEC

RER

SER

Fig. 4-6. A eukaryotic cell.

c04_betsy.qxd 5/11/05 2:29 PM Page 79

hydrate called glycocalyx on its surface. Glycocalyx is made up of covalently

bonded lipids and proteins in order to form glycolipid and glycoprotein in the

plasma membrane. Glycolipid and glycoprotein anchor the glycocalyx to the cell,

giving the cell strength and helping the cell to adhere to other cells. Glycocalyx

is also a molecular signature used to identify the cell to other cells. White blood

cells use this to identify a foreign cell before destroying it.

A eukaryotic cell lacks peptidoglycan, which is critical in fighting bacteria

with antibiotics. A bacterium is a prokaryotic cell. Peptidoglycan is the frame-

work of a prokaryotic cell’s cell wall. Antibiotics such as penicillin attack

peptidoglycan resulting in the destruction of the cell wall of a bacterium.

Eukaryotic cells invaded by the bacterium remain unaffected because eukary-

otic cells lack peptidoglycan.

PLASMA MEMBRANE

The plasma membrane is a selectively permeable membrane enclosing the

cytoplasm of a cell. This is the outer layer in animal cells. Other organisms

have a cell wall as the outer layer and the plasma membrane is between the

cell wall and the cell’s cytoplasm. The cell wall is the outer covering of most

bacteria, algae, fungi, and plant cells. In eubacterium, which is a prokaryotic micro-

organism, the cell wall contains peptidoglycan.

The plasma membrane surrounds a eukaryotic cell and serves as a barrier

between the inner cell and its environment. The cytoplasmic membrane is com-

posed of proteins and lipids. Carbohydrates are used to uniquely identify the

cell to other cells. Lipids, known as sterols, help prevent the destruction of the cell

when there is an increase in osmotic pressure and are mainly used for stability.

Lysis is the destruction of a cell. Prokaryotic cytoplasm lacks certain features

that are found in eukaryotic cytoplasm, such as a cytoskeleton. In a eukaryotic

microorganism, the cytoskeleton provides support and shape for cells and helps

transport substances through the cell.

The plasma membrane of a eukaryotic cell functions like the plasma mem-

brane of a prokaryotic cell, which you learned about previously in this chapter.

That is, substances enter and leave the cell through the cytoplasmic membrane

by using simple diffusion, facilitated diffusion, osmosis, and active transport.

Eukaryotic cells extend parts or sections of plasma membrane. The exten-

sions of the plasma membrane are called pseudopods. The word pseudopod

means “false foot,” and these “feet” enable the cell to have amoeboid motion.

An amoeboid motion consists of muscle-like contractions that move the cell over

a surface. Pseudopods are used to engulf substances and bring them into the cell,

CHAPTER 4 Prokaryotic and Eukaryotic Cells80

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which is called endocytosis (a type of active transport). There are two types of

endocytosis. These are phagocytosis (eat) and pinocytosis (drink). In phago-

cytosis, solid particles are engulfed by the cell. An example is when a white

blood cell engulfs and destroys a bacteria cell. In pinocytosis, liquid particles are

brought into the cell. An example is when extracellular fluid containing a sub-

stance is destroyed by the cell.

CYTOPLASM AND NUCLEUS

The cytoplasm of a eukaryotic cell contains cytosol, organelles, and inclusions,

which is similar to the cytoplasm of the prokaryotic cell. Eukaryotic cytoplasm

also contains a cytoskeleton that gives structure and shape to the cell and assists

in transporting substances throughout the cell.

The nucleus of a eukarytoic cell contains DNA (hereditary information) and

is contained within a nuclear envelope. DNA is also found in the mitochondria

and chloroplasts. Depending on the organism, there can be one or more nucleoli

within the nuclear envelope. A nucleolus (little nucleus) is the site of ribosomal

RNA synthesis, which is necessary for ribosomes to function properly.

In the nucleus, the cell’s DNA is combined to form several proteins called

histones. The combination of about 165 pairs of DNA and nine molecular of his-

tones make up the nucleosome. When a eukaryotic cell is not in the reproduc-

tion phase, the DNA and its proteins look like a threaded mass called chromatin.

When the cell goes through nuclear division, the strands of chromatin condense

and coil together, producing rod-shaped bodies called chromosomes.

A eukaryotic cell uses a method of cell division during reproduction called

mitosis. This is the formation of two daughter cells from a parent cell.

ENDOPLASMIC RETICULUM

The endoplasmic reticulum contributes to the mechanical support and distribu-

tion of the cytoplasm and is the pathway for transporting lipids and proteins

throughout the cell. The endoplasmic reticulum also provides the surface area

for the chemical reaction that synthesizes lipids, it stores lipids and proteins until

the cell needs them.

The endoplasmic reticulum consists of cisterns, which are a network of flat-

tened membranous sacs. The end of these cisterns can be pinched off to become

membrane-enclosed sacs called secretory vesicles. Vesicles transport synthe-

sized material in the cell.

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There are two kinds of endoplasmic reticula.

• Rough endoplasmic reticulum. Covered by ribosomes, which are the sites

for synthesizing protein.

• Smooth endoplasmic reticulum. Not covered by ribosomes, this is the site

for synthesizing lipids.

GOLGI COMPLEX

The Golgi complex is considered the “Fedex System” of the cell because it

packages and delivers proteins, lipids, and enzymes throughout the cell and to

the environment. The Golgi complex contains cisterns stacked on top of each

other. A cistern is a sac or vessel and is filled with proteins or lipids (packaged),

detached from the Golgi complex, and transported to another part of the cell.

LYSOSOME

A lysosome is a sphere in animal cells that is formed by, but is separate from, the

Golgi complex, it contains enzymes used to digest molecules that have entered

the cell. Think of lysosomes as the digestive system of the cell. For example,

lysosomes in a white blood cell digest bacteria that is ingested by the cell dur-

ing phagocytosis.

MITOCHONDRION

The mitochondrion is an organelle that is comprised of a series of folds called

cristae that is responsible for the cell’s energy production and cellular respira-

tion. Chemical reactions occur within the center of the mitrochondrion, called

the matrix; it is filled with semifluid in which adenosine triphosphate (ATP) is

produced. ATP is the energy molecule in the cell. The mitochondrion is the

powerhouse of the cell.

CHLOROPLAST

Eukaryotic cells of green plants and algae contain plastids, one of which is chloro-

plast. Chloroplasts are organelles that contain pigments of chlorophyll and

carotenoids used for gathering light and enzymes necessary for photosynthesis.

Photosynthesis is the process that converts light energy into chemical energy. The

CHAPTER 4 Prokaryotic and Eukaryotic Cells82

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pigment is stored in membranous sacs called thylakoids that are arranged in stacks

called grana.

CENTRIOLE

A centriole is a pair of cylindrical structures near the nucleus that is comprised

of microtubules and aids in the formation of flagella and cilia. The centriole also

has a part in eukaryotic cell division.

Quiz

1. A gram-positive cell wall has

(a) many layers of peptidoglygan, which repels the crystal of violet dye

when the cell is stained

(b) many layers of peptidoglygan, which retains the crystal of violet dye

when the cell is stained

(d) one layer of peptidoglygan, which repels the crystal of violet dye

when the cell is stained

2. A cytoplasmic membrane is

(a) a membrane that provides a selective barrier between the nucleus

and the cell’s internal structures

(b) the cell wall

structures

(d) a membrane that provides a selective barrier between the cell wall and

the cell’s internal structures

3. Amphipathic means

(a) that the cytoplasmic membrane of a cell is bilayered and contains

both polar and nonpolar parts

(b) that the cytoplasmic membrane of a cell is unilayered and contains

polar parts

nonpolar parts

(d) that the cytoplasmic membrane of a cell is resistant to all substances

residing outside the cell

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4. What is the function of the nonpolar part of the cytoplasmic membrane?

(a) The cytoplasmic membrane does not have a nonpolar part.

(b) The nonpolar part of the cytoplasmic membrane prevents extra-

cellular fluid from leaving the cell and intracellular fluid from enter-

ing the cell.

prevents extracellular fluid from entering the cell and intracellular

fluid from exiting the cell.

(d) The nonpolar part of the cytoplasmic membrane is to position organ-

elles within the cell.

5. The function of the transport protein is

(a) to regulate cell division

(b) to regulate the positioning of organelles within the cell

(d) to give a cell its color

6. The function of the channel protein is

(a) to direct movement of a cell through channels in its environment

(b) to channel substances among organelles within the cell

permit the flow of molecules through the cytoplasmic membrane

(d) to form pores (called channels) in the nucleus membrane that permit

the flow of molecules through the nuclei of the cell

7. Passive transport is

(a) the process of moving substances through the cytoplasmic mem-

brane without expending energy by using a concentration gradient

(b) the process of moving substances through the cytoplasmic mem-

brane without expending energy by using a transport protein

brane by expending energy by using a concentration gradient

(d) the process of moving substances through the nucleus membrane

without expending energy by using a concentration gradient

8. What is facilitated diffusion?

(a) A passive transport process in which molecules or ions of a sub-

stance move from a region of lower concentration to a region of

higher concentration without the assistance of an integral protein

(b) A passive transport process in which molecules or ions of a sub-

stance move from a region of lower concentration to a region of

higher concentration with the assistance of an integral protein

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stance move from a region of higher concentration to a region of

lower concentration with the assistance of an integral protein

(d) A passive transport process in which molecules or ions of a sub-

stance move from a region of higher concentration to a region of

lower concentration with the assistance of an integral protein

9. Active transport is

(a) the movement of a substance across the cytoplasmic membrane in

the direction of the gradient by using energy provided by the cell

(b) the formation of pores (called channels) in the cytoplasmic mem-

brane that permit the flow of molecules through the cytoplasmic

membrane

against the gradient by using energy provided by the cell

(d) is a process in which molecules or ions of a substance move from a

region of higher concentration to a region of lower concentration

with the assistance of

an integral protein

10. What are the two types of endocytosis?

(a) Facilitated diffusion and passive transport

(b) Phagocytosis and pinocytosis

(d) Nucleoid and cytosol

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CHAPTER

The Chemical

Metabolism

Those of us who need to shed a few pounds tend to blame our weight gain on our

slow metabolism. Metabolism is the collection of biochemical reactions that hap-

pen in our bodies; an example would be the series of reactions that occur when

our digestive system breaks down the food that we eat to energy. All living organ-

isms have a metabolism, including microorganisms. In this chapter you will learn

about the metabolism of the smallest living part of any organism—the cell.

Riding the Metabolism Cycle

The components of a cell, including its plasma membrane and cell wall (and

organelles in eukaryotic organisms), are composed of macromolecules that are

linked together to form these structures. The macromolecules are assembled from

building blocks called precursor metabolites. Think of precursor metabolites as

the bricks that are used to build a wall and the wall as the macromolecule. With

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the energy from ATP (adenosine triphosphate), these precursor metabolites are

used to construct or build larger molecules. ATP is the short term energy storage

molecule of the cell. Think of it as the battery pack of the cell. Cells use energy

from ATP and enzymes to connect smaller molecules to form macromolecules.

The cell grows as macromolecules are linked together and continue to grow into

cellular structures such as organelles, plasma membranes, and cell walls.

Catabolic and Anabolic:

The Only Reactions You Need

A biochemical reaction is called a metabolic reaction. Metabolic reactions fall

into one of two classifications. These are catabolic reactions (catabolism) and

anabolic reactions (anabolism).

A catabolic reaction is a metabolic reaction that releases energy as large

molecules that are broken down (metabolized) into small molecules. An example is

when triglycerides and diglycerides are metabolized into glycerol and fatty acids.

An anabolic reaction requires energy as small molecules are combined to

form large molecules. This type of reaction is called endergonic because it uses

free energy. For example, an anabolic reaction is the synthesis of phospholipids

from glycerol and fatty acids in order to build the cell plasma membrane.

A Little Give and Take:

Oxidation-Reduction

Metabolic reactions sometime involve the transfer of electrons from one mole-

cule to another. One molecule donates an electron and another molecule

accepts the electron. This transfer of electrons is called oxidation-reduction or

redox reaction. A redox reaction is comprised of two events. The first event

happens when a molecule donates an electron. This is called oxidation. The sec-

ond event happens when another molecule accepts the donated electron. This is

called reduction.

The cell uses electron carrier molecules to carry electrons between areas within

the cell. Think of these carrier molecules as “shuttle buses.” Carrier molecules are

necessary because the cytoplasm of the cell does not contain free electrons.

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Two important electron carrier molecules that are used in cell metabolism are

• nicotinamide adenine dinucleotide (NAD+)

• flavine adenine dinucleotide (FAD)

• nicotinamide adenine dinucleotide phosphate (NADP+)

For example, when synthesizing ATP, NAD+ carries electrons of a hydrogen

(H) atom, making NADH. FAD carries two electrons of hydrogen making

FADH2. Very often electrons of hydrogen atoms are the electrons transported by

the carrier molecule. NADP+ is used to reduce CO2 to carbohydrates during the

Dark Phase of photosynthesis.

Making Power: ATP Production

When enzymes break down nutrients (larger molecules) into smaller molecules,

the energy that is released can be stored and used for future anabolic reactions.

Here are the steps to form ATP:

1. Substrate-level phosphorylation: Phosphate is transferred from another

phosphorylated organic compound to ADP to make ATP during an exer-

gonic reaction.

2. Oxidative phosphorylation: Energy from redox reactions of biochemical

respiration is used to attach an inorganic phosphate to ADP to make ATP.

3. Photophosphorylation: Energy from sunlight is used to phosphorylate ADP

with inorganic phosphate.

What’s Your Name:

Naming and Classifying Enzymes

Enzymes are named according to the substrate that they act upon, and most end

in the suffix “-ase.” Enzymes are classified into six major groups based on their

actions. These classifications are:

• Hydrolases: Enzymes in the hydrolases group increase a catabolic reaction

by introducing water into the reaction. This reaction is called hydrolysis.

For example, lipase (lipid + ase) is an enzyme that is used to break down

lipid molecules.

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• Isomerases: Enzymes in the isomerase group rearrange atoms within the

substrate rather than add or subtract anything from the reaction. Phospho-

glucoisomerase is an example of an isomerase because it converts glucose

6-phosphate into fructose 6-phosphate during the breakdown of glucose.

• Ligases: These are anabolic reactions. These enzymes join molecules together

and use energy in the form of ATP. An example is DNA ligase to synthesis DNA.

• Lyases: Enzymes in the lyases group split molecules without using water in

a catabolic reaction. For example, 1,6-biphosphate aldolase splits fructose

1,6 biphosphate into G-3P and DHAP during glycolysis. These are anabolic

reactions.

• Oxidoreductases: Enzymes in the oxidoreductases group oxidize (remove)

electrons or reduce (add) electrons to a substrate in both catabolic and ana-

bolic reactions. An example is lactic acid dehydrogenase, which oxidizes

pyruvate to form lactic acid during fermentation.

• Transferases: Enzymes in the tranferases group transfer functional groups from

one molecule or another substrate in an anabolic reaction. A functional group

could be amino acids, a phosphate group, or an acetyl group. For example,

hexokinase transfers a phosphate group from ATP to glucose in the first step in

the breakdown of glucose during the process of gycolysis.

Brewing Up Protein

Most enzymes are proteins that can be inactive or active. An inactive enzyme does

not act as a catalyst to increase the speed of a metabolic reaction. An active enzyme

is a catalyst. An inactive enzyme is composed of apoenzyme; when an apoenzyme

binds to its cofactor the enzyme becomes active and is called a holoenzyme.

A cofactor is a substance that is either an inorganic ion, such as iron, mag-

nesium, or zinc, or an organic molecule. Organic cofactors are called coen-

zymes. A coenzyme is a molecule that is required for metabolism. NAD, NADP,

and FAD are examples of coenzymes. Some vitamins are coenzyme precursors.

The Magic of Enzymes: Enzyme Activities

All chemical reactions including those that occur in metabolism, need a boost of

energy to get started. The energy needed to begin a chemical reaction is called

activation energy. An enzyme catalyzes a reaction by lowering the activation

energy. Heat can lower the activation energy and set off a reaction. However, the

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temperature would be so high that the cell would die before the activation energy

threshold could be reached.

Enzymes are needed for metabolism to occur in a timely fashion. The activ-

ity of enzymes depends upon how closely their functional sites fit with their

substrates. The shape of the enzyme’s functional site is called its active site. This

site fits in regard to the shape of the

substrate. The active site of the enzyme

compliments the shape of its substrate. A perfect fit does not occur until the

substrate and enzyme bind together to form an enzyme-substrate complex.

The chemical denaturing of enzymes is caused by very high or very low pH.

H+ ions that are released from acids and accepted by bases interfere with hydro-

gen bonding. If we change the pH of the environment of unwanted microorgan-

isms, we can control their growth by denaturing their proteins. An example is

vinegar, which is acetic acid; it has a pH of 3.0. Vinegar acts as a preservative

in “ pickling” vegetables. Ammonia has a pH of 11. Ammonia is a base, and for

this reason we use ammonia as a cleaner and disinfectant.

ENZYME SUBSTRATE CONCENTRATION

As substrate concentrations increase, enzyme activity also increases. When all

enzyme binding sites have bound to a substrate, the enzymes have reached their

saturation point. If more substrate is added, the rate of enzyme activity will not

increase. One way organisms regulate their metabolism is by controlling the

quantity and timing of enzyme synthesis.

The Right Influences: Factors Affecting Enzymes

The ability of an enzyme to lower the activation required for metabolism is

influenced by three factors. These are pH, temperature, and the concentration of

enzyme, substrate, and product.

Temperature

Changes in temperature change the shape of the active site, and therefore, influ-

ence the fit between the active site and the substrate. Enzymes in humans work

best at about 37 degrees Celsius. This is the same temperature at which en-

zymes work best for some pathogenic microorganisms, too. Once the tempera-

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ture reaches the point that radically changes the shape of the active site, the bond

between the active site and the substrate is broken and makes the enzyme in-

effective. This is called thermal denaturation. Denatured enzymes lose their

specific three-dimensional shape, making them nonfunctional. For example, the

clear liquid portion of an egg turns to a white solid when the egg is heated.

The clear liquid is made up of proteins. Heating these proteins denatures them.

Inhibitors

There are substrates that block active sites from bonding to a substrate. These sub-

stances are called inhibitors. There are two kinds of inhibitors: competitive and

noncompetitive. A competitive inhibitor is a substance that binds to the active site

of an enzyme, thus preventing the active site from binding with the substrate. For

example, sulfa drugs contain the chemical sulfanilamid. Sulfa drugs inhibit micro-

bial growth by fitting into the active site of an enzyme required in the conversion

of paraaminobenzoic acid (PABA) into the B vitamin folic acid. Folic acid is

needed for DNA synthesis in bacteria and thus prevents bacteria from growing. A

noncompetitive inhibitor binds to another site on the enzyme called the allosteric

site and in doing so alters the shape of the active site of the enzyme. The shape of

the active site no longer complements the corresponding site on the substrate and

therefore no binding occurs. Noncompetitive inhibitors do not bind to active sites.

CARBOHYDRATE METABOLISM

Carbohydrates are the main energy source for metabolic reactions and glucose is

the most used carbohydrate in metabolism. Energy is produced by breaking

down (catabolized) glucose in a process called glycolysis, which takes place in

the cytoplasm of most cells. Glycolysis, also known as the Embden-Meyerhof

pathway, is the oxidation of glucose to pyruvic acid. In glycolysis, which

originated from the Greek word glykys meaning “sweet” and lysein meaning

“loosen,” enzymes split a six-carbon sugar into two three-carbon sugars, which

are then oxidized. Oxidation releases energy and rearranges atoms to form two

molecules of pyruvic acid. It is during this process that NAD+ is reduced to

NADH with a net production of two ATP molecules.

In the presence of O2 (aerobic environment), pyruvic acid enters the bridging

pathway and becomes connected to acetyl CoA. It then enters the Krebs cycle,

which will result in the production of three NADH and, one FADH2 molecules. In

the absence of O2 (anaerobic environment), the NADH produced during glycoly-

sis is oxidized and an organic compound accepts the electrons. This process is

called fermentation. This pathway of fermentation results in fewer ATP molecules.

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Embden-Meyerhof Pathway

The Embden-Meyerhof pathway (Fig. 5-1) is used by some bacteria to catabo-

lize glucose to pyruvic acid. For example, Pseudomonas aeruginosa, which is

the bacteria that infects burn victims, uses the Embden-Meyerhof pathway. The

Embden-Meyerhof pathway yields one molecule of ATP.

CHAPTER 5 The Chemical Metabolism 93

Glucose

Glucose 6-phosphate

Fructose 6-phosphate

Fructose 1, 6-diphosphate

Dihydroxyacetone

(DHAP)

Glyceraldehyde

3-phosphate (G-3P)

Glyceraldehyde 3-phosphate (G-3P)

1,3-diphosphoglyceric acid

3-phosphoglyceric acid

2-phosphoglyceric acid

Phosphoenolpyruvic acid (PEP)

Pyruvic acid

2 ATP

2 NADH

2 ATP

2 H2O

ATP ADP

2 ADP

2 NAD +

Fig. 5-1. Diagram of glycolysis: Embden-Meyerhoff pathway.

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Pyruvic Acid

Before entering the Krebs cycle, the pyruvic acid produced from the breakdown

of glucose must be further processed by converting it to acetyl-coenzyme A.

This is accomplished by the enzyme complex pyruvate dehydrogenase. CO2 is

removed from pyruvic acid and the product is an acetyl group (a two carbon

group). The acetyl group is attached to coenxzyme A and the product is called

acetyl-CoA. The removal of CO2 is called decarboxylation.

The Krebs Cycle

The Krebs cycle (Fig, 5-2) is a series of biochemical reactions that occur in the

mitochondria of eukaryotic cells and in the cytoplasm of prokaryotes. The Krebs

CHAPTER 5 The Chemical Metabolism94

Acetyl CoA

Citric acid

Pyruvic acid

NAD+

CO2

Isocitric acid

Alpha -Ketoglutaric acid

Succinyl CoASuccinic acid Fumaric acid

Malic acid

Oxaloacetic acid

CO2

NAD+

CO2

CoA

FADH2

CoA

NADH + H+

NADH

CoA

NAD+

FAD

ADP

ATP

GDP

GTP

NADH + H+

NAD+

NADH + H+

Fig. 5-2. The Krebs Cycle: Citric Acid Cycle

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cycle, also known as the citric acid cycle and the tricarboxylic acid (TCA) cycle,

is named for Sir Hans Krebs, a biochemist, who in the 1940s explained how

these reactions work. In the Krebs cycle, acetyl-CoA is split into carbon dioxide

and hydrogen atoms.

The carbon dioxide diffuses out of the mitochondria in eukaryotic cells and

eventually out of the cell itself. This series of reactions is called a cycle because

as one acetyl group enters the Krebs cycle and is metabolized, oxaloacetate com-

bines with another acetyl group to form citric acid and coenzyme A, which go

through the cycle again. As each acetyl group goes through the cycle, two mole-

cules of CO2 are formed from the oxidation of its two carbon atoms.

Three pairs of electrons are transferred to NAD and one pair to FAD. These

coenzymes are important because they carry large amounts of energy. For every

molecule of acetyl-CoA that enters the Krebs Cycle, a molecule of ATP is pro-

duced. The Krebs cycle also provides substances for bacteria and other prokary-

otic cellular activities.

THE NEW CHAIN GANG:

THE ELECTRON TRANSPORT CHAIN

Glycolysis, the bridging reaction, and the Krebs cycle result in the synthesis of

only four ATP molecules when one glucose is oxidized to six CO2 molecules.

Most of the ATP that is generated comes from the oxidation of NADH and

FADH2 in the electron transport chain.

The electron transport chain, which occurs in the mitochondria in eukaryotic

cells and in the cytoplasm of prokaryotic cells, is composed of a series of elec-

tron carriers that transfer electrons from donor molecules, such as NADH and

FADH2 to

an acceptor atom like O2. The electrons move down an energy gradi-

ent, like water flowing down a series of waterfalls in rapids.

The difference in free energy that occurs between O2 and NADH releases

large amounts of energy. The energy changes that occur at several points in the

chain are very large and can provide the eventual production of large amounts

of ATP. The free energy that electrons have entering the electron transport chain

is greater in the beginning than at the end. It is this energy that enables the pro-

tons (H+) to be pumped out of the mitochondrial matrix.

When the electrons move through the chain they transfer this energy to the

pumps within the plasma membrane. The electron transport chain will separate

the energy that is released into smaller sections, or steps. The reactions of the

electron chain take place in the inner membrane of the mitochondria in eukary-

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otic cells or in the plasma membrane in prokaryotic cells. In the mitochondria

this system is set up into four complexes of carriers.

Each of these carriers transports electrons part of the way to O2 (which is the

final electron acceptor). The carriers, coenzyme Q and cytochrome C, connect

these complexes. This process by which energy comes from the electron trans-

port chain is provided by protons (H+) and are used to make ATP.

Three ATP molecules can be synthesized from ADP and Pi when two elec-

trons pass from NADH to an atom of O2.

The electron transport chain used by bacteria and other prokaryotes can differ

from the mitochondrial chain used in eukaryotic organisms. Bacteria, for exam-

ple, vary in their electron carriers. Bacteria use cytochromes, heme proteins that

carry electrons through the electron transport chain. (A heme is an organic com-

pound, the center of which contains an iron atom surrounded by four nitrogen

atoms.) Electrons can enter at several points and leave through terminal oxidases.

Prokaryotic and eukaryotic electrons work using the same fundamental princi-

ples, although they differ in construction.

The electron transport chain in E. coli bacteria, for example, transports elec-

trons from NADH to acceptors and moves protons across the plasma membrane.

The E. coli electron transport chain is branched and contains different cyto-

chromes. The two branches are cytochrome d and cytochrome o. Coenzyme Q

donates electrons to both branches. These chains operate in different conditions.

For example, the cytochrome d branch will function when O2 levels are low and

does not actively pump protons, whereas the cytochrome o branch operates in

higher O2 concentrations and is a proton pump.

During the aerobic metabolism of a single glucose molecule, ten pairs of elec-

trons from NAD produce thirty ATP molecules, and two pairs of FAD produce

four ATP molecules, making a total of 34 ATP molecules. Four substrate-level

ATPs make a total of 38 molecules of ATP from one molecule of glucose.

The energy captured occurs through a process called chemiosmosis, formu-

lated by British biochemist Peter Mitchell, who won the Nobel Prize in 1978. In

chemiosmosis electrons flow down their electrochemical gradient across the

inner mitochondrial membrane in eukaryotes and the cell membrane in prokary-

otes through ATP syntase.

If the organism is in an aerobic environment, there are enzymes that can break

down harmful chemicals. An example of such a chemical is hydrogen peroxide

(H2O2). If the organism is in an anaerobic environment, they do not possess or

cannot produce these aerobic enzymes and are susceptible to damage by O2. An

example is the free radical superoxide. Organisms that follow this pathway pro-

duce less ATP. An example of these types of organisms is lactobacillus.

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Fermentation

Fermentation is the partial oxidation of glucose or another organic compound to

release energy; it uses an organic molecule as an electron acceptor rather than an

electron transport chain. In a simple fermentation reaction, NADH reduces pyru-

vic acid from glycolysis to form lactic acid. Another example involves two reac-

tions. The first is a decarboxylation reaction where CO2 is given off (this is the

CO2 that causes bakery items to rise), followed by a subsequent reduction reac-

tion that produces ethanol.

The essential function of fermentation is the regeneration of NAD+ for glycol-

ysis so ADP molecules can be phosphorylated to ATP. The benefit of fermentation

is that it allows ATP production to continue in the absence of O2. Microorganisms

that ferment can grow and colonize in an anaerobic environment.

Microorganisms produce a variety of fermentation products. The products of

fermentation of cells are waste products of the cells, but many are useful to

humans. These include ethanol (the alcohol that humans can drink, like in beer,

wine, and liquor), acetic acid (vinegar), and lactic acid (found in cheese, sauer-

kraut, and pickles). Other fermentation products are very harmful to humans. An

example is the bacterium Clostridium perfringens, which ferments hydrogen and

is associated with gas gangrene. Gangrene is involved in necrosis or the “death”

of muscle tissue.

Other Catabolic Pathways

There are two other important catabolic pathways. These are lipid catabolism

and protein catabolism. Both of these convert substances (lipids and proteins)

into ATP, providing the microorganism with energy.

LIPID CATABOLISM

Lipids, including fats, which consist of glycerol and fatty acids, can be involved

in ATP production. Enzymes called lipases hydrolyze the bonds attaching the

glycerol to the fatty acid chains. Glycerol is converted to dihydroxyacetone phos-

phate (DHAP), which is oxidized to pyruvic acid in glycolysis. The fatty acids

are broken down in catabolic reactions called beta-oxidation. In beta-oxidation,

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enzymes split off pairs of hydrogenated carbon atoms that make up the fatty acids.

The enzymes then join these pairs to coenzyme A to form acetyl-CoA. This hap-

pens until the entire fatty acid has been converted to molecules of acetyl-CoA.

Acetyl-CoA is utilized in the cycle to generate ATP.

PROTEIN CATABOLISM

Most organisms break down proteins only when glucose and fats are unavail-

able. Some bacteria that spoil food, pathogenic bacteria, and fungi normally

catabolize proteins as energy sources.

Proteins are too large to cross the cell membrane. Microorganisms secrete an

enzyme called protease, which splits the protein into amino acids outside the

cell. Amino acids are then transported into the cell, where specialized enzymes

split off amino groups in reactions called deamination. These molecules then

enter the Krebs cycle.

These are examples of how the catabolism or breakdown of proteins, carbo-

hydrates, and lipids can be sources of electrons and proteins during cellular res-

piration. The pathways of glycolysis and the Krebs cycle are catabolic roadways

or tunnels where high-energy electrons from these organic molecules can flow

through on their energy-releasing journey.

Photosynthesis

Some organisms use anabolic pathways to synthesize organic molecules from

inorganic carbon dioxide. Most of these phototrophic organisms are autotrophic

and are capable of surviving and growing on carbon dioxide as their only carbon

source. The energy from sunlight is used to reduce CO2 to carbohydrates. This pro-

cess is called photosynthesis. The ability of an organism to “photosynthesize”

depends on the presence of light-sensitive pigments, called chlorophyll, or related

compounds. These pigments are found in plants, algae, and certain bacteria.

The growth of these photosynthetic organisms can be explained by two sep-

arate types of reactions. In light reactions, light energy is converted into chemi-

cal energy and dark reactions in which the chemical energy from the light

reactions is used to reduce carbon dioxide (CO2) to carbohydrates. For the

growth and survival of autotrophic organisms, energy is supplied in the form of

an ATP molecule. Electrons for the reduction of CO2 come from NADPH.

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NADPH is produced from the reduction of NADP+ by electrons from electron

donors such as water.

Purple and green bacteria use light most of the time to form ATP. They pro-

duce NADPH from reducing materials present in their environment, such as

reduced sulfur compounds (H2S), organic compounds, as photosynthetic elec-

tron donors for CO2 fixation. Green plants, algae, and cyanobacteria do not use

reduced sulfur compounds or organic compounds to obtain reducing power.

Instead, they obtain electrons for NADP+ reduction by splitting water molecules.

By splitting water, oxygen (O2) is produced as a byproduct. The reduction of

NADP+ to NADPH by these organisms is dependent on light and therefore a

light-mediated event. Due to the production of molecular oxygen (O2) the

process of photosynthesis in these organisms is called oxygenic photosynthesis.

In contrast, the purple and green bacteria do not produce oxygen. This process

is called anoxygenic photosynthesis.

These photosynthetic organisms capture the light with pigment molecules. An

important pigment molecule is chlorophyll. There are different structures of

chlorophyll, the most common of which are chlorophyll a and chlorophyll b.

Chlorophyll a is the principal chlorophyll of higher plants, most algae, and

cyanobacteria. Purple and green bacteria have chlorophylls of a different struc-

ture, called bacteriochlorophyll.

Accessory pigments, such as carotenoids and phycobilins, are also involved

in capturing light energy. Carotenoids play a photoprotective role, preventing

photooxidative damage to the phototrophic cell. Phycobilins serve as light-

harvesting pigments.

Cells arrange numerous molecules of chlorophyll and accessory pigments

within membrane systems called photosynthetic membranes. The location of

these membranes differs between eukaryotic and prokaryotic microorganisms.

In eukaryotic organisms, photosynthesis occurs in specialized organelles called

chloroplasts. The chlorophyll pigments are attached to “sheet-like” membrane

structures of the chloroplasts. These photosynthetic membrane structures are called

thylakoids. These thylakoids are arranged in stacks called grana. Thylakoids

resemble stacks of pennies. Each stack is called a granum.

In prokaryotic organisms, there are no chloroplasts. The photosynthetic pigments

are integrated in a membrane system that arises from the cytoplasmic membranes.

PHOTOSYSTEMS I AND II

Electron flow in oxygenic phototrophs involves two sets of photochemical

reactions. Oxygenic phototrophs use light energy to generate ATP and

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NADPH. The electrons from NADPH come from the splitting of H2O to get

oxygen (O2) and electrons (H+). The two systems of light reactions are called

photosystem I and photosystem II. Photosystems I and II function together in

the oxygenic process. Under certain conditions many algae and some

cyanobacteria can carry out cyclic photophosphorylation using only photosys-

tem I. These organisms can obtain reducing power from sources other than

water. This requires the presence of anaerobic conditions and a reducing sub-

stance, such as H2 or H2S. Photosystem II is responsible for splitting water to

yield H2 + O.

Dark Phase Reactions

Many photosynthetic bacteria contain carboxysomes in their cytoplasm. These

carbosomes contain many copies of the complex enzyme Rubisco (the most

abundant and probably the most important enzyme on the planet) to start the

Calvin Cycle.

The fixation of CO2 by most photosynthetic and autotrophic organisms in-

volves the biochemical pathway called the Calvin Cycle. The Calvin Cycle is a

reductive, energy-demanding process in which reducing equivalents from

NADPH and energy from ATP are used to reduce CO2 to small carbohydrates that

are metabolized to glucose and ultimately to more complex carbohydrates such as

starch, sucrose and glycogen. Other substances with carbon can be used but CO2

is preferred.

Quiz

1. What is the energy storage molecule?

(a) ATP

(b) Adenosine oxidate

(d) NAAD

2. What reaction releases energy as large molecules are broken down into

small molecules?

(a) Anabolic reaction

(b) Catabolic reaction

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(d) Hydrolase reaction

3. What reaction combines small molecules to form large molecules?

(a) Anabolic reaction

(b) Catabolic reaction

(d) Hydrolase reaction

4. The energy needed to begin a chemical reaction is called?

(a) Metabolism

(b) Activation energy

(d) Inhibitors

5. What process is used to break down glucose?

(a) Anabolic reaction

(b) Catabolic reaction

(d) Hydrolase reaction

6. What pathway is used by some bacteria to catabolize glucose to pyruvic

acid?

(a) Pyruvic acid pathway

(b) Enter-Doudoroff pathway

(d) Aeruginosa pathway

7. What is acetyl-CoA split into in the Krebs cycle?

(a) Hydrogen and oxygen

(b) Oxygen and carbon

(d) Carbon and hydrogen

8. What process partially oxidizes sugar to release energy using an organic

molecule as an electron acceptor?

(a) Fermentation

(b) Oxidation

(d) Lactation

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9. What is caused when there is a chemical denaturing of enzymes?

(a) Protein creation

(b) Lipid creation

(d) Saturation point is reached

10. What blocks active sites from bonding to a substrate?

(a) Carbohydrates

(b) Temperature

(d) Pyruvic acid

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CHAPTER

103

Microbial Growth

and Controlling

Microbial Growth

Microorganisms use chemicals called nutrients for growth and development.

They need these nutrients to build molecules and cellular structures. The most

important nutrients are carbon, hydrogen, nitrogen, and oxygen. Microorganisms

get their nutrients from sources in their environment. When these microorgan-

isms obtain their nutrients by living on or in other organisms, they can cause dis-

ease in that organism by interfering with their host’s nutrition, metabolism, and,

thus disrupting their host’s homeostasis, the steady state of an organism.

Organisms can be classified in two groups depending on how they feed them-

selves. Organisms that use carbon dioxide (CO2) as their source of carbon are

called autotrophs. These organisms “feed themselves,” auto- meaning “self” and

-troph meaning “nutrition.” Autotrophs make organic compounds from CO2

and do not feed on organic compounds from other organisms. Organisms that

obtain carbon from organic nutrients like proteins, carbohydrate, amino acids,

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and fatty acids are called heterotrophs. Heterotrophic organisms acquire or feed

on organic compounds from other organisms.

Organisms can also be categorized according to whether they use chemicals

or light as a source of energy. Organisms that acquire energy from redox re-

actions involving inorganic and organic chemicals are called chemotrophs.

Organisms that use light as their energy source are called phototrophs.

Chemical Requirements for Microbial Growth

A microorganism requires two chemical elements in order to grow. These ele-

ments are carbon and oxygen.

CARBON

Carbon is one of the most important requirements for microbial growth. Carbon

is the backbone of living matter. Some organisms, such as photoautotrophs, get

carbon from carbon dioxide (CO2).

OXYGEN

Microorganisms

that use oxygen produce more energy from nutrients than micro-

organisms that do not use oxygen. These organisms that require oxygen are called

obligate aerobes. Oxygen is essential for obligate aerobes because it serves as

a final electron acceptor in the electron transport chain, which produces most

of the ATP in these organisms. An example of an obligate aerobe is micrococ-

cus. Some organisms can use oxygen when it is present, but can continue to

grow by using fermentation or anaerobic respiration when oxygen is not avail-

able. These organisms are called facultative anaerobes. An example of a fac-

ultative anaerobe is E. coli bacteria, which is found in the large intestine of

vertebrates, such as humans.

Some bacteria cannot use molecular oxygen and can even be harmed by it.

Examples include Clostridium botulinum, the bacterium that causes botulism,

and Clostridium tetani, the bacterium that causes tetanus. These organisms are

called obligate anaerobes. Molecular oxygen (O2) is a poisonous gas to obligate

anaerobes. Toxic forms of oxygen are:

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• Singlet oxygen, which is in an extremely active, high-energy state. This is

present in cells that use phagocytosis to ingest foreign bacteria cells.

• Superoxide free radicals, which is formed during normal respiration of

organisms that use oxygen as a final electron acceptor. In obligate anaer-

obes, they form some superoxide free radicals in the presence of oxygen.

These superoxide free radicals are incredibly toxic to cellular components.

In order for organisms to grow in atmospheric oxygen they must produce

the enzyme superoxide dimutase or (SOD). Superoxide dimutase neutral-

izes superoxide free radicals. Aerobic bacteria, facultative anaerobes grow-

ing aerobically, and aerotolerant anaerobes produce SOD, which converts

the superoxide free radical into molecular oxygen (O2) and hydrogen per-

oxide (H2O2). This can be seen when you place hydrogen peroxide on a

wound infected with bacteria. When hydrogen peroxide is placed on the

colony of bacterial cells that are producing catalase, oxygen bubbles are

released. This is the “foaming” you see when you place hydrogen perox-

ide on a cut. Human cells also produce catalase, which converts hydrogen

peroxide to water and oxygen.

• Hydroxyl radical (OH−); this is a hydroxide ion. Most aerobic respiration

produces some hydroxyl radicals. Aerotolerant anaerobes can tolerate

oxygen, but cannot grow in an oxygen-rich environment. Aerotolerant bac-

teria ferment carbohydrates to lactic acid. Lactic acid inhibits the growth

of aerobic competitors, establishing a good opportunity for the growth of

these organisms. An example of a lactic acid–producing aerotolerant bac-

terium is lactobacillus, used in fermented food such as pickles and yogurt.

Culture Media

A culture medium is nutrient material prepared in the laboratory for the growth

of microorganisms. Microorganisms that grow in size and number on a culture

medium are referred to as a culture.

In order to use a culture medium must be sterile, meaning that it contains no

living organisms. This is important because we only want microorganisms that

we add to grow and reproduce, not others. We must have the proper nutrients, pH,

moisture, and oxygen levels (or no oxygen) for a specific microorganism to grow.

Many culture media are available for microbial growth. Media are constantly

being developed for the use of identification and isolation of bacteria in the

research of food, water, and microbiology studies.

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The most popular and widely used medium used in microbiology laboratories

is the solidifying agent agar. Agar is a complex polysaccharide derived from red

algae. Very few microorganisms can degrade agar, so it usually remains in a

solid form. Agar media are usually contained in test tubes or Petri dishes. The

test tubes are held at a slant and are allowed to solidify on an angle, called a

slant. A slant increases the surface area for organism growth. When they solid-

ify in a vertical tube it is called a deep. The shallow dishes with lids to prevent

contamination are called Petri dishes. Petri dishes are named after their inventor,

Julius Petri, who in 1887 first poured agar into glass dishes.

CHEMICALLY DEFINED MEDIA

For a medium to support microbial growth, it must provide an energy source,

as well as carbon, nitrogen, sulfur, phosphorous, and any other organic growth

factors that the organism cannot make itself, source for the microorganisms

to utilize.

A chemically defined medium is one whose exact chemical composition is

known. Chemically defined media must contain growth factors that serve as a

source of energy and carbon. Chemically defined media are used for the growth

of autotrophic bacteria. Heterotrophic bacteria and fungi are normally grown on

complex media, which are made up of nutrients, such as yeasts, meat, plants, or

proteins (the exact composition is not quite known and can vary with each mix-

ture). In complex media, the energy, carbon, nitrogen, and sulfur needed for

microbial growth are provided by protein. Proteins are large molecules that some

microorganisms can use directly. Partial digestion by acids and enzymes break

down proteins into smaller amino acids called peptones. Peptones are soluble

products of protein hydrolysis. These small peptones can be digested by bacteria.

Different vitamins and organic growth factors can be provided by meat and

yeast extracts. If a complex medium is in a liquid form it is called a nutrient

broth. If agar is added, it is called a nutrient agar. Agar is not a nutrient; it is a

solidifying agent.

ANAEROBIC GROWTH

Because anaerobic organisms can be killed when exposed to oxygen, they must

be placed in a special medium called a reducing medium. Reducing media con-

tain ingredients like sodium thioglycolate that attaches to dissolved oxygen and

depletes the oxygen in the culture medium.

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SELECTIVE AND DIFFERENTIAL MEDIA

In health clinics and hospitals, it is necessary to detect microorganisms that are

associated with disease. Selective and differential media are therefore used.

Selective media are made to encourage the growth of some bacteria while

inhibiting others. An example of this is bismuth sulfite agar. Bismuth sulfite agar

is used to isolate Salmonella typhi from fecal matter. Salmonella typhi is a gram-

negative bacterium that causes salmonella. Differential media make it easy to

distinguish colonies of desired organisms from nondesirable colonies growing

on the same plate. Pure cultures of microorganisms have identifiable reactions

with different media. An example is blood agar. Blood agar is a dark red/brown

medium that contains red blood cells used to identify bacterial species that

destroy red blood cells. An example of this type of bacterium is streptococcus

pyogenes, the agent that causes strep throat.

MacConkey agar is both selective and differential. MacConkey agar contains

bile salts and crystal violet, which inhibit the growth of gram-positive bacteria,

and lactose, in which gram-negative bacteria can grow.

Enrichment cultures are usually liquids and provide nutrients and environ-

mental conditions that provide for the growth of certain microorganisms, but

not others.

PURE CULTURES

Infectious material or materials that contain pathogenic microorganisms can be

located in pus, sputum, urine, feces, soil, water, and food. These infectious

materials can contain several kinds if bacteria. If these materials are placed on

a solid medium, colonies will form that are the exact copies of that same

microorganism. A colony arises from a single spore, vegetative cell, or a group

of the same organism that attaches to others like it into clumps or chains.

Microbial colonies have distinct appearances

that distinguish one microorgan-

ism from another.

The streak plate method is the most common way to get pure cultures of bac-

teria. A device called an inoculating loop is sterilized and dipped into a culture

of a microorganism or microorganisms and then is “streaked” in a pattern over

a nutrient medium. As the pattern is made, bacteria are rubbed off from the loop

onto the nutrient medium. The last cells that are rubbed off the loop onto the

medium are far enough apart to allow isolation of separate colonies of the orig-

inal culture. (See Fig. 6-1.)

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PRESERVING BACTERIAL CULTURES

Two common methods of preserving microbial cultures are deep freezing and

lyophilization or (freeze drying). Deep freezing is a process in which a pure cul-

ture of microorganisms is placed in a suspending liquid and frozen quickly at

temperatures ranging from −50 to −95 degrees Celsius. With this type of freez-

ing method, cultures can usually be thawed and used after several years.

Lyophilization, or freeze drying, quick freezes suspended microorganisms at

temperatures from −54 to −72 degrees Celsius while water is removed by using

a high-pressure vacuum. While under the vacuum the container is sealed with a

torch. The surrounding microbes in the sealed container can last for years. The

organisms can be retained and revived by hydrating them and placing them into

a liquid nutrient medium.

GROWING BACTERIAL CULTURES

Bacteria normally reproduce by a process called binary fission:

1. The cell elongates and chromosomal DNA is replicated.

2. The cell wall and cell membrane pinch inward and begin to divide.

3. The pinched parts of the cell wall meet, forming a cross wall completely

around the divided DNA.

4. The cells separate into two individual cells.

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Fig. 6-1. Streak plate method used

to isolate bacteria.

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Some bacteria reproduce by budding. A small outgrowth or bud emerges from

the bacterium and enlarges until it reaches the size of the daughter cell. It then

separates, forming two identical cells. Some bacteria, called filamentous bac-

teria (or actinomycetes), reproduce by producing chains of spores located at

the tips of the filaments. The filaments fragment and these fragments initiate the

growth of new cells.

GENERATION TIME

The generation time is the amount of time needed for a cell to divide. This varies

among organisms and depends upon the environment they are in and the temper-

ature of their environment. Some bacteria have a generation time of 24 hours,

although the generation time of most bacteria is between 1 to 3 hours. Bacterial

cells grow at an enormous rate. For example, with binary fission, bacteria can dou-

ble every 20 minutes. In 30 generations of bacteria (10 hours), the number could

reach one billion. It is difficult to graph population changes of this magnitude

using arithmetic numbers, so logarithmic scales are used to graph bacterial growth.

Phases of Growth

There are four basic phases of growth: the lag phase, the log phase, the station-

ary phase, and the death phase.

THE LAG PHASE

In the lag phase there is little or no cell division. This phase can last from one

hour to several days. Here the microbial population is involved in intense meta-

bolic activity involving DNA and enzyme synthesis. This is like a factory “shut-

ting down” for two weeks in the summer for renovations. New equipment is

replacing old and employees are working, but no product is being turned out.

THE LOG PHASE

In the log phase, cells begin to divide and enter a period of growth or logarith-

mic increase. This is the time when cells are the most active metabolically. This

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is the time when the product of the factory must be produced in an efficient mat-

ter. In this phase, however, microorganisms are very sensitive to adverse condi-

tions of their environment.

THE STATIONARY PHASE

This phase is one of equilibrium. The growth rate slows, the number of dead

microorganisms equals the number of new microorganisms, and the population

stabilizes. The metabolic activities of individual cells that survive will slow

down. The reasons why the growth of the organisms stops is possibly that the

nutrients have been used up, waste products have accumulated, and drastic harm-

ful changes in the pH of the organisms environment have occurred.

There is a device called a chemostat that drains off old, used medium and

adds fresh medium. In this way a population can be kept in the growth phase

indefinitely.

THE DEATH PHASE

Here the number of dead cells exceeds the number of new cells. This phase con-

tinues until the population is diminished or dies out entirely.

Measurements of Microbial Growth

A plate count is the most common method of measuring bacterial growth. This

method measures the number of viable cells. Plate counts may take 24 hours or

more for visible colonies to form.

A plate count is performed by either a pour plate method or a special plate

method. With the pour plate method either 1.0 milliliter or 0.1 milliliters of a

bacterial solution is placed into a Petri dish. Melted nutrient agar is added, which

is then gently agitated, or mixed. When the agar has solidified, the plate is then

placed under incubation. With this technique, heat-sensitive microorganisms can

be damaged by the melted agar and be unable to form colonies. To avoid death

of cells due to heat, the spread plate method is mostly used. Here a 0.1-milliliter

bacterial solution is added to the surface of a prepored, solid nutrient agar. The bac-

terial solution is then spread evenly over the medium.

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When the amount of bacteria is very small, as in lakes and pure streams, bac-

teria can be counted by filtration methods. Here 100 milliliters of water are

passed through a thin membrane, whose pores are too small for the bacteria to

pass through. The bacteria that are retained from the filter are placed on a Petri

dish containing a pad soaked with liquid nutrient. An example of bacteria that

are grown using this method is coliform bacteria, which are indicators of fecal

pollution of food or water.

When using the direct microscopic count method, a measured volume of bac-

teria is suspended in a liquid placed inside a designated area of a microscopic slide.

For example, a 0.01-milliliter sample is spread over a marked square centimeter of

a slide, stained, and viewed under the 0.1 immersion objective lens. The area for

the viewing field is obtained. Once the number of bacteria is obtained or deter-

mined in several different fields, an average can be taken of the number of bacte-

ria per viewing field. From this data, the number of bacteria in the square

centimeter over which the sample has been spread can be calculated. Because the

area on the slide contained 0.01 milliliters of sample, the number of bacteria in

each milliliter of the suspension is the number of bacteria in the sample times 100.

Establishing Bacterial Numbers

by Indirect Methods

Not all microbial cells must be counted to establish their number. With some

types of work, estimating the turbidity is a practical way of monitoring micro-

bial growth. Turbidity is the cloudiness of a liquid or the loss of transparency

because of insoluble matter.

The instrument used to measure turbidity is a spectrophotometer or col-

orimeter. In the spectrophotometer, a beam of light is transmitted through the

bacteria that are suspended in the liquid medium to a photoelectric cell. As bac-

teria growth increases, less light will reach the photoelectric cell. The change of

light will register on the instrument’s scale as the percentage of transmission.

The amount of light striking the light-sensitive detector on the

Small Is a Microorganism? 7

Your Body Fights Back 7

History of the Microscope 9

How Do Organisms Appear? 10

Germ Theory 12

Vaccination 15

Killing the Microorganism 16

Quiz 19

CHAPTER 2 The Chemical Elements of Microorganisms 23

Everything Matters 24

Chemical Elements and the Atom 24

A Dinner Table of Elements:

The Periodic Table 27

The Glowing Tale of Isotopes 27

Around They Go: Electronic Configuration 29

Before James There Was Bond . . .

Chemical Bond 29

Decoding Chemical Shorthand 31

vii

CONTENTS

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For more information about this title, click here

http://dx.doi.org/10.1036/0071471340

I Just Want to See Your Reaction 31

Molarity: Hey, There’s a Mole Amongst Us 36

An Unlikely Pair: Inorganic and Organic 37

The Blueprint of Protein Synthesis 42

The Power House: ATP 44

Quiz 44

CHAPTER 3 Observing Microorganisms 47

Size Is a Matter of Metrics 47

Here’s Looking at You 51

What Big Eyes You Have: Magnification 52

The Microscope 54

Preparing Specimens 60

Quiz 64

CHAPTER 4 Prokaryotic Cells and Eukaryotic Cells 67

Prokaryotic Cells 68

Eukaryotic Cells 78

Quiz 83

CHAPTER 5 The Chemical Metabolism 87

Riding the Metabolism Cycle 87

Catabolic and Anabolic: The Only Reactions

You Need 88

A Little Give and Take: Oxidation-Reduction 88

Making Power: ATP Production 89

What’s Your Name: Naming and

Classifying Enzymes 89

Brewing Up Protein 90

The Magic of Enzymes: Enzyme Activities 90

The Krebs Cycle 94

Fermentation 97

Other Catabolic Pathways 97

Photosynthesis 98

Quiz 100

CONTENTSviii

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CHAPTER 6 Microbial Growth and Controlling

Microbial Growth 103

Chemical Requirements for Microbial

Growth 104

Culture Media 105

Phases of Growth 109

Measurements of Microbial Growth 110

Establishing Bacterial Numbers

by Indirect Methods 111

Controlling Microbial Growth 112

Microbial Death Rates 113

Action of Antimicrobial Agents 113

Chemical Agents That Control Microbial

Growth 114

Quiz 116

CHAPTER 7 Microbial Genetics 119

Genetics 120

DNA Replication: Take My Genes, Please! 120

Protein Synthesis 123

Controlling Genes: You’re Under My Spell 124

Mutations: Not a Pretty Copy 125

Quiz 127

CHAPTER 8 Recombinant DNA Technology 131

Genetic Engineering: Designer Genes 132

Gene Therapy: Makes You Feel Better 134

DNA Fingerprinting: Gotcha 134

Recombinant DNA Technology and Society:

Too Much of a Good Thing 136

Quiz 137

CHAPTER 9 Classification of Microorganisms 139

Taxonomy: Nothing to Do with the IRS 139

Nomenclature of Taxonomy: Name Calling 140

CONTENTS ix

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Classification: All Natural 146

Quiz 148

CHAPTER 10 The Prokaryotes: Domains Archaea and

Bacteria 151

Archaea 152

Aerobic/Microaerophilic, Motile,

Helical/Vibroid, Gram-Negative Bacteria 154

Gram-Negative Aerobic Rods and Cocci 155

Facultatively Anaerobic Gram-Negative Rods 156

Anaerobic Gram-Negative Cocci and Rods 158

Rickettsias and Chlamydias 158

Mycoplamas 159

Gram-Positive Cocci 160

Endospore-Forming Gram-Positive Rods

and Cocci 162

Regular Nonsporing Gram-Positive Rods 163

Irregular Nonsporing Gram-Positive Rods 164

Mycobacteria 164

Nocardia Forms 165

Quiz 165

CHAPTER 11 The Eukaryotes: Fungi, Algae, Protozoa,

and Helminths 167

Fungi 168

Algae 171

Protozoa 174

Helminths 178

Quiz 182

CHAPTER 12 Viruses, Viroids, and Prions 185

Viruses 185

Viroids 192

Prions 193

Quiz 193

CONTENTSx

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CHAPTER 13 Epidemiology and Disease 197

What Is Epidemiology? 197

Classification of Disease 198

Infection Sites 199

Disease Transmission 201

The Development of Disease 203

Epidemiological Studies 204

Control of Communicable Diseases 205

Nosocomial Infections 206

Who Is Susceptible? 206

Prevention and Control of Nosocomial

Infections 207

Quiz 207

CHAPTER 14 Immunity 211

What Is Immunity? 211

Types of Immunity 213

A Closer Look at Antigens 214

A Closer Look at Binding 214

B Cells 216

Lasting Immunity 218

Antibodies Used for Diagnosing Diseases 218

Chemical Messengers 218

T Cells 219

Macrophages and Natural Killer Cells 220

Quiz 221

CHAPTER 15 Vaccines and Diagnosing Diseases 223

What Is a Vaccine? 223

Types of Vaccines 224

Developing a Vaccine 225

Diagnosing Diseases 226

Quiz 228

CONTENTS xi

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CHAPTER 16 Antimicrobial Drugs 231

Chemotherapeutic Agents: The Silver Bullet 231

Antimicrobial Activity: Who to Attack? 233

The Attack Plan 235

Exploring Antimicrobial Drugs 237

Chemotherapy Tests 246

Quiz 247

Final Exam 249

Answers to Quiz and Exam Questions 265

Index 269

CONTENTSxii

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xiii

When you hear the words “germ,” “bacteria,” and “virus” you might cringe, run-

ning for the nearest sink to wash your hands. These words may bring back mem-

ories of when you caught a cold or the flu—never a pleasant experience. Germs,

bacteria, viruses and other microscopic organisms are called microorganisms, or

microbes for short. And as you’ll learn throughout this book, some microbes

cause disease while others help fight it.

Think for a moment. Right now there are thousands of tiny microbes living

on the tip of your finger in a world that is so small that it can only be visited by

using a microscope. In this book we’ll show you how to visit this world and how

to interact with these tiny creatures that call the tip of your finger home.

The microscopic world was first visited in the late 1600s by the Dutch mer-

chant and amateur scientist Antoni van Leeuwenhoek. He was able to see living

microorganisms by using a single-lens microscope. We’ve come a long way

since Van Leeuwenhoek’s first visit. Today scientists are able to see through

some microbes and study the organelles that bring them to life.

It wasn’t until the Golden Age of Microbiology between 1857 and 1914 when

scientists such as Louis Pasteur and Robert Koch made a series of discoveries

that rocked the scientific community. During this period scientists identified

microbes that caused diseases, learned how to cure those diseases, and then pre-

vented them from occurring through the use of immunization.

Scientists were able to achieve these remarkable discoveries by using cultur-

ing techniques to grow colonies of microbes in the laboratory. Once microbes

could be grown at will, scientists focused their experiments on ways to slow that

growth and stop microbes in their tracks—killing the microbe and curing the dis-

ease caused by the microbe.

Culturing microbes is central to the study of microbiology. You’ll be using

many of the same culturing techniques described in this book to colonize

microbes in your college laboratory. We provide step-by-step instructions on

how to do this.

xiii

INTRODUCTION

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You would find it difficult to live without the aid of microbes. For example,

living inside your intestines are colonies of microorganisms. Just this thought is

enough to make your skin crawl. As frightful as this thought might be, however,

these microbes actually assist your body in digesting food. That is, you might

have difficulty digesting some foods if these microbes did not exist.

Microbes in your intestines are beneficial to you as long as they remain

in your intestines. However, you’ll become very ill should they decide to

wander into other parts of your body. Don’t become too concerned—these

microbes tend to stay at home unless your intestines are ruptured as a result

of trauma.

By the end of this book you’ll learn about the different types of microbes,

how to identify them by using a microscope, and how to cultivate colonies

of microbes.

A Look Inside

Microbiology can be challenging to learn unless you follow the step-by-step

approach that is used in Microbiology Demystified. Topics are presented in an

order in which many students like to learn them—starting with basic compo-

nents and then gradually moving on to those that are more complex.

Each chapter follows a time-tested formula that explains

spectrophotome-

ter is inversely proportional to the number of bacteria under normal cultures: the

less light, the more bacteria.

Another indirect way of measuring bacterial growth is to measure the meta-

bolic activity of the colony. In this method it is assumed that metabolic waste

products, CO2 (carbon dioxide) and acid, are in direct proportion to the number

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of bacteria present. The more bacteria we have, the more waste products we will

also have.

For filamentous organisms, such as molds, a way to measure growth is by dry

weight. The fungus is removed from its growth medium, filtered, and placed in

a weighing bottle dried in a dessicator (a dessicator is a device that removes

water). In bacteria the culture is removed from the medium by centrifugation.

Controlling Microbial Growth

It is very important to control microbial growth in surgical and hospital settings,

as well as in industrial and food preparation facilities. There are many terms

used to describe the fight to control microorganisms.

Sterilization is the destruction of all microorganisms and viruses, as well as

endospores. Sterilization is used in preparing cultured media and canned foods.

It is usually performed by steam under pressure, incineration, or a sterilizing gas

such as ethylene oxide.

Antisepsis is the reduction of pathogenic microorganisms and viruses on liv-

ing tissue. Treatment is by chemical antimicrobials, like iodine and alcohol.

Antisepsis is used to disinfect living tissues without harming them.

Commercial sterilization is the treatment to kill endospores in commercially

canned products. An example is the bacteria Clostridium botulinum, which

causes botulism.

Aseptic means to be free of pathogenic contaminants. Examples include proper

hand washing, flame sterilization of equipment, and preparing surgical environ-

ments and instruments.

Any word with the suffix -cide or –cidal indicates the death or destruction of

an organism. For example, a bactercide kills bacteria. Other examples are fungi-

cides, germicides and virucides. Germicides include ethylene oxide, propylene

oxide, and aldehydes. For the same reason, these germicides are also used in pre-

serving specimens in laboratories.

Disinfection is the destruction or killing of microorganisms and viruses on

nonliving tissue by the use of chemical or physical agents. Examples of these

chemical agents are phenols, alcohols, aldehydes, and surfactants.

Degerming is the removal of microorganisms by mechanical means, such as

cleaning the site of an injection. This area of the skin is degermed by using an

alcohol wipe or a piece of cotton swab soaked with alcohol. Hand washing also

removes microorganisms by chemical means.

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Pasteurization, as noted in Chapter 1, uses heat to kill pathogens and reduce

the number of food spoilage microorganisms in foods and beverages. Examples

are pasteurized milk and juice.

Sanitation is the treatment to remove or lower microbial counts on objects

such as eating and drinking utensils to meet public health standards. This is usu-

ally accomplished by washing the utensils in high temperatures or scalding

water and disinfectant baths. Bacterostatic, fungistatic, and virustastic agents—

or any word with the suffix -static or -stasis—indicate the inhibition of a partic-

ular type of microorganism. These are unlike bactericides or fungicides that kill

or destroy the organism. Germistatic agents include refrigeration, freezing, and

some chemicals.

Microbial Death Rates

Microbial death is the term used to describe the permanent loss of a microor-

ganism’s ability to reproduce under normal environmental conditions. A tech-

nique for the evaluation of an antimicrobial agent is to calculate the microbial

death rate. When populations of particular organisms are treated with heat or

antimicrobial chemicals, they usually die at a constant rate.

The effectiveness of antimicrobial treatments is influenced by the number of

microbes that are present. The larger the population, the longer it takes to destroy

it. The different variations of certain microorganisms influence death rate because,

for example, endospores are difficult to kill.

Environmental influences, such as the presence of blood, saliva, or fecal mat-

ter, inhibits the action of chemical antimicrobials. Time of exposure to heat or

radiation is also important. Many chemical antimicrobials need longer exposure

times to be effective in the death of more resistant microorganisms or endospores.

Action of Antimicrobial Agents

There are two categories that chemical and physical antimicrobial agents fall

into: those that affect the cell walls or cytoplasmic membranes of the microor-

ganism and those that affect cellular metabolism and reproduction. As stated in

Chapter 4, the cell wall is located outside the microorganism’s plasma mem-

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brane. The cell’s plasma membrane regulates substances that enter and exit

the cell during its life. Nutrients enter the cell as waste products exit the cell.

Damage to the plasma membrane proteins or phospholipids by physical or

chemical agents allows the contents of the cell to leak out. This causes the death

of the cell.

Proteins act as regulators in cellular metabolisms, function as enzymes (which

are important in all cellular activities), and form structural components in cell

membranes and cytoplasm. The function of a protein depends on its three-dimen-

sional shape. The hydrogen and disulfide bonds between the amino acids that

make up the protein maintain this shape. Extreme heat, certain chemicals and

very high or low pH can easily break some of these hydrogen bonds. This break-

age is referred to as the denaturing of the protein. The protein’s shape is changed,

thus affecting the function of the protein and ultimately bringing death to the cell.

Certain chemicals, radiation, and heat can damage nucleic acids. The nuclear

acids, DNA and RNA, carry the cell’s genetic information. If these are damaged,

the cell can no longer replicate or synthesize enzymes, which are important in

cell metabolism.

Chemical Agents That Control Microbial Growth

The growth of a microorganism can be controlled through the use of a chemical

agent. A chemical agent is a chemical that either inhibits or enhances the growth

of a microorganism. Commonly used chemical agents include phenols, pheno-

lics, glutaraldehyde, and formaldehyde.

PHENOLS AND PHENOLICS

Phenols are compounds derived from pheno (carbolic acid) molecules. Pheno-

lics disrupt the plasma by denaturing proteins; they also disrupt the plasma

membrane of the cell. As mentioned in Chapter 1, Joseph Lister used phenol in

the late 1800s to reduce infection during surgery.

Alcohols are effective against bacterial fungi and viruses. However, they, are

not effective against fungal spores or bacterial endospores. Alcohols that

are commonly used are isopropanol (rubbing alcohol) and ethanol (the alcohol

we drink).

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Alcohols denature proteins and disrupt cytoplasmic membranes. Pure alcohol

is not as effective as 70 percent because the denaturing of proteins requires

water. Alcohols are good to use because they evaporate rapidly. A disadvantage

is that they may not contact the microorganisms long enough to be effective.

Alcohol is commonly used in swabbing the skin prior to an injection.

Halogens are nonmetallic, highly resistive chemical elements. Halogens are

effective against vegetative bacterial cells, fungal cells, fungal spores, proto-

zoan cysts, and many viruses. Halogen-containing antimicrobial agents include

iodine, which inhibits protein function. Iodine is used in surgery and by

campers to disinfect water. An

iodophur is an iodine-containing compound

that is longer-lasting than iodine and does not stain the skin. Other halogen

agents include:

• Chlorine (Cl2). Used to treat drinking water, swimming pools, and in

sewage plants to treat waste water. Chlorine products such as sodium

hypochlorite (household bleach) are effective disinfectants.

• Chlorine dioxide (ClO2). A gas that can disinfect large areas.

• Chloroamines. Chemicals containing chlorine and ammonia. They are

used as skin antiseptics and in water supplies.

• Bromine. Used to disinfect hot tubes because it does not evaporate as

quickly as chlorine in high temperatures.

• Oxidizing agents. Fill microorganisms by oxidizing their enzymes, thus

preventing metabolism. Hydrogen peroxide, for example, disinfects and

sterilizes inanimate objects, such as food processing and medical equip-

ment, and is also used in water purification.

Arsenic, zinc, mercury, silver, nickel, and copper are called heavy metals due

to their high molecular weights. They inhibit microbial growth because they

denature enzymes and alter the three-dimensional shapes of proteins that inhibit

or eliminate the protein’s function. Heavy metals are bacteriostatic and fungi-

static agents.

An example is silver nitrate. At one time, hospitals required newborn babies

to receive a one percent cream of silver nitrate to their eyes to prevent blindness

caused by Neisseria gonorhoeae, which could enter the baby’s eyes while pass-

ing through the birth canal of a mother who was infected. Today, antibiotic oint-

ments that are less irritating are used. Another example is the use of copper in

swimming pools, fish tanks, and in reservoirs to control algae growth. Copper

interferes with chlorophyll, thus affecting metabolism and energy.

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Aldehydes function in microbial growth by denaturing proteins and inactivat-

ing nucleic acids. Two types are glutaraldehyde that is a liquid and formaldehyde

that is a gas.

GLUTARALDEHYDE AND FORMALDEHYDE

Glutaraldehyde is used in a two percent solution to kill bacteria, fungi, and

viruses on medical and dental equipment. Healthcare workers and morticians

dissolve gaseous formaldehyde in water, making a 37 percent solution of for-

malin. Formalin is used in disinfecting dialysis machines, surgical equipment,

and embalming bodies after death.

Gaseous agents, such as ethylene oxide, propylene oxide, and beta-propiolactone,

are used on equipment that cannot be sterilized easily with heat, chemicals, or

radiation. Certain items, like pillows, mattresses, dried or powered food, plastic-

ware, sutures, and heart-lung machines, are placed in a closed chamber, then filled

with these gases. Gaseous agents denature proteins.

SURFACTANTS

Surfactants are chemicals that act on surfaces by decreasing the tension of water

and disrupting cell membranes. Examples are household soaps and detergents.

Quiz

1. What microorganisms can use oxygen when it is present and continue to

grow without it?

(a) Obligate aerobes

(b) Facultative anaerobes

(d) Free radicals

2. What microorganisms require oxygen?

(a) Obligate aerobes

(b) Facultative anaerobes

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(d) Free radicals

3. What microorganisms do not use oxygen and can actually be harmed by it?

(a) Obligate aerobes

(b) Facultative anaerobes

(d) Free radicals

4. What is not a toxic form of oxygen?

(a) Singlet oxygen

(b) Facultative oxygen

(d) Hydroxyl radical

5. What is a sterile culture medium?

(a) A hydroxyl radical medium

(b) A medium containing no living organisms

(d) A moisture-filled medium

6. What must chemically defined media contain?

(a) Growth factors

(b) Complex media

(d) Protein hydrolysis

7. What is agar?

(a) A nutrient

(b) Vitamins

(d) Broth

8. What is an enrichment culture?

(a) Something that provides growth for all microorganisms

(b) Something that inhibits growth for all microorganisms

(d) Something that provides growth for a certain microorganism but not

for others

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9. What is an inoculating loop?

(a) A tool used to streak a microorganism in a pure culture

(b) A tool used to place agar in a pure medium

(d) A tool used to view colonies of microorganisms

10. How can preserved bacteria cultures can be revived?

(a) Oxygenation

(b) Hydration

(d) Oxygenation and liquid nutrient medium

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CHAPTER

119

Microbial Genetics

“Who does she look like, mom or dad?” That’s probably one of the first few

questions everyone asks when hearing about a new arrival in the family. “Does

she have Aunt Jane’s eyes? Uncle Joe’s nose?” “How about Gramps’ sandy

hair?” These are some of the many noticeable characteristics that can be passed

down from family members.

What is really being asked is what genetic traits did the current generation

inherit from previous generations. Think of genetic traits as our computer

program; it provides us with instructions on how to do everything needed to

stay alive. Some instructions are passed along to the next generation while other

instructions are not.

If microorganisms could speak, they might also ask the same questions as

we do when a new offspring arrives, because microorganisms also pass along

genetic traits to new generations of their species. Those traits preprogram new

microorganisms on how to identify and process food, how to excrete waste prod-

ucts, and how to reproduce, as well as nearly everything the microorganism

needs to know to survive.

In this chapter you’ll learn how microorganisms inherit genetic traits from

previous generations of microorganisms.

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Genetics

Genetics is the branch of science that studies heredity and how traits (expressed

characteristics) are passed to new generations of species and between microor-

ganisms. Scientists who study genetics are called geneticists and are interested in

how traits are expressed within a cell and how traits determine the characteristics

of an organism.

Think of a trait as an instruction that tells an organism how do something,

such as how to form a toe. Each instruction is contained in a gene. As you can

imagine, there are thousands of genes (instructions) necessary for an organism

to grow and flourish. This is why if a youngster looks and behaves like her

mother, family members tend to say she has her mother’s genes—that is, she has

more genes (instructions) from her mom than from her dad.

Genes are actually made up of segments or sections of deoxyribonuclear acid

(DNA), or in the case of a virus, ribonucleic acid (RNA) molecules. These seg-

ments are placed in a specific sequence that code for a functional product.

DNA Replication:

Take My Genes, Please!

In 1868, Swiss biologist Friedrich Miescher carried out chemical studies on the

nuclei of white blood cells in pus. His studies led to the discovery of DNA. DNA

was not linked to hereditary information until 1943 when work performed by

Oswald Avery, Colin MacLeod, and Maclyn McCarty at the Rockefeller Institute

revealed that DNA contained genetic information. These studies also revealed

that genetic information is passed from “parent cells” to “daughter cells,” creat-

ing a pathway through which genetic information is passed to the next genera-

tion of an organism.

Scientists were baffled about how the exchange of DNA occurred. The answer

came in 1953 when American

geneticist James Watson and English physicist

Francis Crick discovered the double-helical structure of DNA at the University

of Cambridge in England. Discovery of the double-helical structure was the key

that enabled Watson and Crick to learn how DNA is replicated.

In the late 1950’s, Mathew Meselson and Franklin Stahl first described the

DNA molecule and how DNA replicates in a process called semiconservative

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replication. DNA is replicated by taking one parent double-stranded DNA mol-

ecule, unzipping it and building two identical daughter molecules. Bases along

the two strands of double-helical DNA complement each other. One strand of the

pair acts as a template for the other.

DNA is replication requires complex cellular proteins that direct the sequence

of replication. Replication begins when the parent double-stranded DNA mole-

cule unwinds; then the two strands separate. The DNA polymerase enzyme uses

a strand as a template to make a new strand of DNA. The DNA polymerase

enzyme examines the new DNA and removes bases that do not match and then

continues DNA synthesis.

The point at which the double-stranded DNA molecule unzips is called

the replication fork (Fig. 7-1). The two new strands of DNA each have a base

CHAPTER 7 Microbial Genetics 121

Parental helix

A T

T A

G C

A T

C G

A T

G C

A T

C G

T A

G C

ParentalNewNew

5′ 3′

5′ 5′3′3′

Parental

A T

G C

A T

C G

T A

G C

Replication fork

Replicas

Fig. 7-1. In semiconservative replication, new strands are synthesized

after the replication fork.

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sequence complimentary to the original strand. Each double-stranded DNA

molecule contains one original and one new strand. In bacteria, each daughter

receives a chromosome that is identical to the parent’s chromosome.

THE CHROMOSOME CONNECTION

Chromosomes are structures that contain DNA. DNA consists of two long chains

of repeating nucleotides that twist around each other, forming a double helix. A

nucleotide in a DNA chain consists of a nitrogenous base, a phosphate group,

and deoxyribose (pentose sugar).

The two DNA chains are held together by hydrogen bonds between their nitro-

genous bases. There are two major types of nitrogenous bases. These are purines

and pyrimidines. There are two types of purine bases: adenine (A) and guanine(G).

There are also two types of pyrimidine bases: cytosine (C) and thymine (T). Purine

and pyrimidine bases are found in both strands of the double helix.

Base pairs are arrangements of nitrogenous bases according to their hydrogen

bonding. Adenine pairs with thymine and cytosine pairs with guanine. Adenine is

said to be complementary to thymine and cytosine is said to be complementary

with guanine. This is known as complementary base pairing and is shown in

Table 7-1.

Genetic information is encoded by the sequence of bases along a strand of

DNA. This information determines how a nucleotide sequence is translated into

an amino acid which is the basis of protein synthesis. The translation of genetic

information from genes to specific proteins occurs in cells.

CHAPTER 7 Microbial Genetics122

Messenger Double-Helical Strand

RNA Base DNA Molecule Base

Adenine (A) Thymine (T)

Guanine (G) Cytosine (C)

Cytosine (C) Guanine (G)

Uricil (U) Adenine (A)

Table 7-1. Complementary Messenger RNA

Bases and DNA Bases

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Protein Synthesis

Protein synthesis is the making of a protein and requires ribonucleic acid

(RNA), which is synthesized from nucleotides that contain the bases A, C, G,

and U (uracil). There are three types of RNA. These are:

• Ribosomal RNA (rRNA), which is the enzymatic part of ribosomes.

• Transfer RNA (tRNA), which is needed to transport amino acids to the

ribosomes in order to synthesize protein.

• Messenger RNA (mRNA), which carries the genetic information from

DNA into the cytoplasm to ribosomes where the proteins are made.

An enzyme called RNA polymerase is required to make (synthesize) rRNA,

tRNA, and mRNA.

Protein synthesis begins with the transcription process, in which DNA

sequences are replicated producing mRNA. The mRNA carries genetic informa-

tion from the DNA to ribosomes. Ribosomes are organelles and the site of pro-

tein synthesis.

Nucleotides contained in DNA are duplicated by enzymes before cell division,

enabling genetic information to be carried between cells and from one generation

to the next. This is referred to as gene expression and happens in RNA only.

During transcription, the bases A, C, G, and uracil (U) pair with bases of the

DNA strand that is being transcribed. The G base in the DNA template pairs with

the C base in the mRNA. The C base in the DNA template pairs with the G base

in the mRNA. The T base in the DNA template pairs with an A in the mRNA.

An A base in the DNA template pairs with the U in the mRNA. This happens

because RNA contains a U base instead of a T base.

Transcription begins when the RNA polymerase binds to DNA at the promo-

tor site. The DNA unwinds. One of the DNA strands, called a coding strand,

serves as a template for RNA synthesis. RNA is synthesized by pairing free

nucleotides of the RNA with nucleotide bases on the DNA template strand. The

RNA polymerase moves along the DNA as the new RNA strand grows. This

continues until the RNA polymerase reaches the terminator site on the DNA or

is physically stopped by a section of RNA transcript. The new single-stranded

mRNA and the RNA polymerase are released from the DNA.

Here is what’s happening: Information of the nucleic acid assembles a protein.

The mRNA strand consists of several sections, one being the reading frame. The

reading frame is made up of codons. These are AUG, AAA, and GGC. Each codon

contains information for a specific amino acid. The sequence of codons on the

RNA determines the sequence that amino acids are used to synthesize proteins.

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Once the transcription process is completed, information of the mRNA is

turned into protein in the translation process. The translation process is one

in which genetic information encoded in mRNA is translated into a specific

sequence of amino acids that produce proteins.

Appropriate amino acids are brought to the translation site in the ribosomes

and are assembled into a growing chain. It is here that tRNA recognizes specific

codons. Each tRNA molecule has an anticodon, which is a sequence of three

bases that is complementary to the bases on the codon. These bases are then

paired, and amino acids are brought to the chain.

This process continues until a polypeptide is produced. The polypeptide is

removed from the ribosome for further processing. The polypeptide may be

stored in the Golgi body of a eukaryotic organism. The mRNA molecule degen-

erates and the nucleotides are returned to the nucleus. The tRNA molecule is

returned to the cytoplasm and combines with new molecules of amino acids.

GENOTYPE AND PHENOTYPE: REALIZING

YOUR POTENTIAL

The genetic makeup of an organism is called a genotype and represents that

organism’s potential properties. Some properties may not have developed. Those

that do develop are called an organism’s phenotype. The phenotype represents

expressed properties, such as blue eyes and curly hair.

A genotype is the organism’s DNA (a collection of genes). The phenotype is

a collection of proteins. The majority of the cell’s properties comes from the

structures and functional properties of these proteins.

Controlling Genes: You’re Under My Spell

The process of making proteins (remember, polypeptides become proteins either

after they are combined with other polypeptides or when they become biologi-

cally functional) begins with the copying of the genetic information found in

DNA, into a complimentary strand of RNA. This copying is called

transcription.

Messenger RNA (mRNA) will carry the coded information or instructions for

assembling the polypeptides from DNA to the ribosomes of the cell’s endoplas-

mic reticulum where the polypeptides will be made.

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The actual building of polypeptides is called translation. Translation involves

the deciphering of nucleic acid information and converting that information into

a language that the proteins can understand.

THE OPERON MODEL

In 1961 Francois Jacob and Jacques Monod formulated the operon model that

described how transcription of mRNA is regulated. Transcription of mRNA is

regulated in two ways. These are repression and induction.

Repression inhibits gene expression and decreases the synthesis of enzymes.

Proteins called repressors stop the ability of RNA polymerase to initiate tran-

scription from repressed genes. Induction activates transcription by producing

inducer, which is the chemical that induces transcription.

Jacob and Monod identified genes in E. coli as structural genes, regulatory

genes, and control regions. Collectively these form a functional unit called the

operon. Certain carbohydrates can induce the presence of enzymes needed to

digest those carbohydrates.

For example when lactose is present, E. coli synthesize enzymes needed to

breakdown lactose. Lactose is an inducer molecule. If lactose is absent, a regu-

lator gene produces a repressor protein that binds to a control region called the

operator site, preventing the structural genes from encoding the enzyme for lac-

tose digestion. Lactose binds to the repressor at the operator site when lactose is

present, freeing the operator site. The structural genes are released and produce

their lactose-digesting enzymes.

Mutations: Not a Pretty Copy

A mutation is a permanent change in the DNA base sequence (Table 7-2). Some

mutations have no expressive effect while other mutations have an expressive

effect. When a gene mutates, the enzyme encoded by the gene can become less

active or inactive because the sequence of the enzyme amino acids may have

changed. The change can be harmful or fatal to the cell, or it can be beneficial—

especially if the mutation creates a new metabolic activity.

The most common type of mutation is point mutation, which is also known

as base substitution mutation. Point mutation occurs when an unexpected base

is substituted for a normal base, causing alteration of the genetic code, which is

then replicated.

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If the mutated gene is used for protein synthesis, the mRNA transcribed from

the gene carries the incorrect base for that position. The mRNA may insert an

incorrect amino acid in the protein. If this happens, the mutation is called a

missence mutation.

Mutations that change or destroy the genetic code are called nonsense muta-

tions. If nucleotides are added or deleted from mRNA, the mutation is called a

frame shift mutation.

A mutation occurring in the laboratory is called an induced mutation; muta-

tions occurring outside the laboratory are called spontaneous mutation. A spon-

taneous mutation occurs when a mutation-causing agent is present.

Base substitution and frame shift mutations occur spontaneously. Agents in

the environment or those introduced by industrial processing can directly or

indirectly cause mutations. These agents are called mutagens. Any chemical

or physical agent that reacts with DNA can potentially cause mutations.

CHAPTER 7 Microbial Genetics126

Type of Mutation Description

Point mutation Also known as base substitution, this is the most common

type of mutation and involves a single base pair in the

DNA molecule. In point mutation, a different base is sub-

stituted for the original base, causing the genetic code to

be altered. The substituted base pair is used when DNA is

replicated.

Missence mutation A mutation when a new amino acid is substituted in the

final protein by the messenger RNA during transcription.

Nonsense mutations A mutation when a terminator codon in the messenger

RNA appears in the middle of a genetic message instead

of at the end of the message, which causes premature

termination of transcription.

Frame shift mutation Pairs of nucleotides are either added or removed from a

DNA molecule.

Loss-of-function mutation This mutation causes a gene to malfunction.

Spontaneous mutation Naturally occurring mutation that happens without the

presence of a mutation-causing agent.

Induced mutation Induced in a laboratory.

Table 7-2. Types of Mutations

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Certain mutations make microorganisms resistant to antibiotics or increase

their pathogenicity. There are many naturally occurring mutagens, such as radi-

ation from x-rays, gamma rays, and ultraviolet light. These rays break the cova-

lent bonds between certain bases of DNA-producing fragments.

Ultraviolet light binds together adjacent thymines in a DNA strand, forming

thymine dimers that cannot function in protein synthesis. Unless repaired, these

dimers cause damage or death to cells due to improper transcription or replica-

tion of DNA. Some bacteria can repair damage caused by ultraviolet radiation

by employing light-repairing enzymes that separate the dimer into the original

two thymines. This process is called photoreactivation.

MUTATION RATE

Mutations occur naturally and can be induced by mutation-causing agents in the

environment. However, not all cells experience mutation even if they are exposed

to mutation-causing agents.

Scientists measure the impact that mutation has on an organism by determin-

ing the mutation rate. The mutation rate is the number of mutations per cell divi-

sion. For example, suppose you observe the growth of 100 cells that began from

a parent cell. If 90 of those cells replicate the parent cell and 10 cells are muta-

tions, than the mutation rate is 10 percent.

Measuring the mutation rate is a way to compare the number of mutations

that occur naturally to the number of mutations that occur when a cell is exposed

to a potential mutation-causing agent.

First, scientists measure the mutation rate that occurs naturally when a cell is

not exposed to a potential mutation-causing agent. Next, the mutation rate is cal-

culated when a cell is not exposed to a potential mutation-causing agent. The

results of these two observations are compared. If both mutation rates are rela-

tively the same, then the substance being tested is not a mutation-causing agent.

However, the substance is a mutation-causing agent if its mutation rate is appre-

ciably higher than the natural mutation rate.

Quiz

1. The point at which the double-stranded DNA molecule unwinds is called

(a) polymerase

(b) replication fork

(d) ribosomes

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2. Protein synthesis begins with the

(a) transcription process

(b) translation process

(d) genotyping

3. Expressed properties such as whether you have blue eyes and curly hair

is called

(a) genotype

(b) exons

(d) phenotype

4. Which of the following is not a type of RNA?

(a) rRNA

(b) uRNA

(d) mRNA

5. What is RNA polymerase?

(a) An enzyme used in the synthesis of RNA

(b) An enzyme used in the synthesis of ribosomes

(d) An enzyme used in the synthesis of pre-DNA

6. What is the promotor site?

(a) The site where RNA polymerase binds to DNA

(b) The site where RNA polymerase binds to protein

(d) The site where RNA polymerase binds to AAA

7. The mRNA language consists of three nucleotides called

(a) amino acid

(b) codons

(d) exons

8. What do repressors do?

(a) They activate transcriptions.

(b) They increase synthesis.

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(c)

They increase gene expression.

(d) They stop the initiation of transcription.

9. An operon consists of structural genes, regulatory genes, and control

genes.

(a) True

(b) False

10. Spontaneous mutation occurs as a result of laboratory intervention in

DNA replication.

(a) True

(b) False

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CHAPTER

131

Recombinant

DNA Technology

Our genes are a strong determining factor of who we are and what we are going

to be because genes program our bodies to express specific characteristics. Some

of those characteristics enable us to carry out basic life functions, such as con-

verting food to energy, while others make us stand out in a crowd, such as being

a seven-foot professional basketball player. The same concept holds true with

microorganisms. A microorganism’s genes determine characteristics expressed

by that microorganism.

Genetic information is encoded in our DNA by the linkage of nucleic acids in

a specific sequence, which you learned about in the previous chapter. Think of

what would happen if you could change the sequence. You could reprogram

genes to express desirable characteristics and to repress undesirable characteris-

tics, such as those that cause diseases.

Reordering genetic information is called genetic engineering. In this chapter,

you’ll learn about genetic engineering and how to use recombinant DNA tech-

nology to alter the genetic program of an organism.

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Genetic Engineering: Designer Genes

The modification of an organism’s genetic information by changing its nucleic

acid genome is called genetic engineering and is accomplished by methods

known as recombinant DNA technology. Recombinant DNA technology opens

up totally new areas in research and applied biology and is an important part of

biotechnology, a field that is increasingly growing. Biotechnology is the term

used for processes in which organisms are manipulated at the genetic level to

form products for medicine, agriculture, and industry.

Recombinant DNA is DNA with a new sequence formed by joining fragments

from different sources. One of the first breakthroughs leading to recombinant

DNA, or rDNA, technology was the discovery of microbial enzymes that make

cuts into the double-stranded DNA. These were discovered by Werner Arber,

Hamilton Smith, and Dan Nathans in the late 1960s. These enzymes recognize

and cleave specific sequences of four to eight base pairs and are known as restric-

tion enzymes. These enzymes recognize specific sequences in DNA and then cut

the DNA to produce fragments called restriction fragments. The enzymes cut the

bonds of the DNA backbone at a point along the exterior of the DNA strands.

There are three types of restriction enzymes. Types I and III cleave DNA away

from recognition sites. Type II restriction endonucleases cleave DNA at specific

recognition sites. The type II enzymes can be used to prepare DNA fragments con-

taining specific genes or portions of genes. A gene can be defined as a segment of

DNA (a segment is a sequence of nucleotides) that codes for a functional product.

ECORI cleaves the DNA between guanine (G) and adenine (A) in the

base sequence GAATTC. In the double-stranded condition, the base sequence

GAATTC will base pair with a sequence, which runs in the opposite direction.

ECORI cleaves both DNA strands between the G and the A. When the two DNA

fragments separate they contain single-stranded complementary ends called

sticky ends.

Each restriction enzyme name begins with the first three letters of the bac-

terium that produces it. This is illustrated in Table 8-1.

In 1972, David Jackson, Robert Symons, and Paul Berg generated recombi-

nant DNA molecules. They allowed the sticky ends of the fragments to base pair

with each other and covalently joined the fragments with the enzyme DNA lig-

ase. The enzyme DNA ligase links the two sticky ends of the DNA molecules at

the point of union. In 1973, Stanley Cohen and Herbert Boyer constructed the

first recombinant plasmid capable of being replicated within a bacterial host. A

plasmid is a circular DNA molecule that a bacterium can replicate without a

chromosome.

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In 1975, Edwin M. Southern developed procedures for detecting specific DNA

fragments so that a particular gene could be isolated from a complex DNA mix-

ture. This technique is called the Southern blotting technique. DNA fragments are

separated by size with agarose gel electrophoresis. Gel electrophoresis takes

advantage of the chemical and physical properties of DNA to separate the frag-

ments. The phosphate groups in the backbone of DNA are negatively charged.

This makes the DNA molecules attracted to anything that is positively charged.

In gel electrophoresis the DNA molecules are placed in an electric field so that

they migrate towards the positive charge.

The DNA is placed in agarose, a semi solid gelatin, and placed in a tank of

buffer. When electrical current is applied, the DNA molecules migrate through

the agarose gel, separate, and travel toward the positive poles of the electric

fields. The entire DNA fragments migrates through the gel. The larger DNA frag-

ments have a harder time moving than the smaller ones, so the small fragments

travel farther through the gel.

ARTIFICIAL DNA: PUTTING TOGETHER THE PIECES

Oligonucleotides, from the Greek word oligo meaning “few,” are short pieces

of DNA or RNA that are 2 to 30 nucleotides long. The ability to synthesize DNA

oligonucleotides of a known sequence is incredibly important and useful. A

DNA probe is used to analyze fragments of DNA. A DNA probe is a single-

stranded fragment of DNA that recognizes and binds to a complementary sec-

tion of DNA in a mixture of DNA molecules.

DNA probes can be synthesized and DNA fragments can be prepared for use

in molecular techniques such as polymerase chain reaction (PCR). Polymerase

chain reaction is a technique that was developed by Kary Mullis in 1985. It pro-

CHAPTER 8 Recombinant DNA Technology 133

Microbial Recognition Cleavage

Enzyme Source Sequence Sites (↓,↑) End Product

EcoRI Escherichia coli GAATTC G↓AATTC G AATTC

CTTAAG CTTAA↑G CTTAA G

Table 8-1. Recombinant DNA Is DNA with a New Sequence Formed by Joining Recognition

Sequence Fragments from Different Sources

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duces large quantities of a DNA fragment without needing a living cell. Starting

with one small piece of DNA, PCR can make billions of copies in a few hours.

These large quantities of DNA can be easily analyzed.

PCR and DNA probes have been of great value to the areas of molecular biol-

ogy, medicine, and biotechnology. Using these tools, scientists can detect the

DNA associated with HIV (the virus that causes AIDS), Lyme disease, chlamy-

dia, tuberculosis, hepatitis, HPV (human papilloma virus), cystic fibrosis, mus-

cular distrophy, and Huntington’s disease.

Gene Therapy: Makes You Feel Better

Gene therapy is a recombinant DNA process, in which cells are taken from the

patient, altered by adding genes, and returned to the patient. A type of genetic

surgery called somatic gene therapy may be possible. Cells of a person with a

genetic disease could be removed, cultured, and transformed with cloned DNA

containing a normal copy of the defective gene. They could be reintroduced into

the individual. If these cells become established, the expression of the normal

genes may be able to cure the patient.

In the early 1990s, gene therapy of this type was used to correct a deficiency

of the enzyme adenosine deaminase (ADA). An immune deficiency disease

patient lacking the enzyme adenosine deaminase, an enzyme that destroys toxic

metabolic byproducts, had been treated. Some of the patient’s lymphocytes were

removed. Lymphocytes are a type of white blood cell that fights infection.

The

lymphocytes were given the adenosine deaminase gene with the use of a modi-

fied retrovirus—which served as a vector—and placed back into the patient’s

body. Once established in the body, the cells with altered genes began to make

the enzyme adenosine deaminase (ADA) and alleviated the deficiency.

DNA Fingerprinting: Gotcha

DNA fingerprinting is an area of molecular biology that involves analyzing

genetic material. It involves the use of restriction enzymes, which cut DNA mol-

ecules into pieces. When DNA samples obtained from different individuals are

cut with the same restriction enzyme, the number and size of restriction frag-

ments produced may be different. This difference provides the basis for DNA

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fingerprinting. The use of DNA fingerprinting depends upon the presence of

repeating base sequences. These sequences are called restriction fragment length

polymorphosis, or the RFLP pattern, which is unique for every individual.

This is a sort of molecular signature or fingerprint. In order to perform DNA

fingerprinting, DNA must be taken from an individual. Samples can be taken

from hair, blood, skin, cheek cells, or other tissue. The DNA is taken from the

cells and is broken down with enzymes. The fragments are separated with elec-

trophoresis. The DNA fragments are then analyzed for RFLPs using DNA

probes. An evaluation enables crime lab scientists (forensic pathologists) to

compare a person’s DNA with the DNA taken from a scene of a crime. This tech-

nique has a 99 percent degree of certainty that a suspect was at a crime scene.

INDUSTRIAL APPLICATION: SHOW ME THE MONEY

Industrial applications of recombinant DNA technology include manufacturing

protein products by the use of bacteria, fungi, and cultured mammal cells. The

pharmaceutical industry is producing several medically important polypeptides

using biotechnology. An example is bacteria that metabolize petroleum and

other toxic materials. These bacteria are constructed by assembling catabolic

genes on a single plasmid and then transforming the appropriate organism.

Another example is vaccines. The hepatitis B vaccine is made up of viral protein

manufactured by yeast cells, which have been recombined with viral particles.

AGRICULTURAL APPLICATIONS: CROPS AND COWS

Recombinant DNA and biotechnology have been used to increase plant growth

by increasing the efficiency of the plant’s ability to fix nitrogen. Scientists take

genes for nitrogen fixation from bacteria and place the genes into plant cells.

Because of this, plants can obtain nitrogen directly from the atmosphere. The

plants can produce their own proteins without the need for bacteria. Another way

to insert genes into plants is with a recombinant tumor-inducing plasmid Ti plas-

mid. This is obtained from the bacterium Agrobacterium tumefaciens. This bac-

teria invades plant cells and its plasmids insert chromosomes that carry the genes

for tumor induction. An example of recombinant DNA with livestock is the

recombinant bovine growth hormone that has been used to increase milk pro-

duction in cows by 10 percent.

U.S. farmers grow substantial amounts of genetically modified crops. About

one-third of the corn and one-half of the soybean and cotton crops are genetically

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modified. Cotton and corn have become resistant to herbicides and insects. Soy-

beans have herbicide resistance and lower saturated fat content. Having herbicidal-

resistant plants is important because many crop plants suffer stress when treated

with herbicides. Resistant crops are not stressed by the chemicals that are used

to control weeds.

Recombinant DNA Technology and Society:

Too Much of a Good Thing

Genetically altering an organism raises scientific and philosophical questions.

Recombinant DNA technology has had a positive impact on society, although

there may be associated dangers with rDNA.

There have been concerns raised by the scientific community that genetically

engineered microorganisms carrying dangerous genes might be released into the

environment and cause widespread infection. Due to these worries, the federal

government has established guidelines to regulate and limit the locations and

types of experiments that are potentially dangerous.

Biomedical rDNA research has been regulated by the Recombinant DNA

Advisory Committee (RAC) of the Natural Institutes of Health. The Food and

Drug Administration (FDA) has principal responsibility in overseeing gene ther-

apy research. The Environmental Protection Agency (EPA) and state govern-

ments have jurisdiction over field experiments in agriculture.

One of the biggest efforts in biotechnology has been the human genome proj-

ect, which began in 1990 and formally ended in 2001. The goal of this project

has been to determine the sequences of all human chromosomes. Advances like

this in biotechnology will make genetic screening incredibly effective.

Physicians will one day be capable of detecting genetic flaws in DNA long

before the disease becomes manifested in a patient.

Another area of controversy is agriculture. Some scientists state that the re-

lease of recombinant organisms without risk assessment may disrupt the ecosys-

tem. Viral nucleic acids, inserted into plants to make them resistant to viruses,

might combine with the genome of an invading virus to make the virus even

stronger. Genetically modified food might even trigger an allergic response in

people or animals that consume them. As of this writing, obvious health or eco-

logical events have not been observed. However, due to the consensus of the

public, many food producers have stopped using genetically modified crops.

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Quiz

1. The nucleotide genome consists of the sequence of nucleic acid that

encodes genetic information on DNA.

(a) True

(b) False

2. What enables scientists to take nucleotide fragments from other DNA

and reassemble fragments into a new nucleotide sequence?

(a) Enzyme DNA technology

(b) Enzyme technology

(d) Recombinant enzyme technology

3. What is used to cut DNA double-helix strand DNA along the exterior of

the strand?

(a) Overhang

(b) Restriction enzymes

(d) Recognition sequence

4. What is the particular nucleotide sequence of a double-helical segment

called?

(a) Overhang

(b) Restriction enzymes

(d) Recognition sequence

5. What is the end of the cut of a double-helical segment called?

(a) Overhang

(b) Restriction enzymes

(d) Recognition sequence

6. What results when two incisions are made in a double-helical segment?

(a) Overhang

(b) Restriction enzymes

(d) Recognition sequence

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7. The four nucleotides are adenine (A), cytosine (C), guanine (G) and

thymine (T).

(a) True

(b) False

8. What is another name for a restriction enzyme?

(a) Vector

(b) Plasmid

(d) Agarose gel

9. The Southern blotting technique is used for detecting specific restriction

fragments.

(a) True

(b) False

10. Scientists synthesize fragments of DNA and RNA using a process known

as polymerase chain reaction (PCR).

(a) True

(b) False

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CHAPTER

139

Classification

of Microorganisms

It is uncanny how a stranger can be at a large family gathering and be able to pick

out who belongs to Mom’s family and who belongs to Dad’s family. Although

no two people at the gathering look the same, there are enough similarities among

some for the unbiased observer to deduce a relationship.

Scientists group together microorganisms much the same way as a stranger

can group family members together. That is, scientists

carefully observe micro-

organisms and classify them into groups based on similar characteristics.

In this chapter, you’ll learn how to use scientific techniques to organize microor-

ganisms into standard classifications based on a microorganism’s characteristics.

Taxonomy: Nothing to Do with the IRS

Organisms have traits that are similar to and different from other organisms.

Scientists organize organisms into groups by developing a taxonomy. Taxonomy

is the science of organisms based on a presumed natural relationship.

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Scientists observe each organism, noting its characteristics. Organisms that

have similar characteristics are presumed to have a natural relationship and

therefore are placed in the same group. Classification tries to show this natural

relationship.

Taxonomy has three components:

• Classification. The arrangement of organisms into groups based on similar

characteristics, evolutionary similarity or common ancestry. These groups

are also called taxa.

• Nomenclature. The name given to each organism. Each name must be

unique and should depict the dominant characteristic of the organism.

• Identification. The process of observing and classifying organisms into a

standard group that is recognized throughout the biological community.

Taxonomy is a subset of systemics. Systemics is the study of organisms in order

to place organisms having similar characteristics into the same group. Using

techniques from other sciences such as biochemistry, ecology, epidemiology,

molecular biology, morphology, and physiology, biologists are able to identify

characteristics of a organism.

BENEFITS OF TAXONOMY

Taxonomy organizes large amounts of information about organisms whose mem-

bers of a particular group share many characteristics. Taxonomy lets scientists

make predictions and design a hypothesis for future research on the knowledge

of similar organisms. A hypothesis is a possible explanation for an observation

that needs experimentation and testing.

If a relative of an organism has the same properties, the organism may also have

the same characteristics. Taxonomy puts microorganisms into groups with precise

names, enabling microbiologists to communicate with each other in an efficient man-

ner. Taxonomy is indispensable for the accurate identification of microorganisms.

For example, once a microbiologist or epidemiologist identifies a pathogen that

infects a patient, physicians know the proper treatment that will cure the patient.

Nomenclature of Taxonomy: Name Calling

In the mid-1700s, Swedish botanist Carl Linnaeus was one of the first scientists

to develop a taxonomy for living organisms. It is for this reason that he is known

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as the father of taxonomy. Linnaeus’ taxonomy grouped living things into two

kingdoms: plants and animals.

By the 1900s, scientists had discovered microorganisms that had characteris-

tics that were dramatically different than those of plants and animals. Therefore,

Linnaeus’ taxonomy needed to be enhanced to encompass microorganisms.

In 1969 Robert H. Whitteker, working at Cornell University, proposed a new

taxonomy that consisted of five kingdoms (see Fig. 9-1). These were monera,

protista, plantae (plants), fungi, and animalia (animals). Monera are organisms

that lack a nucleus and membrane-bounded organelles, such as bacteria. Protista

are organisms that have either a single cell or no distinct tissues and organs, such

as protozoa. This group includes unicellular eukaryotes and algae. Fungi are

organisms that use absorption to acquire food. These include multicellular fungi

and single-cell yeast. Animalia and plantae include only multicellular organisms.

Scientists widely accepted Whitteker’s taxonomy until 1977 when Carl Woese,

in collaboration with Ralph S. Wolfe at the University of Illinois, proposed a

CHAPTER 9 Classification of Microorganisms 141

Fig. 9-1. Whitteker’s five-kingdom taxonomy.

Animalia

Vertebrates Anthropods

Plantae

Green Algae

Fungi

Molds Yeast

Monera

Archaea MycoplasmasGram Positive Bacteria Gram Negative Bacteria

Protista

Red Algae Water MoldsAmoebas

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new six-kingdom taxonomy. This came about with the discovery of archaea,

which are prokaryotes that lives in oxygen-deprived environments.

Before Woese’s six-kingdom taxonomy, scientists grouped organisms into

eukaryotes animals, plants, fungi, and one-cell microorganisms (paramecia)—

and prokaryotes (microscopic organisms that are not eukaryotes).

Woese’s six-kingdom taxonomy consists of:

• Eubacteria (has rigid cell wall)

• Archaebacteria (anaerobes that live in swamps, marshes, and in the intes-

tines of mammals)

• Protista (unicellular eukaryotes and algae)

• Fungi (multicellular forms and single-cell yeasts)

• Plantae

• Animalia

Woese determined that archaebacteria and eubacteria are two groups by study-

ing the rRNA sequences in prokaryotic cells.

Woese used three major criteria to define his six kingdoms. These are:

• Cell type. Eukaryotic cells (cells having a distinct nucleus) and prokaryotic

cell (cells not having a distinct nucleus)

• Level of organization. Organisms that live in a colony or alone and one-cell

organisms and multicell organisms.

• Nutrition. Ingestion (animal), absorption (fungi), or photosynthesis (plants).

In the 1990s Woese studied rRNA sequences in prokaryotic cells (archae-

bacteria and eubacteria) proving that these organisms should be divided into two

distinct groups. Today organisms are grouped into three categories called domains

that are represented as bacteria, archaea, and eukaryotes.

The domains are placed above the phylum and kingdom levels. The term

archaebacteria (meaning from the Greek word archaio “ancient”) refers to the

ancient origin of this group of bacteria that appears to have diverged from

eubacteria. The archaea and bacteria came from the development of eukaryotic

organisms.

The evolutionary relationship among the three domains is:

• Domain Bacteria (eubacteria)

• Domain Archaea (archaebacteria)

• Domain Eulcarya (eukaryotes)

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Different classifications of organisms are:

• Bacteria

• Eubacteria

• Archaea

• Archaebacteria

• Eukarya

• Protista

• Fungi

• Plantae

• Animalia

The three domains are archaea, bacteria, and eukarya (see Fig. 9-2).

• Archaea lack muramic acid in the cell walls.

CHAPTER 9 Classification of Microorganisms 143

Fig. 9-2. Three-domain taxonomy.

Eubacteria

Gram-positive bacteria Mycoplasmas Gram-negative bacteria

Eucarya

Animals Plants Fungi Protists

Archaea

Halophiles Methanogens Thermo-acidophiles

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• Bacteria have a cell wall composed of peptidoglycan and muramic acid.

Bacteria also have membrane lipids with ester-linked, straight-chained

fatty acids that resemble eukaryotic membrane lipids. Most prokaryotes

are bacteria. Bacteria also have plasmids, which are small, double-stranded

DNA molecules that are extrachromosomal.

• Eukarya are of the domain eukarya and have a defined nucleus and mem-

brane bound organelles.

TAXONOMIC RANK AND FILE

A taxonomy has an overlapping hierarchy that forms levels of rank or category

similar to an organization chart. Each rank contains microorganisms that have sim-

ilar characteristics. A rank can also have other ranks that contain microorganisms.

Microorganisms that belong to a lower rank have characteristics that are asso-

ciated with a higher rank to which the lower rank belongs. However, character-

istics of microorganisms of a lower rank are not found in microorganisms that

belong to the same higher rank as the lower-rank microorganism.

Microbiologists use a microbial taxonomy (Fig. 9-3), which is different from

what biologists, who work with larger organisms, use. Microbial taxonomy is

commonly called prokaryotic taxonomy. The widely accepted prokaryotic tax-

onomy is Bergey’s Manual of Systematic Bacteriology, first published in 1923 by

the American Society for Microbiology. David Bergey was chairperson of the

editorial board.

In the taxonomy of prokaryotes, the most commonly used rank (in order from

most general to most specific) is:

Domain

Kingdom

Phyla

Class

Order

Family

Genus

Species

The basic taxonomic group in microbial taxonomy is the species. Taxonomists

working with higher organisms define their species differently than microbiolo-

gists. Prokaryotic species are characterized by differences in their phenotype and

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145

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β-

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c09_betsy.qxd 5/9/05 5:44 PM Page 145

genotype. Phenotype is the collection of visible characteristics and the behavior

of a microorganism. Genotype is the genetic make up of a microorganism.

The prokaryotic species are collections of strains that share many properties

and differ dramatically from other groups or strains. A strain is a group of

microorganisms that share characteristics that are different from microorganisms

in other strains. Each microorganism within a strain is considered to have

descended from the same microorganism.

For example, Biovars is a species that contains strains characterized by differ-

ences in its biochemistry and physiology. Morphovars is also a species whose

strains differ morphologically and structurally. Serovars is another species that has

strains that are characterized by distinct antigenic properties (substances that stim-

ulate the production of antibodies).

Microbiologists use the genus of the taxonomy to name microorganisms,

which you learned in Chapter 1. Microorganisms are given a two-part name. The

first part is the Latin name for the genus. The second part is the epithet. Together

these parts uniquely identify the microorganism. The first part of the name is

always capitalized and the second part of the name is always lowercase. Both

parts are italicized.

For example, Escherichia coli is a bacterium that is a member of the Escherichia

genus and has the epithet coli. Sometimes the name is abbreviated such as

E. coli. However, the abbreviation maintains the same style as the full name

(uppercase, lowercase, italic).

Classification: All Natural

A taxonomy is based on scientists’ ability to characterize organisms into a clas-

sification system. The most widely used classification system is called the natu-

ral classification. The natural classification requires that an organism be grouped

with organisms that have the same characteristics.

In the mid-eighteenth century, Linnaeus developed the first natural classifi-

cation using anatomical characteristics of organisms. Other natural classifica-

tions use classical characteristics to group organisms. These characteristics are:

• Morphological. Morphological characteristics classify organisms by their

structure, which normally remain the same in a changing environment and

are good indications of phylogentic relatedness.

• Ecological. Ecological characteristics classify organisms by the environ-

ment in which they live. For example, some microorganisms live in vari-

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ous parts of the human intestines and others live in marine environments.

Ecological characteristics include the ability to cause disease, temperature,

pH, and oxygen requirements of an organisms, as well as an organism’s

life cycle.

• Genetic. Genetic characteristics classify organisms by the way in which

they reproduce and exchange chromosomes. For example, eukaryotic organ-

isms reproduce sexually by conjugation where two cells come together

and exchange genetic material. Prokaryotic organisms do not reproduce

sexually and instead use transformation to reproduce. Transformation

occurs between strains of prokaryotes if their genomes are dissimilar but

rarely between genera.

In the early 1990s, T. Cavalier-Smith developed the two-empire and eight-

kingdom taxonomy based on phentic and phylogenetic characteristics. Phentic

measures the physical characteristics of an organism using a process called

numerical taxonomy. Numerical taxonomy is a phentic classification based on

physical measurements of an organism. Phylogenetic measures the evolutionary

relationship among organisms.

The two empires are bacteria and eukaryota. The bacteria domain contains

two kingdoms. These are eubacteria and archaeobacteria. The eukaryota empire

contains six kingdoms as shown in Table 9-1.

CHAPTER 9 Classification of Microorganisms 147

Empire Kingdom

Bacteria Eubacteria—Large group of bacteria that have

rigid cell walls.

Archaeobacteria—nonrigid cell walls.

Eukaryota Archezoa—Primitive one-cell eukaryotes.

Chromista—Photosynthetic organisms that

have chloroplasts within the lumen of the

rough endoplasmic reticulum.

Plantae—Photosynthetic organisms that have

chloroplasts in the cytoplasmic matrix.

Fungi—Absorb nutrients.

Animalia—Ingest nutrients.

Protozoa—Single-cell organism.

Table 9-1. Cavalier-Smith Two-Empire and Eight-Kingdom Taxonomy

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Quiz

1. Taxonomy is the classification of organisms based on a presumed natu-

ral relationship.

(a) True

(b) False

2. The arrangement of organisms into groups based on similar characteris-

tics is called

(a) nomenclature

(b) identification

(d) systemics

3. The name given to each group of organism is called

(a) nomenclature

(b) identification

(d) systemics

4. The process of observing and classifying organisms into a standard group

is called

(a) nomenclature

(b) identification

(d) systemics

5. The study of organisms in order to place organisms into groups is called

(a) nomenclature

(b) identification

(d) systemics

6. An animal is an organism that ingests food.

(a) True

(b) False

7. What acquires nutrients through absorption?

(a) Animals

(b) Plants

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(d) Humans

8. What acquires nutrients through photosynthesis?

(a) Animals

(b) Plants

(d) Humans

9. Bacteria have a cell wall composed of peptidoglycan and muramic acid.

(a) True

(b) False

10. A genus consists of one or more lower ranks called species.

(a) True

(b) False

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CHAPTER

151

The Prokaryotes:

Domains Archaea

and Bacteria

Mention the term bacteria and you probably think back to a time when you had

a bacterial infection. Some bacteria do cause disease, but other bacteria are ben-

eficial and live within our bodies, aiding in the digestion of food.

There are many different kinds of bacteria, all of which are prokaryotes.

Bacteria are divided into four divisions called phyla based on characteristics

of their cell wall. Each division is subdivided into sections according to other

characteristics, such as oxygen requirements, motility, shape, and Gram-stain

reaction. Each section is named based on these characteristics. Sections are fur-

ther subdivided into genera.

In this chapter, you’ll learn about major types of bacteria and their charac-

teristics.

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Archaea

Archaea can exist in very hot and very cold environments, making them resilient

microorganisms that can survive attacks that destroy other bacteria. For example,

archaea can survive and grow in an oxygen-free environment (anaerobic) and in

a high-salt (hypersaline) environment.

There are three ways microbiologists identify archaea. Archaea:

• Have a unique sequence of rRNA.

• Have cell walls that lack peptidoglycan. The cell wall of most bacteria con-

tains peptidoglycan.

• Have a membrane lipid that has a branched chain of hydrocarbons con-

nected to glycerol ester links. The membrane lipid of most bacteria has

glycerol connected to fatty acids by ester bonds.

Unfortunately, two of the more common techniques used to identify bacteria

are not very useful in identifying archaea. You’ll recall from Chapter 4 that

microbiologists identify bacteria by using the Gram stain. A bacterium is

either gram-positive or gram-negative. However, archaea could be gram-positive

or gram-negative, which makes the Gram stain test useless when trying to iden-

tify archaea.

The shape of a bacterium is another common way microbiologists identify bac-

teria. Many bacteria have a distinctive appearance. However, archaea are pleo-

morphic, which means they can have various shapes. Sometimes archaea are spiracle,

spiral, lobed, plate-shaped, or irregularly shaped.

Archaea also have various types of metabolism. Some archaea are organ-

otrophs while others are autotrophs. Archaea also break down (catabolize) glu-

cose for energy in various ways. It is these variations that enable archaea to

survive in environments that are fatal to other bacteria.

THE ARCHAEA CLAN

Archaea are not bacteria and can be organized into subgroups. Microbiologists

use one of two subgroup classifications for archaea. One classification method

divides archaea into five subgroups. These are:

• Methanogenic archaea. A single-celled archaea that produces methane

and carbon dioxide (CO2) through the fermentation of simple organic car-

bon compounds or the oxidation of H2 without oxygen to produce CO2.

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• Sulfate reducers. Archaea that function in the presence of air.

• Extreme halophiles. Archaea that live in an extremely salty environment.

• Cell wall–less archaea. Archaea that do not have a cell wall.

• Extremely thermophilic S-metabolizers. Archaea that need sulfur for growth.

The other method used to organize archaea into subgroups is used in Bergey’s

Manual of Systematic Bacteriology that you learned about in Chapter 9; it con-

sists of two branches (phyla). These are:

• Phylum crenarchaeota. Archaea that are within the phylum crenarchaeota

branch are anaerobes (they live in the absence of oxygen) and grow in a sul-

fur-enriched soil or water environment that is at a temperature between 88

and 100 degrees Fahrenheit and has a pH between 0 and 5.5. Extremely

thermophilic S-metabolizers are within the phylum crenarchaeota subgroup.

• Phylum euryarchaeota. The phylum euryarchaeota branch consists of the

following five major groups:

• Methogenic archaea. Methogenic archaea, the largest group of phylum

euryarchaeota, are anaerobic archaea that synthesize organic compounds

in a process called methanogenesis, which produces methane. They also

use inorganic sources (autotrophic) such as H2 and CO2 for growth.

Methogenic archaea thrive in swamps, hot springs, and fresh water as

well as in marshes. They digest sludge and transform undigested food, in

animal intestines and in the rumen of a ruminant, into methane. A rumi-

nant is a herbivoir that has a stomachs which is divided into four com-

partments. The rumen is the expanded upper compartment of the

stomach that contains regurgitated and partially digested food called a

cud. Methogenic archaea transform regurgitated and partially digested

food into methane (CH4), which is a clean-burning fuel. For example, a

cow can belch up to 400 liters of methane a day. Sewage treatment plants

also use methogenic archaea to transform organic waste into methane.

Although methane is a source of energy, it is also a cause for the green-

house effect. Methogenic archaea are further organized into five orders.

These are: methanobacterioles, methanococcales, methanomicrobiales,

methanosareinales, and methanopyrales.

• Extreme halophiles. Extreme halophiles, also known as halobacteria,

absorb nutrients from dead organic matter absorb nutrients in the presents

of oxygen (aerobic chemoheterotrophs). They require proteins, amino

acids, and other nutrients for growth in a high concentration of sodium

chloride. Extreme halophiles can be motile or nonmotile and are found

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in salt lakes and in salted fish and turn lakes and fish red when there is

an abundance of Extreme halophiles.

• Halobacterium salinarium. Halobacterium salinarium is an archaea that

acquires energy through photosynthesis. However, it is able to do so with-

out the need of chlorophyll or bacteriochlorophyll. Halobacterium sali-

narium synthesizes the bacteriorhodopsin protein,which shows as a deep

purple color under high-intensity lighting in a low-oxygen environment.

• Thermophilic archaeon. Thermophilic archaeons are known as thermo-

plasma and grow in hot (55 to 59 degrees Celsius), acidic (pH of

1 to 2) refuse piles of coalmines that contain iron pyrite. These refuse

piles become hot and acidic as chemolithotropic bacteria oxidize iron

pyrite into sulfuric acid. Thermophilic archaeons lack a cell wall.

• Sulfate-reducing archaea. Sulfate-reducing archaea are known as

archaeoglobi and extract electrons from various donors to reduce sulfur

to sulfide in an environment that is approximately 83 degrees Celsius

such as near marine hydrothermal vents (underwater hot springs).

Sulfate-reducing archaea are gram-negative and are shaped as irregular

spheres (coccoid cells).

Aerobic/Microaerophilic, Motile, Helical/Vibroid,

Gram-Negative Bacteria

Another kind of prokaryote is the aerobic/microaerophilic, motile, helical/vibroid,

gram-negative bacterium. This is a mouthful to say, but the name describes char-

acteristics of this group of prokaryote bacteria.

Aerobic/microaerophilic means bacteria within this group require small amounts

of oxygen to grow. Motile implies that the bacterium is self-propelled, using fla-

gella at one or both poles to move in a corkscrew motion. Helical/vibroid indicates

that the bacterium takes the shape of a spiral (helical) or as a curved rod (vibroid).

Gram-negative means that when the bacterium is identified using the Gram stain,

the bacterium loses the violet stain when rinsed and appears red or pink.

Aerobic/microaerophilic, motile, helical/vibroid, gram-negative bacteria thrive

in soil and are found on roots of plants such as the Azospirillum, which improves

a plant’s nutrient uptake. Bacteria within this group are also found in both fresh

and stagnant water.

Some aerobic/microaerophilic, motile, helical/vibroid, gram-negative bacte-

ria cause diseases (pathogenic) such as Campylobacter fetus and Campylobacter

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jejuni. Campylobacter fetus causes spontaneous abortion in domestic animals.

Campylobacter jejuni causes inflammation of the digestive tract (enteritis) result-

ing in food-borne intestinal diseases. Another common aerobic/microaerophilic,

motile, helical/vibroid, gram-negative bacterium that is pathogenic is Helicobacter

pylori. Helicobacter pylori cause gastric ulcers in humans.

Gram-Negative Aerobic Rods and Cocci

Bacteria that are

members of the gram-negative aerobic rods and cocci group

include many bacteria that cause disease in humans and bacteria that are impor-

tant to industry and the environment. There are 11 bacteria in this group:

• Pseudomonads. Pseudomonads are rod-shaped bacteria with polar flagella,

which give the bacteria mobility. They need oxygen to grow and obtain

energy by decomposing organic material. Pseudomonads are found in soil,

fresh water and marine environments.

• Pseudomonas aeruginosa. Pseudomonas aeruginosa is a pathogenic bac-

terium that infects the urinary tract and wounds in humans. It also causes

infections in burn injuries.

• Legionella pneumophilia. Legionella pneumophilia is a bacterium identi-

fied in 1976 when it infected and killed members of the American Legion

at their convention in Philadelphia. Infection caused by the Legionella

pneumophilia bacterium is commonly referred to as Legionnaire’s disease.

• Legionella micdadei. Legionella micdadei is the bacterium that infects lungs

and causes a strain of pneumonia commonly called Pittsburgh pneumonia.

• Moraxella lacunata. Moraxella lacunata is an egg-shaped (coccobacilli)

bacterium that can infect the membrane that lines eyelids called the con-

juntiva, causing a condition known as conjunctivitis (pink eye).

• Neisseria. Neisseria is a double-spherical (diplo-coccus) bacterium that

can live with or without oxygen (anaerobic) and is usually found on

mucous membranes of humans. One type of Neisseria called Neisseria

gonorrhoeae causes the sexually transmitted disease gonorrhea. Another

type is Neisseria meningitidis (N. meningitis), the bacterium that infects

the mucous membranes of the nose and throat (nasopharyngeal), causing

a sore throat. Neisseria meningitidis can cause meningitis if the bacterium

enters blood and cerebral spinal fluid where it can infect the protective

covering (meninges) of the brain and spinal cord. Meningitis is inflamma-

tion of the meninges.

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• Brucella. Brucella bacteria are very small coccobacillus that can not move

themselves (non-motile) and cause brucellosis or undulant fever—daily

episodes of fever and chills. Brucella multiply in white blood cells.

• Bordetella pertussis. Bordetella pertussis is the bacteria that cause pertus-

sis, which is better known as whooping cough. Bordetella pertussis is rod-

shaped and non-motile.

• Franeisella tularensis. Franeisella tularensis is a gram-negative coc-

cobacillus bacterium that lives in contaminated water or wild game. When

such water or wild game is ingested, the bacteria infects the lymph nodes

(lymphadenopathy), causing a disease called tularemia, which is com-

monly known as rabbit fever or deer-fly fever. Franeisella tularensis can

also be inhaled during the skinning of an infected animal or enter through

a lesion in the body.

• Agrobacterium tumefaciens. Agrobacterium tumefaciens is a bacterium

that causes tumor-like growths on plants called crowngull.

• Acetobacter and gluconobacter: Acetobacter and gluconobacter are bacte-

ria that synthesize ethanol to vinegar (acetic acid) and are used in the food

industry to make vinegar.

Facultatively Anaerobic Gram-Negative Rods

Facultatively anaerobic gram-negative rods are a group of bacteria that take on

a rod shape and can live without the presence of oxygen or when oxygen is pres-

ent can carry out metabolism aerobically. These bacteria are gram-negative.

These are three prominent members of the facultatively anaerobic gram-negative

rods bacteria group.

• Enterics. Enterics (Enterobacteriaceae) are small bacteria that are found in

the intestinal tracts of animals and humans (intestinal flora) and have flagella

all over their surface (peritirichous flagella) to move about. Enterics ferment

glucose and produce carbon dioxide and other gases. The word “enteric”

means “pertaining to the intestines.” More predominate Enterics are:

• Escherichia coli. Escherichia coli, commonly known as E.coli is an

example of an enteric bacteria, which makes up some of the normal

flora in the human intestines, but can cause infection if it enters other

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parts of the body (for example, through the ingestion of water that is

contaminated with fecal matter.)

• Shigella. Shigella causes bacillary dysentery or shigellosis, more com-

monly known as traveler’s diarrhea.

• Salmonella. Salmonella is a group (genera) of enteric bacteria that has

members that can infect humans. Species include Salmonella typhi,

which causes typhoid fever and Salmonella choleraesuis and

Salmonella enteritides both of which are food-borne pathogens that

cause salmonellosis, a type of food poisoning.

• Klebsiella. The genera Klebsiella is a bacterium that cause bacterial

pneumonia.

• Erwinia. Erwinia is a bacterium that infects plants and causes what is

commonly called soft root rot.

• Enterobacter. The genus enterobacter consists of the species Enterobacter

cloace and Enterobacter aerogenes. Both of these organisms cause uri-

nary tract infections and nosocomial (hospital) infections in individuals

with a weakened immune system.

• Serratia marcescens, Serratia marcescens bacteria are found on catheters

and instruments that are allegedly sterile; this bacterium causes urinary

and respiratory infections.

• Yersinia pestis. Yersinia pestis, also known as Y.pestis, caused the

bubonic or black plague, which ravaged Europe during the Middle

Ages. It begins by causing abscesses of lymph nodes and then produces

pneumonia-like symptoms when it reaches the lungs, which is called

pneumonia plague.

• Vibrios. Vibrios are facultative anaerobic gram-negative, comma-shaped

bacteria that inhibit aquatic environments and some also live in the intes-

tinal tracts of animals and humans. There are two important species of vib-

rios bacteria. These are:

• Vibrio cholerae. Vibrio cholerae is the bacteria that cause cholera, signs

and symptoms are abdominal pain and watery diarrhea.

• Vibrio parahaemolyticus. Vibrio parahaemolyticus is the bacterium

that causes inflammation and irritation of the stomach and intestine—

better known as gastroenteritis—when contaminated shellfish is ingested

raw or undercooked.

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• Pasteurella-Haemophilus. Pasteurella-Haemophilus are very small faculta-

tively anaerobic gram-negative, rod shaped bacteria, that are named for

Louis Pasteur. Examples include:

• Pasteurella causes blood poisoning (septicemia) in cattle, chickens

(fowl cholera) and pneumonia in various animals.

• P. multocida, the species which was identified by Louis Pasteur, is

transmitted to humans by a dog or cat bite.

• Haemophilus. The genus Haemophilus (which means “blood loving”)

are bacteria that live in mucous membranes of the upper respiratory

tract, mouth, intestinal tract and vagin*.

• H. ducreyi, the species of Haemophilus bacterium that causes chan-

croid, which is an infectious venereal ulcer.

• H. aegyptiusis the species that causes acute conjunctivitis or pink eye.

Anaerobic Gram-Negative Cocci and Rods

Anaerobic gram-negative cocci and rods can live in anaerobic conditions and are

non-motile. They do not form endospores, which are small spores that developed

inside the bacteria as a resistant survival form of the bacteria.

Anaerobic gram-negative cocci are spherically shaped and form a single

chain or are clustered. Veillonella are common anaerobic gram-negative cocci

that are found between teeth and on gums. Veillonella is the cause of abscesses

of teeth and gums.

Anaerobic gram-negative rods are called Bacteroides and are members of the

Bacteriodaceae family of bacteria that live in the intestinal tract of humans.

Bacteroides can cause peritonitis, which is inflammation of the peritoneum due

to infection. Another kind of anaerobic gram-negative rod is Fusobacterium.

These are long slender rods that live in

topics in an easy-

to-read style. You can then compare your knowledge with what you’re ex-

pected to know by taking chapter tests and the final exam. There is little room

for you to go adrift.

CHAPTER 1: THE WORLD OF THE MICROORGANISM

You’ll begin your venture into the microscopic world of microbes by learning

the fundamentals. These are the terms and concepts that all students need to

understand before they can embark on more advanced topics, such as cultivat-

ing their own microbes.

In this chapter, you will be introduced to the science of microbiology with a

look back in time to a period when little was known about microbes except that

some of them could kill people. You’ll also learn about the critical accomplish-

ments made in microbiology that enable scientists to understand and develop

cures for disease.

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CHAPTER 2: THE CHEMICAL ELEMENTS

OF MICROORGANISMS

Chemistry is a major factor in microbiology because microbes are made up of

chemical elements. Scientists are able to destroy microbes by breaking them

down into their chemical elements and then disposing of those elements.

Before you can understand how this process works, you must be familiar with

the chemical principles related to microbiology. You’ll learn about these chemi-

cal principles in this chapter.

CHAPTER 3: OBSERVING MICROORGANISMS

“Wash the germs from your hands!” That was the cry of every mom who knew

that hand washing is the best way to prevent sickness. Most kids balked at hand

washing simply because they couldn’t see the germs on their hands.

We’ll show you how to see germs and other microbes in this chapter by using a

microscope. You’ll learn everything you need to know to bring microbes into clear

focus so you can see with a microscope what you can’t see with the naked eye.

CHAPTER 4: PROKARYOTIC CELLS AND EUKARYOTIC

CELLS

It is time to get down and personal with two common microbe cells. These are

prokaryotic cells and eukaryotic cells. These names are probably unfamiliar to

you, but they won’t be by the time you’re finished reading this chapter.

Prokaryotic cells are bacteria cells and eukaryotic cells are cells of animals,

plants, algae, fungi, and protozoa. Each carries out the six life processes that all

living things have in common. In this chapter you’ll learn about how prokary-

otes and eukaryotes carry out these life processes.

CHAPTER 5: THE CHEMICAL METABOLISM

“It’s my slow metabolism! That’s why I can’t shed a few pounds.” This is a great

excuse for being unable to lose weight, but the reason our metabolisms are slow

is because we tend not to exercise enough.

In this chapter, you’ll learn about the biochemical reactions that change food

into energy—collectively called metabolism—and how the cell is able to con-

vert nutrients into energy.

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CHAPTER 6: MICROBIAL GROWTH

AND CONTROLLING MICROBIAL GROWTH

You and microbes need nutrients to grow—chemical nutrients such as carbon,

hydrogen, nitrogen, and oxygen. However, not all microbes need the same

chemical nutrients. For example, some require oxygen while others can thrive in

an oxygen-free environment.

You’ll learn in this chapter how to classify microbes by the chemical nutri-

ents they need to survive. You’ll also learn how to use this knowledge to grow

microbes and control their growth in the laboratory.

CHAPTER 7: MICROBIAL GENETICS

Just like us, microbes inherit genetic traits from their species’ previous genera-

tions. Genetic traits are instructions on how to everything to stay alive. Some in-

structions are passed along to the next generation while other instructions are not.

In this chapter you’ll learn how microorganisms inherit genetic traits from

previous generations of microorganisms. Some of these traits show them how to

identify and process food, how to excrete waste products, and how to reproduce.

CHAPTER 8: RECOMBINANT DNA TECHNOLOGY

Who we are and what we are going to be is programmed into our genes. The

same is true for microbes. This genetic information is encoded into DNA by the

linking of nucleic acids in a specific sequence.

Genetic information can be reordered in a process called genetic engineering.

You’ll learn about genetic engineering and how to recombinant DNA using

DNA technology in this chapter.

CHAPTER 9: CLASSIFICATION OF MICROORGANISMS

There are thousands of microbes and no two are identical, but many have simi-

lar characteristics. Microbiologists have spent years carefully observing

microbes and organizing them into groups by their similarities.

You’ll learn how microbes are classified in this chapter, which enables you to

efficiently identify microbes that you see under a microscope.

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CHAPTER 10: THE PROKARYOTES:

DOMAINS ARCHAEA AND BACTERIA

Bacteria are one of the most common microbes that you encounter. Some bacte-

ria cause disease and other bacteria help you live by aiding in digestion. There

are many different kinds of bacteria; however, all bacteria can be grouped into

four divisions based on the characteristics of their cell walls.

Each division is further divided into sections based on other characteristics,

such as oxygen requirements, motility, shape, and Gram-stain reaction. In this

chapter, you’ll learn how to use these divisions and sections to identify bacteria.

CHAPTER 11: THE EUKARYOTES:

FUNGI, ALGAE, PROTOZOA, AND HELMINTHS

In this chapter you’ll take a close look at the kingdoms of fungi, protista, and

animalia. These are microbes that are commonly known as fungi, algae, proto-

zoa, and helminths.

Eukaryotes are a type of microbe and are different from bacteria and viruses.

However, they, too, are beneficial to us. They supply food, remove waste, and

cure disease (in the form of antibiotics). And as bacteria, some eukaryotes also

cause disease.

CHAPTER 12: VIRUSES, VIROIDS, AND PRIONS

Probably one of the most feared microbes is a virus because often there is little

or nothing that can be done to kill it. Once you’re infected, you can treat the

symptoms, such as a runny nose and watery eyes, but otherwise you must let the

virus run its course.

Did you ever wonder why this is case? If so, then read this chapter for the

answer and learn what a virus is, how viruses live, and which diseases they cause.

CHAPTER 13: EPIDEMIOLOGY AND DISEASE

It’s flu season and you can only hope that you don’t become infected—otherwise

you’ll have ten days of chills, sneezing, and isolation. No one will want to come

close to you for fear of catching the flu.

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In this chapter, you’ll learn about diseases like the flu and how diseases are

spread. You’ll also learn how to take simple precautions to control and prevent

the spread of diseases.

CHAPTER 14: IMMUNITY

Inside your body there is a war going on. An army of B cells, T cells, natural

killer cells, and other parts of your immune system are on the defense. These

cells seek microbes to rip apart before any of them can give you a runny nose,

cough, or that dreaded feverish feeling.

The immune system is your body’s defense mechanism: Its “soldiers” sur-

round, neutralize, and destroy foreign invaders before they can do harm. In this

chapter you’ll learn about your immune system and how it gives you daily pro-

tection against invading microbes.

CHAPTER 15: VACCINES AND DIAGNOSING DISEASES

Think about this: Each year millions of people pay their doctor to inject them

with the flu virus. On the surface that may not make sense, but after reading this

chapter you’ll find that it makes perfect sense because this injection is actually

a vaccination against the flu.

A vaccine prevents you from catching a certain disease because it has ele-

ments of that disease, triggering your body to create antibodies to the disease.

You’ll learn about vaccines and antibodies in this chapter.

CHAPTER 16: ANTIMICROBIAL

the gingival crevices of teeth and cause

gingivitis, which is a gum infection.

Rickettsias and Chlamydias

Rickettsias and Chlamydias are intracellular parasites that need a host in order

to reproduce and therefore enter the cell of a host. These bacteria were once

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thought to be viruses that invaded cells. They are classified as bacteria because

they have bacterial cell walls and contain DNA and RNA, which is not the case

with a virus. Rickettsias and Chlamydias have no means of mobility because

they lack flagella. They are also gram-negative.

Rickettsias are small rod-shaped or spherical bacteria that live in the cells of

ticks, lice, fleas, and mites (arthropods) and can be transmitted to humans when

bitten by arthropods, causing rickettsial disease. Rickettsial disease causes cap-

illaries to become permeable resulting in a rash. Rickettsias reproduce by binary

fission where a cell wall forms across the cell and the two halves separate to

become individual cells.

Common Rickettsias are:

• Rickettsia prowazekii. Rickettsia prowazekii is transmitted by lice and

causes endemic typhus.

• R. rickettsii. R. rickettsii is transmitted by ticks and causes Rocky Mountain

spotted fever.

• R. tsutsugamushi. R. tsutsugamushi is transmitted by arthropods and cause

scrub typhus that presents with fewer, rash and inflammation of the lymph

nodes.

• Coxiella burnetti. Coxiella burnetti is transmitted by aerosols or contami-

nated milk and causes Q fever, which is similar to pneumonia.

• Bartonella bacilliformis. Bartonella bacilliformis is transmitted by arthro-

pods and causes a wart-like rash called Oroya fever.

Chlamydias are very small spherical or coccoid bacteria that are non-motile

and can be transmitted from person-to-person contact or by airborne respiration.

Chlamydias are not transmitted by arthropods. They are so small that they mul-

tiply in host cells. There are three species of chlamydia:

• Chlamydia trachomatis. C.trachomatis causes trachoma, which is a com-

mon cause of blindness and the non-gonorrhea sexually transmitted dis-

ease urethritis (inflammation of the urethra).

• C. penemoniae causes a mild form of pneumonia in adolescence.

• C. psittaci causes psittacosis.

Mycoplasmas

Mycoplasmas are very small facultatively anaerobic bacteria (some are oblig-

ately anaerobic) that have taken on many shapes (pleomorphic) and were once

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thought to be viruses because they lack a cell wall. However, they have a cell

membrane, DNA and RNA, which distinguishes them from viruses.

Mycoplasmas can also resemble fungi because some Mycoplasmas produce

filaments that are commonly seen in fungi. It is these filaments that led scien-

tists to name it Mycoplasma. Myco means “fungus.”

Many Mycoplasmas are unable to move by themselves because they do not

have flagella, but some are able to glide on a wet surface.

Two of the more common types of Mycoplasma are:

• Mycoplasma pneumoniae. Mycoplasma pneumoniae is the cause of atypi-

cal pneumonia, commonly referred to as walking pneumonia.

• Ureaplasma urealyticum. Ureaplasma urealyticum is a bacterium that is

found in urine and one that can cause urinary tract infection.

Gram-Positive Cocci

Within the gram-positive cocci section are two genera. These are Staphylococcus

and Streptococcus, and each has an important role in medicine.

• Staphylococcus. Staphylococcus bacteria have a grape-like cluster appear-

ance and grow in environments of high osmotic pressure and low moisture.

Osmotic pressure is the pressure required to prevent the net flow of water

by osmosis. Infections caused by the Staphylococcus bacteria are typically

called staph infections. Here are the commonly found Staphylococcus

bacteria:

• Staphylococcus aureus. Staphylococcus aureus, also called S. aureus, is a

bacterium that forms yellow-pigmented colonies that grows with oxygen

(aerobically) or without oxygen (anaerobically). S. aureus is the cause of

toxic shock syndrome that results in high fever, vomiting and sometimes

death. It produces enterotoxins, which affects intestinal mucosa. S. aureus

is also the cause of boils (skin abscess), impetigo (pus-filled blisters on

the skin), styes (an infection at the base of an eye lash), pneumonia,

osteomyelitis, acute bilateral endocarditis (inflammation of the internal

membranes of the heart) and scalded skin syndrome in very young chil-

dren that causes skin to strip off (denude) due to an exfoliative toxin.

S. aureus is one of the major types of infections that occur in hospi-

tals because it is resistant to antibiotics such as penicillin. An infection

of S. aureus is usually identified by the presence of an abscess.

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• Staphylococcus epidermis: Staphylococcus epidermis, also known as S.

epidermis, is the frequent cause of urinary tract infections in the elderly

and also causes subacute bacterial endocarditis, which is a chronic in-

fection of the endocardium (a thin layer of connective tissue that lines

the chambers of the heart) and heart valves.

• Staphylococcus saprophyticus. Staphylococcus saprophyticus, also

known as S. saprophyticus, causes urinary tract infections, usually in

adolescent girls.

• Streptococcus. Streptococcus bacteria appear as a single, paired or chained

spherical gram-positive bacteria. Streptococci do not use oxygen, though

most are aerotolerant. Few may be obligately anarobic. Infections caused

by the Streptococcus bacteria are generally referred to as a strep infection.

Microbiologists classify Streptococcus bacteria in three ways.

• The type of hemolysis (destruction) of red blood cells caused by the

Streptococcus bacteria. There are three types characterized by:

• Alpha-hemolytic group. Incomplete lysis (destruction of the cell)

within green pigment surrounding the colony.

• Beta-hemolytic group. Total lysis and a clear area around the colony.

• Gamma-hemolytic group. Absence of lysis. This group is of no clin-

cal importance.

• The Lance Field classification. There are four groups:

• Group A Streptococci. Characterized by Streptococcus pyogenes and

secrete of erthrogenic exotoxins responsible for scarlet fever.

• Group B Streptococci. Characterized by Streptococcus agalactiae,

which is part of normal oral and vagin*l flora and causes urogenital

(urinary and reproductive systems) infections in females.

• Group C Streptococci. Causes animal diseases.

• Group D Streptococci. Characterized by Streptococcus faecalis, which

is a normal part of oral and intestinal flora. Diseases of S. faecalis are

endocarditis, urinary tract infections and septicemia (blood poisoning).

• Ungrouped Streptococci. There are two kinds:

• Viridans streptococci. Characterized by Streptococcus viridans and

Streptococcus salvarius, which causes subacute bacterial endocardi-

tis, and Streptococcus mutans which causes a biofilm called plague

resulting in tooth decay.

• Pneumococcal streptococci. Characterized by Streptococcus pneu-

moniae which causes lobar pneumonia and otitis media (middle ear

infection).

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Endospore-Forming Gram-Positive Rods and Cocci

Endospore forming, gram-positive rods and cocci consist mainly of rod-shaped

bacteria of the genera Bacillus and Clostridium. Another cocci bacteria included

in this group are of the genus Sporosarcina. These bacteria have no clinical sig-

nificance and are saprophytic soil bacteria. Saphrophytes are organisms that feed

on dead organic matter.

These bacteria can be strict aerobes, facultative anaerobes, obligate anaerobes

or microaerophiles. Microaerophiles are bacteria that grow best in an environ-

ment that has a small amount of free oxygen.

The formation of endospores by bacteria is important in medicine and the food

industry because these endospores are

resistant to heat and many chemicals.

There are three genera in this section. These are:

• Bacillus: Bacillus consists of the following bacterium:

• Bacillus anthracis. Bacillus anthracis causes anthrax, a severe blood

infection that infects cattle, sheep and horses and can be transmitted to

humans. B. anthracis is a non-motile facultative anaerobe and produces

exotoxin. Anthrax can result in central nervous system distress, respira-

tory failure, anoxia and death.

• Bacillus cereus. Bacillus cereus produces enterotoxin (a toxin that affects

the intestine) and causes gastroenteritis (food poisoning).

• Bacillus thuringiensis. Bacillus thuringiensis produces a toxin that attacks

the digestive system of insects, causing the insects to stop feeding by

causing paralysis of the insects guts.

• Sporosarcina. Sporosarcina are bacteria that inhabit the soil and receive

nutrients by feeding on dead organic matter.

• Clostridium. Clostridium are rod-shaped bacteria that exist in water, soil,

and in the intestinal tract of animals and humans. These bacteria do not

require oxygen. They release toxins that cause disease. Here are the com-

mon types of Clostridium:

• Clostridium tetani. Clostridium tetani, also known as C. tetani, causes

tetanus, commonly referred to as lockjaw.

• Clostridium difficile. Clostridium difficile, also known as C. difficile,

causes gastroenteritis.

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• Clostridium perfringes. Clostridium perfringes, also known as C.

perfringes, causes myonecrosis—better known as gas gangrene—which

produces hydrogen gas in deep tissue wounds, resulting in cell death.

• Clostridium botulinum. Clostridium botulinum, also known as C. botu-

linum is a cause of food poisoning usually as a result of improperly

canned food. It produces an exotoxin that causes flaccid paralysis

(weakness of muscle tone) due to the suppression of acetylcholine,

which is a neurotransmitter. The result is vomiting, difficulty speaking,

and difficulty swallowing, which can lead to respiratory paralysis and

death. Physicians use Clostridium botulinum as a neural block that

inhibits muscle contraction. Clostridium botilinum is also used cosmet-

ically to relax muscles that cause facial wrinkles (Botox injections). The

C. botulinum toxin blocks the exocytosis of synaptic vesicle of the neu-

romuscular junction, where motor neurons meet muscle.

Regular Nonsporing Gram-Positive Rods

Regular, non-sporing gram-positive rods are obligate or facultative anaerobes

that have a rod-shaped appearance as is implied by its name. They inhabit fer-

menting plants and animal products. There are four genera within this section.

These are:

• The genus, Lactobacillus are non-sporing gram-positive rods. These are

aerotolerant bacteria that produce lactic acid from simple carbohydrates.

The acidity inhibits competing bacteria. An example of a Lactobacillus

organism is the species Lactobacillus acidophilus.

• Lactobacillus acidophilus is found in the human intestinal tract, oral cav-

ity and adult vagin*. They produce an acidic environment that inhibits the

growth of harmful bacteria by fermenting glycogen into lactic acid.

Lactobacillus acidophilus is also used commercially to produce an assort-

ment of food products including sauerkraut, pickles, buttermilk and yogurt.

Other examples of regular non-sporing gram-positive rod bacteria are:

• Listeria monocytogenes. Listeria monocytogenes contaminates food and

dairy products, if ingested can cause the disease listeriosis, which causes

an inflammation of the brain and meninges (meningitis).

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• Erysipelothrix rhusiopathiae. Erysipelothrix rhusiopathiae causes erysi-

peloid, which is red, swollen and painful lesions, frequently seen in fisher-

men and meat handlers.

Irregular Nonsporing Gram-Positive Rods

These bacteria are irregular, non-sporing rods. Although this group of bacteria

are generally rod-shaped, their shape can vary (pleomorphic). Some resemble a

club while others are long, threadlike cylinders. There are three genera within

this section. These are:

• Corynebacteria. Corynebacteria are club-shaped and receive nutrients from

dead or decaying organic material (saprophytes). Corynebacteria inhabit

airy soil and water and cause diphtheria. Corynebacteria diphtheriae is the

organism which causes diphtheria.

• Propionibacterium. Propionibacterium infects wounds and causes abscesses.

An example would be Propionibacterium acnes.

• Actinomycetales. Actinomycetales is a long, threadlike cylinder (filament)

that inhibits soil and some provide nitrogen to plants. The species

Actinomycetale israelii, which causes actinomycosis, which destroys tis-

sues in the jaw, head, neck, and lungs. Actinomycetales was originally

classified as a fungus because of its shape.

Mycobacteria

Mycobacteria require oxygen (aerobic) and are acid-fast organisms that remain

red while most are blue. Large amounts of lipids in the Mycobacteria’s cell enve-

lope, resists basic dyes. Myco, which means “fungus-like” is how this organism

got its name.

• Mycobacterium tuberculosis. Mycobacterium tuberculosis causes tuberculosis.

• Mycobacterium leprae. Mycobacterium leprae, also known as M. leprae,

causes Hansen’s disease (leprosy).

• Mycobacterium bovis. Mycobacterium bovis, also known as M. bovis,

causes tuberculosis in cattle and can be transmitted to humans.

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Nocardia Forms

Nocardia are a group of a long thread-like cylinder shaped bacteria that inhabits

soil and need oxygen to grow (aerobic). They are gram-positive and cannot

move by themselves (they are non-motile).

Nocardia asteroids, also known as N. asteroids, is a common bacterium

within this group. It causes mycetoma, which causes abscesses on the hands and

feet and also causes lung infection.

Quiz

1. Archaea can exist in very hot and very cold environments, making them

a resilient microorganism that can survive attacks and destroy other

bacteria.

(a) True

(b) False

2. Archaea that function in the presence of air are called

(a) methanogenic archaea

(b) cell wall–less archaea

(d) extreme halophiles

3. Archaea that live in an extreme salty environment are called

(a) methanogenic archaea

(b) cell wall–less archaea

(d) extreme halophiles

4. Single-celled archaea that produce methane and carbon dioxide (CO2) by

fermenting simple organic carbon compounds or oxidizing H2 without

oxygen to produce CO2 are called

(a) methanogenic archaea

(b) cell wall–less archaea

(d) extreme halophiles

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5. Archaea that do not have cell walls are called

(a) methanogenic archaea

(b) cell wall–less Archaea

(d) extreme halophiles

6. “Aerobic/microaerophilic” is a designation for bacteria that require small

amounts of oxygen to grow.

(a) True

(b) False

7. Rod-shaped bacteria with flagella at both ends of the rod, which give the

bacteria mobility, are called

(a) Pseudomonas aeruginosa

(b) Legionella pneumophilia

(d) Legionella micdadei

8. The bacteria that infects lungs and causes a strain of pneumonia com-

monly called Pittsburgh pneumonia is known as

(a) Pseudomonas aeruginosa

(b) Legionella pneumophilia

(d) Legionella micdadei

9. A pathogenic bacterium that infects the urinary tract and wounds in

humans is called

(a) Pseudomonas aeruginosa

(b) Legionella pneumophilia

(d) Legionella micdadei

10. This bacterium, discovered in 1976, infected and killed members of the

American Legion at their convention in Philadelphia.

(a) Pseudomonas aeruginosa

(b) Legionella pneumophilia

(d) Legionella micdadei

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CHAPTER

167

The Eukaryotes:

Fungi, Algae,

Protozoa, and

Helminths

Throughout this book you’ve learned that some kinds of microorganisms are

beneficial to us: They supply food, remove waste, and help prevent disease by

combating bacteria as antibiotics. Other microorganisms however, are patho-

genic; they cause or transmit disease.

In this chapter we take a close look at microorganisms called eukaryotes.

Eukaryotes are organisms within the kingdoms Fungi, Plants, Protists, and Animals.

These microorganisms are called fungi, algae, protozoa, and helminths.

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Fungi

Fungi have been studied systematically for 250 years, although ancient peoples

learned of fermentation (enabled by fungi) thousands of years ago. Scientists

who practice mycology, the study of fungi, are called mycologists. In the early

days of microbiology, mycologists categorized fungi as plants because they

resemble plants in general appearance (they have cell walls) and because both

fungi and plants lack motility (neither can move under its own power).

Today, however, fungi and plants are considered two distinct groups of organ-

isms because plants use chlorophyll to obtain nutrients and fungi do not. Fungi

are heterotrophic: They absorb nutrients from organic matter and organic wastes

(saprophytes) or tissues of other organisms (parasites). Many fungi are multi-

cellular and are called molds. Yeasts are unicellular fungi.

Fungi can be both beneficial and harmful. For example, fungi called mycor-

rhizae are mutualistic and help roots of plants absorb water and minerals from

the soil. The cellulose and lignin of plants are important food sources for ants;

however, ants are unable to digest them unless fungi first break them down.

Ants are known to cultivate fungi for that purpose. Some fungi are beneficial to

humans as food (mushrooms). They are used in the preparation of food such as

bread and beer (yeast). Fungi are also used to fight off bacterial diseases

(antibiotics).

Some fungi can have a harmful effect because they feed on plants, animals,

and humans, causing plants and animals to decay and spoil as a source of nutri-

ents (rotting food). In humans, fungi cause various diseases such as athlete’s foot.

ANATOMY OF FUNGI

The body of a fungus (Fig. 11-1) is referred to as either a soma (meaning

“body”), which is equal to the term “vegetative” in plants, or thallus, which is

also applied to algae and bryophytes (nonflowering plants comprised of mosses

and liverworts). The body of a mold or fleshy fungus consists of long, loosely

packed filaments called hyphae.

Hyphae are divided by cell walls called septa (the singular form is septum). In

most molds the hyphae are divided into one cell units called septate hyphae.

In some fungi, the hyphae have no septa and look like long multinucleated

cells called coenocytic hyphae. Cytoplasm flows or streams throughout the hy-

phae through pores in the septa. Under the right environmental conditions the

hyphae grow to form a filamentous mass known as a mycelium. A fungus can

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have a thallus many meters and penetrate its surroundings. In the hyphae of fungi

there is a portion called the vegetative hyphae. Vegetative hyphae are where nutri-

ents are obtained. The part of the hyphae responsible for reproduction is called

reproductive or aerial hyphae.

Fungi can reproduce both sexually and asexually. Reproduction occurs with

the formation of spores. Spores are always nonmotile and are a common means

of reproduction among fungi. Do not confuse bacterial endospores with fungal

spores; they are different. Bacterial endospores are formed so that the bacterial

cell can survive in harsh environments. Once there is a less threatening env-

ironment, the bacterium leaves the endospore state and becomes active. The

endospore germinates into a single bacterial cell. Asexual reproduction occurs

when asexual spores are formed by the hyphae of one organism. When these

spores germinate, they are identical to the parent. Sexual reproduction happens

when the nuclei of sexual spores from two opposite mating strains of the same

fungus species fuse. Fungi that grow from sexual spores have genetic character-

istics of both parents.

YEASTS

Yeasts are fungi that are unicellular and reproduce using a process called fission,

although some can form filaments. Fission occurs when a cell divides evenly to

form two new cells. When the cell divides by budding, it divides unevenly.

Yeasts are nonfilamentous and have a spherical or oval shape. The white pow-

CHAPTER 11 The Eukaryotes 169

Fig. 11-1. The body of a fungus contains

long filaments called hyphae.

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dery substance that is sometimes found coating fruits and leaves is a yeast.

Yeasts can also reproduce sexually.

MOLDS

When a mold forms an asexual spore, the spore will detach itself from the par-

ent and then germinate into a new mold. This process is considered reproduction

because a second new organism grows from the spore.

FUNGI CLASSIFICATION

Asexual fungal spores are formed on hyphae of fungi. When these hyphal spores

germinate, they are identical to the parent. Asexual spores reproduce by the

process of cell division. In sexual cell reproduction, the spores are produced by

the fusion of nuclei from two opposite fungi of the same species. These fungi

will have the same characteristics of both parents. Asexual spores produce more

frequently than sexual spores. Asexual spores are present in virtually every envi-

ronment on the planet.

Some fungi change their structure based on their natural habitat. This is

referred to as dimorphism, the property of having two forms of growth. For

example, some fungi appear non-filamentous when growing outside their natu-

ral habitat but filamentous when growing in their natural habitat. Such changes

of appearance can make it challenging to identify a particular type of fungus.

Fungal classification is based on the type of sexual spores they produce.

Listed are examples of the divisions of the kingdom Fungi:

• Zygomycota: Zygomycota are conjugative fungi. They reproduce both sex-

ually (zygospores) and asexually (sporangiospores). An example is:

Rhizopus nigricans, a black bread mold.

• Ascomycota: Ascomycota, also called sac fungi, have sac-like cells called

asci. These are yeasts, truffles, morels, and common molds. Fungi in

this group reproduce sexually and asexually. Their sexual spores (conidio-

sphores) freely detach with the slightest movement (conidia) and there-

fore can cause infection (opportunistic disease) or an allergic reaction.

Examples are:

• Blastomyces: Blastomyces causes blastomycosis, which is a general pul-

monary disease.

• Histoplasma: Histoplasma is a fungus found in bird and bat droppings;

it causes histoplasmosis, which is known as the fungus flu.

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• Basidiomycota: Also called club fungus, basidiomycota includes mush-

rooms, toadstools, smuts, and rusts. Sexually produced basidiospores are

formed externally on a base pedestal, producing a club-shaped structure

called a basidium (basidia, plural). Basidia can be found on visible fruit-

ing bodies called basidiocarps, which are positioned on stalks. A mush-

room is a basidiocarp. Some mushrooms, such as Amanita, produce toxins

and are poisonous to humans, while others are very nutritious.

• Deuteromycota: Deutermycota, also known as fungi imperfecti, have no

sexual reproduction (or none that can be observed). They cause pneumo-

cystis which infects people who have a compromised immune system.

Examples are:

• Penicillium notatum, which produces penicillin.

• Candida albicans, which causes vagin*l yeast infections in humas.

FUNGUS NUTRITION

Fungi receive nutrients by absorptive nutrition (chemoheterotrophic), which is

somewhat similar to how bacteria obtain nutrients.

Fungi team up with bacteria

to break down organic molecules and are the principal decomposers on earth.

Fungi can metabolize complex carbohydrates, such as the lignin in wood.

Fungi can decompose substances that have very little moisture and substances

that live in an environment with a pH of 5. Almost all molds are aerobic and

most yeasts are facultative anaerobes.

Algae

Algae are very simple unicellular or multicellular eukaryotic organisms that

obtain energy from sunlight (photoautotrophs). They live in various water envi-

ronments (oceans and ponds) on moist rocks and trees, and in soil.

REPRODUCTION OF ALGAE

Sexual reproduction occurs in most species of algae. In these species the algae

reproduce asexually for generations until there is a change in environmental

conditions; then the algae reproduce sexually. Other types of algae alternate in

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how they reproduce. The algae that reproduce sexually will latter reproduce

asexually. All algae reproduce asexually. Unicellular algae divide by mitosis and

cytokinesis. Multicellular algae that contain thalli and filaments can fragment.

Each new piece can form a thallus and a filament.

TYPES OF ALGAE

Chrysophytes

Chrysophytes are unicellular algae that live in fresh water and contain chloro-

phyll a and chlorophyll c, which are photosynthetic pigments used to transform

sunlight into energy. These are also known as golden algae because they have

golden silica scales. There are 500 known species of chrysophytes. Some chrys-

ophytes are amoeboid that attack bacteria by engulfing and destroying it.

Diatoms

Diatoms are unicellular algae that have a hard, double outer shell made of silica.

Nutrients pass through pores in the shell, then through the diatom’s plasma mem-

brane contained within the shell. There are 5,600 known species of diatoms, most

of which are phototrophic and contain chlorophyll a and chlorophyll c pigments.

They also contain carotenoids, which are yellow and orange pigments. Some

diatoms are heterotrophs and break down and use organic matter as nutrients.

Diatoms accumulate at the bottom of the sea and are commercially mined for both

their value as an abrasive and their filtering and insulating capabilities (used in the

filters in pools).

Dinoflagellates

Dinoflagellates are unicellular algae that have the capability of self-movement

through the use of tail-like projections called flagella. The flagella are located

between grooves in the cellulose plates that cover the dinoflagellate’s body. These

flagella pulsate in both an encircling motion around the body and in a perpendi-

cular motion, causing the dinoflagellates to rotate like a top. There are about

1,200 known species of dinoflagellates that inhabit both fresh water and seawater.

Dinoflagellates live in seawater. Some are heterotrophs and break down

organic matter for nutrients. Some seawater dinoflagellates are luminous, giving

a twinkle to the sea at night. Freshwater dinoflagellates are phototrophic: They

synthesize nutrients from sunlight using photosynthesis.

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Many dinoflagellates have chlorophyll a and c pigments as well as the yellow

and orange pigments, carotenoids. Depending on their photosynthetic pigment,

dinoflagellates can appear yellow-green, green, brown, blue, or red. When

dinoflagellates undergo a population explosion, the sea changes color from an

ocean blue to a sea of red or brown.

Some dinoflagellates, such as Gonyaulax (plankton), can be fatal to humans

because they produce neurotoxins. These dinoflagellates are eaten by fish and are

absorbed by oysters, clams, and other shellfish (mollusks). The neurotoxins build

up in their tissues, making the seafood poisonous to humans. These dinoflagel-

lates also cause “red tides” that have a devastating effect on the fish population.

Red Algae

Red algae, also known as Rhodophyta, are algae that form colonies in warm

ocean currents and in tropical seas. They contribute to the formation of coral

reefs that can be found as deep as 268 meters below the surface of the ocean.

Their stone-like appearance is caused by a build-up of calcium carbonate

deposits on their cell walls.

There are 4,000 known species of red algae, of which fewer than 100 are

found in fresh water. Red algae get their color from the phycobilins and chloro-

phyll a pigments contained in their cells. Phycobilins pigment absorbs green,

violet, and blue light, which are light waves that are capable of penetrating the

deepest waters. It is for this reason that red algae can survive at great depths. The

pigment that makes the algae red is called phycoerythrin.

As you learned in Chapter 6, red algae are used to make agar. Agar is the cul-

ture medium that is extracted from the cell wall of red algae and is used to grow

bacteria. Red algae are also used as a moisture-preserving agent in cosmetics and

baked goods. Red algae are used as a setting agent for jellies and desserts.

Brown Algae

Brown algae, also known as phaeophyta, are multicellular organisms. Some

brown algae are commonly called kelp; they live in the northern rocky shores of

North America and can grow up to 30 meters. There are 1,500 known species of

brown algae.

Brown algae have chlorophyll a and b photosynthetic pigments. They also

have carotenoids. Brown algae can appear dark brown, olive-green, and even

golden depending on the type of pigments in their cells. The pigment that makes

the algae brown is called fucoxanthin. Algin is a gummy substance found in the

cell walls of some species of brown algae and is used as a thickening, emulsify-

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ing, and suspension agent for ice cream, pudding, frozen foods, toothpaste, floor

polish, cough syrup, and even jelly beans.

The organic matter that kelp produces supports the life of invertebrates,

marine mammals, and fish.

Green Algae

Green algae can live in moist places on land, such as tree trunks and in the soil,

as well as in water. There are 7,000 species of green algae that are diverse in

size, morphology, lifestyle, and habits. Scientists believe that some members of

the species are linked structurally and biochemically to the Plant kingdom.

Two common green algae are:

1. Spirogyra: Spirogyra are freshwater algae that have tiny filaments, each

containing spiraling bands of chloroplasts.

2. Volvox: Volvox are colonial multicellular green algae that have flagella and

live in marine, brackish, and freshwater environments.

LICHENS

Lichens are filaments of a fungus and cells of algae (this is a symbiotic rela-

tionship) that are found on exposed soil or rock, on trees, on rooftops, and on

cement structures. There are about 20,000 known species of lichens.

Survival of the green algae and the fungus are interdependent in a symbiotic

association. Neither can live without the other. However, each grows independ-

ently. Lichens are delicate and beautiful in appearance.

Protozoa

This organisms are members of the Kingdom Protista. There are about 20,000

known species of protozoa that live in water and soil. Some feed on bacteria

while others are parasites and feed off their hosts.

Most protozoa are asexual and reproduce in one of three ways. These are:

• Fission: Fission occurs when a cell divides evenly to form two new cells.

• Budding: Budding occurs when a cell divides unevenly.

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• Multiple fission (schizogony): Multiple fission is when the nucleus of the

cell divides multiple times before the rest of the cell divides. Forms around

each nucleus when the nucleus divides then each nuclei separates into a

daughter cell.

Some protists are sexual and exchange genetic material from one cell to

another through conjugation, which is the physical contact between cells.

A protist can survive in an adverse environment by encapsulating itself with

a protective coating called a cyst. The cyst defends the protist in extreme tem-

peratures against toxic chemicals and even when there is a lack of oxygen, mois-

ture, and food.

PROTOZOA NUTRITION

Protists receive nutrients by breaking down organic matter (heterotrophic) and

can grow in both aerobic and anaerobic environments, such as protists that live

in the intestine of animals. Some protists, such as Euglena, receive nutrients

from organic matter and through photosynthesis because they contain chloro-

phyll. These protists are considered both algae and protozoa.

Protists obtain food in one of three ways:

• Absorption: Food is absorbed across the protist’s plasma membrane.

• Ingestion: Cilia outside the protist create a wave-like motion to move food

into a mouth-like opening in the protist called a cytosome. An example is

the paramecium.

• Engulf: Pseudopods (meaning “false feet”) on the protist engulf food, then

pull it into the cell using a process called phagocytosis. An example of this

type of protist is the amoeba.

Food is digested in the vacuole after the food enters the cell. The vacuole is

a membrane-bound organelle. Waste products are excreted using a process

called exocytosis.

AMEBA

Here are common amebas (Fig. 11-2):

• Entamoeba histolytica: Also known as E. histolytica, this microorganism

is transmitted between humans through the ingestion of cysts that are

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excreted in the feces of infected people. It is the causative agent of amebic

dysentery.

• Naegleria fowleri: This ameba causes primary amebic meningoenceph-

alitis (PAM) that results in headache, fever, vomiting, stiff neck, and loss

of bodily control. N. fowleri enters the body through the mucous mem-

branes (when the person swims in warm water) and travels to the brain and

spinal cord.

• Acanthamoeba polyphaga: This ameba lives in water (including tap water)

and infects the cornea of the eye leading to blindness. It can also cause

ulcerations of the eye and the skin. A. polyphaga is also known to invade

the central nervous system, resulting in death.

Flagellates move by structures called flagella. They have two or more spindle-

shaped flagella in the front of the cell that they use to pull themselves through

their environment. Food enters flagellates through a mouth-like grove called a

cytosome.

Here are common flagellates:

• Trichom*onas vagin*lis: Commonly known as T. vagin*lis, this flagellate

is the cause of trichom*oniasis, which is a sexually transmitted disease.

T. vagin*lis is found in the male urinary tract and the vagin* of females.

• Giardia lamblia: This flagellate is commonly known as G. lamblia and

causes giardiasis. Giardiasis causes nausea, cramping, and diarrhea when

food or water contaminated by fecal material is ingested. G. lamblia lives

in the small intestines of humans and other mammals.

CHAPTER 11 The Eukaryotes176

Fig. 11-2. A common type of ameba is the

Amoeba proteus.

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CHAPTER 11 The Eukaryotes 177

BLOOD AND TISSUE PROTOZOA

Hemoflagellates are protozoa that are carried by blood-feeding insects and are

transmitted into the blood stream by the insect’s bite. Here are commonly found

hemoflagellates:

• Trypanosoma gambiense: T. gambiense is transmitted in the saliva of the

tsetse fly as a result of a bite and causes trypanosomiasis, which is better

known as African sleeping sickness.

• Trypanosoma cruzi: T. cruzi is carried by the Reduviid bug or “kissing

bug,” which is commonly called the kissing bug because it bites the face. T.

cruzi causes Chagas’ disease. Chagas’ disease is thought to have made

Charles Darwin sick during his voyage on the H.M.S. Beagle. Typically

there aren’t any symptoms for months after the bite. During this time T.

cruzi spreads through organs of the body, weakening the heart, intestines,

and esophageal. It also cause, both eyes to swell (Romaña’s sign).

CILIATES

Ciliates (Fig. 11-3) are protozoa that have shorter hair-like structures called

cilia that are found in rows on the outer surface of the cell. These cilia are used

to move the protozoa through the environment and are used to bring food into

the cell.

An example of a ciliate is Balantidium coli. It is the only ciliate that causes

disease in humans. When ingested, it enters the large intestine, causing severe

dysentery.

Fig. 11-3. Ciliates are protozoa that have cilia.

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APICOMPLEXANS

Apicomplexans are protozoa that live and grow inside another living organism

(obligate intracellular parasites) and cannot move by themselves (nonmotile).

Apicomplexans have an apical complex of organelles that form an apex (tip).

This tip contains enzymes that enable it to penetrate the tissues of a host.

Here are common Apicomplexans:

• Plasmodium: Plasmodium lives in the female Anopheles mosquito and

causes malaria when the mosquito bites a human. Symptoms of malaria

include severe chills and fever or “rigor” (a sudden chill or coldness that is

followed by fever).

• Bebesia microti: B. microti lives in ticks and causes bebesiosis when the

tick bites someone. B. microti then enters red blood cells where it multi-

plies quickly. At first there aren’t any symptoms (asymptomatic). However,

soon afterwards there is a high fever, headache, and muscle pain as B.

microti destroys red blood cells. This causes the person to become anemic

(insufficient hemoglobin because of the reduction in the number of red

blood cells) and show signs of jaundice (an increase in bile, causing the

skin and eye sclera—the white part of the eye—to yellow).

• Toxoplasma gondii, also known as T. gondii, lives in cat feces and raw

meat and causes lymphadenitis (infection of the lymph nodes), which can

have a devastating effect on people who are immunocompromised, such as

AIDS patients. T. gondii causes congenital infections in a fetus because it

can pass from the mother to the fetus through the placenta.

Helminths

Helminths are parasitic, multicellular eukaryotic animals. The majority of these

animals belong to the phyla Platyhelminthes and Nematoda. There are free-

living members of these phyla; however, in this section, only the parasitic organ-

isms are discussed.

Many parasitic helminths do not have a digestive system and instead absorb

nutrients from the food that is consumed by their host organism, the host’s body

fluids, and the host’s tissues. Parasitic helminths have a very simplistic nervous

system because they have to respond to very few changes in their host’s environ-

ment. They lack or have reduced means of locomotion because they are transferred

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from one host to another. Parasitic helminths have a very complex reproductive

system that produces fertilized eggs (zygotes) that infect the host organism.

LIFE CYCLE OF HELMINTHS

The life cycle of parasitic helminths that go through a developmental larval stage

involves an intermediate host.

Dioecious adult helminths are of one sex. That is, one individual has a male

reproductive system and another has a female reproductive system. When these

two adult helminths with different sex organs occupy the same host organism,

sexual reproduction can occur. Monoecious adult helminths are hermaphroditic

(an organism that has both female and male reproductive organs). Some of

these monoecious helminths can fertilize themselves while others may fertilize

each other.

FLATWORMS

Flatworms, also known as platyhelminths, are mostly parasitic, aquatic organ-

isms that range in size from 1 millimeter to 10 meters, as in the case of a tape-

worm. There are more than 15,000 known species of flatworms. A flatworm has

both male and female reproductive parts (monoecious). Most but not all of their

oxygen and nutrients is absorbed through their body wall.

There are two types of flatworms:

• Flukes: Flukes are flat, leaf-shaped bodies that have an oral and a ventral

sucker

that are used to hang on to the body of a host. Flukes live is inside

the intestines or on tissues of humans. Three common flukes are:

• Schistosoma: This genus of flukes causes the disease schistosomiasis, a

debilitating disease that causes portal hypertension and liver cirrhosis.

• Paragonimus westermani: P. westermani causes paragonimiasis, which

is the result of the fluke’s depositing eggs into the bronchi of the lung.

• Clonorchis sinensis: C. sinensis, also known as Chinese liver fluke,

causes clonorchiasis, which occurs when the fluke latches inside the

liver.

• Tapeworms: Tapeworms have a knob-like “head,” called a scolex, with

hooks that allow it to attach to the wall of the intestine of vertebrate ani-

mals (including humans). Tapeworms have a series of flat, rectangular

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body units called proglottids (compartments that contain reproductive

organs). Proglottids eventually break away from the tapeworm and are

excreted in feces. However, new proglottids take their place. A tapeworm

continues to grow as long as its scolex and neck are intact.

• Taenia saginata: T. saginata, also called beef tapeworm, lives in raw or

poorly cooked beef and can cause taeniasis. T. saginata can grow to a

length of 25 meters in the intestines of a human, leading to an intestinal

blockage and malnutrition as the tapeworm absorbs nutrients intended

for the person.

• Tania solium: T. solium, also called the pork tapeworm, lives in raw or

poorly cooked pork and can cause taeniasis. T. solium can grow to a

length of 7 meters in the intestines leading to an intestinal blockage and

malnutrition.

• Echinococcus granulosus: E. granulosus is a tapeworm that is spread to

humans through contact with an infected dog and is transmitted when a

dog licks a person. This can lead to infection, anaphylactic shock, and

death if the tapeworm enters the body. E. granulosus can lay eggs that

produce cysts called hydatid cysts in the lungs, liver, and brain.

• Hymenolepis nana: H. nana is a tapeworm that lays eggs in cereals and

foods that are contaminated with infected parts of insects. When some-

one ingests the cereal or food he or she also ingests the tapeworm. The

tapeworm then attaches to the intestines, leading to diarrhea, abdominal

pain, and convulsions.

• Diphyllobothrium latum: D. latum is a broad fish tapeworm that lives in

raw or poorly cooked fish. The tapeworm attaches to the intestines of

the fish where it then lays eggs. While attached, the tapeworm absorbs

large quantities of vitamin B12 from the intestine eventually causing the

person to develop vitamin deficiency anemia. This is also, called perni-

cious anemia because there is insufficient vitamin B12 to make red

blood cells.

ROUNDWORMS (NEMATODES)

Roundworms are also known as nematodes and live in soil, fresh water, and salt-

water. Most of the over 80,000 species of roundworms are parasites and live in

plants or animals such as insects. They have a primitive body that consists of a

cylindrical tube that has tapered ends and is covered with a thick protective layer

called a cuticle.

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CHAPTER 11 The Eukaryotes 181

Common roundworms are:

• Ascaris lumbrieoides: A. lumbrieoides is a roundworm that is transmitted

by contaminated human fertilizer, food, or water. It causes ascariasis,

which is an infection of the small intestine.

• Strongyloides stercoralis: S. stercoralis is a roundworm whose larvae pen-

etrates human skin and spread into the small intestine where it causes

strongyloidiasis, which is an infection of the small intestine.

• Trichinella spiralis: T. spiralis is a roundworm whose larvae cause trichi-

nosis and live in undercooked meats, mainly pork. These juvenile worms

that are in the ingested meat mature in the small intestines of the host organ-

ism. The mature females burrow through the wall of the small intestines

and release their offspring (juveniles) into the blood of the host, where skele-

tal muscle is soon infected. It is these juveniles that burrow into the skeletal

muscle of the host. The larvae travel to the muscle where they form into a

sack (encyst), causing muscle pain and fever; this results in a large number

of eosinophilic leukocytes (eosinophilia). An eosinophilic leukocyte is a type

of white blood cell that increases with allergies and infections.

• Wuchereria bancrofti: W. bancrofti is a roundworm that lives in mosqui-

toes and causes elephantiasis when the infected mosquito bites a human.

The mosquito injects the larvae into the skin where they then migrate to the

lymph nodes, causing blockages.

• Onchocerca volvulus: O. volvulus is a roundworm that lives in the black

fly and causes river blindness when the black fly bites a human.

• Dracunculus medinensis: D. medinensis is a roundworm that lives in lob-

sters, crabs, shrimps, and other crustacea. When the infected crustacea is

ingested, this roundworm’s larvae migrate from the person’s intestines

through the abdominal cavity to subcutaneous tissue where they mature.

D. medinensis releases a toxic substance that creates a skin ulcer, which is

the symptom of dracunculosis disease.

• Hookworms are roundworms that have tiny hooks that are used to attach

it to a host, which is typically the intestine. Here are some common hook-

worms:

• Necator americanus: N. americanus, also known as the New World

hookworm, lives in the lower intestine and is the second most common

hookworm infection. Its eggs are passed into the feces. Once it comes

into contact with a human, it penetrates the skin and spreads into the

heart, lungs, and eventually the small intestine where it grows into an

adult. This can lead to severe blood loss and anemia.

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CHAPTER 11 The Eukaryotes182

• Ancylostoma duodenale: A. duodenale, also known as the Old World

hookworm, is similar to N. americanus, but is native to Southern Europe,

North Africa, Northern Asia, and parts of western South America.

• Ancylostoma braziliense: A. braziliense is a hookworm that exists in

cats and dogs and causes cutaneous larva migrans, which is also known

as creeping eruption. Its eggs are passed in feces and the larvae develop

in the soil. The larvae can tunnel into the epidermis of humans and can

cause an infection to develop.

• Ancylostoma caninum: A. caninum is a hookworm that exists in dogs

and frequently infects puppies. It eats away at the tissues in the small

intestine and sucks blood from the dog. This can result in diarrhea,

weight loss, anemia, and death. The larvae can tunnel into the epidermis

of humans and can cause an infection to develop.

PINWORMS

Pinworms can be up to 10 millimeters long and live in the large intestine.

Female pinworms crawl out the anus to lay eggs on the perianal skin.

Afterwards, she dies. Pinworms infect about 10 percent of humans, although

the person may not know he or she is infected: Pinworms cause few or no

symptoms besides a mild gastrointestinal upset and perianal itching, which can

lead to bacterial infections. Pinworms are highly contagious and can be trans-

mitted in bed linens and clothing that has been contaminated with eggs. A com-

mon pinworm is Enterobius vermicularis. Also known as E. vermicularis, it

is the most common pinworm in the United States. E. vermicularis causes

enterobiasis, in which the skin around the anus is so itchy that a person might

not be able to sleep.

QUIZ

1. Helminths are

(a) fungi

(b) algae

(b) worms

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CHAPTER 11 The Eukaryotes 183

2. Fungi are different from plants because

(a) fungi have chlorophyll

(b) plants have chlorophyll

(d) plants absorb nutrients from organic wastes

3. Mushrooms are

(a) fungi

(b) protozoa

(d) algae

4. The body of a mold or fleshy fungus is made up of long, loosely packed

filaments called

(a) soma

(b)

hyphae

(d) mycelium

5. Fungi imperfecti can reproduce

(a) sexually

(b) do not reproduce

(d) both (a) and (b)

6. These are unicellular algae that have a hard, double outer shell made of

silica

(a) diatoms

(b) chrysophytes

(d) phaeophyta

7. What are hemoflagellates?

(a) Protists

(b) Nematodes

(d) Proglottids

8. What are platyhelminths?

(a) Ringworms

(b) Nematodes

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(d) Hookworms

9. An example of a fluke would be

(a) H. ana

(b) D. latum

(d) E. vermicularis

10. Some protists use cilia to move food into a mouth-like opening called

(a) pseudopods

(b) a cytosome

(d) exocytosis

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CHAPTER

185

Viruses, Viroids,

and Prions

In this chapter, you will learn about viruses, how they work, and the diseases

they cause. You will also learn about viroids and prions. A viroid is a small

“naked” infectious RNA molecule that has similar properties of a virus. Prions

are particles of proteins and cause infections.

Viruses

In 1889, Dutch plant microbiologist Martinus Beijerinck described the concept

of viruses through his studies of Tobacco Mosaic Disease. Nobel prize–winner

Sir Peter Medawar described how microbiologists feel about viruses when he

said, “A virus is a piece of bad news wrapped in a protein.”

Viruses are strands of nucleic acids that are encased within a protein coat,

making them difficult to destroy. A microorganism needs both DNA and RNA in

order to reproduce. A virus cannot express genes without a host, because a virus

has either DNA or RNA but not both.

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A virus (Latin for “poison”) is an obligate intracellular parasite that can only

replicate inside a living host cell. Once inside the living host cell, a virus

becomes integrated in the metabolism of its host, making a virus difficult to con-

trol by chemical means. You cannot kill a virus with antibiotics. Drugs that

destroy the host’s ability to be used by a virus for replication tend to also be

highly toxic and have a negatively and sometimes deadly effect on the host cell.

Before a virus enters a cell, it is a free virus particle called a virion. A virion

cannot grow or carry out any biosynthetic or biochemical function because it is

metabolically inert. Viruses are not cells. They vary in size from 20 nanometers

(polio virus) to 300 nanometers (smallpox virus) and cannot be seen under a

light microscope.

In 1933, microbiologist Wendell Stanley of the Rockefeller Institute for Medical

Research showed that viruses could be regarded as chemical matter rather than

as living organisms.

VIRAL STRUCTURE

The major components of a virus are:

• Nucleic acid core. The nucleic acid core can either be DNA or RNA that

makes up the genetic information (genome) of the virus. RNA genomes

only occur in viruses.

• Capsid. A capsid is the protein coat that encapsulates a virus and protects

the nucleic acid from the environment. It also plays a role in how some

viruses attach to a host cell. A capsid consists of one or more proteins that

are unique to the virus and determine the shape of the virus.

• Envelope. An envelope is a membrane bilayer that some viruses have out-

side their capsid. If a virus does not have an envelope, the virus is called a

naked virus. Examples of diseases caused by naked viruses are chickenpox,

shingles, mononucleosis, and herpes simplex. A naked virus is more resist-

ant to changes and is less likely to be affected by conditions that can dam-

age the envelope. Environmental factors that can damage the envelope are:

• Increased temperature

• Freezing temperature

• pH below 6 or above 8

• Lipid solvents

• Some chemical disinfectants (chlorine, hydrogen peroxide, and phenol)

Naked viruses are more resistant to changes in temperature and pH. Examples

of diseases caused by naked viruses include poliomyelitis, warts, and the com-

mon cold.

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SHAPES OF VIRUSES

A virus can have one of two structures. These are:

• Helical virus. A helical virus is rod- or thread-shaped. The virus that causes

rabies is a helical virus.

• Icosahedral virus. An icosahedral virus is spherically shaped. Viruses that

cause poliomyelitis and herpes simplex are icosahedral viruses.

HOW VIRUSES REPLICATE

The easiest way to understand how viruses replicate is to study the life cycles of

viruses called bacteriophages. Bacteriophages replicate by either a lytic cycle or

a lysogenic cycle. The difference in these two cycles is that the cell dies at the

end of the lytic cycle and remains alive in the lysogenic cycle.

The first two scientists to observe bacteriophages were Frederic Twort of

England and Felix d’Herelle of France in the early 1900s. The name bacterio-

phage is credited to d’Herelle and means “eaters of bacteria.”

Lytic Cycle

The most studied bacteriophage is the T-even bacteriophage. The virions of T-

even bacteriophages are big, complex, and do not contain envelopes. The T-even

bacteriophages are composed of a head-and-tail structure and contain genomes

of double-stranded DNA. The lytic cycle of replication begins with the collision

of the bacteriophage and bacteria, called attachment. The tail of the bacterio-

phage attaches to a receptor site on the bacterial cell wall. After attachment, the

bacteriophage uses its tail like a hypodermic needle to inject its DNA (nucleic

acid) into the bacterium. This is called penetration. The bacteriophage uses an

enzyme called lysozyme in its tail to break down the bacterial cell wall, enabling

it to inject its DNA into the cell. The head or capsid of the bacteriophage remains

on the outside of the cell wall. After the DNA is injected into the host’s bacter-

ial cell’s cytoplasm, biosynthesis occurs. Here the T-even bacteriophage uses the

host bacterium’s nucleotides and some enzymes to make copies of the bacterio-

phage’s DNA. This DNA is transcribed to mRNA, which directs the synthesis of

viral enzymes and capsid proteins. Several of these viral enzymes catalyse reac-

tions that make copies of bacteriophage DNA. The bacteriophage DNA will then

direct the synthesis of viral components by the host cell.

Next maturation occurs. Here the T-even bacteriophage DNA and capsids are

put together in order to make virions.

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The last stage is the release of virions from the host bacterium cell. The bac-

teriophage enzyme lysozyme breaks apart the bacterial cell wall (lysis) and the

new virus escapes. The escape of this new bacteriophage virus will then infect

neighboring cells and the cycle will continue in these cells.

The Lysogenic Cycle

Some viruses do not cause lysis and ultimate destruction of their host cells which

they infect. These viruses are called lysogenic phages or temporate phages. These

bacteriophages establish a stable, long-term relationship with their host called

lysogeny. The bacterial cells infected by these phages are called lysogenic cells.

The most studied bacteriophage, which multiplies using the lysogenic cycle,

is the bacteriophage Lambda. This bacteriophage infects the bacterium E. coli.

When the bacteriophage Lambda penetrates an E. coli bacterium, the bacte-

riophage DNA forms a circle. The circle recombines with the circular DNA of

the bacteria. This bacteriophage DNA is called a prophage.

Every time the bacteria host cell replicates normally, so does the prophase

DNA. On occasion, however, the bacteriophage DNA can break out of the

prophage and initiate the lytic cycle.

ANIMAL VIRUSES

Animal viruses infect and replicate animal cells. They differ from bacterio-

phages in the way they enter a host cell. For example, DNA viruses enter an ani-

mal host in this

way:

• Attachment. Animal viruses attach to the host cell’s plasma membrane pro-

teins and glycoproteins (host cell receptors).

• Penetration. Animal viruses do not inject nucleic acid into the host eukary-

otic cell. Instead, penetration occurs by endocytosis, where the virion

attaches to the microvillus of the plasma membrane of the host cell. The

host cell then enfolds and pulls the virion into the plasma membrane, form-

ing a vesicle within the cell’s cytoplasm.

• Transcription in the nucleus by host RNA polymerase.

• Translation by host cell ribosomes.

• DNA replication by host DNA polymerase in the nucleus.

• Assembly of viral particles.

• Release from cell by lysis or exocytosis.

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RNA Viruses

• Attachment to host cell receptor.

• Fusion with membrane of host.

• Nucleocapsid enters the cytoplasm.

• Transcription in cytoplasm by viral RNA polymerase.

• Translation by host cell ribosomes.

• Assembly of viral particles.

• Release from cell.

VIRUSES AND INFECTIOUS DISEASE

Viruses are classified by the type of nucleic acid they contain, chemical and

physical properties, shape, structure, host range, and how they replicate.

DNA viruses

DNA viruses are viruses that have DNA but no RNA. Common DNA viruses are:

• Hepadnaviruses. Hepadnaviruses cause serum hepatitis. The hepatitis B

virus (HBV) is a common form of this virus that enters the body via hypo-

dermic needles, blood transfusion, or sexual relations. (Hepatitis A, C, D,

E, F, and G are not related and are RNA viruses).

• Herpesviridae. Herpesviridae causes the herpes virus. There are about 100

forms of herpes viruses including:

• Herpes simplex virus type I (HSV-1). Herpes simplex virus type I causes

encephalitis and enters the body through lesions on the lip, skin, or eyes.

• Herpes simplex virus type 2 (HSV-2). Herpes simplex virus type 2 is

sexually transmitted, affects the genital and lip area, and can lead to

carcinomas.

• Varicella-Zoster Virus (V2V). Varicella-Zoster virus causes chicken-

pox in the acute form and shingles in the latent form. Shingles appears

as vesicles along a nerve resulting in severe pain along the course of

the nerve.

• Cytomegalovirus (CMV). Cytomegalovirus causes an infection that usu-

ally goes unnoticed unless the person’s immune system is compromised,

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such as in the bodies of AIDS patients or in infants whose immune sys-

tems are not fully developed. This virus can be fatal to some infants.

• Epstein-Barr Virus (EBV). Epstein-Barr virus causes infectious mono-

nucleosis.

• Papovaviridae—Papovaviruses such as the human papilloma virus (HPV),

which causes warts (papillomas) and tumors (polyomas).

• Poxviridae. Poxviridae causes pox (pus-filled lesions) diseases such as

smallpox.

• Adenoviridae. Adenoviruses cause acute respiratory disease, which is the

common cold virus.

RNA virus

An RNA virus is a virus that contains RNA but not DNA. Common RNA

viruses are:

• Flaviviridae. Flaviviruses, such as the Dengue virus that causes Break

Bone Fever, are carried by mosquitoes. Break Bone Fever results in

skin lesions, fever, and muscle and joint pain, and is often fatal. Other

Flaviviruses include:

• St. Louis encephalitis virus. St. Louis encephalitis virus causes an infec-

tion that is not easily recognized. Wild birds and mosquitoes carry St.

Louis encephalitis virus. Monkeys carry a form of this virus called yel-

low fever virus, which is transmitted to humans by mosquitoes and

leads to severe liver damage.

• Hepatitis C virus (HCV). Hepatitis C Virus is called non-A Hepatitis

virus and non-B Hepatitis virus and results in chronic infection. Humans

contract this virus from needle pricks and blood transfusions.

• Picornavirus. Picornavirus such as the Poliovirus causes Poliomyelitis and

kills motor neurons resulting in weakness and loss of muscle tone (flaccid

paralysis). Others include:

• Hepatitis A Virus (HAV). Hepatitis A virus (HAV) is also known as

infectious hepatitis and is transmitted through a fecal-oral route.

• Rhinovirus is the most frequent cause of the common cold. It causes

localized upper respiratory tract infections.

• Retroviridae. Retroviruses are a group of RNA viruses that include the fol-

lowing commonly recognized viruses:

• Human immunodeficiency virus (HIV). (Lentivirus) human immunod-

eficiency virus is a virus that often results in acquired immunodeficiency

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syndrome (AIDS) This virus kills T-cells. A T-cell is a white blood cell

that fights infection and kills spontaneously arising tumors. HIV causes

Kaposi’s sarcoma, which is a rare form of cancer, and Pneumocystic

carinii, which is an opportunistic infection and causes pneumonia in

AIDS patients.

• Human T-cell leukemia virus 1 and 2. Human T-cell leukemia virus 1

and 2 is the virus that causes acute T-cell lymphocytic leukemia and

often contains genes that cause cancer (oncogenic).

• Togaviruses. Togaviruses is a virus, such as Estera equine encephalitis,

that is mainly transmitted through blood-sucking insects (arbovirus), such

as mosquitoes. It causes severe encephalitis. Another is the:

• Rubella virus. The rubella virus causes German measles, which can be

very dangerous if contracted during the first 10 weeks of pregnancy.

The rubella vaccine is used to weaken the disease producing ability of

the rubella virus.

• Orthomytoviruses. Orthomytoviruses, such as influenza viruses A, B, and

C, cause localized infection of the respiratory tract, which is usually not

serious unless the infected person is elderly or the person is infected with

secondary bacterial pneumonia. Influenza viruses A and B can cause

Guillain-Barré Syndrome, which is an inflammation of the nerves that are

outside the brain and spinal cord (peripheral nerves); it appears 3 to 5

weeks after a person contracts the flu or after the person receives a flu vac-

cine. Influenza virus B causes Reyes syndrome, which is lethal to the liver

and the brain and causes a brain disease (encephalopathy) following a mild

flu, chickenpox, or the administration of aspirin.

• Paramyxovirus. Paramyxovirus, such as the parainfluenza virus (Sendai

virus) causes croup in infants. Two other types of paramyxovirus are:

• Mumps virus. The mumps virus causes an enlargement of one or both

parotid glands and swelling and pain in the testes and ovaries. There is

a vaccine to protect humans from the mumps virus.

• Measles virus. The measles virus, which is also known as rubeola,

causes measles. The measles virus causes a slow degeneration of the

nervous system of teenagers and young adults. If not treated, measles

can progress into encephalomyelitis or pneumonia.

• Rhabdovirus. Rhabdovirus, such as the rabies virus (Lyssavirus), causes

rabies following an animal bite. In rare cases, a person can be infected by

inhaling the virus. Some animals such as bats pass the rabies virus through

to their feces.

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• Filoviridae. Filovirus, an example would be the ebola virus which causes

African hemorrhagic fever.

Oncogenic viruses

Oncogenic viruses are viruses that produce tumors when they infect humans.

The more common oncogenic viruses are:

• Human papillomavirus (HPV). Human papillomavirus causes common

warts but also is believed to cause cervical cancer.

• Epstein-Barr virus (EBV). Epstein-Barr virus causes Burkitt’s lymphoma,

which is a tumor of the jaw. It is seen mainly in African children and causes

a tumor in the nasopharyngeal (nasopharyngeal carcinoma).

• Herpes simplex virus 2 (HSV-2). Herpes simplex virus 2 causes genital

herpes, cervical cancer (cervical carcinoma), and oral lesions.

• Human T-cell leukemia virus 1 (HTLV-1). Human T-cell leukemia virus 1

causes acute T-cell lymphocytic leukemia, which

is a cancer that affects T-

cell–forming tissues.

• Human T-cell leukemia virus 2 (HTLV-2). Human T-cell leukemia virus 2

causes atypical hairy cell leukemia.

Plant viruses

Some viruses cause diseases in plants.

RNA plant virus:

• Picornaviridae: Includes the bean mosaic virus.

• Reovirus: Includes the wound tumor virus.

DNA plant virus:

• Papovaviridae: Includes the cauliflower mosaic virus.

Viroids

In 1971, plant pathologist O.T. Diener discovered an infectious RNA particle

smaller than a virus that causes diseases in plants. He called it a viroid. Viroids

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infect potatoes, causing potato, spindle tuber disease. They infect chrysanthe-

mums, stunting their growth. Viroids cause cucumber pale fruit disease. Millions

of dollars are lost each year in crop failures caused by viroids.

A viroid is similar to a virus in that it can reproduce only inside a host cell as

particles of RNA. However, it differs from a virus in that each RNA particle con-

tains a single specific RNA. In addition, a viroid does not have a capsid or an

envelope. Some viruses do not have an envelope.

Prions

A prion is a small infectious particle that contains a protein. Some researchers

believe that a prion consists of proteins without nucleic acids because a prion is

too small to contain a nucleic acid and because a prion is not destroyed by agents

that digest nucleic acids.

Prion diseases referred to as transmissible spongiform encephalopathies

(TSEs) are progressive neurological diseases that are fatal to humans and ani-

mals. Researchers believe that prions cause Creutzfeldt-Jakob disease.

Creutzfeldt-Jakob disease is a neurological disease that causes progressive

dementia first observed by Hans Gerhard Creutzfeldt and Alfon Maria Jakob in

the 1920s. In 1976, Carlton Gajdusek won the Nobel prize for his work with the

TSE Kuru. Kuru is characterized by progressive ataxia incapacitation and death.

In 1982, neurobiologist Stanley Prusiner proposed that proteins cause the

neurological disease Scrapie, which is a degenerative neural conditon in sheep.

Prusiner named this infectious protein prion. Prions also cause other neurologi-

cal diseases such as Kuru and Gerstmann-Strausler-Sheinker syndrome.

However, scientists are still studying prions to learn their origins and how pri-

ons replicate and cause disease.

Quiz

1. A virion is:

(a) another name for a virus

(b) a virus particle

(d) a mature virus

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2. A naked virus is

(a) a virus without an envelope

(b) a virus without a capsid

(d) a virus without DNA

3. A bacteriophage is:

(a) a virus that can be killed by antibiotics

(b) a virus that acts like a bacteria

(d) a naked virus that uses bacteria as a host cell

4. What does a lytic virus inject into a host cell?

(a) Nothing

(b) Cytoplasm

(d) Nucleic acid

5. What is a capsid?

(a) A capsid is the protein coat that encapsulates a virus

(b) A capsid is the membrane bilayer of a virus

(d) A capsid is the envelope around a virus

6. The envelope of a virus is made of:

(a) pieces of the capsid

(b) pieces of the host cell’s membrane

(d) pieces of the nuclei of the host cell

7. A state of lysogeny is:

(a) when the envelope virus and the host cell interact with each other

(b) when the envelope virus and the host cell don’t interact with each

other

(d) when the envelope of a virus interacts with DNA or RNA

8. Oncogenic viruses

(a) cause tumors

(b) cause the common cold

(d) cause influenza

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9. What is a small infectious particle that contains a protein?

(a) Viroid

(b) Capsid

(d) Prion

10. Genetic information of a virus is contained in:

(a) the envelope

(b) central nucleic acid

(d) the viroid

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CHAPTER

197

Epidemiology

and Disease

No one wants to give a friend a cold, so we always cover a sneeze with our

hands. However, the germs are still on our hands and are transferred to door-

knobs, the food we touch, and to friends when we greet them with a handshake.

In this chapter, you’ll learn about diseases and how disease are spread from

one person to another. You’ll also learn ways that outbreaks of disease are con-

trolled and prevented by taking simple precautions.

What Is Epidemiology?

Epidemiology is the study of the distribution and determinants of diseases or

conditions of a population. The word originated from the two Greek words epi

(“among”) and demos (“people”), or “among the people.” An epidemiologist is

a scientist trained to identify and prevent diseases in a given population. They

are concerned with the etiology, or the specific cause of a disease in a given pop-

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ulation. Epidemiologists use this information to design ways of preventing and

controlling outbreaks of disease.

Epidemiology is considered a branch of microbiology because microorgan-

isms cause many diseases. It can also be considered a branch of ecology because

of the relationship among pathogens, their hosts, and the environment. The sci-

ence of epidemiology provides the methods and information that are used to

understand and control outbreaks of diseases in human populations, making it

important for public health. An epidemiologist is a person who is trained to iden-

tify and prevent diseases in a given population or a medical doctor who is trained

to identify and treat diseases in individual people.

Epidemiologists are concerned with the frequency or prevalence of diseases

in a given population. An epidemiologist will identify the factors that cause dis-

ease or how that disease is transmitted and how the spread of communicable and

noncommunicable diseases can be prevented. The incidence rate of a disease is

the total number of new cases seen within a calendar year. The prevalence of a

disease is the number of people infected at any given time. The prevalence rate

is the total number of old and new cases of a disease. Frequencies are also

expressed as proportions of the total population. The morbidity rate is the state

of illness or the number of people in a given population that are ill. This is

expressed as the number of cases per 100,000 people per year. The mortality rate

is the number of people that are dead. This is measured as the number of deaths

from a specific cause per 100,000 people per year.

Classification of Disease

Epidemiologists measure the frequency of diseases within a given population in

regards to the geographical size of the area and the amount of damage the dis-

ease inflicts on the population. Diseases can be classified as endemic, sporadic,

epidemic, or pandemic.

An endemic disease is the average or normal number of cases of a disease in

a certain population.The number of people contracting the disease and the sever-

ity of the disease is so low that it raises little concern and does not constitute a

health problem. An example is the varicella-zoster virus (the virus that causes

chickenpox). Chickenpox is an endemic disease that usually affects children and

is seasonal. An endemic disease can give rise to epidemics.

A sporadic disease occurs when there are small numbers of isolated cases

reported. Sporadic diseases do not threaten the population.

An epidemic disease arises when the level of disease in a certain population

exceeds the endemic level. This disease will cause an increase in mortality rate

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and the rate of morbidity. The level of destruction will be so large that it will

cause a significant public health concern.

A disease becomes pandemic when it is distributed throughout the world. For

example, in 1918 the swine flu (influenza) reached pandemic proportions. Some

experts consider the HIV virus to be pandemic.

In a common source epidemic, large numbers of the population are suddenly

infected from the same source. These epidemics usually are attributed to a con-

taminated supply of water or improperly prepared or handled food. An example is

people who eat contaminated chicken salad at a college cafeteria. Everyone who

eats the chicken salad on this particular day will become infected and feel ill. The

epidemic will subside very fast, though, as the source of infection is eradicated.

A propagated epidemic occurs from person-to-person contact. The disease-

causing agent moves from a person who is infected to a person who is not

infected. In a propagated epidemic, the number of new cases rises and falls

much slower than in common source epidemics, making the pathogen much

harder to isolate and thus eliminate. An example is a “flu” virus.

Pathognomonic is a word that refers to the specific characteristics of disease.

Immunity is the specific resistance to disease. Virulence is the degree of patho-

genicity or the capacity of an organism to produce disease.

Pathology is the study of disease. It is derived from Pathos (“suffering”) and

logos which means (“science”). Pathology is that branch of discourse concerned

with the structural and functional changes that occur due to a disease-causing

agent or pathogen. A pathologist is a scientist or physician who studies the cause of

diseases, or etiology, and pathogenesis, the manner in which a disease develops.

Infection Sites

The sites where a microorganism can infect a host organism are called reservoirs

of infection. In these sites a microorganism can maintain its ability to cause

infection. Reservoirs of infection include humans, some animals, certain non-

living media, and inanimate objects.

HUMAN RESERVOIRS

Humans make good reservoirs because they can transmit organisms to other

humans. Certain disease-causing agents have an incubation period during which

they are contagious and can spread the disease even before a person exhibits

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signs or symptoms. These disease-causing agents can even be contagious during

the recovery period.

When a person becomes symptomatic (feeling sick), the individual seeks

medical attention and receives treatment. In many cases, however, diseases are

spread from a person with subclinical findings—the symptoms are very mild and

not recognizable. These individuals can spread the disease to a healthy person.

Asymptomatic cases are a problem because infected people can infect other indi-

viduals without knowing they are infected. These individuals that are “carriers”

of disease are called disease carriers.

Carriers of disease are classified as:

• Subclinical carriers. These individuals never develop clinical symptoms

of the disease.

• Incubatory carriers. These individuals transmit the disease before be-

coming symptomatic.

• Convalescent carriers are individuals are recovering from the disease; how-

ever, they can still infect other people.

• Chronic carriers. These individuals develop chronic infections and trans-

mit the infection for long periods of time.

ANIMAL RESERVOIRS

Many microorganisms can infect both humans and animals. Many of these dis-

ease-causing agents use animals as reservoirs of infection to infect humans.

Apes and monkeys are good examples of animals that serve as reservoirs for

human infection because they are physiologically similar to humans. When an

animal infects humans, the humans can also serve as reservoirs for the infection.

A disease that is transmitted from domestic and wild animals to humans is

called zoonosis. Two examples of zoonoses are anthrax, which is a bacterial dis-

ease that causes infection in dogs, cats, cattle, and other domestic animals.

Humans become infected with direct contact with the animals, their wool, or

hides, contaminated soil, inhalation of spores, and ingestion of meat or milk.

Another is rabies, a virus that infects dogs, cats, skunks, wolves, and bats.

Humans become infected through infected saliva in bite wounds. Humans and

domestic animals can also be reservoirs for wild animals.

NONLIVING RESERVOIRS

Examples of nonliving reservoirs are water and soil. Soil is a good reservoir for

the bacterium Clostridium tetani, which causes the disease tetanus. Conta-

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minated water infected with human or animal fecal matter can contain many

diseases-causing agents. An example is the bacterium Vibrio cholera, which

causes Asiatic cholera, a disease caused by feces contaminated water where san-

itation is poor. This organism invades the intestines and causes severe vomiting,

diarrhea, abdominal pain, and dehydration.

Disease Transmission

A disease must have a portal of exit from the reservoir and a portal of entry to

the infected host. This is how diseases are spread and new cases of infection occur.

Examples of portal of exit are the respiratory tract, digestive tract, urinary tract,

skin, and utero transmission. Diseases can spread by three different modes of trans-

mission: contact transmission, vehicle transmission, and vector transmission.

CONTACT TRANSMISSION

Contact transmission of a disease-causing agent can either be direct or indirect.

Direct contact transmission occurs from skin-to-skin contact, such as shaking

hands, kissing, sexual contact, or making contact with open sores. Examples of

diseases caused by contact transmission include herpes, syphilis, and staphylo-

coccal infections.

Indirect contact transmission occurs when infection is spread through any

nonliving, inanimate object. These contaminated inanimate objects are called

fomites and include bedding, towels, clothing, dishes, utensils, glasses and cups,

diapers, tissues, and even bars of soap. Examples of diseases caused by indirect

contact transmission include the rhinovirus, hepatitis B, and tetanus.

Droplet transmission is a form of contact transmission that occurs through

sneezing, coughing, and speaking in close contact with an infected individual.

Examples of diseases transmitting in this manner are pneumonia, influenza, the

common cold, and whooping cough.

VEHICLE TRANSMISSION

In vector transmissions, pathogens can be spread through the air and in water,

food products, and body fluids (such as blood and sem*n). Airborne microor-

ganisms mainly come from animals, plants, water, and soil. These microorgan-

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isms can transmit disease through air. They can travel one meter or more through

an air medium to spread infection.

Airborne pathogens have the greatest chance of infecting new individuals when

these individuals are crowded together indoors or in a climate-controlled build-

ing where heating and air conditioning units regulate temperature and very

little fresh air enters the building. Airborne pathogens can fall to the floor and

combine with dust particles. This dust can then be stirred up with walking, dry

mopping, or changing bedding and clothing. Examples of diseases that are trans-

mitted by airborne transmissions and dust particles are measles, chickenpox, histo-

plasmosis, and tuberculosis.

Waterborne microorganisms that cause pathologies do not grow in pure water.

They can survive in water with small amounts of nutrients but thrive in polluted

water, such as water contaminated with fertilizer and sewage (which is rich in

nutrients). Waterborne pathogens are usually transmitted in contaminated water

supplies by either untreated or inadequately treated sewage. Indirect fecal-oral

DRUGS

“Doc, give me a pill to knock out whatever is causing me to be sick!” All of us

say this whenever we come down with an illness. All we want is a magic pill that

makes us feel better. Sometimes that magic pill—or injection—contains a

microbe that seeks out and destroys pathogenic microbes, which are disease-

causing microbes.

In this chapter you’ll learn about antimicrobial drugs that are given as

chemotherapy to cure disease. These antimicrobial drugs contain microbes that

kill other microbes.

INTRODUCTIONxviii

00 Betsy FM 5/11/05 2:20 PM Page xviii

I would like to acknowledge my mentor, colleague, and friend Professor Robert

Highley for all his encouragement and technical support in the production of

this book; my friend Ms. Joan Sisto for all her hours of computer work; and my

friend and coauthor Professor Jim Keogh for asking me to help write this book.

Thank you.

DR. TOM BETSY

Professor Robert Highley has done a magnificent job as technical editor on this

project. His diligence and attention to detail has made Microbiology Demystified

a rewarding addition to every microbiology student’s library.

JIM KEOGH

xix

ACKNOWLEDGMENTS

00 Betsy FM 5/11/05 2:20 PM Page xix

MICROBIOLOGY DEMYSTIFIED

00 Betsy FM 5/11/05 2:20 PM Page xxi

CHAPTER

The World of the

Microorganism

Microbiology is the study of microorganisms, which are tiny organisms that

live around us and inside our body. An organism is a living thing that ingests and

breaks down food for energy and nutrients, excretes undigested food as waste,

and is capable of reproduction. You are an organism and so are dogs, cats,

insects, and other creatures that you see daily.

A microorganism is simply a very, very small organism that you cannot see

with your naked eye, but you sure feel its effect whenever your eyes fill with

water and mucus flows like an open faucet from your nose. You call it a head

cold. Actually, you are under siege by an army of microorganisms attacking

membranes inside your body. Watery eyes and a runny nose are ways that you

fight microorganisms by flushing them out of your body.

Microorganisms are a key component of biological warfare along with chem-

icals that disrupt homeostasis. The anthrax attack that followed the 9/11 terror-

ist attacks clearly illustrated how a dusting of anthrax in an envelope can be

lethal to people in an office building. Anthrax is a disease caused by the micro-

organism Bacillus anthracis, a bacterium that forms endospores and infiltrates

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the body by ingestion, skin contact, and inhalation. An endospore is a bacterium

in a dormant state that forms within a cell.

Fortunately, incidents of biological attacks using microorganisms have been

infrequent. However, there are thousands of microorganisms all around us that

can be just as deadly and debilitating as the microorganisms used in warfare

throughout history.

Types of Microorganisms

UNFRIENDLY MICROORGANISMS

An infection is caused by the infiltration of a disease-causing microorganism

known as a pathogenic microorganism. Some pathogenic microorganisms infect

humans, but not other animals and plants. Some pathogenic microorganisms that

infect animals or plants also infect humans.

Pathogenic microorganisms make headlines and play an important role in his-

tory. Legendary gunfighter John “Doc” Holliday is famous for his escapades in

the Wild West. He dodged countless bullets, showing that he was the best of the

best when it came to gun fighting. Yet Mycobacterium tuberculosis took down

Doc Holliday quietly, without firing a shot. Mycobacterium tuberculosis is the

bacterium that causes tuberculosis (Fig. 1-1). This bacterium affects the lung tis-

sue when droplets of respiratory secretions or particles of dry sputum from a per-

son who is infected with the disease are inhaled by an uninfected person.

CHAPTER 1 The World of the Microorganism2

Fig. 1-1. Mycobacterium tuberculosis is the bac-

terium that causes tuberculosis.

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Yersinia pestis nearly conquered Europe in the fourteenth century with the

help of the flea. Yersinia pestis is the microorganism that caused the Black

Plague (Fig. 1-2) and killed more than 25 million Europeans. You might say that

Yersinia pestis launched a sneak attack. First, it infected fleas that were carried

into populated areas on the backs of rats. Rodents traveled on ships and then

over land in search of food. Fleas jumped from rodents and bit people, trans-

mitting the Yersinia pestis microorganism into the person’s blood stream.

In an effort to prevent the spread of Yersinia pestis, sailors entering Sicily’s

seaports had to wait 40 days before leaving the ship. This gave time for sailors

to exhibit the symptoms of the Black Plague if the Yersinia pestis microorgan-

ism had infected them. Sicilians called this quarantenaria. Today we know it as

quarantine. Sailors who did not exhibit these symptoms were not infected and

free to disembark.

Campers and travelers sometimes become acquainted with Giardia lamblia,

Escherichia coli, or Entameba histolytica whenever they visit tropical countries.

Travelers who become infected typically do not die but come down with a bad

case of diarrhea.

FRIENDLY MICROORGANISMS

Not all microorganisms are pathogens. In fact many microorganisms help to

maintain homeostasis in our bodies and are used in the production of food and

other commercial products. For example, flora are microorganisms found in

our intestines that assist in the digestion of food and play a critical role in the

formation of vitamins such as vitamin B and vitamin K. They help by breaking

down large molecules into smaller ones.

CHAPTER 1 The World of the Microorganism 3

Fig. 1-2. Yersinia pestis is the microorganism

that caused the Black Plague.

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What Is a Microorganism?

Microorganisms are the subject of microbiology, which is the branch of science

that studies microorganisms. A microorganism can be one cell or a cluster of

cells that can be seen only by using a microscope.

Microorganisms are organized into six fields of study: bacteriology, virology,

mycology, phycology, protozoology, and parasitology.

BACTERIOLOGY

Bacteriology is the study of bacteria. Bacteria are prokaryotic organisms. A

prokaryotic organism is a one-celled organism that does not have a true nucleus.

Many bacteria absorb nutrients from their environment and some make their own

nutrients by photosynthesis or other synthetic processes. Some bacteria can

move freely in their environment while others are stationary. Bacteria occupy

space on land and can live in an aquatic environment and in decaying matter.

They can even cause disease. Bacillus anthracis is a good example. It is the bac-

terium that causes anthrax.

VIROLOGY

Virology is the study of viruses. A virus is a submicroscopic, parasitic, acellular

entity composed of a nucleic acid core surrounded by a protein coat. Parasitic

acellular means that a virus receives food and shelter from another organism and

is not divided into cells. An example of a virus is the varicella-zoster virus (Fig.

1-3), which is the virus that causes chickenpox in humans.

CHAPTER 1 The World of the Microorganism4

Fig. 1-3. The varicella-zoster virus causes chickenpox.

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MYCOLOGY

Mycology is the study of fungi. A fungus is a eukaryotic organism, often micro-

scopic, that absorbs nutrients from its external environment. Fungi are not pho-

tosynthetic. A eukaryotic microorganism is a microorganism whose cells have

a nucleus, cytoplasm and organelles. These include yeasts and some molds.

Tinea pedis, better known as athlete’s foot, is caused by a fungus.

PHYCOLOGY

Phycology is the study of algae. Algae are eukaryotic photosynthetic organisms

transmission of pathogens occurs when the disease-causing microorganism liv-

ing in the fecal matter of one organism infects another organism. Bacterial

pathogens infect the digestive system, causing gastrointestinal signs and symp-

toms. Examples of waterborne diseases are shigellosis and cholera.

Foodborne pathogens are normally transmitted through improperly cooked

or improperly refrigerated food, or unsanitary conditions. Improper hygiene of

the part of food handlers also plays a key role in foodborne transmission. Food-

borne pathogens can produce gastrointestinal signs and symptoms. Examples of

foodborne diseases are salmonellosis, typhoid fever, tapeworm, and listeriosos.

Vector Transmission

Vector spread is the transmission of an infectious agent by a living organism

to humans. Most vectors are ticks, flies, and mosquitoes. These organisms are

called arthropods. Vectors can transmit disease in two ways. First, mechanical

vectors can passively transmit disease with their bodies. An example is the

common housefly.

These animals commonly feed on fecal matter. They then fly to feed on human

food, transmitting pathogens along the way. Keeping mechanical vectors away

from food preparation and eating areas are means of prevention. Remember: The

fly that is walking across your picnic lunch may have just walked across dog or

cat feces. Examples of a few diseases transmitted by mechanical vectors are

diarrhea caused by E. coli bacteria, conjunctivitis, and salmonellosis.

The second type of vectors are biological vectors and can actively transmit

disease-causing pathogens that complete part of their life cycle within the vector.

In most vector-transmitted diseases, a biological vector is the host for a phase of

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the life cycle of the pathogen. An example of a host organism is a mosquito that

infects a human with malaria. Other diseases caused by biological transmission

vectors are yellow fever, the plague, typhus, and Rocky Mountain spotted fever.

To cause infection, a microorganism must enter the body and have access to

body tissues. The sites where microorganisms enter the body are called portals

of entry. The portal of entry is similar to the portal of exit for the host to be sus-

ceptible for a certain disease. The portals of entry include the skin, digestive

tract, respiratory tract, and urinary tract. Microorganisms can invade tissues

directly or cross the placenta to infect the fetus. Skin that is intact prevents most

microorganisms from entering the body, although some enter the ducts of sudo-

riferous glands (sweat glands) and hair follicles to gain entrance into the body.

Fungi can invade cells on the surface of the body and some can even invade

other tissues. The larvae of parasitic worms can work their way through the skin

and enter tissues. An example of a parasitic worm is the hookworm.

Mucous membranes make direct contact with the external environment. This

allows microorganisms to enter the body. Examples of mucous membranes are

the eyes, nose, mouth, urethra, vagin*, and anus. The respiratory tract is an area

of the body where microorganisms typically enter on dust particles that are

inhaled with air or in aerosol droplets. Microorganisms that infect the digestive

tract, are normally ingested with contaminated water or food, or even from bit-

ing the nails of contaminated fingers.

Many genitourinary infections are the result of sexual contact. Skin that is not

intact due to injury, surgery, injections, burns, and bites makes it easy for invad-

ing microorganisms to penetrate body tissues. Common portals of entry are

insect bites. Many parasitic diseases are caused by the bites of insects. Some dis-

eases can affect the fetus through the placenta of an infected mother. Viruses

such as the HIV virus, rubella (German measles), and the bacteria that cause

syphilis behave in this way.

The transmission of disease by carriers causes epidemiological problems

because carriers usually do not know they are infected and spread the disease,

causing sudden outbreaks. Carriers can transmit disease by direct and indirect

contact or through vehicles, such as water, air, and food.

The Development of Disease

In order for a pathogen to infect a host, there must be a susceptible host for the

disease to be transmitted. If a host’s resistance is low (resistance is the ability to

ward off disease), its susceptibility increases (its chances of becoming infected

increase). Primary defense mechanisms of the body for resistance include intact

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skin (no cuts or abrasions), mucous membranes, a good cough reflex, normal

gastric juices, and normal bacterial flora.

If a microorganism penetrates these defenses the development of a disease

process begins. First there may be an incubation period. This is the time between

the initial exposure and start of the infection to the first appearance of signs and

the feeling of symptoms. Different microorganisms have different incubation

periods. An examples is the Epstein-Barr virus, which causes infectious mono-

nucleosis and has an incubation period of two to six weeks.

The varicella-zoster virus, which causes varicella (chickenpox), has an incu-

bation period of two weeks. The human immunodeficiency virus, the virus that

causes AIDS, has an incubation period of 7 to 11 years. During this phase, the

disease can be spread from the infected individual to a non-infected individual.

The prodromal period follows the incubation period. This period presents

with mild symptoms.

The period of illness is the acute phase of the disease. Here the individual

presents with signs and symptoms of the disease. Signs are objective findings

that an observer or physician can see. These are physical changes that can be

measured. Examples of signs are fever, skin color or lesions, blood pressure,

inflammation, and paralysis.

Symptoms are subjective and cannot be seen by an observer. Symptoms pres-

ent as changes in bodily functions, such as pain, numbness, chills, general fatigue,

or gastrointestinal discomfort. It is in this period of the disease where white blood

cells may increase and the individual’s immune system responds to combat the

disease-causing pathogen. If the individual’s defense mechanism of the immune

system does not successfully overcome the disease or if the disease is not treated

properly, the person can die.

During the period of decline, the individual’s signs and symptoms subside

and the person feels better. This period may take 24 hours to several days.

During this time, the individual is prone to secondary infections.

The period of convalescence is the phase where recovery has occurred. The

body regains strength and is returned to a state of normality. During this phase,

infection can also be spread.

Epidemiological Studies

Epidemiological studies began in 1855 with the work of English physician John

Snow. Snow conducted studies relating to the cholera outbreak in London,

England. Snow, through careful analysis of deaths related to cholera, case histo-

ries of victims, and interviews with survivors, traced the source of the epidemic

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to a water pump. He concluded that individuals who died from cholera drank

water contaminated with human feces. Snow’s study and his method of analyz-

ing where and when a disease could occur and the transmission of that disease

within a given population gave way to a new approach in medical research and

epidemiological studies.

It was not until 1883 that the cholera bacterium Vibrio cholerae was identi-

fied by Robert Koch. After the studies of Snow, other investigators conducted

epidemiological studies. Epidemiologists now use three types of studies when

determining the occurrence of disease: descriptive, analytical, and experimental.

Descriptive epidemiology is the

that transform sunlight into nutrients using photosynthesis. A eukaryotic photo-

synthetic microorganism is a microorganism whose cells have a nucleus, nuclear

envelope, cytoplasm, and organelles and that is able to carry out photosynthesis.

PROTOZOOLOGY

Protozoology is the study of protozoa, animal-like single-cell microorganisms

that can be found in aquatic environments. Many obtain their food by engulfing

or ingesting smaller organisms. Protozoa are found in aquatic and terrestrial

environments. An example is Amoeba proteus.

PARASITOLOGY

Parasitology is the study of parasites. A parasite is an organism that lives at the

expense of another organism or host. Parasites that cause disease are called

pathogens. Examples of parasites are bacteria, viruses, protozoa, and many ani-

mals such as worms, flatworms, and arthropods (insects).

What’s in a Name: Naming and Classifying

Carl Linnaeus developed the system for naming organisms in 1735. This system

is referred to as binominal nomenclature. Each organism is assigned two latin-

ized names because Latin or Greek was the traditional language used by schol-

ars. The first name is called the genus. The second name is called the specific

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epithet, which is the name of the species, and is not capitalized. The genus and

the epithet appear underlined or italicized.

The name itself describes the organism. For example, Staphylococcus aureus

is a very common bacterium. Staphylococcus is the genus and aureus is the epi-

thet. In this case, the genus describes the appearance of the cells. Staphylo means

a clustered arrangement of the cells and coccus signifies that the cells are spheres.

In other words, this means a cluster of sphere-like cells. Aureus is the Latin word

for golden, which means that the cluster of sphere-like cells has a golden hue.

Sometimes an organism is named for a researcher, as is the case with

Escherichia coli (Fig. 1-4), better known as E. coli. The genus is Escherichia,

which is named for Theodor Escherich, a leading microbiologist. The epithet is

coli, which implies that the bacterium lives in the colon (large intestine).

Organisms were classified into either the animal kingdom or the plant king-

dom before the scientific community discovered microorganisms in the seven-

teenth century. It was at that time when scientists realized that this classification

system was no longer valid.

Carl Woese developed a new classification system that arranged organisms

according to their molecular characteristics and then cellular characteristics.

However, it wasn’t until 1978 when scientists could agree on the new system for

classifying organisms, and it took 12 years after this agreement before the new

system was published.

Woese devised three classification groups called domains. A domain is larger

than a kingdom. These are:

Domains

• Eubacteria: Bacteria that have peptidoglycan cell walls. (Peptidoglycan

is the molecular structure of the cell walls of eubacteria which consists of

N-acetylglucosamine, N-acetylmuramic acid, tetrapeptide, side chain and

murein.)

CHAPTER 1 The World of the Microorganism6

Fig. 1-4. E. coli is a bacterium that lives in the colon.

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• Archaea: Prokaryotes that do not have peptidoglycan cell walls.

• Eucarya: Organisms from the following kingdoms:

Kingdoms

• Protista (Note: This is in the process of changing.)—algae, protozoa, slime

molds.

• Fungi—one-celled yeasts, multicellular molds, and mushrooms.

• Plantae—moss, conifers, ferns, flowering plants, algae.

• Animalia—insects, worms, sponges, and vertebrates.

How Small Is a Microorganism?

Microorganisms are measured using the metric system, which is shown in Table

1.1 In order to give you some idea of the size of a microorganism, let’s compare

a microorganism to things that are familiar to you.

German shepherd 1 meter

Human gamete (egg) from a female ovary 1 millimeter

A human red blood cell 100 micrometers

A typical bacterium cell 10 micrometers

A virus 10 nanometers

An atom 0.1 nanometer

Your Body Fights Back

Immunology is the study of how an organism specifically defends itself against

infection by microorganisms. When a microorganism such as the bacterium

Streptococcus pyogenes, which can cause strep throat, invades your body, white

blood cells engulf the bacterial cells and digest it in an immune response called

phagocytosis. Phagocytosis is the ability of a cell to engulf and digest solid mate-

rials by the use of pseudopods or “false feet.”

Phagocytosis was discovered in 1880 by Russian zoologist Elie Metchnikoff,

who was one of the first scientists to study immunology. Metchnikoff studied the

body’s defense against disease-causing agents and invading microorganisms. He

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discovered that leukocytes (white blood cells) defended the body by engulfing

and eating the invading microorganism.

DRUGS: SEND IN THE CAVALRY

Invading microorganisms activate your body’s immune system. It is at this point

when you experience a fever and feel sick. In an effort to help your immune sys-

tem, physicians prescribe drugs called antibiotics that contain one or more

antimicrobial agents that combat bacteria. An antimicrobial agent is a substance

that specifically inhibits and destroys the attacking microorganism.

One of the most commonly used antimicrobial agent is penicillin. Penicillin

is made from Penicillium, which is a mold that secretes materials that interfere

with the synthesis of the cell walls of bacteria causing “lysis,” or destruction of

the cell wall, and kills the invading microorganism.

IMMUNITY: PREVENTING A MICROORGANISM ATTACK

Our bodies have a wide range of body responses in the fight against pathogens.

These responses are referred to as nonspecific resistance. Resistance is the abil-

ity of the body to ward off disease. The lack of resistance is called susceptibil-

ity. When your immune system is compromised you become susceptible to

pathogens invading your body where they divide into colonies causing disease,

making you sick.

Generally, your first line of defense is to use mechanical and chemical means

to prevent a pathogen from entering your body. Skin is the primary mechanical

means to fight pathogens; it acts as a barrier between the pathogen and the inter-

nal structures of your body. Mucous membranes are another mechanical barrier;

CHAPTER 1 The World of the Microorganism8

Unit Fraction of Standard English Equivalent

meter (m) 3.28 feet

centimeter (cm) 0.01 m = 10−2 0.39 inch

millimeter (mm) 0.001 m = 10−3 0.039 inch

micrometer (µm) 0.000001 m = 10−6 0.000039 inch

nanometer (nm) 0.000000001 m = 10−9 0.000000039 inch

Table 1-1. Quantity and Length: Metric and English Equivalents

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they move the pathogen using tears and saliva (to flush it) and mucus cilia in the

respiratory track to physically move it. Urination, defecation, and vomiting are

other mechanical means to combat a pathogen by forcefully removing the

pathogen from your body.

Chemical means attack a pathogen by changing its pH properties. Skin sebum

is an important defense. Sebum is a thick substance secreted by the sebaceous

glands; it consists of lipids and cellular debris that have a low pH, enabling it to

chemically destroy a pathogen.

Sweat contains the enzyme lysozyme, which attacks the cell walls of bacte-

ria. Hyaluronic acid found in areolar connective tissue sets up a chemical barrier

that restricts a pathogen to a localized area of the body. Likewise, gastric juice

and vagin*l secretions have a low pH that is a natural barrier to many kinds of

pathogens.

History of the Microscope

Diseases are less baffling today than they were centuries ago, when scientists

and physicians were clueless as to what causes disease. Imagine for a moment

that a close relative had taken ill. One day

she was well and the next day she was

sick for no apparent reason. Soon she was dead if her body couldn’t fight the ill-

ness. You couldn’t see whatever attacked her—and neither could the doctor.

ZACHARIAS JANSSEN

In 1590, Zacharias Janssen developed the first compound microscope in

Middleburg, Holland. Janssen’s microscope consisted of three tubes. One tube

served as the outer casing and contained the other two tubes. At either ends of the

inner tubes were lenses used for magnification. Janssen’s design enabled scientists

to adjust the magnification by sliding the inner tubes. This enabled scientists to

enlarge the image of a specimen three and nine times the specimen’s actual size.

ROBERT HOOKE

In 1665, Robert Hooke, an English scientist, popularized the use of the compound

microscope when he placed the lenses over slices of cork and viewed little boxes

that he called cells. It was his discovery that led to the development of cell the-

ory in the nineteenth century by Mathias Schleiden, Theodor Schwann, and

Rudolf Virchow. Cell theory states that all living things are composed of cells.

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ANTONI VAN LEEUWENHOEK

Hooke’s experiments with a crude microscope inspired Antoni van Leeuwenhoek

to further explore the micro world. Van Leeuwenhoek, an amateur lens grinder,

improved Hooke’s microscope by grinding lenses to achieve magnification. His

microscope required one lens. With his improvement, van Leeuwenhoek became

the first person to view a living microorganism, which he called Animalcules.

This discovery took place during the 1600s, when scientists believed that

organisms generated spontaneously and did not come from another organism.

This sounds preposterous today; however, back then scientists were just learning

that a cell was the basic component of an organism.

How Do Organisms Appear?

FRANCESCO REDI

Italian physician Francesco Redi developed an experiment that demonstrated that

an organism did not spontaneously appear. He filled jars with rotting meat.

Some jars he sealed and others he left opened. Those that were open eventually

contained maggots, which is the larval stage of the fly. The other jars did not con-

tain maggots because flies could not enter the jar to lay eggs on the rotting meat.

His critics stated that air was the ingredient required for spontaneous gen-

eration of an organism. Air was absent from the sealed jar and therefore no sponta-

neous generation could occur, they said (Fig. 1-5). Redi repeated the experiment

except this time he placed a screen over the opened jars. This prevented flies from

entering the jar. There weren’t any maggots on the rotting meat.

Until that time scientists did not have a clue about how to fight disease.

However, Redi’s discovery gave scientists an idea. They used Redi’s findings to

conclude that killing the microorganism that caused a disease could prevent

the disease from occurring. A new microorganism could only be generated by

CHAPTER 1 The World of the Microorganism10

Fig. 1-5. No spontaneous generation occurred in the sealed jar.

Open Sealed

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the reproduction of another microorganism. Kill the microorganism and you

won’t have new microorganisms, the theory went—you could stop the spread

of the disease. Scientists called this the Theory of Biogenesis. The Theory of Bio-

genesis states that a living cell is generated from another living cell.

LOUIS PASTEUR

Although the Theory of Biogenesis disproved spontaneous generation, sponta-

neous generation was hotly debated among the scientific community until 1861

when Louis Pasteur, a French scientist, resolved the issue once and for all.

Pasteur showed that microorganisms were in the air. He proved that sterilized

medical instruments became contaminated once they were exposed to the air.

Pasteur came to this conclusion by boiling beef broth in several short-necked

flasks. Some flasks were left open to cool. Other flasks were sealed after boil-

ing. The opened flasks became contaminated with microorganisms while no

microorganisms appeared in the closed flasks. Pasteur concluded that airborne

microorganisms had contaminated the opened flasks.

In a follow-up experiment, Pasteur placed beef broth in an open long-necked

flask. The neck was bent into an S-shape. Again he boiled the beef broth and let

it cool. The S-shaped neck trapped the airborne microorganisms (see Fig. 1-6).

CHAPTER 1 The World of the Microorganism 11

Fig. 1-6. Pasteur placed beef broth into a long-necked flask,

then bent the neck into an S-shape.

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The beef broth remained uncontaminated even after months of being exposed

to the air. The very same flask containing the original beef broth exists today in

Pasteur Institute in Paris and still shows no sign of contamination. Pasteur’s

experiments validated that microorganisms are not spontaneously generated.

Based on Pasteur’s findings, a concerted effort was launched to improve

sterilization techniques to prevent microorganisms from reproducing. Pasteur-

ization, one of the best-known sterilization techniques, was developed and

named for Pasteur. Pasteurization kills harmful microorganisms in milk, alco-

holic beverages, and other foods and drinks by heating it enough to kill most

bacteria that cause spoilage.

JOHN TYNDALL AND FERDINAND COHN

The work of John Tyndall and Ferdinand Cohn in the late 1800s led to one of the

most important discoveries in sterilization. They learned that some microorgan-

isms are resistant to certain sterilization techniques. Until their discovery, scien-

tists had assumed that no microorganism could survive boiling water, which

became a widely accepted method of sterilization. This was wrong. Some ther-

mophiles resisted heat and could survive a bath in boiling water. This meant that

there was not one magic bullet that killed all harmful microorganisms.

Germ Theory

Until the late 1700s, not much was really known about diseases except their

impact. It seemed that anyone who came in contact with an infected person

contracted the disease. A disease that is spread by being exposed to infection is

called a contagious disease. The unknown agent that causes the disease is called

a contagion. Today we know that a contagion is a microorganism, but in the 1700s

many found it hard to believe something so small could cause such devastation.

ROBERT KOCH

Opinions changed dramatically following Robert Koch’s study of anthrax in

the late 1800s. Koch noticed a pattern developing: Anyone who worked with or

ingested animals that were infected with anthrax contracted the disease. In fact,

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people who simply inhaled the air around an infected animal were likely to

inhale the anthrax bacterium spores and come down with the disease. Koch’s

investigations into anthrax led him to discover how microorganisms work.

Anthrax is caused by Bacillus anthracis (Fig. 1-7), which is a bacterial type

of microorganism consisting of one cell. Bacillus anthracis, whether in a dor-

mant or an active state, is called a spore. A spore is not infectious. However,

under the right conditions, the Bacillus anthracis spores germinate and enter the

active state and rapidly multiply and become infectious.

The question that Koch raised is: Would taking active Bacillus anthracis from

one animal and injecting it into a healthy animal cause the healthy animal to

come down with anthrax? If so, then he could prove that a microorganism was

actually the cause of disease.

Bacillus anthracis was present in the blood of infected animals, so Koch

removed a small amount of blood and injected it into a healthy animal. The ani-

mal came down with anthrax. He repeated the experiment by removing a small

amount of blood from the newly infected animal and gave it to another healthy

animal. It, too, came down with anthrax.

Koch expanded

his experiment by cultivating Bacillus anthracis on a slice of

potato. He then exposed the potato to the right blend of air, nutrients, and tem-

perature. Koch took a small sample of his homegrown Bacillus anthracis and

injected it into a healthy animal. The animal came down with anthrax.

Based on his findings, Koch developed the Germ Theory. The Germ Theory

states that a disease-causing microorganism should be present in animals

infected by the disease and not in healthy animals. The microorganism can be

cultivated away from the animal and used to inoculate a healthy animal. The

CHAPTER 1 The World of the Microorganism 13

Fig. 1-7. Bacillus anthracis rapidly multiplies in

the active state and becomes infectious.

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healthy animal should then come down with the disease. Samples of a micro-

organism taken from several infected animals are the same as the original

microorganism from the first infected animal.

Four steps used by Koch to study microorganisms are referred to as Koch’s

Postulates. Koch’s Postulates state:

1. The microorganism must be present in the diseased animal and not present

in the healthy animal.

2. Cultivate the microorganism away from the animal in a pure culture.

3. Symptoms of the disease should appear in the healthy animal after the

healthy animal is inoculated with the culture of the microorganism.

4. Isolate the microorganism from the newly infected animal and culture it in

the laboratory. The new culture should be the same as the microorganism

that was cultivated from the original diseased animal.

Koch’s work with anthrax also developed techniques for growing a culture of

microorganisms. He eventually used a gelatin surface to cultivate microorgan-

isms. Gelatin inhibited the movement of microorganisms. As microorganisms

reproduced, they remained together, forming a colony that made them visible

without a microscope. The reproduction of microorganisms is called colonizing.

The gelatin was replaced with agar that is derived from seaweed and still used

today. Richard Petri improved on Koch’s cultivating technique by placing the

agar in a specially designed disk that was to later be called the Petri dish (Fig.

1-8). It, too, is still used today.

CHAPTER 1 The World of the Microorganism14

Fig. 1-8. A Petri dish is used to grow a culture of microorganisms.

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Vaccination

The variola microorganism was one of the most feared villains in the late

1700s. The variola virus causes smallpox. If variola didn’t kill you, it caused

pus-filled blisters that left deep scars that pitted nearly every part of your body.

Cows were also susceptible to a variation of variola called cowpox. Milkmaids

who tended to infected cows contracted cowpox and exhibited immunity to the

smallpox virus.

EDWARD JENNER

Edward Jenner, an English physician, discovered something very interesting

about both smallpox and cowpox in 1796. Those who survived smallpox never

contracted smallpox again, even when they were later exposed to someone who

was infected with smallpox. Milkmaids who contracted cowpox never caught

smallpox even though they were exposed to smallpox.

Jenner had an idea. He took scrapings from a cowpox blister found on a milk-

maid and, using a needle scratched the scrapings into the arm of James Phipps,

an 8-year-old. Phipps became slightly ill when the scratch turned bumpy. Phipps

recovered and was then exposed to smallpox. He did not contract smallpox

because his immune system developed antibodies that could fight off variola

and vaccinia.

Jenner’s experiment discovered how to use our body’s own defense mecha-

nism to prevent disease by inoculating a healthy person with a tiny amount of

the disease-causing microorganism. Jenner called this a vaccination, which is an

extension of the Latin word vacca (cow). The person who received the vaccina-

tion became immune to the disease-causing microorganism.

ELIE METCHNIKOFF

Elie Metchnikoff, a nineteenth-century Russian zoologist, was interested by

Jenner’s work with vaccinations. Metchnikoff wanted to learn how our bodies

react to vaccinations by exploring our body’s immune system. He discovered

that white blood cells (leukocytes) engulf and digest microorganisms that invade

the body. He called these cells phagocytes, which means “cell eating.” Metch-

nikoff was one of the first scientists to study the new area of biology called

immunology, the study of the immune system.

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Killing the Microorganism

Great strides were made during the late 1800s in the development of antiseptic

techniques. It began with a report by Hungarian physician Ignaz Semmelweis on

a dramatic decline in childbirth fever when physicians used antiseptic tech-

niques when delivering babies. Infections become preventable through the use

of antiseptic techniques.

JOSEPH LISTER

Joseph Lister, an English surgeon, developed one of the most notable antiseptic

techniques. During surgery he sprayed carbolic acid over the patient and then

bandaged the patient’s wound with carbolic acid–soaked bandages. Infection

following surgery dramatically dropped when compared with surgery performed

without spraying carbolic acid. Carbolic acid, also known as phenol was one of

the first surgical antiseptics.

PAUL EHRLICH

Antiseptics prevented microorganisms from infecting a person, but scientists

still needed a way to kill microorganisms after they infected the body. Scientists

needed a magic bullet that cured diseases. At the turned of the nineteenth cen-

tury, Paul Ehrlich, a German chemist, discovered the magic bullet. Ehrlich

blended chemical elements into a concoction that, when inserted into an

infected area, killed microorganisms without affecting the patient. Today we call

Ehrlich’s concoction a drug. Ehrlich’s innovation has led to chemotherapy using

synthetic drugs that are produced by chemical synthesis.

ALEXANDER FLEMING

Scientists from all over set out to use Ehrlich’s findings to find drugs that could

make infected patients well again. One of the most striking breakthroughs came

in 1929 when Alexander Fleming discovered Penicillin notatum, the organ-

ism that synthesizes penicillin. Penicillium notatum is a fungus that kills the

Staphylococcus aureus microorganism (Fig. 1-9), and similar microorganisms.

CHAPTER 1 The World of the Microorganism16

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Fleming grew cultures of Staphylococcus aureus, a bacterium, in the laboratory.

He was also conducting experiments with Penicillium notatim, a mold. By acci-

dent the Staphylococcus aureus was contaminated with the Penicillium notatum,

causing the Staphylococcus to stop reproducing and die. Penicillium notatum be-

came one of the first antibiotics. An antibiotic is a substance that kills bacteria.

A summary of the scientists and their contributions can be found in Table 1-2.

CHAPTER 1 The World of the Microorganism 17

Fig. 1-9. Penicillium notatum is a fungus

that kills the staphylococcus aureus.

Table 1-2. Scientists and Their Contributions

Year Scientist Contribution

1590 Zacharias Janssen Developed the first compound microscope.

1590 Robert Hooke Observed nonliving plant tissue of a thin slice of

cork.

1668 Francesco Redi Discovered that microorganisms did not spontane-

ously appear. His contribution led to the finding that

killing the microorganism that caused the disease

could prevent the disease.

1673 Antoni van Invented the single-lens microscope, grinding the

Leeuwenhoek microscope lens to improve magnification. First

person to view a living organism.

1798 Edward Jenner Developed vaccinations against disease-causing

microorganisms.

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CHAPTER 1 The World of the Microorganism18

Year Scientist Contribution

1850s Mathias Schleiden, Developed cell theory.

Theodore Schwann,

Rudolf Virchow

1847 Ignaz Semmelweis Reported a dramatic decline in childbirth

fever after

physicians used antiseptic techniques when deliver-

ing babies.

1864 Louis Pasteur Discovered that microorganisms were everywhere,

living on organisms and in nonliving things such as air.

His work led to improved sterilization techniques called

pasteurization. One of the founders of bacteriology.

1867 Joseph Lister Reduced infections after surgery by spraying car-

bolic acid over the patient before bandaging the

wound. This was the first surgical antiseptic.

1876 Robert Koch Discovered how microorganisms spread contagious

diseases by studying anthrax. Developed the

Germ Theory. Developed techniques for cultivating

microorganisms.

1870s John Tyndall, Discovered that some microorganisms are resistant to

Ferdinand Cohn certain sterilization techniques. One of the founders

of bacteriology.

1884 Elie Metchnikoff Discovered that white blood cells (leukocytes)

engulf and digest microorganisms that invade the

body. Coined the word phagocytes. Founded the

branch of science called immunology.

1887 Richard Petri Developed the technique of placing agar into a spe-

cially designed dish to grow microorganisms, which

was later called the Petri dish.

1890 Paul Ehrlich Developed the first drug to fight disease-causing

microorganisms that had already entered the body.

1928 Alexander Fleming Discovered Penicillium notatum, the fungus that

kills staphylococcus aureus, a microorganism that is

a leading cause of infection.

Table 1-2. Scientists and Their Contributions (Continued)

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Quiz

1. What is a microorganism?

(a) A microorganism is a small organism that takes in and breaks down

food for energy and nutrients, excretes unused food as waste, and is

capable of reproduction.

(b) A microorganism is a small organism that causes diseases only in

plants.

animals.

(d) A microorganism is a term that refers to a cell.

2. What is a pathogenic microorganism?

(a) A microorganism that multiplies

(b) A microorganism that grows in a host

(d) A disease-causing microorganism

3. Name the parts of this microorganism using the nomenclature system:

Mycobacterium tuberculosis.

(a) A bacterium is a one-cell organism that does not have a distinct

nucleus.

(b) Mycobacterium is the presemous and tuberculosis is the specific

postsemous.

(d) Mycobacterium is the genus and tuberculosis is the specific epithet.

4. Why is a bacterium called a prokaryotic organism?

(a) A bacterium is a one-cell organism that does not have a distinct

nucleus.

(b) A bacterium is a one-cell organism that has a distinct nucleus.

nucleus.

(d) A bacterium is a multicell organism that has a distinct nucleus.

5. Why is a fungus called a eukaryotic microorganism?

(a) Fungus has cells that have a nucleus, nuclear envelope, cytoplasm,

and organelles.

CHAPTER 1 The World of the Microorganism 19

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(b) Fungus has cells that have a nucleus and no nuclear envelope.

but no organelles.

(d) Fungus has cells that have no nucleus, no nuclear envelope, no cyto-

plasm, and no organelles.

6. What is Archaea?

(a) Archaea is a classification for organisms that have two nuclei.

(b) Archaea is a classification for organisms that use phagocytosis.

that do not have peptidoglycan cell walls.

(d) Archaea is a classification of an organism that identifies prokaryotes

that have peptidoglycan cell walls.

7. What is phagocytosis?

(a) The ability of a cell to reproduce.

(b) The ability of a cell to move throughout a microorganism.

pseudopods, or “false feet.”

(d) The ability of a cell to change shape.

8. What is a compound microscope?

(a) A microscope that has one lenses.

(b) A microscope that has two sets of lenses: an ocular lens and an eye-

piece.

(d) A microscope whose lenses are convex.

9. What is Germ Theory?

(a) Germ Theory states that a disease-causing microorganism should be

present in animals infected by the disease and not in healthy animals.

(b) Germ Theory states that a disease-causing microorganism should be

present in healthy animals and not in infected animals.

destroyed.

(d) Germ Theory states that a disease-causing microorganism cannot be

destroyed.

10. What is Edward Jenner’s contribution to microbiology?

(a) Edward Jenner discovered the Germ Theory.

CHAPTER 1 The World of the Microorganism20

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(b) Edward Jenner discovered how to create vaccinations to trigger

the body’s immune system to develop antibodies that fight micro-

organisms.

(d) Edward Jenner discovered the compound nomenclature system.

CHAPTER 1 The World of the Microorganism 21

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CHAPTER

The Chemical

Elements of

Microorganisms

No doubt you’re asking yourself what chemistry has to do with microbiology

since they seem to be two different branches of science. The simple answer is

that microorganisms are made up of chemicals, as is every organism—and all

matter. Remember that matter is anything that occupies space and has mass.

You might say that an organism is a chemical processing plant where things

are broken down into chemical elements; these chemical elements are then re-

arranged to form new things. You do this every time you ingest food. Food is a

group of chemical compounds. The digestive process rearranges these digested

chemical compounds into new substances that provide you with energy and

nutrients that are necessary for you to live. Some microorganisms called auto-

trophic organisms manufacture their own food. Microorganisms that derive energy

from other microorganisms (food) are called heterotopic organisms.

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When you catch a cold or become infected by pathogenic microorganisms,

your body is no longer in homeostasis. You feel rotten, but what’s really hap-

pening is that the microorganism is disrupting your chemical processing plant’s

normal operation. Some microorganisms prevent necessary chemical processing

from occurring. Other microorganisms cause your chemical processing plant to

execute different processes designed to fight the microorganism attack and

return your body to homeostasis—then your body is back to normal.

As you can see, chemistry is a crucial component of microbiology. It is for this

reason that we begin the study of microorganisms with a close look at chemistry.

Everything Matters

Anything that takes up space and has mass is matter. The chair you’re sitting on

is matter. You are matter. And so are the microorganisms crawling over you and

the chair. All nonliving and living things are matter because they take up space

and have mass.

Matter is anything that takes up space and has mass. It is easy to envision

something taking up space, but what is mass?

Mass is the amount of matter a substance or an object contains. A common mis-

conception is that mass is the weight of a substance. It is true that the more there

is of a substance, the more it weighs. However, weight is the force of gravity act-

ing on mass and is calculated as weight = mass × gravity. A trip to the moon will

clarify the difference between mass and weight: You have the same mass on earth

as you do on the moon, but you weigh more on the earth than you do on the moon

because the earth has six times the gravitational force of the moon.

Microbiology Demystified By Belzy - Marketing (2024)

References