

CHAPTER 2 All atoms with the same number of

protons behave the same way chemically and
are classified as the same chemical element.
CHEMICAL PRINCIPLES  Each element has its own name and a
 Knowledge of chemistry is essential to one- or two letter symbol, usually derived
understanding what roles microorganisms play from the English or Latin name for the
in nature, how they cause disease, how element.
methods for diagnosing disease are developed,  For example, the symbol for the element
how the body’s defenses combat infection, and hydrogen is H, and the symbol for carbon is
how antibiotics and vaccines are produced to C.
combat the harmful effects of microbes  The symbol for sodium is Na—the first
 The Bacillus anthracis bacteria in the two letters of its Latin name, natrium—
photograph make a capsule that is not readily distinguish it from nitrogen, N, and from
digested by animal cells sulfur, S.
 Bacillus anthracis bacteria produce heat-  There are 92 naturally occurring
resistant endospores elements. However, only about 26 elements
are commonly found in living things
THE STRUCTURE OF ATOMS  Most elements have several isotopes—
atoms with different numbers of neutrons in
 All matter—whether air, rock, or a living their nuclei.
organism—is made up of small units called  All isotopes of an element have the
atoms. same number of protons in their nuclei, but
 An atom is the smallest component of a their atomic masses differ because of the
substance, and it cannot be subdivided into difference in the number of neutrons.
smaller substances without losing its  Atomic numbers are written as a
properties. subscript to the left of an element’s chemical
 Atoms combine to form molecules. Living symbol.
cells are made up of molecules, some of  Atomic masses are written as a
which are very complex. superscript above the atomic number.
 The science of the interaction between
atoms and molecules is called chemistry. ELECTRONIC CONFIGURATION
 Atoms are the smallest units of matter that
 In an atom, electrons are arranged in
enter into chemical reactions.
electron shells, which are regions
 Every atom has a centrally located nucleus
corresponding to different energy levels. The
and negatively (-) charged particles called
arrangement is called an electronic
electrons that move around the nucleus in
configuration
regions called electron shells
 two electrons in the innermost shell
 The nucleus is made up of positively (+)
(lowest energy level),
charged particles called protons and
 eight electrons in the second shell, and
uncharged (neutral) particles called neutrons.
 eight electrons in the third shell, if it is
 The nucleus, therefore, bears a net positive
the atom’s outermost (valence) shell.
charge. All atoms contain an equal number of
electrons and protons.  The fourth, fifth, and sixth electron
shells can each accommodate 18 electrons,
 Because the total positive charge of the
although there are some exceptions to this
nucleus equals the total negative charge of
generalization
the electrons, each atom is electrically
neutral.  the number of electrons in the outermost
shell determines an atom’s tendency to react
 The nuclei of most atoms are stable—that is,
with other atoms.
they do not change spontaneously—and
nuclei do not participate in chemical  An atom can give up, accept, or share
reactions. electrons with other atoms to fill the outermost
shell.
 Atoms are often listed by their atomic
number, the number of protons in the  When its outer shell is filled, the atom is
nucleus. chemically stable, or inert: it does not tend to
react with other atoms
 Protons and neutrons are approximately the
same weight, which is about 1840 times that  When an atom’s outer electron shell is
of an electron, and the total number of only partially filled, the atom is chemically
protons and neutrons in an atom is its unstable. These unstable atoms react with
approximate atomic mass other atoms

CHEMICAL ELEMENTS
 HOW ATOMS FORM  This positively charged sodium atom is
called a sodium ion and is written as Na+.
MOLECULES: CHEMICAL  Chlorine (Cl) has a total of 17 electrons,
BONDS seven of them in the outer electron shell.
Because this outer shell can hold eight
 The most chemically stable
electrons, chlorine tends to pick up an
configuration for any atom is to have its
electron that has been lost by another atom; it
outermost shell filled.
is an electron acceptor
 The valence, or combining capacity, of
 By accepting an electron, chlorine totals
an atom is the number of extra or missing
18 electrons. However, it still has only 17
electrons in its outermost electron shell.
protons in its nucleus. The chloride ion
 For example, hydrogen has a valence of
therefore has a charge of -1 and is written as
1 (one unfilled space, or one extra electron),
Cl-.
oxygen has a valence of 2 (two unfilled
 The opposite charges of the sodium ion
spaces), carbon has a valence of 4 (four
(Na+) and chloride ion (Cl-) attract each other.
unfilled spaces, or four extra electrons), and
 The attraction, an ionic bond, holds the
magnesium has a valence of 2 (two extra
two atoms together, and a molecule is formed
electrons).
 The formation of this molecule, called
 Basically, atoms achieve the full
sodium chloride (NaCl) or table salt, is a
complement of electrons in their outermost
common example of ionic bonding.
energy shells by combining to form
molecules, which are made up of atoms of  Thus, an ionic bond is an attraction
one or more elements. between ions of opposite charge that holds
them together to form a stable molecule.
 A molecule that contains at least two
different kinds of atoms, such as H2O (the  an ionic bond is an attraction between
water molecule), is called a compound. atoms in which one atom loses electrons and
another atom gains electrons.
 In H2O, the subscript 2 indicates that
there are two atoms of hydrogen; the absence  In general, an atom whose outer
of a subscript indicates that there is only one electron shell is less than half-filled will lose
atom of oxygen. electrons and form positively charged ions,
called cations.
 Molecules hold together because the
valence electrons of the combining atoms  Examples of cations are the potassium
form attractive forces, called chemical bonds, ion (K+), calcium ion (Ca2+), and sodium ion
between the atomic nuclei. (Na+).
 Therefore, valence may also be viewed  When an atom’s outer electron shell is
as the bonding capacity of an element. more than half-filled, the atom will gain
electrons and form negatively charged ions,
 In general, atoms form bonds in one of
called anions.
two ways: by either gaining or losing electrons
from their outer electron shell, or by sharing  Examples are the iodide ion (I-),
outer electrons. chloride ion (Cl-), and sulfide ion (S2-).
 When atoms have gained or lost outer COVALENT BONDS
electrons, the chemical bond is called an ionic
bond.  A covalent bond is a chemical bond
 When outer electrons are shared, the formed by two atoms sharing one or more pairs
bond is called a covalent bond. of electrons.
 bonds range from the highly ionic to the  Covalent bonds are stronger
highly covalent.  The shared pair of electrons actually
orbits the nuclei of both atoms.
IONIC BONDS  Therefore, the outer electron shells of
 If the atom gains electrons, it acquires both atoms are filled. Atoms that share only
an overall negative charge; if the atom loses one pair of electrons form a single covalent
electrons, it acquires an overall positive bond.
charge.  For simplicity, a single covalent bond is
 Such a negatively or positively charged expressed as a single line between the atoms
atom (or group of atoms) is called an ion. (H¬H).
Consider the following examples.  Atoms that share two pairs of electrons
 Sodium tends to lose the single outer form a double covalent bond, expressed as two
electron; it is an electron donor single lines (=).
 When sodium donates an electron to  A triple covalent bond, expressed as
another atom, it is left with 11 protons and three single lines (lll) occurs when atoms share
only 10 electrons and so has an overall three pairs of electrons.\
charge of +1.
 The principles of covalent bonding that  The unit of molecular mass is a dalton
apply to atoms of the same element also apply (da).
to atoms of different elements.  For example, 1 mole of water weighs 18
 Methane (CH4) is an example of grams because the molecular mass of H2O is
covalent bonding between atoms of different 18 da, or [(2 * 12+ 16]
elements
 Elements such as hydrogen and carbon,
whose outer electron shells are half-filled, form
covalent bonds quite easily.
 In fact, in living organisms, carbon
almost always forms covalent bonds; it almost CHEMICAL REACTIONS
never becomes an ion.  chemical reactions involve the making or
 Covalent bonds are formed by the breaking of bonds between atoms.
sharing of electrons between atoms.  After a chemical reaction, the total number
 Ionic bonds are formed by attraction of atoms remains the same, but there are new
between atoms that have lost or gained molecules with new properties because the
electrons and are therefore positively or atoms have been rearranged
negatively charged
ENERGY IN CHEMICAL REACTIONS
HYDROGEN BONDS
 All chemical bonds require energy to form
 Another chemical bond of special or break. It is important to note that initially,
importance to all organisms is the hydrogen activation energy is needed to break a bond
bond, in which a hydrogen atom that is  In the chemical reactions of metabolism,
covalently bonded to one oxygen or nitrogen energy is released when new bonds are
atom is attracted to another oxygen or nitrogen formed after the original bonds break; this is
atom. the energy cells use to do work.
 Such bonds are weak and do not bind  A chemical reaction that absorbs more
atoms into molecules. energy than it releases is called an endergonic
 However, they do serve as bridges reaction (endo = within), meaning that energy
between different molecules or between is directed inward.
various portions of the same molecule.  A chemical reaction that releases more
 When hydrogen combines with atoms of energy than it absorbs is called an exergonic
oxygen or nitrogen, the relatively large nucleus reaction (exo = out), meaning that energy is
of these larger oxygen or nitrogen atoms has directed outward.
more protons and attracts the hydrogen
electron more strongly than does the small
hydrogen nucleus.
SYNTHESIS REACTIONS
 Hydrogen bonds are considerably  When two or more atoms, ions, or
weaker than either ionic or covalent bonds; molecules combine to form new and larger
they have only about 5% of the strength of molecules, the reaction is called a synthesis
covalent bonds. Consequently, reaction.
 hydrogen bonds are formed and broken  To synthesize means to put together, and a
relatively easily synthesis reaction forms new bonds
 temporary bonding that occurs between  The combining substances, A and B, are
certain atoms of large and complex molecules, called the reactants; the substance formed by
such as proteins and nucleic acids. the combination, AB, is the product.
 Even though hydrogen bonds are  The arrow indicates the direction in which
relatively weak, large molecules containing the reaction proceeds.
several hundred of these bonds have  Pathways of synthesis reactions in living
considerable strength and stability. organisms are collectively called anabolic
reactions, or simply anabolism
MOLECULAR MASS & MOLES  The combining of sugar molecules to form
starch and of amino acids to form proteins are
 Molecules are often discussed in terms
two examples of anabolism
of units of measure called molecular mass and
moles. DECOMPOSITION REACTIONS
 The molecular mass of a molecule is
the sum of the atomic masses of all its atoms.  The reverse of a synthesis reaction is a
 To relate the molecular level to the decomposition reaction.
laboratory level, we use a unit called the mole.  To decompose means to break down into
 One mole of a substance is its molecular smaller parts, and in a decomposition reaction
mass expressed in grams. bonds are broken.
  Typically, decomposition reactions split  Some organic molecules, such as
large molecules into smaller molecules, ions, polysaccharides, proteins, and nucleic acids,
or atoms. are very large and usually contain thousands of
 Decomposition reactions that occur in living atoms.
organisms are collectively called catabolic  Such giant molecules are called
reactions, or simply catabolism macromolecules
 An example of catabolism is the
breakdown of sucrose (table sugar) into
simpler sugars, glucose and fructose, during
digestion.

EXCHANGE REACTIONS
 All chemical reactions are based on INORGANIC COMPOUNDS
synthesis and decomposition.
 Many reactions, such as exchange WATER
reactions, are actually part synthesis and part  Water is one of the most important, as well
decomposition. as one of the most abundant, of these
 an exchange reaction occurs when sodium compounds, and it is particularly vital to
hydroxide (NaOH) and hydrochloric acid (HCl) microorganisms
react to form table salt (NaCl) and water (H2O)  water is by far the most abundant
component of almost all living cells.
THE REVERSIBILITY OF CHEMICAL  Water makes up between 65% and 75% of
REACTIONS every cell on average. Simply stated, no
organism can survive without water.
 All chemical reactions are, in theory,
 the total charge on the water molecule is
reversible; that is, they can occur in either
neutral, but the oxygen region of the molecule
direction
has a slightly negative charge, and the
 Some reversible reactions occur
hydrogen region has a slightly positive charge
because neither the reactants nor the end
 Any molecule having such an unequal
products are very stable.
distribution of charges is called a polar
 Other reactions reverse only under
molecule.
special conditions:
 The polar nature of water gives it four
 A and B react to produce AB only when
characteristics that make it a useful medium for
heat is applied, and AB breaks down into A and
living cells.
B only in the presence of water.
 First, every water molecule is capable of
forming four hydrogen bonds with nearby water
IMPORTANT BIOLOGICAL molecules
 This property results in a strong attraction
MOLECULES between water molecules and makes water an
 Biologists and chemists divide compounds excellent temperature buffer.
into two principal classes: inorganic and  Because of this strong attraction, a great
organic. deal of heat is required to separate water
 Inorganic compounds are defined as molecules from each other to form water vapor;
molecules, usually small and structurally thus, water has a relatively high boiling point
simple, which typically lack carbon and in (100°C, 212°F).
which ionic bonds may play an important role.  Because water has such a high boiling point,
 Inorganic compounds include water, it exists in the liquid state on most of the
molecular oxygen (O2), carbon dioxide, and Earth’s surface.
many salts, acids, and bases.  Conversely, water temperatures must drop
 Organic compounds always contain carbon significantly in order for it to freeze.
and hydrogen and typically are structurally  Secondly, the hydrogen bonding between
complex. water molecules affects the density of water,
 Carbon is a unique element because it has depending on whether it occurs as ice or a
four electrons in its outer shell and four unfilled liquid.
spaces. It can combine with a variety of atoms,  For example, the hydrogen bonds in the
including other carbon atoms, to form straight crystalline structure of water (ice) make ice
or branched chains and rings take up more space.
 Organic compounds are held together  As a result, ice has fewer molecules than an
mostly or entirely by covalent bonds. equal volume of liquid water. This makes its
crystalline structure less dense than liquid
water. For this reason, ice floats and can serve  Biochemical reactions—that is, chemical
as an insulating layer on the surfaces of lakes reactions in living systems—are extremely
and streams that harbor living organisms sensitive to even small changes in the acidity
 Third, the polarity of water makes it an or alkalinity of the environments in which they
excellent dissolving medium, or solvent. Many occur.
polar substances undergo dissociation, or  It is convenient to express the amount of H+
separation, into individual molecules in water— in a solution by a logarithmic pH scale, which
that is, they dissolve ranges from 0 to 14
 Substances (such as salts) that are  The term pH means potential of hydrogen.
composed of atoms (or groups of atoms) held On a logarithmic scale, a change of one whole
together by ionic bonds tend to dissociate into number represents a tenfold change from the
separate cations and anions in water previous concentration.
 Fourth, polarity accounts for water’s  Thus, a solution of pH 1 has ten times more
characteristic role as a reactant or product in hydrogen ions than a solution of pH 2 and has
many chemical reactions. 100 times more hydrogen ions than a solution
 Its polarity facilitates the splitting and of pH 3.
rejoining of hydrogen ions (H+) and hydroxide  A solution’s pH is calculated as -log10[H+],
ions (OH-). the negative logarithm to the base 10 of the
 Water is a key reactant in the digestive hydrogen ion concentration (denoted by
processes of organisms, whereby larger brackets), determined in moles per liter [H+].
molecules are broken down into smaller ones.  For example, if the H+ concentration of a
 Water molecules are also involved in solution is 1.0 * 10-4 moles⁄liter, or 10-4, its pH
synthetic reactions; water is an important equals -log1010-4 =-(-4) = 4; this is about the
source of the hydrogen and oxygen that are pH value of wine
incorporated into numerous organic  Acidic solutions contain more H+ than OH-
compounds in living cells. and have a pH lower than 7.
 If a solution has more OH- than H+, it is a
WATER ACIDS, BASES & SALTS basic, or alkaline, solution.
 sodium chloride (NaCl) are dissolved in  In pure water, a small percentage of the
water, they undergo ionization or dissociation; molecules are dissociated into H+ and OH-, so
that is, they break apart into ions. it has a pH of 7.
 Substances called acids and bases show  Because the concentrations of H+ and OH-
similar behavior. are equal, this pH is said to be the pH of a
 An acid can be defined as a substance that neutral solution.
dissociates into one or more hydrogen ions  We can increase its acidity by adding
(H+) and one or more negative ions (anions). substances that will increase the concentration
 Thus, an acid can also be defined as a of hydrogen ions.
proton (H+) donor.  organisms possess natural pH buffers,
 A base dissociates into one or more compounds that help keep the pH from
negatively charged hydroxide ions (OH-) that changing drastically.
can accept, or combine with, protons, and one  But the pH in our environment’s water and
or more positive ions (cations). soil can be altered by waste products from
 A salt is a substance that dissociates in organisms, pollutants from industry, or
water into cations and anions, neither of which fertilizers used in agricultural fields or gardens.
is H+ or OH-  When bacteria are grown in a laboratory
medium, they excrete waste products such as
ACID-BASE BALANCE: THE acids that can alter the pH of the medium.
CONCEPT OF PH  If this effect were to continue, the medium
would become acidic enough to inhibit bacterial
 An organism must maintain a fairly constant
enzymes and kill the bacteria.
balance of acids and bases to remain healthy
 To prevent this problem, pH buffers are
 In the aqueous environment within
added to the culture medium. One very
organisms, acids dissociate into hydrogen ions
effective pH buffer for some culture media uses
(H+) and anions.
a mixture of K2HPO4 and KH2PO4
 Bases, in contrast, dissociate into hydroxide
 Different microbes function best within
ions (OH- ) and cations.
different pH ranges, but most organisms grow
 The more hydrogen ions that are free in a
best in environments with a pH value between
solution, the more acidic the solution is.
6.5 and 8.5.
 Conversely, the more hydroxide ions that
 Among microbes, fungi are best able to
are free in a solution, the more basic, or
tolerate acidic conditions, whereas the
alkaline, it is.
prokaryotes called cyanobacteria tend to do  Functional groups help us classify organic
well in alkaline habitats. compounds.
 Propionibacterium acnes, a bacterium that  ¬OH group, they are grouped together in a
causes acne, has as its natural environment class called alcohols.
human skin, which tends to be slightly acidic,  The ¬OH group is called the hydroxyl group
with a pH of about 4. and is not to be confused with the hydroxide
 Acidithiobacillus ferrooxidans is a ion (OH-) of bases.
bacterium that metabolizes elemental sulfur  The hydroxyl group of alcohols does not
and produces sulfuric acid (H2SO4). Its pH ionize at neutral pH; it is covalently bonded to
range for optimum growth is from 1 to 3.5. a carbon atom.
 Inorganic compounds, excluding water,  the letter R can be used to stand for the
constitute about 1–1.5% of living cells. These remainder of the molecule.
relatively simple components, whose  Small organic molecules can be combined
molecules have only a few atoms, cannot be into very large molecules called
used by cells to perform complex biological macromolecules (macro = large).
functions.  Macromolecules are usually polymers (poly
 Organic molecules, whose carbon atoms = many; mers = parts): polymers are formed
can combine in an enormous variety of ways by covalent bonding of many repeating small
with other carbon atoms and with atoms of molecules called monomers (mono = one).
other elements, are relatively complex and thus  When two monomers join together, the
are capable of more complex biological reaction usually involves the elimination of a
functions. hydrogen atom from one monomer and a
hydroxyl group from the other; the hydrogen
THE STRUCTURE & CHEMISTRY
atom and the hydroxyl group combine to
 In the formation of organic molecules, produce water:
carbon’s four outer electrons can participate  This type of exchange reaction is called
in up to four covalent bonds, and carbon dehydration synthesis (de = from; hydro =
atoms can bond to each other to form water), or a condensation reaction
straight-chain, branched-chain, or ring
structures.
 In addition to carbon, the most common CARBOHYDRATES
elements in organic compounds are hydrogen  The carbohydrates are a large and diverse
(which can form one bond), oxygen (two group of organic compounds that includes
bonds), and nitrogen (three bonds). sugars and starches.
 Sulfur (two bonds) and phosphorus (five  Carbohydrates perform a number of major
bonds) appear less often. functions in living systems.
 The chain of carbon atoms in an organic  For instance, one type of sugar
molecule is called the carbon skeleton; a (deoxyribose) is a building block of
huge number of combinations is possible for deoxyribonucleic acid (DNA), the molecule that
carbon skeletons. carries hereditary information.
 Most of these carbons are bonded to  Other sugars are needed for the cell walls.
hydrogen atoms. The bonding of other  Simple carbohydrates are used in the
elements with carbon and hydrogen forms synthesis of amino acids and fats or fatlike
characteristic functional groups, specific substances, which are used to build cell
groups of atoms that are most commonly membranes and other structures.
involved in chemical reactions and are  Macromolecular carbohydrates function as
responsible for most of the characteristic food reserves. The principal function of
chemical properties carbohydrates, however, is to fuel cell activities
 the hydroxyl group of alcohols is hydrophilic with a ready source of energy.
(water-loving) and thus attracts water  Carbohydrates are made up of carbon,
molecules to it. hydrogen, and oxygen atoms.
 This attraction helps dissolve organic  The ratio of hydrogen to oxygen atoms is
molecules containing hydroxyl groups. always 2:1 in simple carbohydrates.
Because the carboxyl group is a source of
 This ratio can be seen in the formulas for the
hydrogen ions, molecules containing it have
carbohydrates ribose (C5H10O5), glucose
acidic properties.
(C6H12O6), and sucrose (C12H22O11).
 Amino groups, by contrast, function as
 The general formula for carbohydrates is
bases because they readily accept hydrogen
(CH2O)n, where n indicates that there are
ions.
three or more CH2O units.
 The sulfhydryl group helps stabilize the
 Carbohydrates can be classified into three
intricate structure of many proteins.
major groups on the basis of size:
monosaccharides, disaccharides, and  Chitin is a polysaccharide that makes up
polysaccharides. part of the cell wall of most fungi and the
exoskeletons of lobsters, crabs, and insects.
Monosaccharides  Starch is a polymer of glucose produced by
 Simple sugars are called monosaccharides plants and used as food by humans
(sacchar = sugar); each molecule contains  Many animals, including humans, produce
three to seven carbon atoms. enzymes called amylases that can break the
 Pentoses and hexoses are extremely bonds between the glucose molecules in
important to living organisms. glycogen.
 Deoxyribose is a pentose found in DNA.  However, this enzyme cannot break the
Glucose, a very common hexose, is the main bonds in cellulose.
energy-supplying molecule of living cells.  Bacteria and fungi that produce enzymes
called cellulases can digest cellulose.
Disaccharides  Cellulases from the fungus Trichoderma are
 Disaccharides (di = two) are formed when used for a variety of industrial purposes.
two monosaccharides bond in a dehydration  One of the more unusual uses is producing
synthesis reaction.* stone-washed or distressed denim. Because
 For example, molecules of two washing the fabric with rocks would damage
monosaccharides, glucose and fructose, washing machines, cellulase is used to digest,
combine to form a molecule of the disaccharide and therefore soften, the cotton.
sucrose (table sugar) and a molecule of water
 Similarly, the dehydration synthesis of the LIPIDS
monosaccharides glucose and galactose forms  lipids are essential to the structure and
the disaccharide lactose (milk sugar). function of membranes that separate living
 ] Two molecules with the same chemical cells from their environment.
formula but different structures and properties  Lipids (lip = fat) are a second major group of
are called isomers (iso = same). organic compounds found in living matter.
 Disaccharides can be broken down into  Like carbohydrates, they are composed of
smaller, simpler molecules when water is atoms of carbon, hydrogen, and oxygen, but
added. lipids lack the 2:1 ratio between hydrogen and
 This chemical reaction, the reverse of oxygen atoms.
dehydration synthesis, is called hydrolysis  they are nonpolar molecules so, unlike
(hydro = water; lysis = to loosen) water, do not have a positive and a negative
 the cell walls of bacterial cells are composed end (pole).
of disaccharides and proteins, which together  Therefore, most lipids are insoluble in water
are called peptidoglycan. but dissolve readily in nonpolar solvents, such
as ether and chloroform.
Polysaccharides
 Lipids provide the structure of membranes
 Carbohydrates in the third major group, the and some cell walls and function in energy
polysaccharides, consist of tens or hundreds of storage.
monosaccharides joined through dehydration
synthesis. Simple Lipids
 Polysaccharides often have side chains  Simple lipids, called fats or triglycerides,
 Like disaccharides, polysaccharides can be contain an alcohol called glycerol and a group
split apart into their constituent sugars through of compounds known as fatty acids.
hydrolysis  Glycerol molecules have three carbon atoms
 They usually lack the characteristic to which are attached three hydroxyl (¬OH)
sweetness of sugars such as fructose and groups
sucrose and usually are not soluble in water.  Fatty acids consist of long hydrocarbon
 One important polysaccharide is glycogen, chains (composed only of carbon and
which is composed of glucose subunits and is hydrogen atoms) ending in a carboxyl
synthesized as a storage material by animals (¬COOH, organic acid) group
and some bacteria.  A molecule of fat is formed when a molecule
 Cellulose, another important glucose of glycerol combines with one to three fatty
polymer, is the main component of the cell acid molecules.
walls of plants and most algae.  The number of fatty acid molecules
 The polysaccharide dextran, which is determines whether the fat molecule is a
produced as a sugary slime by certain bacteria, monoglyceride, diglyceride, or triglyceride
is used in a blood plasma substitute.  The chemical bond formed where the water
molecule is removed is called an ester linkage.
 In the reverse reaction, hydrolysis, a fat  When an ¬OH group is attached to one of
molecule is broken down into its component the rings, the steroid is called a sterol (an
fatty acid and glycerol molecules. alcohol).
 The primary function of lipids is to form  Sterols are important constituents of the
plasma membranes that enclose cells. plasma membranes of animal cells and of one
 A plasma membrane supports the cell and group of bacteria (mycoplasmas), and they are
allows nutrients and wastes to pass in and out; also found in fungi and plants.
therefore, the lipids must maintain the same  The sterols separate the fatty acid chains
viscosity, regardless of the surrounding and thus prevent the packing that would
temperature. harden the plasma membrane at low
 animal fats (such as butter) are usually solid temperatures
at room temperature, whereas vegetable oils
are usually liquid at room temperature. PROTEINS
 The difference in their respective melting  Proteins are organic molecules that contain
points is due to the degrees of saturation of the carbon, hydrogen, oxygen, and nitrogen. Some
fatty acid chains. also contain sulfur
 A fatty acid is said to be saturated when it  Proteins are essential ingredients in all
has no double bonds aspects of cell structure and function.
 Saturated chains become solid more easily  Enzymes are the proteins that speed up
because they are relatively straight and are biochemical reactions.
thus able to pack together more closely than  Transporter proteins help transport certain
unsaturated chains. chemicals into and out of cells.
 The double bonds of unsaturated chains  Other proteins, such as the bacteriocins
create kinks in the chain, which keep the produced by many bacteria, kill other bacteria.
chains apart from one another  Certain toxins, called exotoxins, produced
Complex Lipids by some disease-causing microorganisms are
also proteins.
 Complex lipids contain such elements as  Some proteins play a role in the contraction
phosphorus, nitrogen, and sulfur, in addition to of animal muscle cells and the movement of
the carbon, hydrogen, and oxygen found in microbial and other types of cells.
simple lipids.  Other proteins are integral parts of cell
 The complex lipids called phospholipids are structures such as walls, membranes, and
made up of glycerol, two fatty acids, and, in cytoplasmic components.
place of a third fatty acid, a phosphate group  Still others, such as the hormones of certain
bonded to one of several organic groups organisms, have regulatory functions.
 Phospholipids are the lipids that build  proteins called antibodies play a role in
membranes; they are essential to a cell’s vertebrate immune systems.
survival.
 Phospholipids have polar as well as Amino Acids
nonpolar regions  Just as monosaccharides are the building
 Polar portions consist of a phosphate group blocks of larger carbohydrate molecules, and
and glycerol. just as fatty acids and glycerol are the building
 In contrast to the polar regions, all nonpolar blocks of fats, amino acids are the building
(hydrophobic) parts of the phospholipid make blocks of proteins.
contact only with the nonpolar portions of  Amino acids contain at least one carboxyl
neighboring molecules. (¬COOH) group and one amino (¬NH2) group
 (Hydrophobic means water-fearing.) attached to the same carbon atom, called an
Nonpolar portions consist of fatty acids alpha-carbon
 Phospholipids enable the membrane to act  The side group can contain functional
as a barrier that separates the contents of the groups, such as the sulfhydryl group (¬SH), the
cell from the water-based environment in which hydroxyl group (¬OH), or additional carboxyl or
it lives. amino groups
 Cell walls rich in such complex lipids are  Most amino acids exist in either of two
characteristic of all members of the genus configurations called stereoisomers,
Mycobacterium. designated by D and L.
Steroids  These configurations are mirror images,
corresponding to “right-handed” (D) and “left-
 steroid cholesterol, with the four handed” (L) three-dimensional shapes
interconnected carbon rings that are  The amino acids found in proteins are
characteristic of steroids. always the L-isomers (except for glycine, the
simplest amino acid)
 However, D- amino acids occasionally occur  Both structures are held together by
in nature—for example, in certain bacterial cell hydrogen bonds between oxygen or nitrogen
walls and antibiotics. atoms that are part of the polypeptide’s
backbone.
Peptide Bonds
 Tertiary structure refers to the overall three-
 Amino acids bond between the carbon atom dimensional structure of a polypeptide chain
of the carboxyl (¬COOH) group of one amino  The folding is not repetitive or predictable,
acid and the nitrogen atom of the amino as in secondary structure.
(¬NH2) group of another  Hydrogen bonds between side groups, and
 The bonds between amino acids are called ionic bonds between oppositely charged side
peptide bonds. groups, also contribute to tertiary structure.
 For every peptide bond formed between two  Proteins that contain the amino acid
amino acids, one water molecule is released; cysteine form strong covalent bonds called
thus, peptide bonds are formed by dehydration disulfide bridges
synthesis.  Cysteine molecules contain sulfhydryl
 Adding another amino acid to a dipeptide groups (¬SH), and the sulfur of one cysteine
would form a tripeptide. Further additions of molecule bonds to the sulfur on another,
amino acids would produce a long, chainlike forming (by the removal of hydrogen atoms) a
molecule called a peptide (4–9 amino acids) or disulfide bridge (S¬S) that holds parts of the
polypeptide (10–2000 or more amino acids). protein together.
 Some proteins have a quaternary structure,
which consists of an aggregation of two or
Levels of Protein Structure more individual polypeptide chains (subunits )
that operate as a single functional unit.
 Proteins vary tremendously in structure.
 More commonly, proteins have two or more
Different proteins have different architectures
kinds of polypeptide subunits.
and different three-dimensional shapes.
 The bonds that hold a quaternary structure
 This variation in structure is directly related
together are basically the same as those that
to their diverse functions.
maintain tertiary structure.
 When a cell makes a protein, the
 The overall shape of a protein may be
polypeptide chain folds spontaneously to
globular (compact and roughly spherical) or
assume a certain shape. One reason for
fibrous (threadlike).
folding of the polypeptide is that some parts of
 If a protein encounters a hostile
a protein are attracted to water and other parts
environment in terms of temperature, pH, or
are repelled by it.
salt concentrations, it may unravel and lose its
 The unique shape of each protein permits it
characteristic shape.
to interact with specific other molecules in
 This process is called denaturation
order to carry out specific functions.
 As a result of denaturation, the protein is no
 Proteins are described in terms of four levels
longer functional.
of organization: primary, secondary, tertiary,
 The proteins we have been discussing are
and quaternary.
simple proteins, which contain only amino
 The primary structure is the unique
acids.
sequence in which the amino acids are linked
 Conjugated proteins are combinations of
together to form a polypeptide chain
amino acids with other organic or inorganic
 But proteins do not exist as long, straight
components.
chains.
 Conjugated proteins are named by their
 Each polypeptide chain folds and coils in
non–amino acid component.
specific ways into a relatively compact
 Thus, glycoproteins contain sugars,
structure with a characteristic three-
nucleoproteins contain nucleic acids,
dimensional shape.
metalloproteins contain metal atoms,
 A protein’s secondary structure is the
lipoproteins contain lipids, and
localized, repetitious twisting or folding of the
phosphoproteins contain phosphate groups.
polypeptide chain.
 Phosphoproteins are important regulators of
 This aspect of a protein’s shape results from
activity in eukaryotic cells.
hydrogen bonds joining the atoms of peptide
 Bacterial synthesis of phosphoproteins may
bonds at different locations along the
be important for the survival of bacteria such as
polypeptide chain.
Legionella pneumophila that grow inside host
 The two types of secondary protein
cells.
structures are clockwise spirals called helices
(singular: helix) and pleated sheets, which form NUCLEIC ACIDS
from roughly parallel portions of the chain
  In 1944, three American microbiologists—  The bases are held together by hydrogen
Oswald Avery, Colin MacLeod, and Maclyn bonds; A and T are held by two hydrogen
McCarty—discovered that a substance called bonds, and G and C by three.
deoxyribonucleic acid (DNA) is the substance  DNA does not contain uracil (U).
of which genes are made.  The order in which the nitrogen base pairs
 Nine years later, James Watson & Francis occur along the backbone is extremely specific
Crick, working with molecular models and X- and in fact contains the genetic instructions for
ray information supplied by Maurice Wilkins the organism.
and Rosalind Franklin, identified the physical  Nucleotides form genes, and a single DNA
structure of DNA. molecule may contain thousands of genes.
 In addition, Crick suggested a mechanism  Genes determine all hereditary traits, and
for DNA replication and how it works as the they control all the activities that take place
hereditary material. DNA and another within cells.
substance called ribonucleic acid (RNA) are  bases are said to be complementary
together referred to as nucleic acids because
they were first discovered in the nuclei of cells. RNA
 Just as amino acids are the structural units  RNA, the second principal kind of nucleic
of proteins, nucleotides are the structural units acid, differs from DNA in several respects.
of nucleic acids.  Whereas DNA is double-stranded, RNA is
 Each nucleotide has three parts: a nitrogen- usually single-stranded.
containing base, a pentose (five-carbon) sugar  The five-carbon sugar in the RNA nucleotide
(either deoxyribose or ribose), and a phosphate is ribose, which has one more oxygen atom
group (phosphoric acid). than deoxyribose.
 The nitrogen-containing bases are cyclic  Also, one of RNA’s bases is uracil (U)
compounds made up of carbon, hydrogen, instead of thymine
oxygen, and nitrogen atoms.  The other three bases (A, G, C) are the
 The bases are named adenine (A), thymine same as DNA.
(T), cytosine (C), guanine (G), and uracil (U).  Three major kinds of RNA have been
 A and G are double-ring structures called identified in cells.
purines, whereas T, C, and U are single-ring  They are messenger RNA (mRNA),
structures referred to as pyrimidines. ribosomal RNA (rRNA), and transfer RNA
 Nucleotides are named according to their (tRNA), each of which has a specific role in
nitrogen- containing base. protein synthesis
 Thus, a nucleotide containing thymine is a
thymine nucleotide, one containing adenine is ADENOSINE TRIPHOSPHATE
an adenine nucleotide, and so on.
 Adenosine triphosphate (ATP) is the
 The term nucleoside refers to the
principal energy-carrying molecule of all cells
combination of a purine or pyrimidine plus a
and is indispensable to the life of the cell.
pentose sugar; it does not contain a phosphate
 It stores the chemical energy released by
group.
some chemical reactions, and it provides the
DNA energy for reactions that require energy.
 ATP consists of an adenosine unit,
 According to the model proposed by Watson
composed of adenine and ribose, with three
and Crick, a DNA molecule consists of two long
phosphate groups attached
strands wrapped around each other to form a
 adenine nucleotide (also called adenosine
double helix
monophosphate, or AMP) with two extra
 The double helix looks like a twisted ladder,
phosphate groups.
and each strand is composed of many
 ATP is called a high-energy molecule
nucleotides.
because it releases a large amount of usable
 Every strand of DNA composing the double
energy when the third phosphate group is
helix has a “backbone” consisting of alternating
hydrolyzed to become adenosine diphosphate
deoxyribose sugar and phosphate groups.
(ADP).
 The deoxyribose of one nucleotide is joined
 A cell’s supply of ATP at any particular time
to the phosphate group of the next.
is limited.
 The nitrogen- containing bases make up the
 Whenever the supply needs replenishing,
rungs of the ladder.
the reaction goes in the reverse direction; the
 Note that the purine A is always paired with addition of a phosphate group to ADP and the
the pyrimidine T and that the purine G is input of energy produces more ATP.
always paired with the pyrimidine C.  The energy required to attach the terminal
phosphate group to ADP is supplied by the
cell’s various oxidation reactions, particularly
the oxidation of glucose.
 ATP can be made in every cell, where its
potential energy is released when needed.