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3

CHEMICAL BONDING,
MACROMOLECULES,
AND WATER

3.1 Strong and Weak Chemical Bonds

3.2 An Overview of Macromolecules


and Water as the Solvent of Life 52
II

NONINFORMATIONAL
MACROMOLECULES

3.3 Polysaccharides

Chemistry of Cellular
Components

51
51

3.4 Lipids
III

55

55

56

INFORMATIONAL
MACROMOLECULES

3.5 Nucleic Acids

57

57

3.6 Amino Acids and the Peptide Bond

59

3.7 Proteins: Primary and Secondary


Structure 61
3.8 Proteins: Higher Order Structure and
Denaturation 62

All microbial cells, regardless of type, are composed of


macromoleculesproteins, nucleic acids, polysaccharides,
and lipids.

50

CHEMICAL BONDING,
MACROMOLECULES,
AND WATER

s we learned in the first two chapters, all cells have much


in common. The heart of microbial diversity lies in the
variations that cells display in the chemistry and arrangement
of their cellular components. These variations confer special
properties on each type of cell and allow the cell to carry out
specific functions.
To really understand how a cell works, it is necessary to
know the molecules that are present and the chemical processes
that take place. Molecules, especially macromolecules, are the
guts of the cell and are the subject of this chapter. It is assumed
that the reader has some background in elementary chemistry,
especially regarding the nature of atoms and atomic bonding.
Here we will expand on this background with a primer on relevant biochemical bonds, followed by a discussion of the
structure and function of the four classes of macromolecules.

3.1

Strong and Weak Chemical Bonds

The major chemical elements in living things include hydrogen, oxygen, carbon, nitrogen, phosphorus, and sulfur
(l Section 5.1). These elements bond in various ways to
form the molecules of life. A molecule consists of two or more
atoms chemically bonded to one another. Thus, two oxygen
(O) atoms can combine to form a molecule of oxygen (O2).
Likewise, carbon (C), hydrogen (H), and O atoms can combine
to form glucose, C6H12O6, a hexose sugar (see Figure 3.4).

Covalent Bonds
In living things, chemical elements typically form strong
bonds in which electrons are shared more or less equally between atoms. These are called covalent bonds. To envision a
covalent bond, consider the formation of a molecule of water
from the elements O and H:
O + 2H

HOH

Oxygen has six electrons in its outermost shell, and


hydrogen contains only a single electron. When O and 2H
combine to form H2O, covalent bonds maintain the three
atoms in tight association as a water molecule. In some
compounds, double and even triple covalent bonds can
form (Figure 3.1). The strength of these bonds increases
dramatically with their number. In cells single and double
covalent bonds are most common; triply bonded substances
are rare.
Chemical elements bond in different combinations to form
monomers, small molecules that in turn bond with each other to
form larger molecules called polymers. Covalently bonded polymers in living things are called macromolecules. Thousands of
different monomers are known but only a relatively small number play important roles in the four classes of macromolecules.
To a large extent it is the chemical properties of monomers that
give macromolecules their distinctive structure and function.

H C C H
H H

51

H
H C

C H

Acetylene, a triple-bonded
organic compound

Ethylene, a double-bonded
organic compound
(a)

O
O

O (CO2)

Carbon dioxide

N (N2)

Nitrogen

O- (PO43-)

OPhosphate

(b)
NH2

H O

C C N C
H

(c)

Peptide bond
of proteins

H H O

C C C
O

H
Cytosine (nitrogen
base of DNA and RNA)

OH

H NH2

Phenylalanine (amino
acid in proteins)

Figure 3.1 Covalent bonding of some molecules containing


double or triple bonds. (a) For acetylene and ethylene, both the
electronic configuration of the molecules and the conventional
shorthand for bonds is shown. (b) Some inorganic compounds with
double bonds. (c) Some organic compounds with double bonds.

Hydrogen Bonding and Polarity


In addition to covalent bonds, several weaker chemical bonds
also play an important role in biological molecules. Foremost
among these are hydrogen bonds. Hydrogen bonds form as
the result of weak electrostatic interactions between hydrogen
atoms and more electronegative (electron attracting) atoms,
such as oxygen or nitrogen (Figure 3.2). For example, because
an oxygen atom is electronegative but a hydrogen atom is not,
in the covalent bond between oxygen and hydrogen the
shared electrons orbit slightly nearer the oxygen nucleus than
the hydrogen nucleus. Because electrons carry a negative
charge, this creates a slight charge separation, oxygen slightly
negative and hydrogen slightly positive; this bridge is the
hydrogen bond. An individual hydrogen bond by itself is very
weak. However, when many hydrogen bonds form within and
between molecules, overall stability of the molecules can increase dramatically.
Water is a polar substance. Because of this, water molecules tend to associate with one another and remain apart
from nonpolar (hydrophobic) molecules. Water is extensively
hydrogen bonded. As water molecules orient themselves in solution, the slight positive charge on a hydrogen atom can
bridge the negative charges on oxygen atoms (Figure 3.2a).
Hydrogen bonds also form between atoms in macromolecules
(Figure 3.2b,c). As these weak forces accumulate in a large
molecule such as a protein, they increase the stability of the
molecule and can also affect its overall structure. We will
see in Sections 3.5, 3.7, and 3.8 that hydrogen bonds play
major roles in the biological properties of proteins (Figure
3.2b) and nucleic acids (Figure 3.2c).

UNIT 1

Chapter 3 Chemistry of Cellular Components

UNIT 1 Principles of Microbiology

52

Amino terminus

H
H
O

()

()

H (+)
O()

H C R2
C O

(+)

H N
C O
H C R4
H N

(+)

H N

()

(+)

(+)

C O

C R5

H N

(+) H

()

H(+)

O () H

NH2
H C R1

H O

(+)H

()

C O
H C R3

(b) Amino acids in a protein

(a) Water
H
N H

N
Guanine

Cytosine

H N

N
H

N
O

H N
H
H

CH3

H N

N
Adenine

N H

Thymine
N
H

often control how different subunits in a multisubunit


protein associate with one another (quaternary structure,
Section 3.8) to form the biologically active molecule, and
they also help stabilize RNA and cytoplasmic membranes.

Bonding Patterns in Biological Molecules


The element carbon is a major component of all macromolecules. Carbon can bond not only with itself, but with many
other elements as well, to yield large structures of considerable diversity and complexity. Different organic (carboncontaining) compounds have different bonding patterns.
Each of these patterns, called functional groups, has unique
chemical properties that are important in determining their
biological role within the cell. An awareness of key functional
groups will make our later discussion of macromolecular
structure, cell physiology, and biosynthesis easier to follow.
Table 3.1 lists several functional groups of biochemical importance and examples of molecules or macromolecules that
contain them.
3.1 MiniReview

N
N

O
Hydrogen
bonds

(c) Nitrogen bases in DNA

Covalent bonds are strong bonds that bind elements in macromolecules. Weak bonds, such as hydrogen bonds, van der Waals
forces, and hydrophobic interactions, also affect macromolecular
structure, but they do so through more subtle atomic interactions. Various functional groups are common in biomolecules.

Figure 3.2 Hydrogen bonding in water and organic compounds.


Hydrogen bonds are shown as highlighted dotted lines. (b) Proteins.
R represents the side chain of the amino acid (Figure 3.12). (c) Hydrogen
bonds formed during complementary base pairing in DNA.

Why are covalent bonds stronger than hydrogen bonds?

Other Weak Bonds

3.2

Weak interactions other than hydrogen bonds are also important in cells. For instance, van der Waals forces are weak
attractive forces that occur between atoms when they become closer than about 34 angstroms (); van der Waals
forces can play significant roles in the binding of substrates
to enzymes (l Section 5.5) and in proteinnucleic acid
interactions.
Ionic bonds, such as that between Na and Cl- in NaCl,
are weak electrostatic interactions that support ionization in
aqueous solution. Many important biomolecules, such as carboxylic acids and phosphates (Table 3.1), are ionized at
cytoplasmic pH (typically pH 68) and thus can be dissolved
to high levels in the cytoplasm.
Hydrophobic interactions are also considered weak
bonds. Hydrophobic interactions occur when nonpolar
molecules or nonpolar regions of molecules associate
tightly in a polar environment. Hydrophobic interactions
can play major roles in controlling the folding of proteins
(Sections 3.7 and 3.8). Like van der Waals forces, hydrophobic interactions help bind substrates to enzymes
(l Section 5.5). In addition, hydrophobic interactions

How can a hydrogen bond play a role in macromolecular


structure?

An Overview of Macromolecules
and Water as the Solvent of Life

If you were to chemically analyze a cell of the common intestinal bacterium Escherichia coli, what would you find? You
would find water as the major constituent, but after removing
the water, you would find large amounts of macromolecules,
much smaller amounts of monomers, and a variety of inorganic ions (Table 3.2). About 95% of the dry weight of a cell
consists of macromolecules, and of these, proteins are by far
the most abundant class (Table 3.2).
Proteins are polymers of monomers called amino acids.
Proteins are found throughout the cell, playing both structural and enzymatic roles (Figure 3.3a). An average cell will
have over a thousand different types of proteins and multiple
copies of each (Table 3.2).
Nucleic acids are polymers of nucleotides and are found
in the cell in two forms, RNA and DNA. After proteins, ribonucleic acids (RNAs) are the next most abundant
macromolecule in an actively growing cell (Table 3.2 and
Figure 3.3b). This is because there are thousands of ribosomes
(the machines that make new proteins) in each cell, and

Table 3.1

53

Some functional groups of biochemical importance

Functional group

Structurea

Biological relevance

Example

Organic, amino, and fatty acids; lipids; proteins

Acetateb

Functional group of reducing sugars such as glucose;


aldehydes

Formaldehyde

Lipids; carbohydrates

Glucose

Citric acid cycle intermediates

-ketoglutarate

Triglycerides

Lipids of Bacteria and


Eukarya

Nucleic acids

DNA, RNA

Energy metabolism; biosynthesis of fatty acids

Acetyl-CoA

Certain types of lipids

Lipids of Archaea

Energy metabolism

Acetyl phosphate

Energy metabolism

Adenosine triphosphate
(ATP)

Proteins

Cellular proteins

O
Carboxylic acid

C OH
O

Aldehyde

C H
H

Alcohol

C OH
H
O

Keto

C
H

O
Ester

C O C
H
O

Phosphate ester

O P O C
O
O

Thioester

C~S
H

H
Ether

Acid anhydride

Phosphoanhydride

C O C
H

C~O P O
O
O
O
O P~O P O
O

O
O

Peptide

R C C N C R

A squiggle-type bond depiction (~) indicates an energy-rich bond (l Section 5.8).


Acetate (H3CCOO-) is the ionized form of acetic acid (H3CCOOH).

ribosomes are composed of a mixture of RNAs and protein. In


addition, smaller amounts of RNA are present in the form of
messenger and transfer RNAs, other key players in protein
synthesis. In contrast to RNA, DNA makes up a small fraction
of the bacterial cell (Table 3.2).
Lipids have both hydrophobic and hydrophilic properties
and play crucial roles in the cell as the backbone of membranes and as storage depots for excess carbon (Figure 3.3d).
Polysaccharides are polymers of sugars and are present in
the cell, primarily in the cell wall. Like lipids, however, polysaccharides such as glycogen (discussed in the next section)
can be major forms of carbon and energy storage in the cell
(Figure 3.3c).

Water as a Biological Solvent


Macromolecules and all other molecules in cells are bathed in
water. Water has several important features that make it an
ideal biological solvent. Two key features are its polarity and
cohesiveness.
The polar properties of water are important because
many biologically important molecules (Table 3.2) are themselves polar and thus readily dissolve in water. As we will see
in Chapter 4, dissolved substances are continually passing
into and out of the cell through transport activities of the
cytoplasmic membrane (l Sections 4.3 and 4.4). These substances include nutrients needed to build new cell material
and waste products of metabolic processes.

UNIT 1

Chapter 3 Chemistry of Cellular Components

54

UNIT 1 Principles of Microbiology

Table 3.2

Chemical composition of a prokaryotic cella

Molecule
Total macromolecules
Protein
Polysaccharide
Lipid
Lipopolysaccharide
DNA
RNA
Total monomers
Amino acids and
precursors
Sugars and precursors
Nucleotides and
precursors
Inorganic ions
Total

Percent of
dry weightb

Molecules per cell


(different kinds)

96
55
5
9.1
3.4
3.1
20.5

24,610,000 (~2,500)
2,350,000 (~1,850)
4,300 (2)c
22,000,000 (4)d
1,430,000 (1)
2.1 (1)
255,500 (~660)

Flagellum

Cell wall
Cytoplasm

(a) Proteins

Nucleoid

Ribosomes

3.0
0.5

(~350)
(~100)

2
0.5

(~50)
(~200)
(b) Nucleic

1
100%

Cytoplasmic
membrane

Acids:

DNA RNA

(18)

Data from Neidhardt, F.C., et al. (eds.), 1996. Escherichia coli and Salmonella
typhimuriumCellular and Molecular Biology, 2nd edition. American Society for
Microbiology, Washington, DC.
b
Dry weight of an actively growing cell of E. coli 2.8 1013g; total weight
(70% water) 9.5 1013 g.
c
Assuming peptidoglycan and glycogen to be the major polysaccharides present.
d
There are several classes of phospholipids, each of which exists in many kinds
because of variability in fatty acid composition between species and because of
different growth conditions.
e
Reliable estimates of monomer and inorganic ion composition are lacking.

The polar properties of water also promote the stability of


large molecules because of the increased opportunities for hydrogen bonding. Water forms three-dimensional networks,
both with itself (Figure 3.2a) and within macromolecules. By
so doing, water molecules help to position atoms within biomolecules for potential interaction. The high polarity of water
is also beneficial to the cell because it forces nonpolar substances to aggregate and remain together. Membranes, for
example, contain large amounts of lipids, which have major
nonpolar (hydrophobic) components, and these aggregate in
such a way as to prevent the unrestricted flow of polar molecules into and out of the cell.
The polar nature of water makes it highly cohesive. This
means that water molecules have a high affinity for one another and form ordered arrangements in which hydrogen
bonds (Figure 3.2a) are constantly forming, breaking, and
re-forming. The cohesiveness of water is responsible for
some of its biologically important properties, such as high
surface tension and high specific heat (heat required to
raise the temperature 1C). Also, the fact that water expands
on freezing to yield a less dense solid form (ice) has a profound effect on life in temperate and polar aquatic
environments. In a lake, for example, ice on the surface insulates the water beneath the ice and prevents it from
freezing, thus allowing aquatic organisms to survive under
the overlying ice.
Life originated in water about 3.9 billion years ago
(l Figure 1.6), and virtually anywhere on Earth where liquid
water exists, microorganisms are likely to be found. With

(c) Polysaccharides

Storage
granules

(d) Lipids

Figure 3.3

Macromolecules in the cell. (a) Proteins (brown) are


found throughout the cell both as parts of cell structures and as
enzymes. The flagellum is a structure involved in swimming motility.
(b) Nucleic acids. DNA (green) is found in the nucleoid of prokaryotic
cells and in the nucleus of eukaryotic cells. RNA (orange) is found in the
cytoplasm (mRNA, tRNA) and in ribosomes (rRNA). (c) Polysaccharides
(yellow) are located in the cell wall and occasionally in internal storage
granules. (d) Lipids (blue) are found in the cytoplasmic membrane, the
cell wall, and in storage granules.

these important properties of water in mind, we now consider


the structure of the major macromolecules of life (Table 3.2
and Figure 3.3) in more detail.
3.2 MiniReview
Proteins are the most abundant class of macromolecule in the
cell. Other macromolecules include the nucleic acids, lipids,
and polysaccharides. Water is an excellent solvent for life
because of its polarity and cohesiveness.
Why do protein and RNA make up such a large proportion
of an actively growing cell?
Why does the high polarity of water make it useful as a
biological solvent?

II

NONINFORMATIONAL
MACROMOLECULES

Sugar
Pentoses

In this unit we examine the structure and function of noninformational macromoleculespolysaccharides and lipids.
The sequence of monomers in these macromolecules does not
carry genetic information, but the macromolecules themselves play important roles in the cell, primarily as structural
or reserve materials.

The Glycosidic Bond


Polysaccharides are carbohydrates containing many (sometimes hundreds or even thousands) of monomeric units called
monosaccharides. The latter are connected by covalent bonds
called glycosidic bonds (Figure 3.6). If two monosaccharides
are bonded by a glycosidic linkage, the resulting molecule is
a disaccharide. The addition of one more monosaccharide
yields a trisaccharide, and several more an oligosaccharide. An
extremely long chain is then a polysaccharide.
Glycosidic bonds can form in two different geometric orientations, alpha () and beta () (Figure 3.6a). Polysaccharides
with a repeating structure composed of glucose units
bonded between carbons 1 and 4 in the alpha orientation
(for example, glycogen and starch, Figure 3.6b) function as
important carbon and energy reserves in bacteria, plants,
and animals. Glucose units joined by -1,4 linkages are present in cellulose (Figure 3.6b), a stiff plant and algal cell wall
component. Thus, even though both starch and cellulose
contain only D-glucose, their functional properties differ
because of the different configurations, or , of their glycosidic bonds.

O
OH

5
4C

OH

H
H
H

C
4

OH

Glucose

HO C
H
H

OH

Backbone
of DNA

C1

C2 H

3C

HOCH2
5

OH

OH

OH

OH

O
H

CH2OH

OH

Backbone
of RNA

C1

C2 H

HOCH2

Hexoses

OH

CH2OH

OH

H C
3

OH

Significance

HOCH2

Polysaccharides

Carbohydrates (sugars) are organic compounds that contain


carbon, hydrogen, and oxygen in a ratio of 1:2:1. The structural formula for glucose, the most abundant sugar on Earth is
C6H12O6 (Figure 3.4). The most biologically relevant carbohydrates are those containing four, five, six, and seven carbon
atoms (designated as C4, C5, C6, and C7). C5 sugars (pentoses)
are of special significance because of their role as structural
backbones of nucleic acids. Likewise, C6 sugars (hexoses) are
the monomeric constituents of cell wall polymers and energy
reserves. Figure 3.4 shows the structure of a few common
sugars.
Derivatives of simple carbohydrates are common in cells.
When other chemical species replace one or more of the
hydroxyl groups on the sugar, derivatives are formed. For
example, the important bacterial cell wall polymer peptidoglycan (l Section 4.6) contains the glucose derivative
N-acetylglucosamine (Figure 3.5). Besides sugar derivatives,
sugars having the same structural formula can differ in their
stereoisomeric properties. For example, a polysaccharide composed of D-glucose differs from one containing L-glucose
(Section 3.6). Hence, a large number of different sugars are
available to the cell for the construction of polysaccharides.

H
H

Deoxyribose

3.3

H
H

Ribose

Ring

Open
chain

55

OH

4C

C1

OH

HO

OH

3C

CH2OH

Energy
source;
cell walls

C2
OH

Fructose

CH2OH

HO C
H
H

O
H
OH
OH

HOCH2
5C

OH

Energy
source;
OH C2
fruit sugar
CH
OH
C 1 2

H C
4

OH

CH2OH

Figure 3.4 Structural formulas of a few common sugars. The


formulas can be depicted in two alternate ways, open chain and ring.
The open chain is easier to visualize, but the ring form is the commonly
used structure. Note the numbering system on the ring. Glucose and
fructose are isomers of one another; they have the same molecular
composition but have different structures (Section 3.6).

Complex Polysaccharides
Polysaccharides can also combine with other classes of
macromolecules, such as proteins and lipids, to form complex polysaccharidesglycoproteins and glycolipids. These

1 O
C H O

H
2

HO

HO C H
H

C OH
C OH

CH2OH

OH
1

OH

H
H

N replaces O
in the sugar

CH2OH

H C N C CH3
H

Acetyl group

NH
C O
CH3

Open chain

Ring structure

Figure 3.5 N-acetylglucosamine, a derivative of glucose. The O


on C-2 is replaced with an N- acetyl group.

UNIT 1

Chapter 3 Chemistry of Cellular Components

UNIT 1 Principles of Microbiology

56

6 CH2OH
5

6 CH2OH

O
H

OH

HO

H
2

OH

How can glycogen and cellulose differ so much in their physical


properties when they both consist of 100% D-glucose?

OH

OH

molecules. Polysaccharides can also contain other molecules


such as protein or lipid, forming complex polysaccharides.

OH

-1,4-Glycosidic bond

3.4

6 CH2OH

CH2

H
1

H
O

OH

H
H

OH
HO

OH

OH
3

-1,4-Glycosidic bond

-1,6-Glycosidic bond
(a)

Starch

-1,4 bonds

-1,6 bonds

Lipids

Lipids are essential components of cells and are amphipathic


macromolecules, meaning that they show both hydrophilic
and hydrophobic character. Lipid structure varies between
the domains of life, and even within a domain many different
lipids are known. Fatty acids are major constituents of
Bacteria and Eukarya lipids. By contrast, lipids of Archaea
contain a hydrocarbon (phytanyl) side chain not composed of
fatty acids (l Section 4.3).
Fatty acids contain both hydrophobic and hydrophilic
components. Palmitate (the ionized form of palmitic acid),
is a common fatty acid in membrane lipids. Palmitate is a
16-carbon fatty acid composed of a chain of 15 saturated
(fully hydrogenated and thus highly hydrophobic) carbon
atoms and a single carboxylic acid group (the hydrophilic portion) (Figure 3.7). Other common fatty acids in the lipids of
Bacteria include saturated or monounsaturated forms, from
C12 to C20 (Figure 3.7).

Triglycerides and Complex Lipids


Glycogen

Cellulose

-1,4 bonds

-1,4 bonds

(b)

Figure 3.6 The glycosidic bond and polysaccharides. (a) Structure


of different glycosidic bonds. Note that both the linkage (position on
the ring of the carbon atoms bonded) and the geometry ( or ) of the
linkage can vary about the glycosidic bond. (b) Structures of some
common polysaccharides. Compare color coding to (a).

compounds play important roles in cells, in particular as


cell-surface receptor molecules in cytoplasmic membranes.
The compounds typically reside on the external surfaces of
the membrane where they are in contact with the environment. Glycolipids constitute a major portion of the cell wall of
gram-negative bacteria and, as such, impart a number of
unique surface properties to these organisms (lSection 4.9).
3.3 MiniReview
Sugars can form long polymers called polysaccharides. The
two different orientations of the glycosidic bonds that link
sugar residues impart different properties to the resultant

Simple lipids (fats) consist of fatty acids (or phytanyl units in


Archaea) bonded to the C3 alcohol glycerol (Figure 3.7a, b).
Simple lipids are also called triglycerides because three fatty
acids are linked to the glycerol molecule. We will see when we
consider membrane structure (l Section 4.3) that the bond
between glycerol and the hydrophobic side chain is an ester
bond (Table 3.1) in cells of Bacteria and Eukarya but an ether
bond (Table 3.1) in Archaea.
Complex lipids are simple lipids that contain additional
elements such as phosphorus, nitrogen, or sulfur, or small hydrophilic organic compounds such as sugars (Figure 3.7d),
ethanolamine (Figure 3.7c), serine, or choline. Lipids containing a phosphate group, called phospholipids, are an important
class of complex lipids because they play a major structural
role in the cytoplasmic membrane (l Section 4.3).
The amphipathic property of lipids makes them ideal
structural components of membranes. Lipids aggregate to
form membranes; the hydrophilic (glycerol) portion is in contact with the cytoplasm and the external environment
whereas the hydrophobic portion remains buried away inside
the membrane (l Section 4.3 and Figures 4.4 and 4.5).
Because of this property, membranes are ideal permeability
barriers. The inability of polar substances to flow through the
hydrophobic region of the lipids renders the membrane impermeable and prevents leakage of cytoplasmic constituents.
However, this also means that polar substances necessary for
cell function do not leak in, either, but we reserve this story for
the next chapter (transport, l Section 4.5)

Common fatty acids:

16 15 14 13 12 11 10 9

H3C

C OH

Simple lipids (triglycerides):


Fatty acids linked to glycerol by ester linkage

Glycerol
O

C16 saturated (palmitic)


O
C OH

CH3
C16 monounsaturated (palmitoleic)

H3C
H3C

C O C H
O
C O C H
H
Ester
linkage

Fatty acids
(a)

(b)

Complex lipid:
Phosphatidyl ethanolamine (a phospholipid)

Complex lipid:
Monogalactosyl diglyceride (a glycolipid)

H3C
H 3C
Fatty acids
Phosphate
Ethanolamine

C O C H
O
C O C H
O
O P O C H
O
H

OH
4

CH2OH
O

OH
2

Galactose

Fatty acids

CH2

O C H
O
C O C H
O

H3C

C O C H
H

H3C
(c)

OH

CH2
+NH

C O C H
O

H3C

57

(d)

Figure 3.7 Lipids. (a) Fatty acids differ in length, in position, and in number of double bonds. (b) Simple
lipids are formed by a dehydration reaction between fatty acids and glycerol to yield an ester linkage. The fatty
acid composition of a cell varies with growth temperature. (c, d) Complex lipids are simple lipids containing
other molecules.

3.4 MiniReview
Lipids contain both hydrophobic and hydrophilic components;
their chemical properties make them ideal structural components for cytoplasmic membranes.
What part of a fatty acid molecule is hydrophobic? Hydrophilic?
How does a phospholipid differ from a triglyceride?
Draw the chemical structure of butyrate, a C4 fully saturated
fatty acid.

we already know, DNA carries the genetic blueprint for the


cell and RNA is the intermediary molecule that converts
the blueprint into defined amino acid sequences in proteins
(l Figure 1.4).
A nucleotide is composed of three components: a pentose
sugar, either ribose (in RNA) or deoxyribose (in DNA), a
nitrogen base, and a molecule of phosphate, PO43-. The general structure of nucleotides of both DNA and RNA is very
similar (Figure 3.8).

III

INFORMATIONAL
MACROMOLECULES

The sequence of monomers in nucleic acids carries genetic information, and the sequence of monomers in proteins carries
structural and functional information. In contrast to polysaccharides and lipids, nucleic acids and proteins are thus
informational macromolecules.

Phosphate

O
5

CH2
C 4 H
3
H C
OH

Base
H
C

1 C

OH

H
Ribose
H only
in DNA

3.5

Nucleic Acids

The nucleic acids deoxyribonucleic acid, DNA, and ribonucleic


acid, RNA, are macromolecules composed of monomers called
nucleotides. Therefore, DNA and RNA are polynucleotides. As

Figure 3.8 Nucleotides. The numbers on the sugar contain a prime


() after them because the ring structure in the nitrogen base is also
numbered (Figure 3.9).

UNIT 1

Chapter 3 Chemistry of Cellular Components

UNIT 1 Principles of Microbiology

58

Pyrimidine bases
O

NH2
5 4 3N
6
2
1

N
H

H3C

Purine bases

O
N

NH2
N

N
H

N
H

5 6 1N
2
4
3

N
H

O
N

N
H

Cytosine
(C)

Thymine
(T)

Uracil
(U)

Adenine
(A)

Guanine
(G)

DNA
RNA

DNA
only

RNA
only

DNA
RNA

DNA
RNA

NH2

Figure 3.9 Structure of the nitrogen bases of DNA and RNA.


Note the numbering system of the rings. In attaching itself to the 1
carbon of the sugar phosphate shown in Figure 3.8, a pyrimidine base
bonds through N-1 and a purine base bonds at N-9.

Nucleotides
The nitrogen bases of nucleic acids belong to one of two chemical classes. Purine basesadenine and guaninecontain two
fused heterocyclic rings (a heterocyclic ring contains more
than one kind of atom). Pyrimidine basesthymine, cytosine,
and uracilcontain a single six-membered heterocyclic ring
(Figure 3.9). Guanine, adenine, and cytosine are present in
both DNA and RNA. Thymine is present (with minor exceptions) only in DNA, and uracil is present only in RNA.
Nucleotides consist of a nitrogen base attached to a pentose sugar by a glycosidic linkage between carbon atom 1 of
the sugar and a nitrogen atom of the base, either the nitrogen
atom labeled 1 (in a pyrimidine base) or 9 (in a purine base).
Without the phosphate, a nitrogen base bonded to its sugar is
called a nucleoside. Nucleotides are thus nucleosides containing one or more phosphates (Figure 3.10).
Nucleotides play other roles in the cell besides their major
role as components of nucleic acids. Nucleotides, especially
adenosine triphosphate (ATP) (Figure 3.10), are key forms of
chemical energy within the cell, releasing sufficient energy
during the hydrolysis of a phosphate bond to drive energyrequiring reactions in the cell (l Section 5.8). Other

Phosphoanhydride

Phosphate
ester

Ribose
NH2

O P ~ O P ~O P O CH
2
O

O
H

OH

OH

5 6 1N
2
4
3

Adenine

Phosphates

Figure 3.10 Components of the important nucleotide, adenosine


triphosphate. The energy of hydrolysis of a phosphoanhydride bond
(shown as squiggles) is greater than that of a phosphate ester bond,
which is significant in bioenergetics (l Section 5.8). With the
phosphate group removed, the molecule would be the nucleoside
adenosine.

nucleotides or nucleotide derivatives function in oxidation


reduction reactions in the cell (l Section 5.7) as carriers of
sugars in the biosynthesis of polysaccharides (l Section
5.15) and as regulatory molecules inhibiting or stimulating
the activities of certain enzymes or metabolic events. However, we discuss here only the role of nucleotides as building
blocks of nucleic acids, the major informational function of
nucleotides.

Nucleic Acids
The nucleic acid backbone is a polymer of alternating sugar
and phosphate molecules. Polynucleotides consist of nucleotides covalently bonded via phosphate from carbon
3called the 3 (3 prime) carbonof one sugar to the 5 carbon of the adjacent sugar (Figure 3.11a). The phosphate
linkage is called a phosphodiester bond because a phosphate molecule connects two sugar molecules by ester linkage
(Figure 3.11a; Table 3.1).
The sequence of nucleotides in a DNA or RNA molecule is
called its primary structure. As we have discussed, the sequence of bases in a DNA or RNA molecule is informational,
encoding the sequence of amino acids in proteins or encoding
specific ribosomal or transfer RNAs. The replication of DNA
and the synthesis of RNA are key events in the life of a cell
(l Section 1.2 and Figure 1.4). We will see later that a virtually error-free mechanism is employed to ensure the faithful
transfer of genetic traits from one generation to another
(l Chapter 7).

DNA
In the genome of cells, DNA is double-stranded. Each chromosome consists of two strands of DNA, with each strand
containing hundreds of thousands to several million nucleotides linked by phosphodiester bonds. The strands
associate with one another by hydrogen bonds that form
between the nitrogen bases in nucleotides of one strand and
the nitrogen bases in nucleotides of the other strand. When
positioned adjacent to one another, purine and pyrimidine
bases can undergo hydrogen bonding (see Figure 3.2c).
Hydrogen bonding is most stable when guanine (G)
bonds with cytosine (C) and adenine (A) bonds with thymine
(T) (see Figure 3.2c). Specific base pairing, A with T and G
with C, thus ensures that the two strands of DNA are
complementary in base sequence; that is, wherever a G is
found in one strand, a C is found in the other, and wherever a
T is present in one strand, its complementary strand has an A
(Figure 3.11b).

RNA
With a few exceptions, all RNAs are single-stranded molecules.
However, RNAs typically fold back upon themselves in regions where complementary base pairing is possible to form
folded structures. This pattern of folding in RNA is called its
secondary structure (Figure 3.11c). In certain very large
RNA molecules, such as ribosomal RNA (l Sections 7.15
and 14.9), some parts of the molecule contain only primary

59

5 position
H 2C

Base
1

H
3 position

5 A G C

T T A G C 3

Hydrogen bonds

3 T C G A A T C G 5
(b)

O
O P

Phosphodiester
bond

Nitrogen base attached


to 1 position

Deoxyribose

(i) 5 C A G U G A C C A

U C G 3

O
O

H2C
H

(ii) 5 C C G A C A C G U C G G 3
A C

O
O P

Base

Region of
complementary
base pairing

(a)

(c)

C
5

G
3

Primary structure
Secondary
structure

Figure 3.11 Nucleic acids: DNA and RNA. (a) Structure of part of a DNA chain. The nitrogen bases can be
adenine, guanine, cytosine, or thymine. In RNA, an OH group is present on the 2 carbon of the pentose sugar
(see Figure 3.8) and uracil replaces thymine. (b) Simplified structure of DNA in which only the nitrogen bases
are shown. The two strands are complementary in base sequence, with A joined to T by two hydrogen bonds
and G joined to C by three hydrogen bonds (note that the hydrogen bonds are indicated by two and three lines
rather than by dots as in Figure 3.2). (c) RNA: (i) a sequence showing only primary structure; (ii) a sequence that
allows for secondary structure. In RNA, secondary structures form when opportunities for intrastrand base pairing
arise, as shown here.

structure but others contain both primary and secondary


structure. This leads to highly folded and twisted molecules
whose biological function is critically dependent on their final
three-dimensional shape.
At least four classes of RNA exist in cells. Messenger RNA
(mRNA) carries the genetic information of DNA in a singlestranded molecule complementary in base sequence to that of
DNA. Transfer RNAs (tRNAs) convert the genetic information
present in mRNA into the language of amino acids, the building blocks of proteins. Ribosomal RNAs (rRNAs), of which
there are several types, are important structural and catalytic
components of the ribosome, the protein-synthesizing system
of the cell. In addition to these, a variety of small RNAs exist
in cells. These RNAs function to regulate the production or activity of other RNAs. These various types of RNA are
discussed in detail in Chapters 7, 9, and 11.
3.5 MiniReview
The informational content of a nucleic acid is determined by the
sequence of nitrogen bases along the polynucleotide chain.
Both RNA and DNA are informational macromolecules. RNA can
fold into various configurations to obtain secondary structure.
What components are found in a nucleotide?
How does a nucleoside differ from a nucleotide?
Distinguish between the primary and secondary structure
of RNA.

3.6

Amino Acids and the Peptide Bond

Amino acids are the monomers of proteins. Most amino


acids consist of carbon, hydrogen, oxygen, and nitrogen only,
but 2 of the 22 genetically encoded amino acids also contain
sulfur, and 1 contains selenium. All amino acids contain two important functional groups, a carboxylic acid group (COOH)
and an amino group (NH2) (Table 3.1 and Figure 3.12a).
These groups are key to the structure of proteins because covalent bonds can form between the carboxyl carbon of one
amino acid and the amino nitrogen of a second amino acid
(with elimination of a molecule of water) to form the peptide
bond (Figure 3.13).

Structure of Amino Acids


All amino acids have the general structure shown in Figure 3.12a. But each type of amino acid is unique because of its
unique side group (abbreviated R in Figure 3.12a) attached to
the -carbon. The -carbon is the carbon atom adjacent to the
carboxylic acid group. The side chains vary considerably in
structure, from as simple as a hydrogen atom in the amino
acid glycine to aromatic rings in phenylalanine, tyrosine, and
tryptophan (Figure 3.12b).
The chemical properties of an amino acid are governed by
its side chain. Amino acids that have similar chemical properties are grouped into related amino acid families as shown
in Figure 3.12b. For example, the side chain may contain a
carboxylic acid group, such as in aspartic acid or glutamic

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60

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H
-carbon
H 2N C

Carboxylic
acid group

Glu Glutamate (E)

CH3

Lys Lysine (K)

CH3

O
H
H
H3C C C C N (CH2)4 Pyl Pyrrolysine (O)
N
H2 C
C
H2
+NH C H
N CH2 CH2 CH2 Arg Arginine (R)
2

Ser Serine (S)

CH3 CH
O OH
NH2 C CH2
O

Thr Threonine (T)

NH2 C CH2 CH2

Gln Glutamine (Q)

HS CH2

-O C CH CH
2
2

+NH CH CH CH CH
3
2
2
2
2

(a)General structure of an amino acid

OH CH2

Asp Aspartate (D)

C OH

Amino group

O
-O C CH
2
O

Asn Asparagine (N)

NH2

+HN

CH2

Cys Cysteine (C)


Sec Selenocysteine (U)

CH2

Ionizable: acidic

Tyr Tyrosine (Y)

Nonionizable polar
Nonpolar
(hydrophobic)

(b)Structure of the amino acid R groups

CH3

Ala Alanine (A)

CH

Val Valine (V)

CH CH2 Leu Leucine (L)


CH3

CH3 CH2

CH

CH3 S CH2 CH2

N
H

Ionizable: basic
HO

CH3

Gly Glycine (G)

Ile Isoleucine (I)


Met Methionine(M)

CH2

Phe Phenylalanine (F)

CH2

Trp Tryptophan(W)

His Histidine (H)

Key
HSe CH2

CH3

H2C

N
H
CH2

H2C

CH COO

N
H

Pro Proline (P)

(Note: Because proline lacks a free amino group,


the entire structure of this amino acid is shown,
not just the R group.

Figure 3.12 Structure of the 22 genetically encoded amino acids. (a) General structure. (b) R group
structure. The three-letter codes for the amino acids are to the left of the names, and the one-letter codes are
in parentheses to the right of the names. Pyrrolysine has thus far been found only in certain methanogenic
Archaea (l Sections 2.10 and 17.4).
acid, rendering the amino acid acidic. Others contain additional amino groups, rendering them basic. Alternatively,
several amino acids contain hydrophobic side chains and are
grouped together as nonpolar amino acids. The amino acid
cysteine contains a sulfhydryl group (SH). Sulfhydryl groups
can connect one chain of amino acids to another by disulfide
linkage (RSSR) through two cysteine molecules, one
from each chain.

H O
H O
H
H2N C C OH + H N C C OH
R2

R1

H2O
N-terminus

C-terminus
H O H H O
H2N C C N C C OH
R1

R2
Peptide
bond

Figure 3.13 Peptide bond formation. R1 and R2 refer to the


variable portions (side chains) of the amino acids (Figure 3.12). Note
how, following peptide bond formation, a free OH group is present at
the C-terminus for formation of the next peptide bond.

The diversity of chemically distinct amino acids makes


possible an enormous number of unique proteins with widely
different biochemical properties. For example, if one assumes
that an average polypeptide contains 100 amino acids, there
are 22100 different polypeptide sequences that are theoretically
possible. No cell has anywhere near this many different proteins. However, a cell of Escherichia coli contains almost
2,000 different kinds of proteins (Table 3.2). These include
different soluble and membrane-integrated enzymes, structural proteins, transport proteins, sensory proteins, and many
others.

Isomers
Two molecules may have the same molecular formula but exist in different structural forms. These related but
nonidentical molecules are called isomers. For example, the
hexose sugars glucose and fructose (Figure 3.4) are isomers.
Louis Pasteur, the famous early microbiologist who quashed
the theory of spontaneous generation (l Section 1.7), began
his scientific career as a chemist studying a class of isomers
called optical isomers. Optical isomers that have the same
molecular and structural formulas, except that one is a
mirror image of the other (just as the left hand is a mirror
image of the right), are called enantiomers. The enantiomers
of a given compound can never be superimposed one over the
other and are designated as either D or L (Figure 3.14),
depending on whether a pure solution rotates light to the right

or left, respectively. Sugars of the D enantiomer predominate


in biological systems.
Amino acids also have D or L enantiomers. However, in
proteins cells employ the L-amino acid rather than the D form
(Figure 3.14c). Nevertheless, D-amino acids are occasionally
found in cells, most notably in the cell wall polymer peptidoglycan (l Section 4.6) and in certain peptide antibiotics
(l Section 27.9). Cells can interconvert certain enantiomers
by the activity of enzymes called racemases. For instance,
some prokaryotes can grow on L-sugars or D-amino acids
because they have racemases that can convert these forms
into the opposite enantiomer before metabolizing them.

Why can it be said that all amino acids are structurally


similar yet different simultaneously?
Draw the complete structure of a dipeptide containing the
amino acids alanine and tyrosine. Outline the peptide bond.
Which enantiomeric forms of sugars and amino acids are
commonly found in living organisms? Why doesnt the
amino acid glycine have different enantiomers? (Hint: Look
carefully at Figure 3.14c and replace the alanine shown with
glycine.)

3.7

Proteins: Primary and


Secondary Structure

Proteins play several key roles in cell function. In essence, a


cell is what it is and does what it does because of the kinds
and amounts of proteins it contains; that is, every different
type of cell has a different complement of proteins. An understanding of protein structure is therefore essential for
understanding how cells work.
Two major classes of proteins are catalytic proteins
(enzymes) and structural proteins. Enzymes are the
catalysts for chemical reactions that occur in cells (lChapters 5, 20, and 21). By contrast, structural proteins are
integral parts of the major structures of the cell: membranes,
walls, cytoplasmic components, and so on. However, all
proteins show certain basic features in common, and we
discuss these now.

Primary Structure
As we have said, proteins are polymers of amino acids covalently bonded by peptide bonds (Figure 3.13). Two amino acids
bonded by peptide linkage constitute a dipeptide, three amino
acids, a tripeptide, and so on. When many amino acids are covalently linked via peptide bonds, they form a polypeptide.

(a)

D-Glucose

3.6 MiniReview
Twenty-two different amino acids are found in cells and can
bond to each other via the peptide bond. Mirror image
(enantiomeric) forms of sugars and amino acids exist, but only
one optical isomer of each is found in most cell polysaccharides
and proteins.

61

O
C

H C OH
HO C H

L-Alanine

L-Glucose

O
C

H2N C H

HO C H

COOH
H C NH2

CH3

CH3

COOH

H C OH

H C OH

HO C H

COOH

H C OH

HO C H

CH2OH

D-Alanine

COOH

H2N

CH2OH

CH3

NH2
CH3

Three-dimensional projection
(b)

(c)

Figure 3.14 Isomers. (a) Ball-and-stick model showing mirror images.


(b) Enantiomers of glucose. (c) Enantiomers of the amino acid alanine.
In the three-dimensional projection the arrow should be understood as
coming toward the viewer and the dashed line indicates a plane away
from the viewer. Note that no matter how the three-dimensional views
are rotated, the L and D forms can never be superimposed. This is a
characteristic of enantiomers.

A protein consists of one or more polypeptides. The number of amino acids differs greatly from one protein to another;
proteins containing as few as 15 or as many as 10,000 amino
acids are known. Because proteins differ in their composition,
sequence, and number of amino acids, it is obvious that enormous variation in protein structure (and thus function) is
possible.
The linear array of amino acids in a polypeptide is called
its primary structure. The primary structure of a polypeptide
is critical to its final function because it is consistent with only
certain types of folding patterns. And it is only the final, folded
polypeptide that assumes biological activity. The two ends
of a polypeptide are so designated by whether a free carboxylic acid group or a free amino group exists; the terms
C-terminus and N-terminus are used to describe these two
ends, respectively (Figure 3.2b).

Secondary Structure
Once formed, a polypeptide does not remain a linear structure. Instead it folds to form a more stable structure.
Interactions of the R groups on the amino acids in a polypeptide force the molecule to twist and fold in a specific way.
This forms the secondary structure. Hydrogen bonds, the
weak noncovalent linkages discussed earlier (Section 3.1),

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62

UNIT 1 Principles of Microbiology

R C

R C

R C
C O H N
C O
H N
C O H N
C R
C R
C R
N H O C
O C

O
N

C
C
C
H
CH
C
H
N
C
CH N
R
CH N
R H
R
R
H
H
O
O
C
C
CH N
H
C N
R H
Hydrogen bonds
R
between nearby
H
O
amino acids
O
C
C
H
CH N C
N
R
R
H
H
O
O
C
N
C
CH
N
CH
H
H R
R
(a) -helix

N H
N H O C
R C
R C
C O
C O H N

R C

H N
C R
O C

C O H N
C R
C R
C
N H O

N H
N H O C
R C
R C
C O
C O H N

R C

H N
C R
O C

( b) -sheet

C O H N
C R
C R
N H O C

Hydrogen bonds
between distant
amino acids

Figure 3.15 Secondary structure of polypeptides. (a) -helix secondary structure.

(b) -sheet secondary structure. Note that the hydrogen bonding is between atoms in the
peptide bonds and does not involve the R groups.

play important roles in polypeptide secondary structure. One


common type of secondary structure is the -helix. To envision an -helix, imagine a linear polypeptide wound around
a cylinder (Figure 3.15a). In this twisted structure, oxygen
and nitrogen atoms from different amino acids become
positioned close enough to allow hydrogen bonding. These
hydrogen bonds give the -helix its inherent stability (Figure 3.15a).
The primary structure of some polypeptides induces a different type of secondary structure, called a -sheet. In the
-sheet, the chain of amino acids in the polypeptide folds back
and forth upon itself instead of forming a helix. However, as in
the -helix, the folding in a -sheet exposes hydrogen atoms
that can undergo hydrogen bonding (Figure 3.15b). Typically,
a -sheet secondary structure yields a polypeptide that is
rather rigid and -helical secondary structures are more flexible. Thus, an enzyme, for example, whose activity may
depend on its being rather flexible, may contain a high degree
of -helix secondary structure. By contrast, a structural protein that functions in cellular scaffolding may contain large
regions of -sheet secondary structure.
Many polypeptides contain regions of both -helix and
-sheet secondary structure, the type of folding and its location in the molecule being determined by the primary
structure and the available opportunities for hydrogen bonding and hydrophobic interactions (see Figure 3.16). A typical
protein is thus made up of many domains, as they are called,
regions of the protein that have a specific structure and function in the final, biologically active, molecule.

3.8

Proteins: Higher Order Structure


and Denaturation

Once a polypeptide has achieved secondary structure it continues to fold to form an even more stable molecule. This
folding results in a unique three-dimensional shape called the
tertiary structure of the protein.
Like secondary structure, tertiary structure is ultimately
determined by primary structure. However, tertiary structure
is also governed to some extent by the secondary structure of
the molecule because the side chain of each amino acid in the
polypeptide is positioned in a specific way (Figure 3.15). If
additional hydrogen bonds, covalent bonds, hydrophobic interactions, or other atomic interactions are able to form, the
polypeptide will fold to accommodate them (Figure 3.16).
The tertiary folds of the polypeptide ultimately form exposed regions or grooves in the molecule (Figure 3.16 and see
Figure 3.17) that are important for binding other molecules
(for example, in the binding of a substrate to an enzyme or the
binding of DNA to a specific regulatory protein) (l Sections
5.5 and 9.2).
Frequently a polypeptide folds in such a way that adjacent
sulfhydryl groups of cysteine residues are exposed. These free
SH groups can form a disulfide bond between the two
amino acids. If the two cysteine residues are located in different polypeptides in a protein, the disulfide bond covalently
links the two molecules (Figure 3.16a). In addition, a single
polypeptide chain can fold and bond to itself if a disulfide
bond can form within the molecule.

A chain

Chains

-helix

SS

SS
S

Chains

63

B chain
S

-sheet

(a) Insulin

Chains

(b) Ribonuclease

Chains

(a)

Figure 3.16 Tertiary structure of polypeptides. (a) Insulin, a protein containing two polypeptide chains; note how the B chain contains
both -helix and -sheet secondary structure and how disulfide linkages (SS) help in dictating folding patterns (tertiary structure).
(b) Ribonuclease, a large protein with several regions of -helix and
-sheet secondary structure.

(b)

Figure 3.17 Quaternary structure of human hemoglobin.


(a) There are two kinds of polypeptide in human hemoglobin, chains
(shown in blue and red) and chains (shown in orange and yellow), but
a total of four polypeptides in the final protein molecule (two chains
and two chains). Separate colors are used to distinguish each chain.
(b) Molecular structure of human hemoglobin as determined by X-ray
crystallography. In this view each chain is red and each chain is blue.

Quaternary Structure
If a protein consists of two or more polypeptides, and many
proteins do, the number and type of polypeptides that form
the final protein molecule are referred to as its quaternary
structure (Figure 3.17). In proteins showing quaternary
structure, each polypeptide, called a subunit, contains primary, secondary, and tertiary structure. Some proteins contain
multiple copies of a single subunit. A protein containing two
identical subunits, for example, would be called a homodimer.
Other proteins may contain nonidentical subunits, each
present in one or more copies (a heterodimer, for example,
contains one copy each of two different polypeptides). The
subunits in multisubunit proteins are held together by noncovalent interactions (hydrogen bonding, van der Waals forces,
and hydrophobic interactions) or by covalent linkages, typically disulfide bonds.

Gentle
denaturation;
urea

Active
protein

Harsh
denaturation;
100C

Denaturation
When proteins are exposed to extremes of heat or pH or to
certain chemicals or metals that affect their folding, they may
undergo denaturation (Figure 3.18). Denaturation causes
the polypeptide chain to unfold, destroying the higher order
(secondary, tertiary, and quaternary, if relevant) structure of
the molecule. Depending on the severity of the denaturant or
denaturing conditions, the polypeptide may refold after the
denaturant is removed (Figure 3.18). Typically, however, denatured proteins unfold such that their hydrophobic regions
become exposed and stick together to form protein aggregates
that lack biological activity.
The biological properties of a protein are usually lost
when it is denatured. Peptide bonds (Figure 3.13) are unaffected, however, and so a denatured molecule retains its
primary structure. This shows that biological activity is not
inherent in the primary structure of a protein but instead is a
function of the uniquely folded form of the molecule as ultimately directed by primary structure. In other words, folding

Inactive
Remove urea;
reactivation

Inactive
Cool

Active
protein

Inactive

Figure 3.18 Denaturation of the protein ribonuclease. Ribonuclease


structure was shown in Figure 3.16b. Note how harsh denaturation
permanently destroys a molecule (from the standpoint of biological
function) because of improper folding but primary structure is retained.

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64

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of a polypeptide confers upon it a unique shape that is compatible with a specific biological function.
Denaturation of proteins is a major means of destroying
microorganisms. For example, alcohols such as phenol and
ethanol are effective disinfectants because they readily penetrate cells and irreversibly denature their proteins. Such
chemical agents are thus useful for disinfecting inanimate
objects such as surfaces and have enormous practical value in
household, hospital, and industrial disinfectant applications.
We discuss disinfectants, along with other chemical and physical agents used to destroy microorganisms, in Chapter 27.

As the contemporary microbiologist Norman Pace has


put it, life is fundamentally chemistry. And as any microbiologist will attest, a feeling for the biochemistry of proteins,
lipids, nucleic acids, and polysaccharides is essential to a
grasp of modern microbiology and will accelerate the understanding of both basic and more advanced principles.

Moving On
Now that we have reviewed the chemistry of cellular components, we are in a better position to understand the structural
details of cells. In the next chapter we will see how macromolecules come together to form major structures of the cell,
such as the cytoplasmic membrane, the cell wall, and the flagellum. From there we will consider the basic metabolic properties
of cells in Chapter 5. Metabolism, the machine function of a cell,
drives the biosynthesis and assembly of new copies of macromolecules; these processes result in cell growth (lChapter 6).
The metabolic events themselves are directed by the coding
functions of the cell, the essential genetic events carried out by
all cells. We discuss molecular biology in Chapters 79.

3.7 and 3.8 MiniReview


The primary structure of a protein is determined by its amino
acid sequence, but the folding (higher order structure) of the
polypeptide determines how the protein functions in the cell.
Define the terms primary, secondary, and tertiary with
respect to protein structure.
How does a polypeptide differ from a protein?
What secondary structural features tend to make -sheet
proteins more rigid than -helices?
Describe the number and kinds of polypeptides present in a
homotetrameric protein.
Describe the structural and biological effects of the denaturation of a protein. Of what practical value is knowledge of
protein denaturation?

Review of Key Terms


Amino acid one of the 22 different monomers
that make up proteins; chemically, a twocarbon carboxylic acid containing an amino
group and a characteristic substituent on the
alpha carbon

Covalent bond a chemical bond in which


electrons are shared between two atoms

Denaturation destruction of the folding properties of a protein leading (usually) to protein


aggregation and loss of biological activity

Domain in the context of proteins, a portion


of the protein typically possessing a specific
structure or function

DNA (deoxyribonucleic acid) a polymer of deoxyribonucleotides linked by phosphodiester


bonds that carries genetic information

Enantiomer a form of a molecule that is the


mirror image of another form of the same
molecule

Enzyme a protein or an RNA that catalyzes a


specific chemical reaction in a cell

Fatty acid an organic acid containing a carboxylic acid group and a hydrocarbon chain

of various lengths; major components of


lipids of Bacteria and Eukarya

Glycosidic bond a covalent bond linking


sugars together in a polysaccharide

Hydrogen bond a weak chemical interaction


between a hydrogen atom and a second,
more electronegative element, usually an
oxygen or nitrogen atom

Isomers two molecules with the same


molecular formula but a difference in
structure

Lipid a polar compound such as glycerol


bonded to fatty acids or other hydrophobic
molecules by ester or ether linkage, often
also containing other groups, such as phosphate or sugars

Macromolecule a polymer of covalently


linked monomeric units, such as DNA, RNA,
polysaccharides, and lipids

Molecule two or more atoms chemically


bonded to one another

Monomer a small molecule that is a building


block for larger molecules

Nonpolar possessing hydrophobic (waterrepelling) characteristics and not easily


dissolved in water

Nucleic acid DNA or RNA


Nucleotide a monomer of a nucleic acid containing a nitrogen base (adenine, guanine,
cytosine, thymine, or uracil), one or more
molecules of phosphate, and a sugar, either
ribose (in RNA) or deoxyribose (in DNA)

Peptide bond a type of covalent bond linking


amino acids in a polypeptide

Phosphodiester bond a type of covalent


bond linking nucleotides together in a
polynucleotide

Polar possessing hydrophilic (water-loving)


characteristics and generally water soluble

Polymer a large molecule made up of


monomers

Polynucleotide a polymer of nucleotides


bonded to one another by covalent bonds
called phosphodiester bonds

Polypeptide a polymer of amino acids


bonded to one another by peptide bonds

Polysaccharide a polymer of sugar units


bonded to one another by glycosidic bonds

Primary structure in an informational


macromolecule such as a polypeptide or a
nucleic acid, the precise sequence of
monomeric units

Protein a polypeptide or group of


polypeptides forming a molecule of specific
biological function

Purine one of the nitrogen bases of nucleic


acids that contain two fused rings; adenine
and guanine

Pyrimidine one of the nitrogen bases of


nucleic acids that contain a single ring; cytosine, thymine, and uracil

Quaternary structure in proteins, the number and types of individual polypeptides in


the final protein molecule

65

usually dictated by opportunities for hydrogen bonding

Tertiary structure the final folded structure


of a polypeptide that has previously attained
secondary structure

RNA (ribonucleic acid) a polymer of ribonucleotides linked by phosphodiester bonds


that plays many roles in cells, in particular,
during protein synthesis

Secondary structure the initial pattern of


folding of a polypeptide or a polynucleotide,

Review Questions
1. Which are the major elements found in living organisms? Why
are oxygen and hydrogen particularly abundant in living organisms (Section 3.1)?
2. Define the word molecule. How many atoms are in a molecule of hydrogen gas? How many atoms are in a molecule of
glucose (Sections 3.1 and 3.3)?
3. Refer to the structure of the nitrogen base cytosine shown in
Figure 3.1. Draw this structure and then label the positions of
all single bonds and double bonds in the cytosine molecule
(Section 3.1).
4. Compare and contrast the words monomer and polymer.
Give three examples of biologically important polymers and
list the monomers of which they are composed. Which classes
of macromolecules are most abundant (by weight) in a cell
(Sections 3.1 and 3.2)?
5. List the components that would make up a simple lipid. How
does a triglyceride differ from a complex lipid (Section 3.4)?
6. Examine the structures of the triglyceride and of phosphatidyl
ethanolamine shown in Figure 3.7. How might the substitution
of phosphate and ethanolamine for a fatty acid alter the chemical properties of the lipid (Section 3.4)?

7. RNA and DNA are similar types of macromolecules but show


distinct differences as well. List three ways in which RNA
differs chemically or physically from DNA. What is the cellular
function of DNA and RNA (Section 3.5)?
8. Why are amino acids so named? Write a general structure for
an amino acid. What is the importance of the R group to final
protein structure? Why does the amino acid cysteine have special significance for protein structure (Section 3.6)?
9. What type of reaction between two amino acids leads to formation of the peptide bond (Section 3.6)?
10. Define the types of protein structure: primary, secondary, tertiary, and quaternary. Which of these structures are altered by
denaturation (Sections 3.7 and 3.8)?
11. Fill in the blanks. A glycosidic bond is to a ___________ as a
___________ bond is to a polypeptide and a ___________ is to a
nucleic acid. All of these bonds are examples of ___________
bonds, which are chemically much stronger than weak bonds,
such as ___________, ___________, and ___________

Application Questions
1. Observe the following nucleotide sequences of RNA:
(a) GUCAAAGAC, (b) ACGAUAACC. Can either of these RNA
molecules have secondary structure? If so, draw the potential
secondary structure(s).
2. A few soluble (cytoplasmic) proteins contain a high content of
hydrophobic amino acids. How would you predict these proteins would fold into their tertiary structure and why?
3. Cells of the genus Halobacterium, an organism that lives in very
salty environments, contain over 5 molar (M) potassium (K).
Because of this high K content, many cytoplasmic proteins of
Halobacterium cells are enriched in two specific amino acids
that are present in much higher proportions in Halobacterium
proteins than in functionally similar proteins from Escherichia
coli (which has only very low levels of K in its cytoplasm).
Which amino acids are enriched in Halobacterium proteins and

why? (Hint: Which amino acids could best neutralize the positive charges due to K?)
4. When a culture of the bacterium Escherichia coli, an inhabitant
of the human gut, is placed in a beaker of boiling water, significant changes in the cells occur almost immediately. However,
when a culture of Pyrodictium, a hypothermophile that grows
optimally in boiling hot springs is put in the same beaker, similar
changes do not occur. Explain.
5. Review Figure 3.6b and then describe the differences that make
each of these polymers unique. If all of the glycosidic bonds in
these polymers were hydrolyzed, what single molecule would
remain?
6. Review Figure 3.12b. Of all the amino acids shaded in blue,
what is it about their chemistry that unites them as a family?

UNIT 1

Chapter 3 Chemistry of Cellular Components

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