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CHEMICAL BONDING,
MACROMOLECULES,
AND WATER
NONINFORMATIONAL
MACROMOLECULES
3.3 Polysaccharides
Chemistry of Cellular
Components
51
51
3.4 Lipids
III
55
55
56
INFORMATIONAL
MACROMOLECULES
57
57
59
50
CHEMICAL BONDING,
MACROMOLECULES,
AND WATER
3.1
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
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)
UNIT 1
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
(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
N
N
O
Hydrogen
bonds
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.
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
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
Functional group
Structurea
Biological relevance
Example
Acetateb
Formaldehyde
Lipids; carbohydrates
Glucose
-ketoglutarate
Triglycerides
Nucleic acids
DNA, RNA
Acetyl-CoA
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
UNIT 1
54
Table 3.2
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
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.
(c) Polysaccharides
Storage
granules
(d) Lipids
Figure 3.3
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.
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
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
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
UNIT 1
56
6 CH2OH
5
6 CH2OH
O
H
OH
HO
H
2
OH
OH
OH
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
Cellulose
-1,4 bonds
-1,4 bonds
(b)
16 15 14 13 12 11 10 9
H3C
C OH
Glycerol
O
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.
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
UNIT 1
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
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
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
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.
3.6
UNIT 1
60
H
-carbon
H 2N C
Carboxylic
acid group
CH3
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
CH3 CH
O OH
NH2 C CH2
O
HS CH2
-O C CH CH
2
2
+NH CH CH CH CH
3
2
2
2
2
OH CH2
C OH
Amino group
O
-O C CH
2
O
NH2
+HN
CH2
CH2
Ionizable: acidic
Nonionizable polar
Nonpolar
(hydrophobic)
CH3
CH
CH3 CH2
CH
N
H
Ionizable: basic
HO
CH3
CH2
CH2
Trp Tryptophan(W)
Key
HSe CH2
CH3
H2C
N
H
CH2
H2C
CH COO
N
H
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
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
3.7
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)
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),
UNIT 1
62
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
(b) -sheet secondary structure. Note that the hydrogen bonding is between atoms in the
peptide bonds and does not involve the R groups.
3.8
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)
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
UNIT 1
64
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.
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.
Fatty acid an organic acid containing a carboxylic acid group and a hydrocarbon chain
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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)?
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