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Chapter 5:
The Structure and Function
of Large Biological (Macro)molecules
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Overview: The Molecules of Life
• All living things are made up of four classes
of large biological molecules: carbohydrates,
lipids, proteins, and nucleic acids
• Macromolecules are large molecules
composed of thousands of covalently
connected atoms
© 2011 Pearson Education, Inc.
Jerome Karle – a biochemist most renound for
his work on macromolecules
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Concept 5.2: Carbohydrates serve as fuel
and building material
• Carbohydrates include sugars and the
starches
• The simplest carbohydrates are
monosaccharides, or single sugars
© 2011 Pearson Education, Inc.
Figure 5.3
Aldoses (Aldehyde Sugars)
Ketoses (Ketone Sugars)
Trioses: 3-carbon sugars (C3H6O3)
Glyceraldehyde
Dihydroxyacetone
Pentoses: 5-carbon sugars (C5H10O5)
Ribose
Ribulose
Hexoses: 6-carbon sugars (C6H12O6)
Glucose
Galactose
Fructose
• A disaccharide is formed when a dehydration
reaction joins two monosaccharides
• A common dissaccharide is sucrose (table
sugar).
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Storage Polysaccharides
• Starch, a storage polysaccharide of plants,
consists entirely of glucose monomers
• Plants store surplus starch as granules within
chloroplasts and other plastids
• The simplest form of starch is amylose
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Storage polysaccharides of plants and animals
Chloroplast
Starch
Mitochondria
Giycogen granules
0.5 m
1 m
Amylose
Amylopectin
(a) Starch: a plant polysaccharide
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Glycogen
(b) Glycogen: an animal polysaccharide
• Glycogen is a storage polysaccharide in
animals
• Humans and other vertebrates store
glycogen mainly in liver and muscle cells
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Structural Polysaccharides
• The polysaccharide cellulose is a major
component of the tough wall of plant cells
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Cellulose-digesting bacteria are found in grazing
animals such as this cow
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Chitin, a structural polysaccharide
H
OH
CH2OH
O OH
H
OH H
H
H
NH
C
O
CH3
(a) The structure of the
chitin monomer.
(b) Chitin forms the exoskeleton
of arthropods. This cicada
is molting, shedding its old
exoskeleton and emerging
in adult form.
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
(c) Chitin is used to make a
strong and flexible surgical
thread that decomposes after
the wound or incision heals.
Figure 5.9b
Chitin is used to make a strong and flexible surgical
thread that decomposes after the wound or incision
heals.
Fats
• Fats are constructed from two types of smaller
molecules: glycerol and fatty acids
• Fats (and oils) are considered very high energy
food items with roughly twice the energy per
gram as any other food item.
© 2011 Pearson Education, Inc.
The synthesis and structure of a fat, or
triacylglycerol
H
H
C
O
H
C
OH
HO
H
H
C
C
C
H
OH
H
C
H
H
C
H
H
C
H
H
H
C
C
H
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
Fatty acid
(palmitic acid)
OH
H
Glycerol
(a) Dehydration reaction in the synthesis of a fat
Ester linkage
O
H
H
C
O
C
H
C
H
O
H
C
O
C
H
C
H
O
H
C
H
O
C
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
(b) Fat molecule (triacylglycerol)
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
H
C
H
H
H
C
H
H
H
C
H
H
Examples of saturated and unsaturated fats and
fatty acids
Stearic acid
(a) Saturated fat and fatty acid
Oleic acid
(b) Unsaturated fat and fatty acid
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
cis double bond
causes bending
• A diet rich in saturated fats may contribute to
cardiovascular disease through plaque deposits
• Hydrogenation is the process of converting
unsaturated fats to saturated fats by adding
hydrogen
• Hydrogenating vegetable oils also creates
unsaturated fats with trans double bonds
• These trans fats may contribute more than
saturated fats to cardiovascular disease
© 2011 Pearson Education, Inc.
The structure of a phospholipid
+N(CH )
CH2
3 3
Choline
CH2
O
O
P
–
O
Phosphate
O
CH2
CH
O
O
C
O C
CH2
Glycerol
O
Fatty acids
Hydrophilic
head
Hydrophobic
tails
(a) Structural formula
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
(b) Space-filling model
(c) Phospholipid
symbol
Bilayer structure formed by self-assembly of
phospholipids in an aqueous environment
WATER
Hydrophilic
head
WATER
Hydrophobic
tail
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Cholesterol, a steroid
H3C
CH3
CH3
HO
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
CH3
CH3
Concept 5.4: Proteins include a diversity of
structures, resulting in a wide range of
functions
• Proteins account for more than 50% of the dry
mass of most cells
• Protein functions include structural support,
storage, transport, cellular communications,
movement, and defense against foreign
substances
© 2011 Pearson Education, Inc.
Figure 5.15-a
Enzymatic proteins
Defensive proteins
Function: Selective acceleration of chemical reactions
Example: Digestive enzymes catalyze the hydrolysis
of bonds in food molecules.
Function: Protection against disease
Example: Antibodies inactivate and help destroy
viruses and bacteria.
Antibodies
Enzyme
Virus
Bacterium
Storage proteins
Transport proteins
Function: Storage of amino acids
Function: Transport of substances
Examples: Hemoglobin, the iron-containing protein of
vertebrate blood, transports oxygen from the lungs to
other parts of the body. Other proteins transport
molecules across cell membranes.
Examples: Casein, the protein of milk, is the major
source of amino acids for baby mammals. Plants have
storage proteins in their seeds. Ovalbumin is the
protein of egg white, used as an amino acid source
for the developing embryo.
Transport
protein
Ovalbumin
Amino acids
for embryo
Cell membrane
Figure 5.15-b
Hormonal proteins
Receptor proteins
Function: Coordination of an organism’s activities
Example: Insulin, a hormone secreted by the
pancreas, causes other tissues to take up glucose,
thus regulating blood sugar concentration
Function: Response of cell to chemical stimuli
Example: Receptors built into the membrane of a
nerve cell detect signaling molecules released by
other nerve cells.
High
blood sugar
Insulin
secreted
Normal
blood sugar
Receptor
protein
Signaling
molecules
Contractile and motor proteins
Structural proteins
Function: Movement
Examples: Motor proteins are responsible for the
undulations of cilia and flagella. Actin and myosin
proteins are responsible for the contraction of
muscles.
Function: Support
Examples: Keratin is the protein of hair, horns,
feathers, and other skin appendages. Insects and
spiders use silk fibers to make their cocoons and webs,
respectively. Collagen and elastin proteins provide a
fibrous framework in animal connective tissues.
Actin
Myosin
Collagen
Muscle tissue
100 m
Connective
tissue
60 m
Amino Acid Monomers
• Amino acids are organic molecules with
carboxyl and amino groups
• Amino acids differ in their properties due to
differing side chains, called R groups
© 2011 Pearson Education, Inc.
Figure 5.UN01
Side chain (R group)
 carbon
Amino
group
Carboxyl
group
The 20 amino acids of proteins
CH3
CH3
H
H3N+
C
CH3
O
H3N+
C
H
Glycine (Gly)
O–
C
H3N+
C
H
Alanine (Ala)
O–
CH
CH3
CH3
O
C
CH2
CH2
O
H3N+
C
H
Valine (Val)
CH3
CH3
O–
C
O
H3N+
C
H
Leucine (Leu)
H3C
O–
CH
C
O
C
H
Isoleucine (Ile)
O–
Nonpolar
CH3
CH2
S
NH
CH2
CH2
H3N+
C
H
CH2
O
H3N+
C
O–
Methionine (Met)
C
H
H3N+
C
C
O–
Phenylalanine (Phe)
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CH2
O
H
O
H2C
CH2
H2N
C
O
C
O–
H
C
O–
Tryptophan (Trp)
Proline (Pro)
OH
OH
Polar
CH2
H3N+
C
CH
O
H3N+
C
O–
H
Serine (Ser)
C
CH2
O
H3N+
C
O–
H
C
CH2
O
C
H
O–
H3
N+
C
CH2
O
H3N+
C
Electrically
charged
H3N+
NH3+
O
CH2
C
CH2
CH2
CH2
CH2
CH2
CH2
O
CH2
C
H
H3N+
C
O
CH2
C
H
O–
H3N+
C
H
O–
C
O
C
O–
H
Glutamine
(Gln)
Glutamic acid
(Glu)
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NH+
C
O–
Lysine (Lys)
NH2+
H3N+
CH2
O
CH2
H3N+
C
H
Aspartic acid
(Asp)
H3
NH2
C
O–
C
Asparagine
(Asn)
C
C
CH2
N+
Basic
O–
O
CH2
O
H
Acidic
–O
C
O–
H
Tyrosine
(Tyr)
Cysteine
(Cys)
Threonine (Thr)
C
NH2 O
C
SH
CH3
OH
NH2 O
NH
CH2
O
C
C
O–
H
O
C
O–
Arginine (Arg)
Histidine (His)
Making a polypeptide chain
Peptide
bond
OH
CH2
SH
CH2
H
N
H
OH
C C
CH2
H
H
N C C OH H
N C
H O
H O
H
(a)
C OH
O
DESMOSOMES
H2O
OH
DESMOSOMES
DESMOSOMES
OH
CH2
H
H N C C
H O
(b)
Side chains
SH
Peptide
CH2 bond CH2
H
H
N C C
H O
N C C
Amino end
(N-terminus)
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H O
Carboxyl end
(C-terminus)
OH
Backbone
Four Levels of Protein Structure
• The primary structure of a protein is its unique sequence
of amino acids
• Secondary structure, found in most proteins, consists of
coils and folds in the polypeptide chain
• Tertiary structure is determined by interactions among
various side chains (R groups)
• Quaternary structure results when a protein consists of
multiple polypeptide chains
© 2011 Pearson Education, Inc.
Spider Web
Abdominal glands of the
spider secrete silk fibers
that form the web
The radiating strands, made
of dry silk fibers maintained
the shape of the web
The spiral strands (capture
strands) are elastic, stretching
in response to wind, rain,
and the touch of insects
Spider silk: a structural protein
containing  pleated sheets
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Levels of protein structure
1
+H N
3
Gly Pro ThrGly
5
Thr
Gly
Amino end
Leu
Met
Val
15 Lya
Val
Leu
Asp
Glu
Seu
Pro CyaLya
10
pleated sheet
Amino acid
subunits
R H
C
O C N H
N H
N H
O C
O C
H C RH C
H C RHC R
R
N HO C
N HO C
O C
O C N H
N H
C
C
R
R
H
N
N H
20
Ala Val Arg
Gly
Ser
Pro
25
Ala
O H
O H H
O H
H
H
R
R
R
C
C CH
C C H
C C N C N CC N
CC N
C C
R
R
R
R
H
H
OH
OH
O
O HH
R
R
R
R
O
O
O
C H
C H O
C
H
C H
H
H
N
N C H
N C
C
C
C NH CN
H CN
C
H
C
H N
C
H
H O C
C
H ON
H O C
O
R
R
R
R H
C
O C
C N
H
O H
H
C C N
 helix
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Exploring Levels of Protein Structure: Primary structure
Gly Pro Thr Gly
Thr
+H N
3
Amino acid
subunits
Gly
Amino end
Leu
Seu
Pro Cys Lys
Glu
Met
Val
Lys
Val
Leu
Asp
Ala Val Arg Gly
Ser
Pro
Ala
Glu Lle
Asp
Thr
Lys
Ser
Tyr
Lys Trp
Leu Ala
Gly
lle
Ser
Pro Phe
His Glu
His
Ala
Glu
Ala Thr Phe Val
Val
Asn
Asp
Arg
Ser
Gly Pro
Thr
Tyr
Thr
lle
Ala
Ala
Arg
Leu
Ser Tyr
Ser
Tyr Pro
Leu
Ser
Thr
Ala
Val
Val
Thr
Asn Pro
Lys Glu
c
o
o–
Carboxyl end
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Exploring Levels of Protein Structure:
Secondary structure
 pleated sheet
H
O
Amino acid
subunits
C
N
C
R
C
C
N
C
R
C
C
R
H
H
C
H
C
O
C
O
H
N
C
H
H
R
H C
O
H
C
N
C
C
O
C
N
N
C
R
N
C
O
H
H
C
R
C
O
C
N
H
C
C
R
H
C
H
H
H
C
O
H
R
H
N
O
N
O
C
C
H
N
O
R
H
C
H
R
H
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H
 helix
N
H
O
H
H
H
R
C
C
N
N
C
C
R
H
O
H
N
C
N
C
R
H
O
H
H C
O
H
C
N
C
R
R
C
N
H
C
O
R
C
H
R
R
C
C
O
H
R
C
N
R
N
R
O
O
H
N
C
O
H
H
O
H
O
H
H
H
C
O
C
N
C
R
C
N
H
H
H C
O
N
C
Exploring Levels of Protein Structure:
Tertiary structure
CH
CH2
Hydrogen
bond
H3C
CH3
H3C
CH3
CH
O
H
O
Hydrophobic
interactions and
van der Waals
interactions
OH C
CH2
CH2 S S CH2
Disulfide bridge
O
CH2 NH3+ -O C CH2
Ionic bond
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Polypeptide
backbone
Exploring Levels of Protein Structure: Quaternary
Structure
Polypeptide
chain
Collagen
 Chains
Iron
Heme
 Chains
Hemoglobin
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• Enzymes are a type of protein that acts as a
catalyst to speed up chemical reactions
• Enzymes can perform their functions
repeatedly, functioning as workhorses that
carry out the processes of life
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The catalytic cycle of an enzyme
2 Substrate binds to
enzyme.
1 Active site is available for
a molecule of substrate, the
reactant on which the enzyme acts.
Substrate
(sucrose)
Glucose
OH
Enzyme
(sucrase)
H2O
Fructose
H O
4 Products are released.
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3 Substrate is converted
to products.
Sickle-Cell Disease: A Change in Primary
Structure
• A slight change in primary structure can affect
a protein’s structure and ability to function
• Sickle-cell disease, an inherited blood
disorder, results from a single amino acid
substitution in the protein hemoglobin
© 2011 Pearson Education, Inc.
A single amino acid substitution in a protein causes
sickle-cell disease
Primary
structure
Normal hemoglobin
Val
His
Leu
Glu
Glu
Sickle-cell hemoglobin
Val
His
Leu


Molecules do
not associate
with one
another; each
carries oxygen
Normal cells are
full of individual
hemoglobin
molecules, each
carrying oxygen


Thr
Pro
Val
Glu
...
structure 1 2 3 4 5 6 7
Secondary
 subunit and tertiary
structures
Quaternary Hemoglobin A
structure
Red blood
cell shape
Pro
1 2 3 4 5 6 7
Secondary
and tertiary
structures
Function
Thr
. . . Primary
Quaternary
structure
 subunit




Function
10 m
10 m
Red blood
cell shape
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Exposed
hydrophobic
region
Hemoglobin S
Molecules
interact with
one another to
crystallize into a
fiber, capacity to
carry oxygen is
greatly reduced
Fibers of abnormal
hemoglobin deform
cell into sickle
shape
Denaturation and renaturation of a protein
Denaturation
Normal protein
Denatured protein
Renaturation
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A chaperonin in action
Polypeptide
Cap
Correctly
folded
protein
Hollow
cylinder
Chaperonin
(fully assembled)
Steps of Chaperonin
Action:
1 An unfolded polypeptide enters the
cylinder from one end.
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2 The cap attaches, causing
3 The cap comes
the cylinder to change shape in off, and the properly
such a way that it creates a
folded protein is
hydrophilic environment for the released.
folding of the polypeptide.
Research Method x-ray crystallography
X-ray
diffraction pattern
Photographic film
Diffracted X-rays
X-ray
source
X-ray
beam
Crystal
(a) X-ray diffraction pattern
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Nucleic acid
Protein
(b) 3D computer model
DNA  RNA  protein: a diagrammatic overview of
information flow in a cell
DNA
1 Synthesis of
mRNA in the nucleus
mRNA
NUCLEUS
CYTOPLASM
mRNA
2 Movement of
mRNA into cytoplasm
via nuclear pore
Ribosome
3 Synthesis
of protein
Polypeptide
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Amino
acids
The DNA double helix and its replication
3 end
5 end
G
C
Sugar-phosphate
backbone
G
C
A
T
C
G
A
T
A
T
G
C
A
A
A
Old strands
T
T
A
T
Base pair (joined by
hydrogen bonding)
Nucleotide
about to be
added to a
new strand
3 end
5 end
New
strands
3 end
5 end
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
5 end
3 end