AG 1301 / FT 1202 - Biology – 2C (30 L)

The Structure and Function of Large Biological Molecules

Dr. Jayani J. Wewalwela

Overview: The Molecules of Life

• All living things are made up of four classes of

large biological molecules: carbohydrates,
lipids, proteins, and nucleic acids
• Within cells, small organic molecules are joined
together to form larger molecules
• Macromolecules are large molecules
composed of thousands of covalently
connected atoms
Macromolecules are polymers, built from
monomers

• A polymer is a long molecule consisting of

many similar building blocks
• These small building-block molecules are
called monomers
• Three of the four classes of life’s organic
molecules are polymers:
– Carbohydrates
– Proteins
– Nucleic acids
The Synthesis and Breakdown of Polymers

• A condensation reaction or more specifically

a dehydration reaction occurs when two
monomers bond together through the loss of a
water molecule
• Enzymes are macromolecules that speed up
the dehydration process
• Polymers are disassembled to monomers by
hydrolysis, a reaction that is essentially the
reverse of the dehydration reaction
HO 1 2 3 H HO H

Short polymer Unlinked monomer

Dehydration removes a water

molecule, forming a new bond
H2O

HO 1 2 3 4 H

Longer polymer
(a) Dehydration reaction in the synthesis of a polymer

HO 1 2 3 4 H

Hydrolysis adds a water H2O

molecule, breaking a bond

HO 1 2 3 H HO H

(b) Hydrolysis of a polymer

HO 1 2 3 H HO H

Short polymer Unlinked monomer

Dehydration removes a water

molecule, forming a new bond
H2O

HO 1 2 3 4 H

Longer polymer
(a) Dehydration reaction in the synthesis of a polymer
 HO 1 2 3 4 H

Hydrolysis adds a water H2O

molecule, breaking a bond

HO 1 2 3 H HO H

(b) Hydrolysis of a polymer

The Diversity of Polymers

• Each cell has thousands of different kinds of

macromolecules2 3 H HO

• Macromolecules vary among cells of an

organism, vary more within a species, and vary
even more between species
• An immense variety of polymers can be built
from a small set of monomers
Carbohydrates serve as fuel and building material

• Carbohydrates include sugars and the

polymers of sugars
• The simplest carbohydrates are
monosaccharides, or single sugars
• Carbohydrate macromolecules are
polysaccharides, polymers composed of many
sugar building blocks
Sugars

• Monosaccharides have molecular formulas

that are usually multiples of CH2O
• Glucose (C6H12O6) is the most common
monosaccharide
• Monosaccharides are classified by
– The location of the carbonyl group (as aldose
or ketose)
– The number of carbons in the carbon skeleton
Trioses (C3H6O3) Pentoses (C5H10O5) Hexoses (C6H12O6)

Glyceraldehyde

Ribose
Glucose Galactose

Dihydroxyacetone

Ribulose
Fructose
Trioses (C3H6O3) Pentoses (C5H10O5) Hexoses (C6H12O6)

Glyceraldehyde

Ribose
Glucose Galactose
Trioses (C3H6O3) Pentoses (C5H10O5) Hexoses (C6H12O6)

Dihydroxyacetone

Ribulose
Fructose
• Though often drawn as linear skeletons, in
aqueous solutions many sugars form rings
• Monosaccharides serve as a major fuel for
cells and as raw material for building molecules
(a) Linear and ring forms (b) Abbreviated ring structure
(a) Linear and ring forms
(b) Abbreviated ring structure
• A disaccharide is formed when a dehydration
reaction joins two monosaccharides
• This covalent bond is called a glycosidic
linkage
 1–4
glycosidic
linkage

Glucose Glucose Maltose

(a) Dehydration reaction in the synthesis of maltose
1–2
glycosidic
linkage

Glucose Fructose Sucrose

(b) Dehydration reaction in the synthesis of sucrose
Polysaccharides

• Polysaccharides, the polymers of sugars,

have storage and structural roles
• The structure and function of a polysaccharide
are determined by its sugar monomers and the
positions of glycosidic linkages
Storage Polysaccharides

• Starch, a storage polysaccharide of plants,

consists entirely of glucose monomers
• Plants store surplus starch as granules within
chloroplasts and other plastids
 Chloroplast Starch Mitochondria Glycogen granules

0.5 µm

1 µm

Amylose Glycogen

Amylopectin

(a) Starch: a plant polysaccharide (b) Glycogen: an animal polysaccharide

• Glycogen is a storage polysaccharide in
animals
• Humans and other vertebrates store glycogen
mainly in liver and muscle cells
Structural Polysaccharides

• The polysaccharide cellulose is a major

component of the tough wall of plant cells
• Like starch, cellulose is a polymer of glucose,
but the glycosidic linkages differ
• The difference is based on two ring forms for
glucose: alpha () and beta ()
(a)  and  glucose
ring structures

 Glucose  Glucose

(b) Starch: 1–4 linkage of  glucose monomers (b) Cellulose: 1–4 linkage of  glucose monomers
  Glucose  Glucose

(a)  and  glucose ring structures

(b) Starch: 1–4 linkage of  glucose monomers

(c) Cellulose: 1–4 linkage of  glucose monomers

• Polymers with  glucose are helical
• Polymers with  glucose are straight
• In straight structures, H atoms on one
strand can bond with OH groups on other
strands
• Parallel cellulose molecules held together
this way are grouped into microfibrils, which
form strong building materials for plants
Cell walls
Cellulose
microfibrils
in a plant
cell wall
Microfibril

10 µm

0.5 µm

Cellulose
molecules

 Glucose
monomer
• Enzymes that digest starch by hydrolyzing 
linkages can’t hydrolyze  linkages in cellulose
• Cellulose in human food passes through the
digestive tract as insoluble fiber
• Some microbes use enzymes to digest
cellulose
• Many herbivores, from cows to termites, have
symbiotic relationships with these microbes
• Chitin, another structural polysaccharide, is
found in the exoskeleton of arthropods
• Chitin also provides structural support for the
cell walls of many fungi
(a) The structure (b) Chitin forms the (c) Chitin is used to make
of the chitin exoskeleton of a strong and flexible
monomer. arthropods. surgical thread.
Lipids are a diverse group of hydrophobic
molecules

• Lipids are the one class of large biological

molecules that do not form polymers
• The unifying feature of lipids is having little or
no affinity for water
• Lipids are hydrophobic because they consist
mostly of hydrocarbons, which form nonpolar
covalent bonds
• The most biologically important lipids are fats,
phospholipids, and steroids
Fats

• Fats are constructed from two types of smaller

molecules: glycerol and fatty acids
• Glycerol is a three-carbon alcohol with a
hydroxyl group attached to each carbon
• A fatty acid consists of a carboxyl group
attached to a long carbon skeleton
 Fatty acid
(palmitic acid)

Glycerol
(a) Dehydration reaction in the synthesis of a fat

Ester linkage

(b) Fat molecule (triacylglycerol)

 Fatty acid
(palmitic acid)

Glycerol
(a) Dehydration reaction in the synthesis of a fat
 Ester linkage

(b) Fat molecule (triacylglycerol)

• Fats separate from water because
water molecules form hydrogen bonds
with each other and exclude the fats
• In a fat, three fatty acids are joined to
glycerol by an ester linkage, creating a
triacylglycerol, or triglyceride
• Fatty acids vary in length (number of carbons)
and in the number and locations of double
bonds
• Saturated fatty acids have the maximum
number of hydrogen atoms possible and no
double bonds
• Unsaturated fatty acids have one or more
double bonds
Structural
formula of a
saturated fat
molecule

Stearic acid, a
saturated fatty
acid
(a) Saturated fat

Structural formula
of an unsaturated
fat molecule

Oleic acid, an
unsaturated
fatty acid
cis double
bond causes
(b) Unsaturated fat bending
Structural
formula of a
saturated fat
molecule

Stearic acid, a
saturated fatty
acid
(a) Saturated fat
Structural formula
of an unsaturated
fat molecule

Oleic acid, an
unsaturated
fatty acid
cis double
bond causes
(b) Unsaturated fat bending
• Fats made from saturated fatty acids are called
saturated fats, and are solid at room
temperature
• Most animal fats are saturated
• Fats made from unsaturated fatty acids are
called unsaturated fats or oils, and are liquid at
room temperature
• Plant fats and fish fats are usually unsaturated
• 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
• The major function of fats is energy storage
• Humans and other mammals store their fat in
adipose cells
• Adipose tissue also cushions vital organs and
insulates the body
Phospholipids

• In a phospholipid, two fatty acids and a

phosphate group are attached to glycerol
• The two fatty acid tails are hydrophobic, but the
phosphate group and its attachments form a
hydrophilic head
 Hydrophilic head

Choline

Phosphate

Glycerol
Hydrophobic tails

Fatty acids

Hydrophilic
head

Hydrophobic
tails

(a) Structural formula (b) Space-filling model (c) Phospholipid symbol

 Hydrophilic head
Choline

Phosphate

Glycerol
Hydrophobic tails

Fatty acids

(a) Structural formula (b) Space-filling model

• When phospholipids are added to water, they
self-assemble into a bilayer, with the
hydrophobic tails pointing toward the interior
• The structure of phospholipids results in a
bilayer arrangement found in cell membranes
• Phospholipids are the major component of all
cell membranes
Hydrophilic WATER
head

Hydrophobic
WATER
tail
Steroids

• Steroids are lipids characterized by a carbon

skeleton consisting of four fused rings
• Cholesterol, an important steroid, is a
component in animal cell membranes
• Although cholesterol is essential in animals,
high levels in the blood may contribute to
cardiovascular disease
Proteins have many 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
• 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
 Substrate
(sucrose)

Glucose
Enzyme
(sucrase)
OH
H2O
Fructose

HO
Polypeptides

• Polypeptides are polymers built from the

same set of 20 amino acids
• A protein consists of one or more polypeptides
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
  carbon

Amino Carboxyl
group group
 Nonpolar

Glycine Alanine Valine Leucine Isoleucine

(Gly or G) (Ala or A) (Val or V) (Leu or L) (Ile or I)

Methionine Phenylalanine Trypotphan Proline

(Met or M) (Phe or F) (Trp or W) (Pro or P)

Polar

Serine Threonine Cysteine Tyrosine Asparagine Glutamine

(Ser or S) (Thr or T) (Cys or C) (Tyr or Y) (Asn or N) (Gln or Q)

Electrically
charged
Acidic Basic

Aspartic acid Glutamic acid Lysine Arginine Histidine

(Asp or D) (Glu or E) (Lys or K) (Arg or R) (His or H)
 Nonpolar

Glycine Alanine Valine Leucine Isoleucine

(Gly or G) (Ala or A) (Val or V) (Leu or L) (Ile or I)

Methionine Phenylalanine Tryptophan Proline

(Met or M) (Phe or F) (Trp or W) (Pro or P)
 Polar

Serine Threonine Cysteine Tyrosine Asparagine Glutamine

(Ser or S) (Thr or T) (Cys or C) (Tyr or Y) (Asn or N) (Gln or Q)
 Electrically
charged
Acidic Basic

Aspartic acid Glutamic acid Lysine Arginine Histidine

(Asp or D) (Glu or E) (Lys or K) (Arg or R) (His or H)
Amino Acid Polymers

• Amino acids are linked by peptide bonds

• A polypeptide is a polymer of amino acids
• Polypeptides range in length from a few to
more than a thousand monomers
• Each polypeptide has a unique linear sequence
of amino acids
 Peptide
bond

(a)

Side chains
Peptide
bond

Backbone

Amino end Carboxyl end

(b) (N-terminus) (C-terminus)
Protein Structure and Function

• A functional protein consists of one or more

polypeptides twisted, folded, and coiled into a
unique shape
• The sequence of amino acids determines a
protein’s three-dimensional structure
• A protein’s structure determines its function
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
• Primary structure, the sequence of amino
acids in a protein, is like the order of letters in a
long word
• Primary structure is determined by inherited
genetic information
 Primary Secondary Tertiary Quaternary
Structure Structure Structure Structure

 pleated sheet
+H N
3
Amino end
Examples of
amino acid
subunits

 helix
 Primary Structure
1

+H 5
3N
Amino end

10

15 Amino acid
subunits

20

25
 1

+H
5
3N
Amino end

10

15 Amino acid
subunits

20

25

75

80

85 90

95

105
100
110

115

120

125
Carboxyl end
• The coils and folds of secondary structure
result from hydrogen bonds between repeating
constituents of the polypeptide backbone
• Typical secondary structures are a coil called
an  helix and a folded structure called a 
pleated sheet
 Secondary Structure
 pleated sheet

Examples of
amino acid
subunits

 helix
 Abdominal glands of the
spider secrete silk fibers
made of a structural protein
containing  pleated sheets.
The radiating strands, made
of dry silk fibers, maintain
the shape of the web.

The spiral strands (capture

strands) are elastic, stretching
in response to wind, rain,
and the touch of insects.
• Tertiary structure is determined by
interactions between R groups, rather than
interactions between backbone constituents
• These interactions between R groups include
hydrogen bonds, ionic bonds, hydrophobic
interactions, and van der Waals interactions
• Strong covalent bonds called disulfide
bridges may reinforce the protein’s structure
Tertiary Structure Quaternary Structure
 Hydrophobic
interactions and
van der Waals
interactions

Polypeptide
backbone
Hydrogen
bond

Disulfide bridge

Ionic bond
Polypeptide  Chains
chain

Iron
Heme

 Chains
Hemoglobin
Collagen
• Quaternary structure results when two or
more polypeptide chains form one
macromolecule
• Collagen is a fibrous protein consisting of three
polypeptides coiled like a rope
• Hemoglobin is a globular protein consisting of
four polypeptides: two alpha and two beta
chains
Nucleic acids store and transmit hereditary
information

• The amino acid sequence of a polypeptide is

programmed by a unit of inheritance called a
gene
• Genes are made of DNA, a nucleic acid
The Roles of Nucleic Acids

• There are two types of nucleic acids:

– Deoxyribonucleic acid (DNA)
– Ribonucleic acid (RNA)

• DNA provides directions for its own replication

• DNA directs synthesis of messenger RNA
(mRNA) and, through mRNA, controls protein
synthesis
• Protein synthesis occurs in ribosomes
Fig. 5-26-1

DNA

1 Synthesis of
mRNA in the
nucleus mRNA

NUCLEUS
CYTOPLASM
Fig. 5-26-2

DNA

1 Synthesis of
mRNA in the
nucleus mRNA

NUCLEUS
CYTOPLASM

mRNA
2 Movement of
mRNA into cytoplasm
via nuclear pore
Fig. 5-26-3

DNA

1 Synthesis of
mRNA in the
nucleus mRNA

NUCLEUS
CYTOPLASM

mRNA
2 Movement of
mRNA into cytoplasm Ribosome
via nuclear pore

3 Synthesis
of protein

Amino
Polypeptide acids
The Structure of Nucleic Acids

• Nucleic acids are polymers called

polynucleotides
• Each polynucleotide is made of monomers
called nucleotides
• Each nucleotide consists of a nitrogenous
base, a pentose sugar, and a phosphate group
• The portion of a nucleotide without the
phosphate group is called a nucleoside
Fig. 5-27

5 end
Nitrogenous bases
Pyrimidines
5C

3C

Nucleoside

Nitrogenous
base Cytosine (C) Thymine (T, in DNA) Uracil (U, in RNA)

Purines

Phosphate
group Sugar
5C (pentose)
Adenine (A) Guanine (G)
3C (b) Nucleotide

Sugars
3 end
(a) Polynucleotide, or nucleic acid

Deoxyribose (in DNA) Ribose (in RNA)

(c) Nucleoside components: sugars

Fig. 5-27ab
5' end

5'C

3'C

Nucleoside

Nitrogenous
base

5'C

Phosphate 3'C
group Sugar
5'C (pentose)

3'C (b) Nucleotide

3' end
(a) Polynucleotide, or nucleic acid
Fig. 5-27c-1

Nitrogenous bases
Pyrimidines

Cytosine (C) Thymine (T, in DNA) Uracil (U, in RNA)

Purines

Adenine (A) Guanine (G)

(c) Nucleoside components: nitrogenous bases

Fig. 5-27c-2

Sugars

Deoxyribose (in DNA) Ribose (in RNA)

(c) Nucleoside components: sugars

Nucleotide Monomers

• Nucleoside = nitrogenous base + sugar

• There are two families of nitrogenous bases:
– Pyrimidines (cytosine, thymine, and uracil)
have a single six-membered ring
– Purines (adenine and guanine) have a six-
membered ring fused to a five-membered ring
• In DNA, the sugar is deoxyribose; in RNA, the
sugar is ribose
• Nucleotide = nucleoside + phosphate group
Nucleotide Polymers

• Nucleotide polymers are linked together to build

a polynucleotide
• Adjacent nucleotides are joined by covalent
bonds that form between the –OH group on the
3 carbon of one nucleotide and the phosphate
on the 5 carbon on the next
• These links create a backbone of sugar-
phosphate units with nitrogenous bases as
appendages
• The sequence of bases along a DNA or mRNA
polymer is unique for each gene
The DNA Double Helix

• A DNA molecule has two polynucleotides spiraling

around an imaginary axis, forming a double helix
• In the DNA double helix, the two backbones run in
opposite 5 → 3 directions from each other, an
arrangement referred to as antiparallel
• One DNA molecule includes many genes
• The nitrogenous bases in DNA pair up and form
hydrogen bonds: adenine (A) always with thymine
(T), and guanine (G) always with cytosine (C)
Fig. 5-28
5' end 3' end

Sugar-phosphate
backbones

Base pair (joined by

hydrogen bonding)

Old strands

Nucleotide
about to be
added to a
new strand
3' end

5' end

New
strands

3' end 5' end

5' end 3' end

DNA and Proteins as Tape Measures of Evolution

• The linear sequences of nucleotides in DNA

molecules are passed from parents to offspring
• Two closely related species are more similar in
DNA than are more distantly related species
• Molecular biology can be used to assess
evolutionary kinship
The Theme of Emergent Properties in the
Chemistry of Life: A Review

• Higher levels of organization result in the

emergence of new properties
• Organization is the key to the chemistry of life
Fig. 5-UN2
Fig. 5-UN2a
Fig. 5-UN2b
Fig. 5-UN3
Fig. 5-UN4
Fig. 5-UN5
Fig. 5-UN6
Fig. 5-UN7
Fig. 5-UN8
Fig. 5-UN9
Fig. 5-UN10
You should now be able to:

1. List and describe the four major classes of molecules

2. Describe the formation of a glycosidic linkage and
distinguish between monosaccharides,
disaccharides, and polysaccharides
3. Distinguish between saturated and unsaturated fats
and between cis and trans fat molecules
4. Describe the four levels of protein structure

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

You should now be able to:

5. Distinguish between the following pairs: pyrimidine

and purine, nucleotide and nucleoside, ribose and
deoxyribose, the 5 end and 3 end of a nucleotide