Chapter 3

The Structure and Function of

Large Biological Molecules
Overview: The Molecules of Life

• Four classes of large biological molecules:

carbohydrates, lipids, proteins, and nucleic
acids.
– small organic molecules are joined together to
form larger molecules.
• Macromolecules: large molecules of
thousands of covalently connected atoms.
– Molecular structure and function are
inseparable.

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Why do scientists study the structures of macromolecules?
Scientists study the structures of macromolecules—such as proteins, nucleic acids,
carbohydrates, and lipids—because the structure of a macromolecule is closely related to its
function in biological processes. Understanding the specific shape and arrangement of
atoms within these large molecules helps scientists to:

1.Identify Function: The structure of a macromolecule can reveal its role in cellular
processes, such as enzyme activity, DNA replication, or cell signaling.

2.Understand Mechanisms: By examining structural details, scientists can understand how

macromolecules interact with other molecules and how they carry out biochemical reactions.

3.Develop Treatments: Structural insights can inform the development of drugs and
therapies that target specific molecules, as seen in drug design for diseases like cancer or
Alzheimer’s.

4.Study Evolution: Comparing macromolecular structures across different species helps

researchers trace evolutionary relationships and understand how life has adapted to various
environments.

5.Improve Biotechnology: Knowing the structure allows scientists to modify

macromolecules for various applications, such as engineering enzymes for industrial use or
creating synthetic biomaterials.
Macromolecules are polymers, built from
monomers

• Polymer: long chain-like molecule consisting

of many similar building blocks, monomers.
• Three of the four classes of life’s organic
molecules are polymers:
– Carbohydrates
– Proteins
– Nucleic acids

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The Synthesis and Breakdown of Polymers

• condensation reaction (dehydration

reaction): two monomers bond together
through the loss of a water :
– dehydration synthesis = build by removing
HOH.

• Enzymes: organic catalysts, speed up rxn

• Polymers are disassembled to monomers by

hydrolysis: breaking down by adding HOH.

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The synthesis
and HO 1 2 3 H HO H
breakdown of Short polymer Unlinked monomer
polymers
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

 Carbohydrates

Four classes of large biological molecules:

carbohydrates, lipids, proteins, and nucleic acids.
Carbohydrates : fuel and building material

• Carbohydrates: sugars
– Monosaccharides: single sugars

• CH2O

• Glucose (C6H12O6): most common

• Disaccharide: two monosaccharides by removing HOH

to form a covalent bond.
– glycosidic linkage.
– dehydration synthesis

– C6H12O6 + C6H12O6 = C12H22O11

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Linear and ring forms of glucose

Linear and ring forms Abbreviated

ring structure
Examples of disaccharide synthesis
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
Here are some common types of sugars, categorized by their structure:

Monosaccharides (Simple Sugars)

1. Glucose - A primary energy source for cells; found in fruits, vegetables, and honey.

2. Fructose - Found in fruits, honey, and root vegetables; it’s the sweetest naturally occurring sugar.

3. Galactose - Less sweet than glucose; commonly found in milk as part of lactose.

Disaccharides (Two Sugars Linked)

1. Sucrose - Composed of glucose and fructose; commonly known as table sugar.

2. Lactose - Composed of glucose and galactose; found in milk and dairy products.

3. Maltose - Composed of two glucose molecules; found in germinating grains and malted products.

Oligosaccharides (3-10 Sugars Linked)

1. Raffinose - Made of galactose, glucose, and fructose; found in beans, cabbage, and whole grains.

2. Stachyose - Contains two galactose molecules, one glucose, and one fructose; found in beans and
legumes.

Polysaccharides (Many Sugars Linked)

1. Starch - A long chain of glucose units; found in potatoes, grains, and legumes.

2. Glycogen - A storage form of glucose in animals, stored in the liver and muscles.

3. Cellulose - A structural component of plant cell walls; made of glucose units but not digestible by
humans.

These sugars play various roles in energy storage, structural support, and cellular functions across different
organisms.
Storage polysaccharides of plants and animals
Chloroplast Starch Mitochondria Glycogen granules

0.5 µm

1 µm

Amylose Glycogen

Amylopectin

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

Structural Polysaccharides

• Cellulose: plant cell walls.

– polymer of glucose, but the glycosidic linkages
differ.
• grouped into microfibrils, which form strong
building materials for plants.

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 The Cell walls
arrangement of Cellulose
microfibrils
cellulose in in a plant
plant cell cell wall
Microfibril
walls

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.

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• Chitin, another structural polysaccharide, is
found in the exoskeleton of arthropods.
• Chitin also provides structural support for the
cell walls of fungi.
– polysaccharide with nitrogen ( N ) in each
sugar monomer.

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Chitin = a structural polysaccharide

(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

Four classes of large biological molecules:

carbohydrates, lipids, proteins, and nucleic acids.
Lipids

• do not form polymers.

• Hydrophobic: little or no affinity for water.

– nonpolar covalent bonds.

• Lipids = fats, phospholipids, and steroids

– fats  energy storage

– Adipose: fat cells, cushions vital organs,

insulates the body

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1. Fats = type of lipid
• fatty acid : 2 types

• Saturated fatty acids: maximum number of

hydrogen & no double bonds; single C bonds
– Unsaturated fatty acids have one or more
double bonds C = C

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The
Synthesis
and
Structure
of a fat = Fatty acid
triacylglycerol (palmitic acid)

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

Ester linkage

(b) Fat molecule (Triglyceride)

Examples
of
Saturated Structural
formula of a
and saturated fat
molecule
Unsaturated
Fats and Stearic acid, a
saturated fatty
Fatty acids acid
(a) Saturated fat

Structural formula
of an unsaturated
fat molecule.
The chain bends

Oleic acid, an
unsaturated
fatty acid
cis double
bond causes
(b) Unsaturated fat bending
• saturated fatty acids
– solid at room temperature.

– animal fats.

• unsaturated fatty acids

– Oils

– liquid at room temperature.

– Plant and fish fats

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2. Phospholipids (Cell Membranes) – type of
lipid
• two fatty acids and a phosphate group are
attached to glycerol.
– Hydrophobic: fatty acid tails

– Hydrophillic head: phosphate group

• amphipathic: both hydrophillic and hydrophobic

• added to water, self-assemble into a bilayer,

with the hydrophobic tails pointing toward the
interior.

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The structure of a phospholipid
Hydrophilic head
amphipathic

Choline

Phosphate

Glycerol
Hydrophobic tails

Fatty acids

Hydrophilic
head
Hydrophobic
tails
(a) Structural formula (b) Space-filling model (c) Phospholipid symbol
Bilayer structure formed by self-assembly of phospholipids
into a membrane in an aqueous environment

Hydrophilic WATER
head

Hydrophobic
WATER
tail
3. Steroids = type of Lipids with 4 fused rings
…
• Cholesterol: in animal cell membranes.

• high blood levels  cardiovascular disease.

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 Proteins

Four classes of large biological molecules:

carbohydrates, lipids, proteins, and nucleic acids.
Proteins

• more than 50% of the dry mass of most cells.

• structural support, storage, transport, cellular

communications, movement, defense against foreign
substances, and organic catalysts (enzymes).
• Enzymes: LARGE proteins; catalysts
– Specific, shape-match to molecules

– Used repeatedly

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The catalytic cycle of an
enzyme
Substrate is the reactant
(sucrose)

Products
Enzyme
(sucrase)
OH
H2O
Glucose
Fructose
HO
Proteins

• 20 amino acids (monomers)  Polypeptides

(polymers)
– AA linked by covalent peptide bond, C-N

• sequence of amino acids determines a

protein’s 3D three-dimensional structure & fxn
• Amino acids: organic molecules with carboxyl
and amino groups attached to a central carbon.
– variable side chains, called R group

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The 20 Nonpolar
amino acids
of
proteins 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
Acidic
charged Basic

Aspartic acid Glutamic acid Lysine Arginine Histidine

(Asp or D) (Glu or E) (Lys or K) (Arg or R) (His or H)
Of the 20 standard amino acids, 9 are considered essential for humans because the body cannot
synthesize them, so they must be obtained through the diet. Here are the essential amino acids:

1.Histidine - Important for growth, tissue repair, and the production of histamine, a neurotransmitter.

2.Isoleucine - Involved in muscle metabolism, immune function, hemoglobin production, and energy
regulation.

3.Leucine - Plays a key role in protein synthesis and muscle repair; also helps regulate blood sugar
levels.

4.Lysine - Crucial for protein synthesis, enzyme production, and calcium absorption; supports immune
function.

5.Methionine - Aids in metabolism and detoxification; important for tissue growth and the absorption of
zinc and selenium.

6.Phenylalanine - Precursor for neurotransmitters like dopamine, epinephrine, and norepinephrine; helps
in the formation of other amino acids.

7.Threonine - Involved in the formation of collagen and elastin; supports immune function and fat
metabolism.

8.Tryptophan - Precursor for serotonin, a neurotransmitter involved in mood regulation; also important
for sleep and nitrogen balance.

9.Valine - Vital for muscle growth and tissue repair; helps regulate energy levels and is involved in the
functioning of the nervous system.

These amino acids are essential for various bodily functions, including protein synthesis, enzyme
production, and the maintenance of muscle and immune health. They can be obtained through a
balanced diet that includes protein-rich foods like meat, fish, eggs, dairy products, legumes, and certain
Making a
polypeptide Peptide
chain bond

(a)

Side chains
Peptide
bond

Backbone

Amino end Carboxyl end

(b) (N-terminus) (C-terminus)
A protein folds into a specific Shape / Structure so
it can perform its Function. Scientists draw it 2
different ways:

Groove
Groove

(a) A ribbon model of lysozyme (b) A space-filling model of lysozyme

An antibody binding to a protein from a flu virus

Antibody protein Protein from flu virus

4 Levels of protein structure due to folding

Primary Secondary Tertiary Quaternary

Structure Structure Structure Structure
 pleated sheet
H3 N
+

Amino end
Examples of
amino acid
subunits

 helix
 A single amino acid substitution in a protein causes sickle-cell disease
Normal hemoglobin Sickle-cell hemoglobin
Val His Leu Thr Pro Glu Glu
Primary
Primary Val His Leu Thr Pro Val Glu
structure
structure 1 2 3 4 5 6 7 1 2 3 4 5 6 7

Exposed
Secondary Secondary hydrophobic
and tertiary  subunit and tertiary region  subunit
structures structures

 


Quaternary Normal Quaternary Sickle-cell
structure hemoglobin structure hemoglobin
(top view) 

 

Function Molecules do Function Molecules

not associate interact with
with one one another and
another; each crystallize into
carries oxygen. a fiber; capacity
to carry oxygen
is greatly reduced.

10 µm 10 µm

Red blood Normal red blood Red blood Fibers of abnormal

cell shape cells are full of cell shape hemoglobin deform
individual red blood cell into
hemoglobin sickle shape.
moledules, each
carrying oxygen.
Environmental Factors Affect Protein Structure

• Denaturation: shape change in protein is

biologically inactive
– pH, salt concentration, temperature

– protein unravels and looses its shape.

• Chaperonins: protein molecules that assist the

proper folding of other proteins.

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Denaturation and renaturation of a protein

Denaturation

Normal protein Renaturation Denatured protein

 Nucleic Acids

Four classes of large biological molecules:

carbohydrates, lipids, proteins, and nucleic acids.
Nucleic acids store and transmit hereditary
information
• Genes: sequences of DNA nucleotides.
– Determines the amino acid sequence of
polypeptides

– Deoxyribonucleic acid (DNA)

– Ribonucleic acid (RNA)
• DNA: directions for its own replication and the
synthesis of messenger RNA (mRNA) 
protein synthesis in ribosomes.

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Central Dogma: DNA → RNA → protein
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

• Polynmer: Nucleic acids

• monomers : nucleotides.
– nitrogenous base

– pentose sugar

– phosphate group.

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 Components of nucleic acids
5 end
Nitrogenous bases
Pyrimidines
5C

3C

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

Nucleotide Monomers

• Pyrimidines: C T (U) (cytosine, thymine,

and uracil) have a single six-membered ring
– Remember the acronym “CUT”
• Purines: A G (adenine and guanine) have a
6-membered ring fused to a 5-membered ring
• Nucleotide = nucleoside + phosphate group.
Nucleoside = nitrogenous base + sugar

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The DNA Double Helix

• Double helix: two polynucleotides spiraling around

• antiparallel : two backbones run in opposite 5 →

3 directions
• One DNA molecule includes many genes

• The nitrogenous bases in DNA pair-up forming

hydrogen bonds: A - T and C-G

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The DNA double helix 5' end 3' end
and its Replication
Semi-Conservative Sugar-phosphate
Replication 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

Nucleic Acid :
Chain of
Nucleotides

Be sure you can

Identify the 5’
end vs. the 3’
ends)
You should be able to draw and explain a review chart of
organic molecules: