The Molecules of Life

Within cells, small organic molecules are joined

together to form larger molecules
Macromolecules are large molecules composed
of thousands of connected atoms

Most macromolecules are polymers, built from

monomers
A polymer is a long molecule consisting of many
similar building blocks called monomers
Three of the four classes of lifes organic
molecules are polymers:
Carbohydrates
Proteins
Nucleic acids

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 is the most common monosaccharide
Monosaccharides are classified by location of the
carbonyl group and by number of carbons in the
carbon skeleton

Triose sugars
(C3H6O3)

Pentose sugars
(C5H10O5)

Hexose sugars
(C6H12O6)

Glyceraldehyde

Ribose
Galactose

Glucose

Dihydroxyacetone

Ribulose
Fructose

Linear and
ring forms

Abbreviated ring
structure

 A disaccharide is formed when a dehydration

reaction joins two monosaccharides
This covalent bond is called a glycosidic bond
Lactose = Glu + Gal
Maltose = Glu + Glu
Sucrose = Glu + Fru

Dehydration
reaction in the
synthesis of maltose

14
glycosidic
linkage

Glucose

Glucose

Dehydration
reaction in the
synthesis of sucrose

Maltose

12
glycosidic
linkage

Glucose

Fructose

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

Starch granules
in a potato tuber cell

Starch (amylose)

Glucose
monomer
Glycogen granules
in muscle
tissue

Cellulose microfibrils
in a plant cell wall
Cellulose
molecules

Glycogen

Cellulose
Hydrogen bonds
between OH groups
(not shown) attached to
carbons 3 and 6

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

1 m

Amylose

Amylopectin

Starch: a plant polysaccharide

 Glycogen is a storage polysaccharide in animals

Humans and other vertebrates store glycogen

mainly in liver and muscle cells

Mitochondria Glycogen granules

0.5 m

Glycogen

Glycogen: an animal polysaccharide

Structural Polysaccharides
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 Glucose

b Glucose

a and b glucose ring structures

Starch: 14 linkage of a glucose monomers.

Cellulose: 14 linkage of b glucose monomers.

Cellulose microfibrils
in a plant cell wall
Cell walls

Microfibril

0.5 m
Plant cells

Cellulose
molecules

b Glucose
monomer

 Enzymes that digest starch by hydrolyzing alpha

linkages cant hydrolyze beta 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
Chitin can be used as 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

Dehydration reaction in the synthesis of a fat

 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

Ester linkage

Fat molecule (triacylglycerol)

 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
The major function of fats is energy storage

(a) Saturated fat

Structural
formula of a
saturated fat
molecule

Space-filling
model of
stearic acid,
a saturated
fatty acid

(b) Unsaturated fat

Structural
formula
of an
unsaturated
fat molecule

Space-filling
model of oleic
acid, an
unsaturated
fatty acid
Double bond
causes bending.

 Fats made from saturated fatty acids are called

saturated fats

Most animal fats are saturated

Saturated fats are solid at room temperature
A diet rich in saturated fats may contribute to
cardiovascular disease through plaque deposits

Stearic acid

Saturated fat and fatty acid.

 Fats made from unsaturated fatty acids are called

unsaturated fats

Plant fats and fish fats are usually unsaturated

Plant fats and fish fats are liquid at room
temperature and are called oils

Oleic acid

cis double bond

causes bending
Unsaturated fat and fatty acid.

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
Hydrophobic tails

Choline
Phosphate
Glycerol

Fatty acids

(a) Structural formula

Hydrophilic
head
Hydrophobic
tails
(b) Space-filling model

(c) Phospholipid
symbol

(d) Phospholipid
bilayer

 When phospholipids are added to water, they selfassemble 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
head

Hydrophobic
tails

WATER

WATER

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

Enzymatic proteins

Defensive proteins

Function: Selective acceleration of

chemical reactions

Function: Protection against disease

Example: Digestive enzymes catalyze the

hydrolysis of bonds in food molecules.

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: 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.

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.
Transport
protein

Ovalbumin

Amino acids
for embryo

Cell membrane

Hormonal proteins

Receptor proteins

Function: Coordination of an organisms

activities

Function: Response of cell to chemical

stimuli

Example: Insulin, a hormone secreted by

the pancreas, causes other tissues to
take up glucose, thus regulating blood
sugar concentration.

Example: Receptors built into the

membrane of a nerve cell detect signaling
molecules released by other nerve cells.
Receptor
protein

Insulin
secreted

High
blood sugar

Signaling molecules
Normal
blood sugar

Contractile and motor 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.
Actin

Structural proteins
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.

Myosin
Collagen

Muscle tissue

30

Connective tissue 60 m

 Enzymes are a type of protein that acts as a

catalyst, speeding up chemical reactions
Enzymes can perform their functions repeatedly,
functioning as workhorses that carry out the
processes of life

Substrate
(sucrose)

Glucose
Enzyme
(sucrose)
Fructose

Defensive proteins
Function: Protection against disease
Example: Antibodies inactivate and help
destroy viruses and bacteria.

Antibodies
Virus

Bacterium

Storage proteins
Function: Storage of amino acids
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.

Ovalbumin

Amino acids
for embryo

Transport proteins
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.
Transport
protein

Cell membrane

Hormonal proteins
Function: Coordination of an organisms
activities
Example: Insulin, a hormone secreted by
the pancreas, causes other tissues to
take up glucose, thus regulating blood
sugar concentration.

High
blood sugar

Insulin
secreted

Normal
blood sugar

Receptor proteins
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.
Receptor
protein
Signaling molecules

Contractile and motor 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.
Actin

Muscle tissue

30

Myosin

Structural proteins
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.
Collagen

Connective tissue

60

Polypeptides
Polypeptides are polymers of 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

Cells use 20 amino acids to make thousands of

proteins

a carbon

Amino
group

Carboxyl
group

Nonpolar side chains; hydrophobic

Side chain
(R group)

Glycine
(Gly or G)

Methionine
(Met or M)

Alanine
(Ala or A)

Valine
(Val or V)

Phenylalanine
(Phe or F)

Leucine
(Leu or L)

Tryptophan
(Trp or W)

Isoleucine
( le or )

Proline
(Pro or P)

Polar side chains; hydrophilic

Serine
(Ser or S)

Threonine
(Thr or T)

Cysteine
(Cys or C)

Tyrosine
(Tyr or Y)

Asparagine
(Asn or N)

Glutamine
(Gln or Q)

Electrically charged side chains; hydrophilic

Basic (positively charged)
Acidic (negatively charged)

Aspartic acid Glutamic acid

(Asp or D)
(Glu or E)

Lysine
(Lys or K)

Arginine
(Arg or R)

Histidine
(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

monomers to more than a thousand
Each polypeptide has a unique linear sequence of
amino acids
Each polypeptide has a unique linear sequence of
amino acids, with a carboxyl end (C-terminus)
and an amino end (N-terminus)
NCC-NCC-NCC-NCC

Peptide bond

New peptide
bond forming
Side
chains

Backbone

Amino end
(N-terminus)

Peptide
bond

Carboxyl end
(C-terminus)

Protein Conformation 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
proteins three-dimensional conformation
A proteins conformation determines its function
Ribbon models and space-filling models can
depict a proteins conformation

Antibody protein

Protein from flu virus

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

Secondary
structure

Tertiary
structure

Quaternary
structure

Transthyretin
polypeptide

Transthyretin
protein

helix

pleated sheet

 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 structure
Amino
acids
1

10

Amino end
30

35

15

20

25

45

40

50

Primary structure of transthyretin

65

70

55

60

75
80

90

85

95

115

120

110

105

100

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
alpha helix and a folded structure called a beta
pleated sheet

Secondary structure

helix

Hydrogen bond

pleated sheet
strand

Hydrogen
bond

Tertiary structure

Transthyretin
polypeptide

Hydrophobic
interactions and
van der Waals
interactions
Polypeptide
backbone
Hydrogen
bond

Disulfide bridge

Ionic bond

Quaternary structure

Transthyretin
protein

 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

Polypeptide
chain

b Chains

Iron
Heme

Polypeptide chain

Collagen

a Chains
Hemoglobin

Sickle-Cell Disease: A Simple Change in

Primary Structure
A slight change in primary structure can affect a
proteins conformation and ability to function
Sickle-cell disease, an inherited blood disorder,
results from a single amino acid substitution in the
protein hemoglobin

10 m

Red blood Normal cells are

cell shape full of individual
hemoglobin
molecules, each
carrying oxygen.

10 m

Red blood
cell shape

Fibers of abnormal
hemoglobin deform
cell into sickle
shape.

Figure 3.22

Sickle-cell

Normal

Primary
Structure
1
2
3
4
5
6
7

1
2
3
4
5
6
7

Secondary
and Tertiary
Structures

Quaternary
Structure
Normal
hemoglobin

Function

Red Blood Cell

Shape

Molecules do not
associate with one
another; each carries
oxygen.

subunit

Exposed hydrophobic region

Sickle-cell
hemoglobin

Molecules crystallized
into a fiber; capacity to
carry oxygen is reduced.

subunit

What Determines Protein Conformation?

In addition to primary structure, physical and
chemical conditions can affect conformation
Alternations in pH, salt concentration,
temperature, or other environmental factors can
cause a protein to unravel
This loss of a proteins native conformation is
called denaturation

A denatured protein is biologically inactive

Denaturation

Normal protein

Denatured protein
Renaturation

The Protein-Folding Problem

It is hard to predict a proteins conformation from
its primary structure
Most proteins probably go through several states
on their way to a stable conformation

Chaperonins are protein molecules that assist the

proper folding of other proteins

Cap

Hollow
cylinder

Chaperonin
(fully assembled)

Polypeptide

Steps of Chaperonin
Action:
An unfolded polypeptide enters the
cylinder from one
end.

Correctly
folded
protein

The cap attaches, causing

the cylinder to change
shape in such a way that
it creates a hydrophilic
environment for the
folding of the polypeptide.

The cap comes

off, and the
properly folded
protein is released.

 Scientists use X-ray crystallography to

determine a proteins conformation

Another method is nuclear magnetic resonance

(NMR) spectroscopy, which does not require
protein crystallization

X-ray
diffraction pattern
Photographic film
Diffracted X-rays
X-ray
source

X-ray
beam

Crystal

Nucleic acid

X-ray diffraction pattern

3D computer model

Protein

Experiment
Diffracted
X-rays
X-ray
source X-ray
beam

Crystal

Digital detector

X-ray diffraction
pattern

Results
RNA

DNA

RNA
polymerase

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

DNA

Synthesis of
mRNA in the nucleus
mRNA

NUCLEUS
CYTOPLASM

mRNA
Movement of
mRNA into cytoplasm
via nuclear pore

Ribosome

Synthesis
of protein

Polypeptide

Amino
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

end

Sugar-phosphate backbone
(on blue background)

Nitrogenous bases
Pyrimidines

5 C
3 C

Nucleoside
Nitrogenous
base

Cytosine (C)

Thymine
(T, in DNA)

Uracil
(U, in RNA)

Purines

5 C

Phosphate
group

3 C

Sugar
(pentose)

Adenine (A)

Guanine (G)

(b) Nucleotide
3

end

Sugars

(a) Polynucleotide, or nucleic acid

Deoxyribose (in DNA)

(c) Nucleoside components

Ribose (in RNA)

5 end

Nucleoside
Nitrogenous
base

Phosphate
group
Nucleotide
3 end

Polynucleotide, or
nucleic acid

Pentose
sugar

Sugar-phosphate
backbones
Hydrogen bonds

Base pair joined

by hydrogen bonding

Nucleotide Monomers
Nucleotide monomers are made up of
nucleosides and phosphate groups

Nucleoside = nitrogenous base + sugar

There are two families of nitrogenous bases:
Pyrimidines have a single six-membered ring
Purines have a six-membered ring fused to a
five-membered ring

In DNA, the sugar is deoxyribose

In RNA, the sugar is ribose

Nitrogenous bases
Pyrimidines

Cytosine
C

Thymine (in DNA) Uracil (in RNA)

U
T
Purines

Adenine
A

Guanine
G

Pentose sugars

Deoxyribose (in DNA)

Nucleoside components

Ribose (in RNA)

Nucleotide Polymers
Nucleotide polymers are linked together, building 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 to 3 directions from each other, an
arrangement referred to as antiparallel
One DNA molecule includes many genes
The nitrogenous bases in DNA form hydrogen
bonds in a complementary fashion: A always
with T, and G always with C

5 end

3 end
Sugar-phosphate
backbone
Base pair (joined by
hydrogen bonding)
Old strands
Nucleotide
about to be
added to a
new strand

5 end

New
strands

5 end

3 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

Animations and Videos

Macromolecules 1
Macromolecules 2
Polymers
Biomolecules Carbohydrates
Carbohydrates
Glucose in Water
Dehydration and Hydrolysis

Animations and Videos

Disaccharides

Polysaccharides
Bozeman Carbohydrates

Fats
Lipids

Biomolecules Lipids
Bozeman - Lipids

Animations and Videos

Proteins
Protein Structure 1
Protein Structure 2
Life Cycle of a Protein
Peptide Bond Formation

Dehydration Synthesis of Amino Acids

Protein Folding - 1

Animations and Videos

Protein Folding 2
Protein Organization
Protein Denaturation

Bozeman Proteins
How Enzymes Work

Enzyme Action and the Hydrolysis of Sucrose

Enzyme Catalysis - 1

Animations and Videos

Enzyme Catalysis 2
Allosteric Regulation of Enzymes

Allosteric Enzyme
Enzyme Changing Shape

Bozeman Enzymes
Bozeman - Nucleic Acids
Testing Organic Substances
Chapter Quiz Questions 1

Animations and Videos

Chapter Quiz Questions 2