Molecules

of Life

Structure and Function

Biochemistry Department
The Molecules of Life
the organic molecules are the unique constituents of cells,
accounts for 25-30% of the cell weight.
Within cells, small organic molecules are joined together to
form larger molecules
Macromolecules are large molecules composed of thousands
of covalently 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
The Synthesis and Breakdown of Polymers

Monomers form larger molecules by condensation reactions

called dehydration reactions
Polymers are disassembled to monomers by hydrolysis, a
reaction that is essentially the reverse of the dehydration
reaction
 Short polymer Unlinked monomer

Dehydration removes a water

molecule, forming a new bond

Longer polymer
Dehydration reaction in the synthesis of a polymer

Hydrolysis adds a water

molecule, breaking a bond

Hydrolysis of a polymer
 The Diversity of Polymers
1 2 3 H HO

Each cell has thousands of different kinds of macromolecules

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 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 Pentose sugars Hexose sugars
(C3H6O3) (C5H10O5) (C6H12O6)

Glyceraldehyde

Ribose
Glucose Galactose

Dihydroxyacetone

Ribulose
Fructose
 Monosaccharides serve as a major fuel for cells and as raw
material for building molecules
Though often drawn as a linear skeleton, in aqueous solutions
they form rings
Linear and Abbreviated ring
ring forms 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
14
reaction in the glycosidic
synthesis of maltose linkage

Glucose Glucose Maltose

Dehydration
12
reaction in the glycosidic
synthesis of sucrose 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 Glycogen

Cellulose microfibrils
in a plant cell wall Cellulose

Cellulose
Hydrogen bonds
molecules
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.

 Polymers with alpha glucose are helical
Polymers with beta 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
 Cellulose microfibrils
in a plant cell wall
Cell walls Microfibril

0.5 m

Plant cells

Cellulose
molecules

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 (b) Unsaturated fat

Structural
formula of a
saturated fat
molecule
Structural
formula
of an
unsaturated
Space-filling fat molecule
model of
stearic acid,
a saturated
fatty acid
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

Choline

Phosphate

Glycerol
Hydrophobic tails

Fatty acids

Hydrophilic
head

Hydrophobic
tails
(a) Structural formula (b) Space-filling model (c) Phospholipid (d) Phospholipid
symbol bilayer
 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
 WATER
Hydrophilic
head

Hydrophobic
WATER
tails
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
Function: Selective acceleration of
chemical reactions
Example: Digestive enzymes catalyze the
hydrolysis of bonds in food molecules.
Defensive proteins
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
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.
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

Ovalbumin Amino acids

for embryo Cell membrane
 Hormonal proteins Receptor proteins
Function: Coordination of an organisms Function: Response of cell to chemical
activities stimuli
Example: Insulin, a hormone secreted by Example: Receptors built into the
the pancreas, causes other tissues to membrane of a nerve cell detect signaling
take up glucose, thus regulating blood molecules released by other nerve cells.
sugar concentration.
Receptor
protein

Insulin Signaling molecules

High secreted Normal
blood sugar blood sugar
Structural proteins
Contractile and motor proteins Function: Support
Function: Movement Examples: Keratin is the protein of hair,
Examples: Motor proteins are responsible horns, feathers, and other skin appendages.
for the undulations of cilia and flagella. Insects and spiders use silk fibers to make
Actin and myosin proteins are their cocoons and webs, respectively.
responsible for the contraction of Collagen and elastin proteins provide a
muscles. fibrous framework in animal connective
tissues.
Actin Myosin
Collagen

Muscle tissue 30 m 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.

Insulin
High secreted Normal
blood sugar 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 Myosin

Muscle tissue 30 m
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 m
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
 carbon

Amino Carboxyl
group group
Nonpolar side chains; hydrophobic
Side chain
(R group)

Glycine Alanine Valine Leucine Isoleucine

(Gly or G) (Ala or A) (Val or V) (Leu or L) (le or )

Methionine Phenylalanine Tryptophan Proline

(Met or M) (Phe or F) (Trp or W) (Pro or P)
Polar side chains; hydrophilic

Serine Threonine Cysteine

(Ser or S) (Thr or T) (Cys or C)

Tyrosine Asparagine Glutamine

(Tyr or Y) (Asn or N) (Gln or Q)
Electrically charged side chains; hydrophilic

Basic (positively charged)

Acidic (negatively charged)

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 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

Back-
bone

Amino end Peptide Carboxyl end

(N-terminus) bond (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 Tertiary Quaternary
structure structure structure

helix

pleated sheet
Transthyretin Transthyretin
polypeptide protein
 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 5 10

Amino end
30 25 20 15

35 40 45 50

Primary structure of transthyretin

55
70 65 60

75
80 85 90

95

115 110 105 100

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 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 Chains

Iron
Heme

Chains
Polypeptide chain Collagen 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 10 m

Red blood Normal cells are Red blood Fibers of abnormal

cell shape full of individual cell shape hemoglobin deform
hemoglobin cell into sickle
molecules, each shape.
carrying oxygen.
Figure 3.22

Secondary
Primary Quaternary Red Blood Cell
and Tertiary Function
Structure Structure Shape
Structures
Normal Molecules do not
1 hemoglobin associate with one
2 another; each carries
3 oxygen.
Normal

4

5 subunit
6
7
5 m

Exposed hydro- Sickle-cell Molecules crystallized

1 phobic region hemoglobin into a fiber; capacity to
carry oxygen is reduced.
2
Sickle-cell

3
4

5
6 subunit
7
5 m
 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 (=terurai)
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)
 Correctly
Polypeptide folded
protein

Steps of Chaperonin The cap attaches, causing The cap comes

Action: the cylinder to change off, and the
An unfolded poly- shape in such a way that properly folded
peptide enters the it creates a hydrophilic protein is released.
cylinder from one environment for the
end. folding of the polypeptide.
 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
X-ray
source
beam

Crystal
 Nucleic acid Protein

X-ray diffraction pattern 3D computer model

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
Ribosome
via nuclear pore

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
 Sugar-phosphate backbone
5 end (on blue background) Nitrogenous bases
Pyrimidines
5C

3C

Nucleoside

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

Phosphate
5C group Sugar
(pentose) Adenine (A) Guanine (G)
3C
(b) Nucleotide
Sugars
3 end
(a) Polynucleotide, or nucleic acid

Deoxyribose (in DNA) Ribose (in RNA)

(c) Nucleoside components

 5 end

Nucleoside
Nitrogenous
base

Phosphate
group Pentose
sugar
Nucleotide

3 end
Polynucleotide, or
nucleic acid
5 3 Sugar-phosphate
backbones
Hydrogen bonds

3 5 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 Thymine (in DNA) Uracil (in RNA)

C T U

Purines

Adenine Guanine
A G

Pentose sugars

Deoxyribose (in DNA) Ribose (in RNA)

Nucleoside components
 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

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