Chapter 3

Molecules of Life
BIO 121
Instructor: Dr. Marisa Khoo
Chapter 3 overview

From structure to function Carbohydrates

Lipids Proteins Nucleic Acids

FROM STRUCTURE TO
FUNCTION
 Carbon, the Stuff of Life
• Carbon’s ability to bond with four other atoms
is the basis for building large and diverse
organic compounds.
• Organic compounds consist primarily carbon
and hydrogen atoms.
• Carbon chains form the backbone of most
organic molecules.
• By sharing electrons, carbon can bond to four
other atoms.
 Carbon, the Stuff of Life
• Methane (CH4) is one of the simplest organic
compounds
• Four covalent bonds link four hydrogen atoms to
the carbon atom
• Each of the four lines in the formula for methane
represents a pair of shared electrons
Structural Ball-and-stick Space-filling
formula model model

Methane

The four single bonds of carbon point to the corners

of a tetrahedron.

Figure: Three representations of methane (CH4).

 Carbon, the Stuff of Life
• Methane and other compounds composed of
only carbon and hydrogen are called
hydrocarbons
• Carbon atoms bond covalently with up to four other atoms,
often in long chains or rings
• An organic compound’s properties depend on the
– size and shape of its carbon backbone and
– atoms attached to that skeleton.
• Functional groups attach to a carbon backbone
– Influence organic compound’s properties
A few chemical groups are key to the functioning
of biological molecules
• The functional groups are
• Hydroxyl group—consists of a hydrogen bonded to an
oxygen
• Carbonyl group—a carbon linked by a double bond to
an oxygen atom
• Carboxyl group—consists of a carbon double-bonded
to both an oxygen and a hydroxyl group
• Amino group—composed of a nitrogen bonded to
two hydrogen atoms and the carbon skeleton
• Phosphate group—consists of a phosphorus atom
bonded to four oxygen atoms
• Methyl group-consist of a carbon bonded to three
hygrogen atoms
Checkpoint question Identify the chemical groups that do
not contain carbon.
A few chemical groups are key to the functioning
of biological molecules
• A functional group affects a biological
molecule’s function in a characteristic way
• An example of similar compounds that differ
only in functional groups is sex hormones
• Male and female sex hormones differ only in
functional groups
• The differences cause varied molecular actions
• The result is distinguishable features of males and
females
 Testosterone

Methyl and carbonyl group

Hydroxyl group

Estradiol

© 2018 Pearson Education Ltd.

 Metabolic Reactions
• Cells use energy to grow and maintain
themselves
• Enzyme-driven reactions build, rearrange, and
split organic molecules
• Cells form complex organic molecules
– Simple sugars → carbohydrates
– Fatty acids → lipids
– Amino acids → proteins
– Nucleotides → nucleic acids
 Metabolic Reactions

Carbohydrates Lipids

Four
classes of
biological
molecules

Proteins Nucleic acids

 Cells make large molecules from a
limited set of small molecules
• The four classes of biological molecules contain
very large molecules.
– They are often called macromolecules because of
their large size.
– They are also called polymers because they are made
from identical or similar building blocks strung
together.
– The building blocks of polymers are called monomers.
– Eg: Proteins are made from only 20 different amino
acids, and DNA is built from just four kinds of
nucleotides
What do cells do to organic
compounds?
 Cells make large molecules from a
limited set of small molecules
• Monomers are linked together to form
polymers through condensation.
• Polymers are broken apart by hydrolysis.
• These reactions are mediated by enzymes,
which speed up chemical reactions in cells
Condensation and Hydrolysis
CARBOHYDRATES
 Carbohydrates in living system
• Carbohydrates are organic compounds that
consist of carbon, hydrogen and oxygen in 1:2:1
ratio.
– Sugar monomers are monosaccharides.
– A monosaccharide has a formula that is a multiple
of CH2O and contains hydroxyl groups and a
carbonyl group.
Checkpoint question Write the formula for a
monosaccharide that has three carbons.
 Carbohydrates in living system
• Three main types of carbohydrates
– Monosaccharides (simple sugars)
– Oligosaccharides (short chains)
– Polysaccharides (complex carbohydrates)

• Carbohydrate functions
– Instant energy sources
– Transportable or storable forms of energy
– Structural materials
 Carbohydrates in living system
• The carbon skeletons of monosaccharides vary
in length with 2 or more hydroxyl (-OH) group
• Glucose and fructose are six carbons long
• Others have three to seven carbon atoms
• Monosaccharides are the main fuels for
cellular work
• Monosaccharides are also used as raw materials
to manufacture other organic molecules
Formation of a sucrose molecule through condensation process
 Polysaccharides are long chains of
sugar units
• Polysaccharides are polymers of monosaccharides
• They can function in the cell as a storage molecule or as a
structural compound
• Starch is a storage polysaccharide composed of glucose
monomers and found in plants
• Glycogen is a storage polysaccharide composed of
glucose, which is hydrolyzed by animals when glucose
is needed
• Cellulose is a polymer of glucose that forms plant cell
walls
• Chitin is a polysaccharide used by insects and
crustaceans to build an exoskeleton
 Starch granules in Starch
a potato tuber cell

Glucose
monomer
Glycogen granules
in muscle
tissue Glycogen

Cellulose microfibrils Cellulose

in a plant cell wall
Cellulose
molecules Hydrogen bonds
 Starch granules in Starch
a potato tuber cell

Glucose
monomer

Starch is a storage polysaccharide composed of glucose

monomers and found in plants
-Starch molecules coil in to helical shape and may be
unbranched or branched.
-Potato, grain, corn and rice are major source of starch.
 Glycogen granules
in muscle
tissue Glycogen

Glycogen is a storage polysaccharide composed of glucose, which

is hydrolyzed by animals when glucose is needed It is especially
abundant in the liver and muscles of highly active animals,
including fishes and people. It is highly branched than starch.
 Cellulose microfibrils Cellulose
in a plant cell wall
Cellulose
molecules Hydrogen bonds

Cellulose is a polymer of glucose that forms plant cell walls.

Arranged parallel to each other, cellulose molecules are joined
by hydrogen bond, forming cable-like microfibrils.
Checkpoint question
Compare and contrast starch and
cellulose, two plant polysaccharides.

-Both are polymers of glucose, but the bonds

between glucose monomers have different shapes.
-Starch functions mainly for sugar storage. Cellulose
is a structural polysaccharide that is the main
material of plant cell walls.
LIPIDS
 Fats are lipids that are mostly energy-
storage molecules
• Lipids are fatty, oily, and waxy organic compounds.
• Lipids are water insoluble (hydrophobic, or water
fearing) compounds that are the most abundant
energy storage
• They contain twice as much energy as a polysaccharide
• Fats (triglycerides) are lipids made from glycerol and
fatty acids
• Fatty acids link to glycerol by a condensation reaction
• A fat contains one glycerol linked to three fatty acids
• Fats are often called triglycerides because of their
structure
 glycerol

Figure: A
condensation
reaction linking a
fatty acid to
glycerol.

three fatty acid tails Triglyceride, a neutral fat

Fig. 3.11, p. 40
 Fats are lipids that are mostly energy-
storage molecules
• Some fatty acids contain one or more double bonds,
forming unsaturated fatty acids. Unsaturated fatty
acids are typical of plant oils, which are in liquid form
at room temperature.
• Fats with the maximum number of hydrogens are
called saturated fatty acids. Saturated fatty acids are
found in animal fats and appears solid in room
temperature.
Saturated fats Unsaturated fats
• Checkpoint question Explain why fats are
hydrophobic.
• The three fatty acid tails of a fat molecule
contain only nonpolar C—H bonds, which do
not mix well with polar water molecules.
 Lipids in living system
•Phospholipids consist of 2 long hydrocarbon tail and a
head with phosphate group which makes the head
hydrophilic.
•This opposing properties give rise to the basic
components of cell membranes.
Water
Hydrophilic heads

Hydrophobic tails

Symbol for phospholipid

Water
Phosphate
group
Glycerol

Hydrophilic heads

Hydrophobic tails
• Checkpoint question Compare the structure
of a phospholipid with that of a fat.
• A phospholipid has two fatty acids and a
phosphate group attached to glycerol. Three
fatty acids are attached to the glycerol of a fat
molecule.
 Lipids in living system
• Steroids are lipids composed of fused ring structures
(no fatty acid tails)
• Functional groups attached to the rings define the
type of steroid
• Cholesterol is an example of a steroid that plays a
significant role in the structure of the cell membrane
• In addition, cholesterol is the compound from which we
synthesize sex hormones

Figure: Cholesterol, a steroid

 Lipids in living system
• A wax is a water repelling substances consist of a
complex , varying mixture of lipids with long fatty
acid tails bonded to a long chain alcohols.
• Firm and water repelling because these
molecules can pack together very tightly
• Functions: lubricating, make feathers water proof,
beeswax secretion.
PROTEINS
 Proteins- Diversity in structure and
function
• Proteins are involved in nearly every dynamic
function in your body and are very diverse.
• Proteins function as
– enzymes,
– transport proteins embedded in cell membranes,
– defensive proteins, such as antibodies,
– signal proteins such as many hormones,
– receptor proteins,
– contractile proteins found within muscle cells,
– structural proteins such as collagen, and
– storage proteins.
 Proteins- Diversity in structure and
function
• Proteins are composed of differing arrangements
of a common set of just 20 amino acid
monomers.
• Protein diversity is based on different sequences
of amino acids, monomers that contain
– an amino group,
– a carboxyl group,
– an H atom, and
– an R group, all attached to a central carbon.
• The R groups distinguish 20 amino acids, each
with specific properties.
Amino
group Carboxyl
group

General structure of an amino acid

 Proteins- Diversity in structure and
function
• Amino acid monomers are linked together in a
dehydration reaction,
– joining the carboxyl group of one amino acid to
the amino group of the next amino acid, and
creating a peptide bond.
• Additional amino acids can be added by the
same process to create a chain of amino acids
called a polypeptide.
Protein Synthesis
Protein Synthesis
Protein Synthesis
• Checkpoint question By what process do you
digest the proteins you eat into their
individual amino acids?

• By hydrolysis, adding a molecule of water back

to break each peptide bond
 Four Levels of Protein Structure
1. Primary structure
– Amino acids joined by peptide bonds form a linear polypeptide
chain

2. Secondary structure
– Polypeptide chains form sheets and coils

3. Tertiary structure
– Sheets and coils pack into functional domains

4. Quaternary structure
– Many proteins (e.g. enzymes) consist of two or more chains
 Four Levels of Protein Structure

Primary structure

Amino acids
Hydrogen
bond

Secondary structure

Alpha helix Pleated sheet

Tertiary structure Polypeptide

(single subunit
of transthyretin)

Transthyretin, with
Quaternary structure four identical
polypeptide subunits
 A protein’s shape depends on four
levels of structure
• The primary structure of a protein is its unique
amino acid sequence in polypeptide chain.
• The correct amino acid sequence is determined by the
cell’s genetic information
• The slightest change in this sequence affects the protein’s
ability to function
PRIMARY STRUCTURE
+H N
3
Amino end
Peptide bonds
connect amino acids. +
 A protein’s shape depends on four
levels of structure
• Protein secondary structure results from coiling or
folding of the polypeptide
• Coiling results in a helical structure called an alpha helix
• Folding may lead to a structure called a pleated sheet
• Coiling and folding result from hydrogen bonding between certain
areas of the polypeptide chain
Two types of
SECONDARY STRUCTURES Secondary structures Beta pleated sheet
are maintained by
Alpha helix hydrogen bonds
between atoms of
the backbone.
 A protein’s shape depends on four
levels of structure
The overall three-dimensional shape of a protein
is called its tertiary structure
• Tertiary structure generally results from
interactions between the R groups of the various
amino acids
• Disulfide bridges are covalent bonds that further
strengthen the protein’s shape
TERTIARY STRUCTURE

Tertiary structure is stabilized

by interactions between R
groups.
 A protein’s shape depends on four
levels of structure
Two or more polypeptide chains (subunits) associate
providing quaternary structure
• Collagen is an example of a protein with quaternary
structure
• Its triple helix gives great strength to connective tissue,
bone, tendons, and ligaments
QUATERNARY STRUCTURE
Polypeptides are associated
into a functional protein.
 PRIMARY STRUCTURE
+H N
3
Amino end
Peptide bonds
connect amino acids.
+

Two types of Secondary structures

SECONDARY STRUCTURES are maintained by Beta pleated sheet
Alpha helix hydrogen bonds
between atoms of
the backbone.

TERTIARY STRUCTURE

Tertiary structure is
stabilized by interactions
between R groups.

QUATERNARY STRUCTURE

Polypeptides are associated

into a functional protein.

© 2018 Pearson Education Ltd.

 The importance of protein structure
• The shape of a protein defines its biological
activities.
• If a protein unfolds and loses its three-dimensional
shape (denatures), it also loses its function
• One wrong amino acid in the polypeptide will cause
the whole protein to change to another protein.
• A few factors, such as heat, and shifts of pH, can
alter its shape (denaturation)
• Disrupts hydrogen bonds and other molecular interactions
responsible for protein’s shape
NUCLEIC ACIDS
 Nucleotide Functions:
Reproduction, Metabolism, and Survival
• The monomers that make up nucleic
acids are nucleotides.
• Nucleotides are composed
– a five-carbon sugar called ribose in RNA and
deoxyribose in DNA
– a phosphate group,
– a nitrogenous base.
 Nucleotide

Nitrogenous
base (A)

Phosphate
group

Sugar
Figure: A nucleotide, consisting of phosphate
group, sugar, and nitrogenous bases
Sugar-phosphate
backbone

Figure: Part of polynucleotide

 Nucleotide Functions:
Reproduction, Metabolism, and Survival
• DNA and RNAs are nucleic acids, each composed of
four kinds of nucleotide subunits
– DNA is a double helix while RNA is a single polynucleotide
chain.
– DNA and RNA serve as the blueprints for proteins and thus
control the life of a cell.
– DNA is the molecule of inheritance.
• ATP energizes many kinds of molecules by
phosphate-group transfers
• Other nucleotides function as coenzymes or as
chemical messengers
 Nucleic acids are information-rich
polymers of nucleotides
• DNA nitrogenous bases are adenine (A), thymine
(T), cytosine (C), and guanine (G)
• RNA also has A, C, and G, but instead of T, it has uracil
(U)
• A nucleic acid polymer, a polynucleotide, forms
from the nucleotide monomers when the
phosphate of one nucleotide bonds to the sugar
of the next nucleotide
• The result is a repeating sugar-phosphate backbone
with protruding nitrogenous bases
 Nucleic acids are information-rich
polymers of nucleotides
• Two polynucleotide strands
wrap around each other to
form a DNA double helix
• The two strands are
associated because particular Base
bases always hydrogen bond pair

to one another
Nitrogenous
• A pairs with T, and C pairs base (A)

with G, producing base pairs

• RNA is usually a single
polynucleotide strand
Figure: DNA double helix