BIO122

HISTOLOGY OF CELL AND TISSUE

CHAPTER 4: BIOLOGICAL MOLECULES

RAR 2019
 Chapter 4: Biological Molecules
• Course outline
4.1. FUNCTIONAL GROUPS
4.1.1. Hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, methyl
4.2. MACROMOLECULE (BASIC PROCESSES – CONDENSATION & HYDROLYSIS)
4.3. CARBOHYDRATES
4.3.1. Monosaccharides
4.3.2. Disaccharides
4.3.3. Polysaccharides
4.4. LIPIDS
4.4.1. Fatty acids and glycerol
4.4.2. Simple lipids (steroids, prostaglandins)
4.4.3. Complex lipids (triacylglycerol, phospholipids, sphingolipids, waxes)
4.5. PROTEINS
4.5.1. Amino acids, peptide formation, polypeptide chains, levels of protein structure (primary,
secondary, tertiary, quaternary), denaturation, renaturation
4.6. NUCLEIC ACIDS
4.6.1. Functions of nucleic acids, nucleotides, bases
4.6.2. Introduction to double helix (Watson-Crick model)
4.6.3. Types of RNA and functions (mRNA, tRNA, rRNA)

At the end of the study, student should be able to state and define concepts and principles in biology, basic
biochemistry and cytology
 Chapter 4: Biological molecules
Introduction
Carbon: The Backbone of Life

• Living organisms consist mostly of carbon-based compounds

• Carbon is unparalleled in its ability to form large, complex, and diverse

molecules

• Proteins, DNA, carbohydrates, and other molecules that distinguish living

matter are all composed of carbon compounds

• With four valence electrons, carbon can form four covalent bonds with a
variety of atoms

• This ability makes large, complex molecules possible

 Table 4.1 The shapes of three simple organic molecules.
Name and Molecular Structural Ball-and- Space-Filling
Comment Formula Formula Stick Model Model
(a) Methane

CH4

(b) Ethane

C2H6

(c) Ethene
(ethylene)
C2H4
 Chapter 4: Biological molecules
Introduction
• Organic chemistry is the study of compounds that contain carbon

• Organic compounds range from simple molecules to colossal ones

• Most organic compounds contain hydrogen atoms in addition to

carbon atoms
 Chapter 4: Biological Molecules
4.1. Functional Groups
A few chemical groups are key to the functioning of
biological molecules
• Distinctive properties of organic molecules depend
on the carbon skeleton and on the molecular
components attached to it

• A number of characteristic groups can replace the

hydrogens attached to skeletons of organic
molecules
 Chapter 4: Biological Molecules
4.1. Functional Groups
• Functional groups are the components of organic
molecules that are most commonly involved in
chemical reactions

• The number and arrangement of functional groups

give each molecule its unique properties
Estradiol
Testosterone
 Chapter 4: Biological Molecules
4.1. Functional Groups
• The seven functional groups that are most
important in the chemistry of life:
• Hydroxyl group
• Carbonyl group
• Carboxyl group
• Amino group
• Sulfhydryl group
• Phosphate group
• Methyl group
 Hydroxyl

STRUCTURE Alcohols NAME OF

(Their specific COMPOUND
names usually
(may be written end in -ol.)
HO—)

EXAMPLE • Is polar as a result FUNCTIONAL

of the electrons PROPERTIES
spending more
time near the
electronegative
oxygen atom.
Ethanol • Can form hydrogen
bonds with water
molecules, helping
dissolve organic
compounds such
as sugars.
 Carbonyl

STRUCTURE Ketones if the carbonyl NAME OF

group is within a COMPOUND
carbon skeleton
Aldehydes if the carbonyl
group is at the end of the
carbon skeleton

EXAMPLE • A ketone and an FUNCTIONAL

aldehyde may be PROPERTIES
structural isomers
with different properties,
as is the case for
acetone and propanal.
• Ketone and aldehyde
Acetone groups are also found
in sugars, giving rise
to two major groups
of sugars: ketoses
(containing ketone
groups) and aldoses
(containing aldehyde
Propanal groups).
 Carboxyl

STRUCTURE Carboxylic acids, or organic NAME OF

acids COMPOUND

EXAMPLE • Acts as an acid; can FUNCTIONAL

donate an H+ because the PROPERTIES
covalent bond between
oxygen and hydrogen is so
polar:

Acetic acid

Nonionized Ionized

• Found in cells in the ionized

form with a charge of 1– and
called a carboxylate ion.
 Amino

STRUCTURE Amines NAME OF

COMPOUND

EXAMPLE • Acts as a base; can FUNCTIONAL

pick up an H+ from the PROPERTIES
surrounding solution
(water, in living
organisms):

Glycine

Nonionized Ionized

• Found in cells in the

ionized form with a
charge of 1+.
 Sulfhydryl

STRUCTURE Thiols NAME OF

COMPOUND

(may be
written HS—)

EXAMPLE • Two sulfhydryl groups can FUNCTIONAL

react, forming a covalent PROPERTIES
bond. This “cross-linking”
helps stabilize protein
structure.

• Cross-linking of cysteines
in hair proteins maintains
the curliness or straightness
Cysteine
of hair. Straight hair can be
“permanently” curled by
shaping it around curlers
and then breaking and
re-forming the cross-linking
bonds.
 Phosphate

STRUCTURE Organic phosphates NAME OF

COMPOUND

EXAMPLE • Contributes negative FUNCTIONAL

charge to the molecule PROPERTIES
of which it is a part
(2– when at the end of
a molecule, as at left;
1– when located
internally in a chain of
phosphates).
Glycerol phosphate • Molecules containing
phosphate groups have
the potential to react
with water, releasing
energy.
 Methyl

STRUCTURE Methylated compounds NAME OF

COMPOUND

EXAMPLE • Addition of a methyl group FUNCTIONAL

to DNA, or to molecules PROPERTIES
bound to DNA, affects the
expression of genes.
• Arrangement of methyl
groups in male and female
sex hormones affects their
shape and function.
5-Methyl cytidine
CHEMICAL
GROUP Hydroxyl Carbonyl Carboxyl

STRUCTURE

(may be written HO—)

NAME OF Alcohols (Their specific names Ketones if the carbonyl group is Carboxylic acids, or organic acids
COMPOUND usually end in -ol.) within a carbon skeleton

Aldehydes if the carbonyl group

is at the end of the carbon skeleton

EXAMPLE

Ethanol Acetone Acetic acid

Propanal

FUNCTIONAL • Is polar as a result of the • A ketone and an aldehyde may be • Acts as an acid; can donate an
PROPERTIES electrons spending more time structural isomers with different H+ because the covalent bond
near the electronegative oxygen properties, as is the case for between oxygen and hydrogen
atom. acetone and propanal. is so polar:
• Can form hydrogen bonds with • Ketone and aldehyde groups are
water molecules, helping dissolve also found in sugars, giving rise
organic compounds such as to two major groups of sugars:
sugars. ketoses (containing ketone
groups) and aldoses (containing
aldehyde groups). Nonionized Ionized

• Found in cells in the ionized form

with a charge of 1− and called a
carboxylate ion.
 Amino Sulfhydryl Phosphate Methyl

(may be
written HS—)

Amines Thiols Organic phosphates Methylated compounds

Glycine Cysteine Glycerol phosphate 5-Methyl cytidine

• Acts as a base; can • Two sulfhydryl groups can • Contributes negative charge to • Addition of a methyl group
pick up an H+ from the react, forming a covalent the molecule of which it is a part to DNA, or to molecules
surrounding solution bond. This “cross-linking” (2– when at the end of a molecule, bound to DNA, affects the
(water, in living helps stabilize protein as above; 1– when located expression of genes.
organisms): structure. internally in a chain of • Arrangement of methyl
phosphates). groups in male and female
• Cross-linking of cysteines • Molecules containing phosphate sex hormones affects their
in hair proteins maintains groups have the potential to react shape and function.
the curliness or straightness with water, releasing energy.
of hair. Straight hair can be
Nonionized Ionized “permanently” curled by
shaping it around curlers
and then breaking and
• Found in cells in the re-forming the cross-linking
ionized form with a bonds.
charge of 1+.
 Chapter 4: Biological Molecules
• Course outline
4.1. FUNCTIONAL GROUPS
4.1.1. Hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, methyl
4.2. MACROMOLECULE (BASIC PROCESSES – CONDENSATION & HYDROLYSIS)
4.3. CARBOHYDRATES
4.3.1. Monosaccharides
4.3.2. Disaccharides
4.3.3. Polysaccharides
4.4. LIPIDS
4.4.1. Fatty acids and glycerol
4.4.2. Simple lipids (steroids, prostaglandins)
4.4.3. Complex lipids (triacylglycerol, phospholipids, sphingolipids, waxes)
4.5. PROTEINS
4.5.1. Amino acids, peptide formation, polypeptide chains, levels of protein structure (primary,
secondary, tertiary, quaternary), denaturation, renaturation
4.6. NUCLEIC ACIDS
4.6.1. Functions of nucleic acids, nucleotides, bases
4.6.2. Introduction to double helix (Watson-Crick model)
4.6.3. Types of RNA and functions (mRNA, tRNA, rRNA)

At the end of the study, student should be able to state and define concepts and principles in biology, basic
biochemistry and cytology
 Chapter 4: Biological Molecules
4.2. Macromolecules
The Molecules of Life

• All living things are made up of four classes of large

biological molecules:

• Carbohydrates
• Lipids
• Proteins
• Nucleic acids
 Chapter 4: Biological Molecules
4.2. Macromolecules
The Molecules of Life

• Macromolecules are large molecules composed of

thousands of covalently connected atoms

• Molecular structure and function are inseparable

 Chapter 4: Biological Molecules
Polymer
• 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
 Chapter 4: Biological Molecules
Polymer
• A dehydration reaction occurs when two monomers bond together
through the loss of a water molecule (Dehydration reaction:
synthesizing a polymer)

• Polymers are disassembled to monomers by hydrolysis, a reaction

that is essentially the reverse of the dehydration reaction.
(Hydrolysis: breaking down a polymer)
(a) Dehydration reaction: synthesizing a polymer

1 2 3

Short polymer Unlinked monomer

Dehydration removes
a water molecule,
forming a new bond.

1 2 3 4

Longer polymer
(b) Hydrolysis: breaking down a polymer

1 2 3 4

Hydrolysis adds
a water molecule,
breaking a bond.

1 2 3
 Chapter 4: Biological Molecules
• Course outline
4.1. FUNCTIONAL GROUPS
4.1.1. Hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, methyl
4.2. MACROMOLECULE (BASIC PROCESSES – CONDENSATION & HYDROLYSIS)
4.3. CARBOHYDRATES
4.3.1. Monosaccharides
4.3.2. Disaccharides
4.3.3. Polysaccharides
4.4. LIPIDS
4.4.1. Fatty acids and glycerol
4.4.2. Simple lipids (steroids, prostaglandins)
4.4.3. Complex lipids (triacylglycerol, phospholipids, sphingolipids, waxes)
4.5. PROTEINS
4.5.1. Amino acids, peptide formation, polypeptide chains, levels of protein structure (primary,
secondary, tertiary, quaternary), denaturation, renaturation
4.6. NUCLEIC ACIDS
4.6.1. Functions of nucleic acids, nucleotides, bases
4.6.2. Introduction to double helix (Watson-Crick model)
4.6.3. Types of RNA and functions (mRNA, tRNA, rRNA)

At the end of the study, student should be able to state and define concepts and principles in biology, basic
biochemistry and cytology
 Chapter 4: Biological Molecules
4.3. Carbohydrate

• Carbohydrates: substances found in food and living cells include

sugars and the polymers of sugars

• 3 main classes of carbohydrates:

1. Monosaccharides
2. Disaccharides
3. Polysaccharides

Function : storage and transport of energy

* Saccharide = sugar
 Chapter 4: Biological Molecules
4.3. Carbohydrate
• 1. Monosaccharides a carbohydrate that cannot be hydrolyzed
to a simpler carbohydrate

• they have the general formula CnH2nOn , where n varies from

3 to 8

• The simplest carbohydrates are monosaccharides, or single

sugars

• Example: sugar such as Glucose (C6H12O6), Galactose and

Fructose
Molecular structure of monosaccharide
• Monosaccharides are classified by :
• The location of the carbonyl group (as aldose or ketose)
• The number of carbons in the carbon skeleton

(a) The location of the carbonyl group (as aldose or ketose)

• aldose: a monosaccharide containing an aldehyde group
• ketose: a monosaccharide containing a ketone group

(b) The number of carbons in the carbon skeleton

Name Formula Number of carbon atoms

Triose C3H6O3
Tetrose C4H8O4
Pentose C 5 H 1 0 O5
Hexose C 6 H 1 2 O6
Heptose C 7 H 1 4 O7
Octose C 8 H 1 6 O8
Aldose (Aldehyde Sugar) Ketose (Ketone Sugar)
Trioses: 3-carbon sugars (C3H6O3)

Glyceraldehyde Dihydroxyacetone
Aldose (Aldehyde Sugar) Ketose (Ketone Sugar)
Pentoses: 5-carbon sugars (C5H10O5)

Ribose Ribulose
Aldose (Aldehyde Sugar) Ketose (Ketone Sugar)

Hexoses: 6-carbon sugars (C6H12O6)

Glucose Galactose Fructose

• Though often drawn as linear skeletons, in aqueous solutions many sugars form rings

1 6 6
2
5 5
3
4 1 4 1
4
2 2
5 3 3

(a) Linear and ring forms

6
5
4 1
3 2

(b) Abbreviated ring structure

 Chapter 4: Biological Molecules
4.3. Carbohydrate
• 2. disaccharide is a carbohydrate that is formed when two
monosaccharides are joined together by glycosidic linkage through
dehydration (the loss of sugar)

• General Formula= =C12H22O11

• Example:
- Maltose (glucose + glucose) = used in the production of alcohol by
fermentation.
- Lactose (galactose + glucose) = milk sugar found in milk.
- Sucrose (glucose + fructose) = found in table sugar and maple
syrup.
 1–4
glycosidic
1 linkage 4

Glucose Glucose Maltose

(a) Dehydration reaction in the synthesis of maltose

1–2
glycosidic
1 linkage 2

Glucose Fructose Sucrose

(b) Dehydration reaction in the synthesis of sucrose
Molecular structure of
disaccharide
 Chapter 4: Biological Molecules
4.3. Carbohydrate
• 3. Polysaccharides is a carbohydrate that can be decomposed by
hydrolysis into two or more molecules of monosaccharides.

General Formula: (C6H12O5)n

• The structure and function of a polysaccharide are determined by:

1- its sugar monomers
2- the positions of glycosidic linkages

• Polysaccharides can be divided into:

1- storage polysaccharides
2- structural polysaccharides
Molecular structure of polysaccharide
 Chapter 4: Biological Molecules
4.3. Carbohydrate
1- STORAGE POLYSACCHARIDES

• Starch, a storage polysaccharide in plants, consists entirely of

glucose monomers

• Plants store extra starch as granules within chloroplasts and

other plastids

• Example of starch are amylose and amylopectin

• Glycogen is a storage polysaccharide in animals

• Humans and other vertebrates store glycogen mainly in liver

and muscle cells
Chloroplast Starch granules
Amylopectin

Amylose
(a) Starch: 1 m
a plant polysaccharide

Mitochondria Glycogen granules

Glycogen
(b) Glycogen: 0.5 m
an animal polysaccharide
 Chapter 4: Biological Molecules
4.3. Carbohydrate
2- 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 ()
 4 1 4 1

 Glucose  Glucose

(a)  and  glucose ring structures

 1 4

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

1 4

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

 Chapter 4: Biological Molecules
4.3. Carbohydrate
• 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 wall Cellulose
microfibrils in a
plant cell wall
Microfibril

10 m

0.5 m

Cellulose
molecules

 Glucose
monomer
 Chapter 4: Biological Molecules
4.3. Carbohydrate
• 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
 Chapter 4: Biological Molecules
4.3. Carbohydrate
• Chitin, another structural polysaccharide, is found
in the exoskeleton of arthropods

• Chitin also provides structural support for the cell

walls of many fungi

• Chitin is also used as surgical thread

Chitin forms the exoskeleton
of arthropods.
Chitin is used to make a strong and flexible surgical
thread that decomposes after the wound or incision
heals.
 Chapter 4: Biological Molecules
4.3. Carbohydrate
Summary

Monosaccharides Disaccharides
• Example: • Example: sucrose, maltose
Glucose,
galactose, • Dehydration → Glycosidic linkage
fructose

• Carbonyl Polysaccharides
group: Aldose, • storage polysaccharides : starch (amylose,
ketose amylopectin), glycogen
• structural polysaccharides : cellulose, chitin
• Linear & ring • alpha () and beta () glucose
form
 Chapter 4: Biological Molecules
• Course outline
4.1. FUNCTIONAL GROUPS
4.1.1. Hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, methyl
4.2. MACROMOLECULE (BASIC PROCESSES – CONDENSATION & HYDROLYSIS)
4.3. CARBOHYDRATES
4.3.1. Monosaccharides
4.3.2. Disaccharides
4.3.3. Polysaccharides
4.4. LIPIDS
4.4.1. Fatty acids and glycerol
4.4.2. Simple lipids (steroids, prostaglandins)
4.4.3. Complex lipids (triacylglycerol, phospholipids, sphingolipids, waxes)
4.5. PROTEINS
4.5.1. Amino acids, peptide formation, polypeptide chains, levels of protein structure (primary,
secondary, tertiary, quaternary), denaturation, renaturation
4.6. NUCLEIC ACIDS
4.6.1. Functions of nucleic acids, nucleotides, bases
4.6.2. Introduction to double helix (Watson-Crick model)
4.6.3. Types of RNA and functions (mRNA, tRNA, rRNA)

At the end of the study, student should be able to state and define concepts and principles in biology, basic
biochemistry and cytology
 Chapter 4: Biological Molecules
4.4. Lipids
• Lipids are a diverse group of hydrophobic molecules

• Lipids are the one class of large biological molecules that do not form polymers

• Lipids are hydrophobic because they consist mostly of hydrocarbons, which form
nonpolar covalent bonds

• 3 groups of Lipids:
1- Fats (fatty acid and glycerol)
2- simple lipids (steroids and prostaglandins)
3- complex lipids (triacylglycerol, phospholipids, sphingolipids, waxes)

Functions of Lipids:
1. Energy storage
2. Cell membrane formation
 Chapter 4: Biological Molecules
4.4. Lipids
1- FATS (fatty acid and glycerol)

• 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
 Chapter 4: Biological Molecules
4.4. Lipids
• Functions of fatty acids:
1. As building blocks of phospholipid in cell membrane
2. As messenger molecules where products of fatty acids used as
hormones and messenger molecules.

• Functions of glycerol:

1. Used as food additives and sweeteners

2. Used in skin care products, shaving cream, hair care products.
 Fatty acid
(in this case, palmitic acid)

Glycerol
(a) One of three dehydration reactions in the synthesis of a fat
 Chapter 4: Biological Molecules
4.4. Lipids
• Fats insoluble in 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
 Glycerol
Ester linkage Fatty acid

(b) Fat molecule (triacylglycerol)

 Chapter 4: Biological Molecules
4.4. Lipids
❖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
 Chapter 4: Biological Molecules
4.4. Lipids
The “tail” of a fatty acid is a long hydrocarbon chain, making it hydrophobic.
The “head” of the molecule is a carboxyl group which is hydrophilic.
(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
Cis double bond
causes bending.
Chapter 4: Biological Molecules
4.4. Lipids
 Chapter 4: Biological Molecules
4.4. Lipids
• 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

 Chapter 4: Biological Molecules
4.4. Lipids
• 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
 Chapter 4: Biological Molecules
4.4. Lipids
• Certain unsaturated fatty acids are not synthesized
in the human body

• These must be supplied in the diet

• These essential fatty acids include the omega-3

fatty acids, required for normal growth, and
thought to provide protection against
cardiovascular disease
 Chapter 4: Biological Molecules
4.4. Lipids
• 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
Differences between saturated and unsaturated fats
SATURATED FAT UNSATURATED FAT

Saturated with hydrogen

atoms and does not
Contains double bonds in
contain double bonds
the hydrocarbons of their
between carbon atoms in
fatty acids
Chemical Structure the hydrocarbons of their
fatty acids

Maximum number of
Fewer hydrogen atoms
hydrogen atoms

Solid at room Liquid at room

Physical Structure temperature temperature
- fats - oils
 Chapter 4: Biological Molecules
4.4. Lipids
2- simple lipids (steroids and prostaglandins)
❖Steroids

• Steroids are lipids characterized by a carbon skeleton consisting of four fused rings

• Example:
- Cholesterol, an important steroid, (is a component in animal cell membranes)
- hormones

• Although cholesterol is essential in animals, high levels in the blood may contribute to
cardiovascular disease

• Functions:
1- help control metabolism
2- regulate immune response,
MOLECULAR STRUCTURE OF
CHOLESTEROL
 Chapter 4: Biological Molecules
4.4. Lipids
❖prostaglandins

• Prostaglandins are a group of lipid compounds that are made of fatty acids

• Example: prostaglandin E2 (PGE2) and prostaglandin F2 (PGF2 ).

• Functions:
1- maintenance of tissues such as the lining of the stomach
2- help in blood clotting
3- control of blood pressure

• each prostaglandin is named using the prefix 'PG‘.

MOLECULAR STRUCTURE OF PROSTAGLANDIN
 Chapter 4: Biological Molecules
4.4. Lipids
3- complex lipids (triacylglycerol, phospholipids,
sphingolipids, waxes)

❖Phospholipid

• 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
 Chapter 4: Biological Molecules
4.4. Lipids
• Importance/Functions of Phospholipids:
 Choline
Hydrophilic head

Phosphate

Glycerol
Hydrophobic tails

Fatty acids

Hydrophilic
head

Hydrophobic
tails

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

 Choline

Hydrophilic head
Phosphate

Glycerol
Hydrophobic tails

Fatty acids

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

 Chapter 4: Biological Molecules
4.4. Lipids
Phospholipid

• 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
tail WATER
 Chapter 4: Biological Molecules
4.4 Lipids
❖Sphingolipids

• Sphingolipids are a class of lipids with a polar head group and two nonpolar
tails.

• The core of a sphingolipid is an amino alcohol called sphingosine.

• A fatty acid is attached to the amine through amide bond.

• Sphingolipids found in cell membranes, particularly nerve cells and brain tissues.

• Functions of Sphingolipids:
1. Involve in signal transmission
2. Help in cell recognition.

Example: Ceramides (found in within the cell membrane of cells).

Chapter 4: Biological Molecules
4.4 Lipids
 Chapter 4: Biological Molecules
4.4 Lipids
❖Waxes

• A wax is a simple lipid which is an ester of a long-chain

alcohol and a fatty acid.
• The alcohol may contain from 12-32 carbon atoms.

• Examples and Functions of Wax:

1. Carnuba wax is found on the leaves of Brazilian palm
trees and is used in floor and automobile waxes.
2. Beeswax is secreted by bees to make cells for honey and
eggs.
3. Spermaceti wax is found in the fats of the sperm whale.
Chapter 4: Biological Molecules
4.4 Lipids
Chapter 4: Biological Molecules
4.4 Lipids
Chapter 4: Biological Molecules
4.4 Lipids
 Chapter 4: Biological Molecules
• Course outline
4.1. FUNCTIONAL GROUPS
4.1.1. Hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, methyl
4.2. MACROMOLECULE (BASIC PROCESSES – CONDENSATION & HYDROLYSIS)
4.3. CARBOHYDRATES
4.3.1. Monosaccharides
4.3.2. Disaccharides
4.3.3. Polysaccharides
4.4. LIPIDS
4.4.1. Fatty acids and glycerol
4.4.2. Simple lipids (steroids, prostaglandins)
4.4.3. Complex lipids (triacylglycerol, phospholipids, sphingolipids, waxes)
4.5. PROTEINS
4.5.1. Amino acids, peptide formation, polypeptide chains, levels of protein structure (primary,
secondary, tertiary, quaternary), denaturation, renaturation
4.6. NUCLEIC ACIDS
4.6.1. Functions of nucleic acids, nucleotides, bases
4.6.2. Introduction to double helix (Watson-Crick model)
4.6.3. Types of RNA and functions (mRNA, tRNA, rRNA)

At the end of the study, student should be able to state and define concepts and principles in biology, basic
biochemistry and cytology
 Chapter 4: Biological Molecules
4.5. Protein
• A protein is a biological molecule that consists of one or more
polypeptides

• Protein molecules are made up of hydrogen, carbon, oxygen,

nitrogen and other elements

• Polypeptides are polymers built from the same set of 20 amino acids

• Amino acids are organic molecules with carboxyl group and amino
group

• The properties of Amino acids depends on their side chains, called R

groups
PROTEIN STRUCTURE

Polypeptide Chain

Amino acid
 Chapter 4: Biological Molecules
4.5. Amino Acid Structure
 carbon
Side chain (R group)

Amino
group Carboxyl
group
Nonpolar side chains; hydrophobic
Side chain

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 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)
 Chapter 4: Biological Molecules
4.5. Protein
How Protein is formed (peptide bond formation):
• A polypeptide is a polymer of amino acids

• Amino acids are linked by peptide bonds

• Polypeptides range in length from a few to more than a thousand

monomers

• Each polypeptide has a unique linear sequence of amino acids, with a

carboxyl end (C-terminus) and an amino end (N-terminus)
 Peptide bond

New peptide
bond forming

Side
chains

Back-
bone

Amino end Peptide Carboxyl end

(N-terminus) bond (C-terminus)
PEPTIDE BOND FORMATION
 Chapter 4: Biological Molecules
4.5. Protein Structure
• A functional protein consists of one or more polypeptides precisely
twisted, folded, and coiled into a unique shape

Groove

Groove

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

 Chapter 4: Biological Molecules
4.5. Protein Structure
• A protein’s structure determines its function

• The sequence of amino acids determines a protein’s three-

dimensional structure
Antibody protein Protein from flu virus
 Chapter 4: Biological Molecules
4.5. Protein Structure
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
Four Levels of
Protein Structure
 Chapter 4: Biological Molecules
4.5. Protein Structure
❑Primary structure

• The sequence of amino acids in a protein, is like the order of letters

in a long word
 Chapter 4: Biological Molecules
4.5. Protein Structure
❑Secondary structure

• The coils and folds of secondary structure result from hydrogen

bonds between repeating components of the polypeptide backbone

• Typical secondary structures are a coil called an  helix and a folded

structure called a  pleated sheet
 Secondary structure

 helix

Hydrogen bond
 pleated sheet

 strand, shown as a flat

arrow pointing toward
the carboxyl end

Hydrogen bond
 Chapter 4: Biological Molecules
4.5. Protein Structure
❑Tertiary structure

• Tertiary structure is determined by interactions between R groups,

rather than interactions between backbone components

• 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
 Hydrogen
bond
Hydrophobic
interactions and
van der Waals
interactions
Disulfide
bridge
Ionic bond

Polypeptide
backbone
 Chapter 4: Biological Molecules
4.5. Protein Structure
❑Quaternary structure
• Quaternary structure results when two or more polypeptide chains
form one macromolecule or one protein
 Chapter 4: Biological Molecules
4.5. Protein Structure
❑Quaternary structure
• Example: Collagen is a fibrous protein consisting of three
polypeptides coiled like a rope Collagen

Example: Hemoglobin is a globular protein consisting of four

polypeptides: two alpha and two beta subunits
 Heme
Iron
 subunit

 subunit

 subunit

 subunit

Hemoglobin
 Chapter 4: Biological Molecules
4.5. Protein Denaturation and
Renaturation

• Denaturation = this process changes the shape of a protein without

breaking its peptide bonds

• Renaturation = this process is where a protein folds back into its

original shape (also known as ‘reconfiguration’)
Chapter 4: Biological Molecules
4.5. Protein Denaturation and
Renaturation
Chapter 4: Biological Molecules
4.5. Protein Denaturation and
Renaturation
Chapter 4: Biological Molecules
4.5. Protein Denaturation and
Renaturation
Denaturation agents:

1. Heat
e.g: fry eggs, heating water

2. Mechanical treatment
e.g: beating eggs and kneading bread

3. Very high or very low pH

e.g: adding lemon juice for example can sour milk, causing the milk to
separate from the liquid – forming curds (solid substance of sour milk)
and whey (liquid substance of sour milk)
 Chapter 4: Biological Molecules
Protein Types and Functions /
Importance
Protein functions/importance include:

1. Structural support
2. Storage
3. Transport
4. Response of cell to chemical stimuli
5. Coordination of organism’s activities
6. Movement
7. Defense against foreign substances
8. Speed up chemical reaction
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
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
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
Signaling protein
molecules
Hormonal proteins
Function: Coordination of an organism’s 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
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
100 m
Defensive proteins
Function: Protection against disease
Example: Antibodies inactivate and help destroy
viruses and bacteria.

Antibodies

Virus Bacterium
Enzymatic proteins
Function: Selective acceleration of chemical reactions
Example: Digestive enzymes catalyze the hydrolysis
of bonds in food molecules.

Enzyme
 Chapter 4: Biological Molecules
• Course outline
4.1. FUNCTIONAL GROUPS
4.1.1. Hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, methyl
4.2. MACROMOLECULE (BASIC PROCESSES – CONDENSATION & HYDROLYSIS)
4.3. CARBOHYDRATES
4.3.1. Monosaccharides
4.3.2. Disaccharides
4.3.3. Polysaccharides
4.4. LIPIDS
4.4.1. Fatty acids and glycerol
4.4.2. Simple lipids (steroids, prostaglandins)
4.4.3. Complex lipids (triacylglycerol, phospholipids, sphingolipids, waxes)
4.5. PROTEINS
4.5.1. Amino acids, peptide formation, polypeptide chains, levels of protein structure (primary,
secondary, tertiary, quaternary), denaturation, renaturation
4.6. NUCLEIC ACIDS
4.6.1. Functions of nucleic acids, nucleotides, bases
4.6.2. Introduction to double helix (Watson-Crick model)
4.6.3. Types of RNA and functions (mRNA, tRNA, rRNA)

At the end of the study, student should be able to state and define concepts and principles in biology, basic
biochemistry and cytology
 Chapter 4: Biological Molecules
4.6. Nucleic Acid
Nucleic acids are:
• large molecules consisting of long chains of monomers called
nucleotides.
• Example: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).

The Components 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,
• one or more phosphate groups
nucleotide

125
 Chapter 4: Biological Molecules
Nucleic Acid
• The portion of a nucleotide without the phosphate
group is called a nucleoside

• Nucleotide = nitrogenous base + sugar + phosphate

group

• Nucleoside = nitrogenous base + sugar

• In DNA, the sugar is deoxyribose

• in RNA, the sugar is ribose
NUCLEOTIDE AND NUCLEOSIDE
 Chapter 4: Biological Molecules
Nucleic Acid
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
 Sugar-phosphate backbone
5 end
5C

3C

Nucleoside

Nitrogenous
base

5C

1C
Phosphate 3C
5C group Sugar
(pentose)
3C (b) Nucleotide

3 end
(a) Polynucleotide, or nucleic acid
 Chapter 4: Biological Molecules
Nucleic Acid
• There are two families of nitrogenous bases

• Pyrimidines [cytosine (C), thymine (T), and uracil

(U)] have a single six-membered ring

• Purines [adenine (A) and guanine (G)] have a six-

membered ring fused to a five-membered ring
 Nitrogen Bases
The nitrogen bases in
DNA and RNA are:

• pyrimidines C, T, and U.
• purines A and G.

131
 Nitrogenous bases
Pyrimidines

Cytosine Thymine Uracil

(C) (T, in DNA) (U, in RNA)
Sugars
Purines

Deoxyribose Ribose
Adenine (A) Guanine (G) (in DNA) (in RNA)

(c) Nucleoside components

Nitrogen-Containing Bases in DNA and RNA
DNA contains the nitrogen bases
• Cytosine (C)
• Guanine (G) same in both DNA and RNA
• Adenine (A)
• Thymine (T) different in DNA than RNA

RNA contains the nitrogen bases

• Cytosine (C)
• Guanine (G) same in both DNA and RNA
• Adenine (A)
• Uracil (U) different in DNA than RNA

133
 Pentose Sugars
The pentose (five-carbon) sugar
• in RNA is ribose.
• in DNA is deoxyribose with no O atom on carbon 2’.
• has carbon atoms numbered with primes to distinguish them from the
atoms in nitrogen bases.

134
 Nucleosides
A nucleoside
• has a nitrogen base linked by a
glycosidic bond to C1’ of a sugar
(ribose or deoxyribose).

• is named by changing the the

nitrogen base ending to -osine for
purines and
–idine for pyrimidines.

135
 Nucleotides
A nucleotide
• is a nucleoside that forms a
phosphate ester with the C5’ –
OH group of a sugar (ribose or
deoxyribose).
• is named using the name of the
nucleoside followed by
5’-monophosphate.

136
 Formation of a Nucleotide

A nucleotide forms when the −OH on C5’ of a

sugar bonds to phosphoric acid.
NH2 NH2

N N

O 5’ O N
O 5’ O N
O- P OH + HO CH2 O- P O CH2
O O
-
O- O

OH OH

deoxycytidine and phosphate deoxycytidine monophosphate (dCMP)

137
Nucleosides and Nucleotides with Purines

138
Nucleosides and Nucleotides with
Pyrimidines

139
Names of Nucleosides and Nucleotides

140
 Chapter 4: Biological Molecules
Nucleic Acid
❖Functions of nucleic acids:
1. to store and transmit genetic information
2. To synthesize of new protein

❖ Functions of nucleotides:
1. to form the nucleic acids ribonucleic acid (RNA) and
deoxyribonucleic acid (DNA)
2. Involve in cell signaling and metabolism

❖ Functions of bases:
1. To construct nucleotides
Learning Check
Give the name and abbreviation for the following and list its
nitrogen base and sugar.

142
Primary Structure of Nucleic Acids
In the primary structure of nucleic acids

• nucleotides are joined by phosphodiester bonds.

• the 3’-OH group of the sugar in one nucleotide forms an ester

bond to the phosphate group on the 5’-carbon of the sugar of
the next nucleotide.

143
Primary Structure of Nucleic Acids

144
 Structure of Nucleic Acids
A nucleic acid
• has a free 5’-phosphate group at
one end and a free 3’-OH group at
the other end.
• is read from the free 5’-end using
the letters of the bases.
• This example reads
—A—C—G—T—.

145
 Example of RNA Structure
The primary structure
of RNA,
• is a single strand of
nucleotides with bases A,
C, G, and U.
• is linked by
phosophodiester bonds
between ribose and
phosphate.

Copyright © 2005 by Pearson Education, Inc.

Publishing as Benjamin Cummings

146
 Chapter 4: Biological Molecules
• Course outline
4.1. FUNCTIONAL GROUPS
4.1.1. Hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, methyl
4.2. MACROMOLECULE (BASIC PROCESSES – CONDENSATION & HYDROLYSIS)
4.3. CARBOHYDRATES
4.3.1. Monosaccharides
4.3.2. Disaccharides
4.3.3. Polysaccharides
4.4. LIPIDS
4.4.1. Fatty acids and glycerol
4.4.2. Simple lipids (steroids, prostaglandins)
4.4.3. Complex lipids (triacylglycerol, phospholipids, sphingolipids, waxes)
4.5. PROTEINS
4.5.1. Amino acids, peptide formation, polypeptide chains, levels of protein structure (primary,
secondary, tertiary, quaternary), denaturation, renaturation
4.6. NUCLEIC ACIDS
4.6.1. Functions of nucleic acids, nucleotides, bases
4.6.2. Introduction to double helix (Watson-Crick model)
4.6.3. Types of RNA and functions (mRNA, tRNA, rRNA)

At the end of the study, student should be able to state and define concepts and principles in biology, basic
biochemistry and cytology
Chapter 4: Biological Molecules
Introduction to Double Helix
DNA Double Helix

Copyright © 2005 by Pearson Education, Inc.

Publishing as Benjamin Cummings

148
 Example of DNA
In DNA,
• nucleotides
containing bases A, C,
G, and T are linked by
ester bonds between
deoxyribose sugars
and phosphate
groups.

Copyright © 2005 by Pearson Education, Inc.

Publishing as Benjamin Cummings

149
 DNA Double Helix
A double helix
• is the structure of DNA.
• has two strands of nucleotides that wind together.
• is held in place by of two hydrogen bonds that form between the
base pairs A-T.
• is held in place by three hydrogen bonds that form between the
base pairs G-C.

150
Complementary Base Pairs
DNA contains complementary base pairs in which
• Adenine is always linked by two hydrogen bonds
with thymine (A−T).
• Guanine is always linked by three hydrogen with
Cytosine (G−C).

151
Double Helix of DNA

In the double helix of DNA

• two strands of nucleotides form
a double helix structure like a
spiral stair case.
• hydrogen bonds link bases A–T
and G–C.
• the bases along one strand
complement the bases along
the other.

Copyright © 2005 by Pearson Education, Inc.

Publishing as Benjamin Cummings

152
Learning Check
Write the complementary base sequence for the matching strand in
the following DNA section:

—A—G—T—C—C—A—A—T—C—

153
DNA Replication

In DNA replication
• genetic information is maintained
each time a cell divides.
• the DNA strands unwind.
• each parent strand bonds with new
complementary bases.
• two new DNA strands form that
are exact copies of the original
DNA.

Copyright © 2005 by Pearson

Education, Inc.
Publishing as Benjamin
Cummings

154
Chapter 4: Biological Molecules
RNA

Copyright © 2005 by Pearson Education, Inc.

Publishing as Benjamin Cummings

155
 Chapter 4: Biological Molecules
Types of RNA and Functions
RNA
• transmits information from DNA to make proteins.
• has several types:
1. Messenger RNA (mRNA) carries genetic information from DNA to
the ribosomes.
2. Transfer RNA (tRNA) brings amino acids to the ribosome to make
the protein.
3. Ribosomal RNA (rRNA) makes up 2/3 of ribosomes where protein
synthesis takes place.

156
Types of RNA

157
 Chapter 4: Biological Molecules
4.6. Nucleic Acid
• 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 made of monomers called

nucleotides

• DNA directs synthesis of messenger RNA (mRNA) and, through

mRNA, controls protein synthesis

• Protein synthesis occurs in ribosomes

Figure 5.25-1
DNA

1 Synthesis of
mRNA
mRNA

NUCLEUS
CYTOPLASM
Figure 5.25-2
DNA

1 Synthesis of
mRNA
mRNA

NUCLEUS
CYTOPLASM

mRNA
2 Movement of
mRNA into
cytoplasm
Figure 5.25-3
DNA

1 Synthesis of
mRNA
mRNA

NUCLEUS
CYTOPLASM

mRNA
2 Movement of
mRNA into Ribosome
cytoplasm

3 Synthesis
of protein

Amino
Polypeptide acids
 Chapter 4: Biological Molecules
4.6. Nucleic Acid
The Structures of DNA and RNA Molecules
• RNA molecules usually exist as single polypeptide chains

• DNA molecules have 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

 Chapter 4: Biological Molecules
4.6. Nucleic Acid
The Structures of DNA and RNA Molecules
• The nitrogenous bases in DNA pair up and form hydrogen bonds:
adenine (A) always with thymine (T), and guanine (G) always with
cytosine (C)

• Called complementary base pairing

• Complementary pairing can also occur between two RNA molecules or

between parts of the same molecule

• In RNA, thymine is replaced by uracil (U) so A and U pair

5 3 Sugar-phosphate
backbones
Hydrogen bonds

Base pair joined

by hydrogen
bonding

3 5 Base pair joined

by hydrogen bonding
(a) DNA (b) Transfer RNA
 Chapter 4: Biological Molecules
DNA vs RNA
DNA RNA
Type of sugar Deoxyribose Ribose
Double stranded Single stranded
Number of strands
(Double helix) (Single helix)
Adenine, Cytosine, Adenine, Cytosine,
Nitrogenous Bases Guanine and Guanine and
Thymine Uracil
Location in cell Nucleus Nucleus & Cytoplasm
Chapter 4: Biological Molecules
DNA vs RNA
Chapter 4: Biological Molecules
Summary
Nucleus

(ER)

(Nuclear
envelope)
Nucleus

(ER)
(Nuclear
envelope)