CHAPTER 4

BIOLOGICAL MOLECULES
Carbon-based life forms
• Living organisms =
Carbon- based life
forms or
Organic life forms.

• Carbon= basic building

block for life forms.
 Functional Groups
• Components of organic molecules – involved in chemical
reactions.
• Each functional group = consistently found in each organic
molecule.
• Number and arrangement = organic molecules unique
properties.
• Example Testosterone – male sex hormone and estradiol
(estrogen) – female sex hormone
• Six functional groups
most important in the
chemistry of life:
1. Hydroxyl
2. Carbonyl
3. Carboxyl
4. Amino
5. Sulfhydryl
6. Phosphate
• These groups are
hydrophilic and
increase solubility of
organic compounds in
water.
 Macromolecules
• Large biological molecules.
• Four classes:
 carbohydrates,
 lipids,
 proteins,
 nucleic acids
• Exist as polymer : long molecules consist of
similar / identical repeating units (monomers)
linked by covalent bonds.
• Monomer = building blocks of a polymer.
The Synthesis of Polymers
• Monomers are connected by a reaction in which two molecules
are covalently bonded to each other through loss of a water
molecule – condensation reaction (dehydration reaction)
• Each monomer contributes a hydroxyl group (OH) and a
hydrogen (H) that will form water molecule
• The reaction requires energy, with the help of enzymes to speed
up the reaction
The Breakdown of Polymers
• Involved hydrolysis process : to break with water
• Bonds between monomers are broken by the addition of
water molecules, with the help of enzymes to speed up
the reactions
 Carbohydrates
• Include both sugars and polymers of sugars
• Sugars, starches and cellulose are carbohydrates
• Simplest carbohydrates : monosaccharides
• Double sugars : disaccharides – consisting of two
monosaccharides joined by a condensation reaction
• Macromolecules : polysaccharides

Monosaccharides
• Formula molecule : CnH2nOn
• Example : Glucose (C6H12O6)
• 2 groups : aldose and ketose – depending on the location
of the carbonyl group
• Example : Glucose is an aldose and fructose is a structural
isomer of glucose is a ketose
• The name or sugars end up with –ose
• Sugars that have three carbons called trioses; have five
cabons called pentoses; six carbons called hexoses
• In aqueous solutions, glucose molecules as well as other
sugars form rings
Disaccharide
• Consists of two monosaccharides joined by a
glycosidic linkage – a covalent bond formed between
two molecules by a dehydration reaction
• Example:
Glucose + glucose  Maltose
(Malt sugar in
brewing beer)
Glucose + fructose  Sucrose
(Table sugar)
Glucose + galactose  Lactose
(sugar in milk)
Polysaccharides
• Macromolecules, polymers with a few hundred to a few
thousand monosaccharides joined by glycosidic linkages
• Serve as storage material, hydrolyzed to provide sugar for
cells and building material
Storage Polysaccharides
• Starch
Storage in plants. Consists entirely of glucose monomers
which is joined by 14 linkages.
2 simplest form starch
amylose – unbranched
amilopectin – branch with 16 linkages at the branch points.
Plants store starch as granules within cellular structures called
plastids which include chloroplasts.
• Glycogen
Similar to amylopectin but more extensively branched.
Storage polysaccharide in human and other vertebrates
mainly in liver and muscle cells.
Structural polysaccharides
• Cellulose
The most abundant organic compound on Earth. Major
component of the tough walls that enclose plant cells. A
polymer of glucose but the glycosidic linkages in these two
polymers differ.
Forms from two ring forms for glucose called:  and 
In starch, all glucose monomers are in  configuration and in
cellulose, all glucose monomers are in  configuration.
Chitin
• Used by arthropods (insects, spiders,
crustaceans and related animals) to build their
exoskeleton
• Exoskeleton : a hard case that surrounds the
soft part of an animal NH

• Also found in many fungi cell wall C=O

• Chitin is similar to cellulose except that the CH3
glucose monomer of chitin had a nitrogen-
containing appendage
 Lipid
•Soluble in nonpolar substance (ex. Ether
and chloroform) and insoluble in water
•These properties are caused by the
molecule having mainly of carbon and
hydrogen with few oxygen-containing
functional group
•Therefore lipids tend to be hydrophobic:
little or no affinity for water
•Types of lipid : fats, phospholipids,
waxes and steroids
Fats - Triacylglycerol
•Form from smaller molecules by three dehydration reactions
•Consists of three fatty acids + one glycerol (example of complex
lipid)
•Fat molecule is build from three fatty acids molecules each join to
glycerol by an ester linkage, a bond between a hydroxyl group and
a carboxyl group.
•The reaction also involves the removal of three water molecules
• Fatty acids vary in length and in the number and locations of
double bonds
• 2 types : saturated and unsaturated fats
• Saturated fatty acid : No double bonds between carbon
atoms composing the chain, it is saturated with hydrogen
• Unsaturated fatty acid : has one or more double bonds, form
by the removal of hydrogen atoms from the carbon skeleton
Saturated fat
• Mostly animal fats
• Solid at room temperature
Example : butter
• High melting point

Unsaturated fat
• Mostly from plants and fishes
• Liquid at room temperature
Example : Olive oil, cod liver oil
• Low melting point
• The kinks where the cis double bond are located prevent the
molecule from packing closely enough to solidify at room
temperature
• Major function of fats is energy storage
A gram of fat stores more than twice as
much energy as a gram of
polysaccharide

• In human fat is deposited in adipose

cells as a storage energy and also
cushions such vital organs as the
kidneys and as an insulator under the
skin
 Simple Lipids
Steroids
• A carbon skeleton consisting of four fused rings
• Among the steroids of biological importance are cholesterol,
bile salts, reproductive hormones and cortisol and other
hormones secreted by adrenal cortex
• Cholesterol : common components of animal cell
membranes and is also a precursor from which other
steroids are synthesized, example : sex hormones
Prostaglandins

•It is an unsaturated carboxylic acids, consisting of a 20 carbon

skeleton that also contains a five member ring. They are
biochemically synthesized from the fatty acid, arachidonic acid.
•Activation of the inflammatory response, production of pain, and
fever, form blood clot and some involved with the induction of
labor
 Complex Lipids
Phospholipids
• Similar to fat but only has two
fatty acids attached to glycerol
• The third hydroxyl group of
glycerol is joined to a
phosphate group which has a
negative electrical charge
• Additional small molecules
usually charged or polar can be
linked to the phosphate group
to form a variety of
phospholipids
Sphingolipids
A group of lipids that are abundant in brain and nerve
tissue. Its three-carbon backbone is sphingosine, a
nitrogen-containing alcohol (amino alcohol).
It is an amphipathic molecule – having a polar head group
and two nonpolar fatty acid tails.
It contains : sphingosine backbone, the amide of a fatty acid
which is linked to the sphingosine molecule by an amide
linkage and a polar molecule.
Waxes
Texture is harder and less greasy than fats.
Less dense than water and are soluble in alcohol and
ether.
Solid in room temperature.
Found naturally as coating on fruits, leaves, insect
exoskeleton (water retaining), birds gland that produced
wax for feathers (water repelling).
 Protein

• 50% of the dry mass of most cells

• Functions: speed up chemical reactions, structural
support, storage, transport, cellular communications,
movement and defense against foreign substances.
• Most important type of protein : enzymes – regulate
metabolism by acting as catalysts, chemical agents
that selectively speed up chemical reactions in the cell
without being consumed by the reaction
Polypeptides
• Polymers of amino acids are called polypeptides
• A protein consists of one or more polypeptides folded and coiled
into specific conformations
Amino acid monomer side chain

R  carbon
H O
NCC
H OH
amino H carboxyl
group group

• the physical and chemical properties of the side chain determine

the unique characteristics of a particular amino acid
• Amino acid are grouped according to the properties of their side chains
1. Nonpolar group : hydrophohic
2. Polar group : hydrophilic
3. Electrically charged group : acidic amino acid (negatively
charged)
basic amino acid (positively
charged)
- both are hydrophilic
Amino acid polymers
Protein Conformation and Function

• A protein specific conformation determines how it works

• The function of the protein depends on its ability to recognize and
bind to some other molecule

Conformation of a protein, the enzyme lysozyme

The Primary Structure of a Protein

• Primary structure is represented in a simple,

linear form
• Example : Transthyretin – a globular protein
found in the blood that transport vitamin A
and a particular thyroid hormone throughout
the body
• Four identical polypeptide chains make it
composed of 127 amino acids
The Secondary Structure of a
Protein

•Composed of coils and folds of

polypeptide protein
•Hydrogen bonds linked the
repeating constituents of the
polypeptide backbone.
•These hydrogen bonds are weak,
because it is repeated so many
times over a relatively long region of
the polypeptide chain, they can
support a particular shape for that
part of the protein
•The bond formed between the
weakly positive hydrogen atom
attached to the nitrogen atom and
oxygen atom of a nearby peptide
bond
 helix
A delicate coil held together by hydrogen
bonding between every fourth amino acid
Example :  keratin – the structural protein
of hair, hairs, nails and wool

 pleated sheet
Two or more regions of the polypeptide
chain lying side by side are connected by
hydrogen bonds between parts of the two parallel
polypeptide backbones.
Example : silk protein of a spider’s web
The Tertiary Structure of a Protein
• Involved the interactions between the side chains (R group)
• Hydrophobic interaction : caused by the action of water
molecules, which exclude nonpolar substances as they form
hydrogen bonds with each other and with hydrophilic part of the
protein. Van der Waals interaction holds amino acid chain close
together.
• Hydrogen bonds will occur between the polar amino acid side
chains.
• Ionic bond : formed between
positively and negatively
charged side chains stabilize the
structure
These are all weak interactions,
but give a cumulative effects to
the shape of protein.
• Disulfide bridge : a covalent
bond between amino acids with
sulfhydryl groups at their side
chains
The Quaternary Structure of Proteins

• Include overall protein structure that results from the aggregation of

these polypeptide subunits
• Example :
Collagen : a fibrous protein that has helical subunits intertwined into
a larger triple helix giving the long fibers great strength
Hemoglobin : consists of four polypeptide subunits, two of one kind
( chains) and two of another kind ( chains)
• Each subunit has a nonpolypeptide component called heme with an
iron atom that binds oxygen
Review: the four levels of protein structure
What determines protein conformation?
• A polypeptide chain of a given amino acid sequence can
spontaneously arrange itself into a three-dimensional shape
determined and maintained by the interactions responsible for
secondary and tertiary structure
• Protein conformation depends of the physical and chemical
conditions of the protein’s environment
• If the pH, salt concentration, temperature or other aspect of its
environment are altered, the protein may unravel and lose its
native conformation, a condition called as denaturation
• A denatured protein is biologically inactive
• Denaturation can be caused by:
1. a transfer from an aqueous environment to an organic
environment
2. chemicals that disrupt the hydrogen bonds, ionic bonds
and disulfide bridges that maintain a protein shape
3. excessive heat

• Denatured protein (by heat or chemicals) will often returned to its

functional shape when the denaturing agent is removed
 Nucleic Acid

• Two types of nucleic acids : deoxyribonucleic acid (DNA) and

ribonucleic acid (RNA)
• These molecules enable living organisms to reproduce their
complex components from one generation to the next
• DNA provides directions for its own replication, directs RNA
synthesis and control protein synthesis
• DNA is the genetic material that organisms inherit from their
parents
• Each chromosome contains one long DNA molecule
• DNA encoded the information that program all the cells activities
• Each gene along the length of a DNA molecule directs the
synthesis of a type of RNA called messenger RNA (mRNA)
• The flow of genetic information: DNA  RNA  protein
• The actual site of
protein synthesis are
ribosomes which
located in cytoplasm
• In eukaryotic cells,
mRNA conveys the
genetic instructions for
building proteins from
the nucleus to the
cytoplasm
• In prokaryotic cells,
lack nuclei but use
RNA to send a
message from the
DNA to the ribosomes
and other cells that
translate the coded
information into amino
acid sequences.
The Structure of Nucleic Acids
• Nucleic acids are macromolecules that exists as polymers called
polynucleotides
• Each nucleotides consists of monomers called nucleotides
• Nucleotides composed of three parts : a nitrogenous base, a
pentose (five-carbon sugar) and a phosphate group.

• Without a phosphate group it is called as nucleoside

Nucleotide monomers
Nucleotide Polymers
• Nucleotides are joined by covalent bonds called phosphodiester
linkage between the OH group on the 3’ carbon of one
nucleotide and the phosphate on the 5’ carbon of the next
• The two free ends of the polymers : phosphate attached to a 5’
carbon (5’ end) and a hydroxyl group on a 3’ carbon (3’ end)

5’C

3’C 5’C

3’C
 • James Watson and Francis Crick first
The DNA Double Helix proposed the double helix structure
of DNA
• It is called as Watson-Crick Model
• Two sugar-phosphate backbones run
in opposite 5’  3’ directions –
antiparallel
• 2 polynucleotides held together by
hydrogen bonds between the paired
bases and Van der Waals
interactions between the stacked
bases
• Paired bases:
In DNA
Adenine(A) – Thymine(T)
Guanine(G) – Cytosine(C)
In RNA
Adenine(A) – Uracil (U)
Guanine(G) – Cytosine(C)
• The two strands are complementary
RNA

Messenger RNA Transfer RNA Ribosomal RNA

Carries information The RNA that moves RNA that constructed
specifying amino acid amino acids to the the ribosomal subunit
sequences of ribosome to be
proteins from DNA to placed in the order
ribosomes prescribed by the
messenger RNA
5’ 3’
5’ 3’
5’
5’

3’
3’
3’

Messenger RNA Transfer RNA

Messenger
(mRNA) RNA Transfer
(tRNA) RNA Ribosomal RNA
(mRNA) (tRNA) (rRNA)