➢ Biochemistry : Is the biological chemistry that provides us the knowledge

of the chemistry of living organisms & molecular basis for changes taking
place in plants, animals & microbial cells.

➢ It develops the foundation for understanding :

i. All biological processes & communication within & between cells
ii. Chemical basis of inheritance & diseases in animals & plants.

➢ Chemical analysis of all living organisms indicate the presence of the most
common elements like
i. Carbon,
ii. Hydrogen,
iii. Nitrogen,
iv. Oxygen,
v. Sulphur,
vi. Calcium,
vii. Phosphorus,
viii. Magnesium & others with their respective content per unit mas of living
tissue.
Chemically all living organisms have basic 3 types of macromolecules which
are POLYMERS of simple sub-units called monomers.

1. Polysaccharides (Carbohydrates)

2. Polypeptides ( Proteins)

3. Polynucleotides (Nucleic acids)

Lipids are water insoluble and small molecular weight compounds as

compared to these high molecular weight macromolecules
 CLASSIFICATION OF MONOSACCHARIDES
(BASED ON FUNCTIONAL GROUP)
ALDOSES KETOSES
CLASSIFICATION OF MONOSACCHARIDES
(BASED ON NO. OF CARBON ATOMS)
1. STARCH
Amylose
α 1, 4 glycosidic bond

Amylopectin
α 1, 4 glycosidic bond
α 1, 6 glycosidic bond
 1. STARCH

A. AMYLOSE (15-20%) – STRAIGHT CHAIN , WATER SOLUBLE

 1. STARCH

B. AMYLOPECTIN (80-85%) – BRANCHED CHAIN, WATER INSOLUBLE

3. GLYCOGEN
 HETEROPOLYSACCHRIDE:
1. Hyaluronic acid
(Hi – lu- ronic acid )
D- Glucuronic Acid & N- Acetyl glucosamine (1,4 linkage)
 HETEROPOLYSACCHRIDE:
[Link]
D- Glucuronate -2- sulfate & N- sulfoglucosamine-6-sulfate
(1,4 linkage)
 HETEROPOLYSACCHRIDE:
[Link] Sulphate
D- Glucuronic Acid & N- Acetyl – D-galactosamine
Lipids
Simple : Esters of fatty acids with alcohol
• Fats & Oils : Esters of fatty acids with glycerol
• Waxes: Esters of fatty acids with long chain alcohol
(Ex: Cetyl alcohol.

Compound: Esters of fatty acids with

alcohol and other groups

Derived: Composed of hydrocarbon rings

and a long hydrocarbon side chain
 LIPIDS

Simple Lipids Compound Lipids Derived Lipids

Fats & Oils Waxes Phospholipids Glycolipids Sterols

Terpenes
Triacyl Cetyl Glycero Sphingo
Glycerides Alcohol Phospholipids Phospholipids
Carotenoids
1. Simple Lipids (Fats & oils) : Esters of fatty acids + glycerol

Palmitic Acid : 16 Carbon

Glycerol
Palmitoleic Acid : 16 Carbon
Unsaturated fatty acids have one or more double bonds between the carbon atoms of
hydrocarbon chain.
Ex: Oleic (18 C) is found in nearly all fats & Linoleic acid (18 C) found in many oil seeds
18 Carbon, 1 Double bond
Oleic Acid – Mono unsaturated fatty acid

18 Carbon, 2 double bond

Linoleic Acid – Poly unsaturated fatty acid
Unsaturated fatty acids have one or more double bonds between the carbon atoms of
hydrocarbon chain.
18 Carbon, 3 Double bond
Linolenic Acid – Poly unsaturated fatty acid
1. B. Simple Lipids (Wax) :

Esters of fatty acids + Cetyl alcohol (long chain alcohol).

➢ They are abundantly found in the blood, gonads & sebaceous glands of the
skin.
➢ Waxes are not as readily hydrolyzed as fats. They are solid at room
temperature.
➢ They form water insoluble coating on hair & skin in animals, and also form
outer covering on stems, leaves & fruits.

Cetyl Alcohol
2. Compound Lipids :
Esters of fatty acids + Glycerol + Nitrogen or Phosphorus (Phospho lipids) or
Sulphur or Protein or sugars (Glyco lipids).
A. Phospholipids :

i. Glycero-phospholipids :

Esters of fatty acids + glycerol + Phosphorus + Nitrogenous Base.

( Found in abundance in the cell membrane)

Sat Fatty acid

Unsat Fatty acid

Glycerol

PO4 Nit Base

32
 Nitrogenous Bases/ Amino Alcohol

CH3
+ +
HO−CH2−CH2−N−CH3 HO−CH2−CH2−NH3

Choline CH3 + Ethanolamine

NH3

HO−CH2−CH−COO−
Serine
A i. Glycero-phospholipids :
➢ Example 1 : Lecithin [Phosophotidyl Choline].
(Brain & nerve tissues, Yolk, Wheat germ, yeast)

➢ Example 2: Cephalin [Phosophotidyl ethanolamine]

(Brain & nerve tissues, Yolk, Wheat germ, yeast)
➢ Phospho lipids have both hydrophilic polar groups (Phosphate & nitrogenous
group & glycerol) & hydrophobic non-polar groups ( fatty acids)
A. Phospholipids :

ii. Sphingo-phospholipids/ Sphingomyelin:

Sphingosine + Fatty acids [Amide bond]+ Phosphorus + Nitrogenous Base

( Imp constituent of myelin sheath found of nerves in brain & nervous tissue)

Fatty acid
Sphingosine

PO4 Nit Base

36
B. Glycolipids/ Glyco sphingolipids :

Sphingosine + Fatty acids [Amide bond]+ Simple Sugar.

( Found in abundance in the brain white matter & myelin sheath)

Fatty acid

Sphingosine
Simple
Sugar
37
B. Glycolipids/ Glyco sphingolipids :

Sphingosine + Fatty acids [Amide bond]+ Simple Sugar.

( Found in abundance in the brain white matter & myelin sheath)

Example 1: Cerebrosides (Sphingosine + Fatty acids + Simple Sugar )

i. Galacto-Cerebroside [Galactose]
ii. Gluco-Cerebroside [Glucose]

Fatty acid

Sphingosine
Simple
Sugar
38
B. Glycolipids/ Glyco sphingolipids :

Sphingosine + Fatty acids [Amide bond]+ Simple Sugar.

( Found in abundance in the brain white matter & myelin sheath)

Example 2 : Gangliosides -
i. N-acetyl Neuramic acid (NANA) (Sugar derivative)

Fatty acid

Sphingosine

Sugar
Derivative
39
Derived Lipids : Hydrolytic products of lipids. They include Steroid hormones, Fat
soluble vitamins, hydrocarbons, ketone bodies.

Steroids : Each molecule has

carbon atoms arranged in 4 inter
locking rings. (Steroid nucleus) &
long hydrocarbon side chain.

Ex : Cholesterol , exists as free or

as cholesterol ester.

Cyclopentanoperhydrophenanthrene (CPPP)
Derived Lipids : Hydrolytic products of lipids. They include Steroid hormones, Fat
soluble vitamins, hydrocarbons, ketone bodies..

➢ Adrenocorticoids , sex hormones (Progesterone, testosterone ) & Vit. D are

synthesized from cholesterol.

➢ Cholesterol is absent in plants.

➢ In plants, sterols exist chiefly as Phyto-sterols .

➢ Yam plants (Dioscorea) produces a steroid compound called diosgenin.

➢ Diosgenin is used in manufacture of anti-fertility pills. (birth control pills)

✓ Terpenes are naturally occurring
chemical compounds found in
plants and some animals.

✓ They're responsible for the aromas,

flavors, and even colors associated
with various types of vegetation.
Carotenoids: Pigments composed of two, 6- carbon rings with highly unsaturated
straight chain of hydrocarbons.
Occurrence: Thylakoids of chloroplast & chromoplast of all higher plants
Ex: Alpha & beta carotene, Xanthophyll's.
Sr. No Amino Acid Sr. No Amino Acid
1. Glycine 11. Asparagine
2. Alanine 12. Glutamic Acid
3. Valine 13. Glutamine
4. Leucine 14. Lysine
5. Isoleucine 15. Arginine
6. Serine 16. Histidine
7. Threonine 17. Phenyl Alanine
8. Cysteine 18. Tyrosine
9. Methionine 19. Tryptophan
10. Aspartic Acid 20. Proline
AMINO ACID 1 + AMINO ACID 2

DIPEPTIDE
➢ Proteins are large molecules
containing amino acids units ranging
from 100-3000.

➢ A protein molecule consists of 1 or

more polypeptide chain.

➢ PRIMARY STRUCTURE :
Linear structure of A.A in polypeptide
chain of a protein forms it primary
structure.
➢ Linear structure of A.A in polypeptide chain of a protein forms it
primary structure

➢ Ex: INSULIN is made up of A chain & B chain i.e. 2 polypeptides.

➢ SECONDARY STRUCTURE :

➢ Some proteins such as keratin of hair,

consists of polypeptide chain
arranged like a spiral helix.

➢ Right handed spiral is called Alpha

helix , while left handed is called Beta
helix.
➢ The spiral conformation is held together by
HYDROGEN BOND.

➢ The HYDROGEN BOND is formed between the C

= O group of amino acid 1 & N-H group of the
amino acid No. 5.

AA1 AA2 AA3 AA4 AA5 AA6 7 6

8
5
3 2

1
4
➢ The sequence of A.A in polypeptide
chain determines :
✓ The location of its bend or fold &
✓ Position of formation of hydrogen
bond

between different portions of chain or

between different chains.

➢ Due to formation of H- bond peptide

chain assume a secondary structure.
➢ In some proteins , 2 or more polypeptide chains are linked together by
inter-molecular hydrogen bonds.

➢ Such structures are called pleated structures.

Ex: Protein of Silk fibres , Hair Protein : Kertain.

➢ In a β pleated sheet, 2 or more segments of a polypeptide chain line up
next to each other, forming a sheet-like structure held together by
hydrogen bonds.

➢ The hydrogen bonds form between carbonyl and amino groups of

backbone, while the R groups extend above and below the plane of the
sheet.
➢ The strands of a β pleated sheet may be parallel, pointing in the same
direction (meaning that their N- and C-termini match up), OR

➢ Antiparallel, pointing in opposite directions (meaning that the N-terminus

of one strand is positioned next to the C-terminus of the other).
TERTIARY STRUCTURE:

➢ In large proteins like MYOGLOBIN &

ENZYMES, peptide chains are looped,
twisted and folded back on
themselves.

➢ Such loops and bends give the protein

a tertiary structure.

➢ Thus, the overall three-dimensional

structure of a polypeptide is called
its tertiary structure.
MYOGLOBIN STRUCTURE
➢ The tertiary structure is primarily due to interactions between the R
groups of the amino acids that make up the protein.

➢ R group interactions that contribute to tertiary structure include hydrogen

bonding, ionic bonding, dipole-dipole interactions, London dispersion
forces ( Non-covalent bonds) & Di-sulphide bond (Only COVALENT BOND)
QUATERNARY STRUCTURE:

➢ In large proteins like HAEMOGLOBIN

protein sub-units are held together to
form quaternary structure.
➢ In large proteins like HAEMOGLOBIN protein sub-units are held together to
form quaternary structure.
Properties of proteins
• Extremely reactive & highly specific in behavior.
• Amphoteric in nature . i.e act both as acid & base.
• Their behavior is influenced strongly by pH.
• Like A.A, they are dipolar ions at iso-electric point i.e. sum of the
positive charges & sum of negative charges is equal. The net charge
is zero.
• The ionic groups of a protein are contributed by the side chains of
polyvalent amino acids.
Properties of proteins :
• A protein consists of more basic amino acids such as lysine &
arginine exists as a cation (positive charged) & behaves as a base at
physiological pH of 7.4. Such proteins are called basic proteins.
Ex: Histones of nucleoproteins are basic proteins.

➢ A protein rich in acidic amino acids exists as a anion (negative

charged) and behaves as an acid. Such proteins are called acidic
proteins.
Ex: Most of blood proteins are acidic proteins.
 Types Function Examples

Enzymes Bio- catalyst ▪ Amylase

▪ Insulin, Growth Hormone

Hormones Regulate body functions
(GH)

▪ Keratin (In Hair, Nails, Skin)

▪ Elastin ( Connective Tissue:
Give shape & structure to cell
Structural Ligaments)
& its organelles
▪ Collagen ( Connective
Tissue: Tendons)

Contractile Contraction ▪ Myosin (Muscles)

Transportation of certain ▪ Hemoglobin (R.B.C)
Transport
materials. ▪ Myoglobin ( Muscles)
▪ Immunoglobulin
Protection of the body against
Defense (Antibodies)
diseases
▪ Thrombin (Blood Clotting)
Sr. PROTEIN DESCRIPTION EXAMPLES
No
1. SIMPLE PROTEINS • The simplest • Histones
• Made of amino acid units only, joined • Albumin
by peptide bond • Globulin
• Upon hydrolysis they give mixture of
amino acid & nothing else

2. CONJUGATED • Composed of simple proteins + non- • Glycoprotein

PROTEINS protein substance. • Lipoprotein
• The non-protein substance is called • Nucleoprotein
prosthetic group or co-factor • Chromoprotein
Ex: Hemoglobin,
Mucin of saliva,
Heparin of blood

3. DERIVED • Not naturally occurring proteins. • Peptones

PROTEINS • Obtained from simple proteins by • Peptides
action of enzymes & chemical agents. • Proteoses
• They are also obtained by hydrolysis
of proteins.
 NUCELOSIDE = BASE + SUGAR

NUCELOTIDE = BASE + SUGAR+ PHOSPHATE GROUP

 Nucleoside

Sugar –Phosphate bond

Glycosidic bond

Nucleotide
James Watson &
Francis Crick
 5’ 3’
5’ 3’

Phospho-
diester bond

3’ 5’ 3’ 5’
Central Dogma :
✓ ds-DNA molecule gives rise to m-RNA which acts as a messenger to programme the synthesis of a
polypeptide chain (protein).
✓ This type of unidirectional flow of information from DNA to RNA to protein/ proteins is referred as
central dogma of molecular biology. It was postulated by F.H.C. Crick in 1958.
✓ The present concept of central dogma in retroviruses or Riboviruses is given by Temin (1970) and
Baltimore (1970)
Erwin Chargaff’s Rule:

✓ In 1949, Erwin Chargaff gave the Chargaff rule, according to which,

a. In a ds- DNA , the amount of Purines is equal to amount of pyrimidines.

b. In a ds- DNA , Adenine (A) is equal to Thymine (T) and Guanine (G) is equal to Cytosine (C)
i.e.
A =1 G =1
T C

Hence A+G
=1
C+T

The ratio is constant for a given species and varies from species to species.
DNA v/s RNA
RNA (Ribose Nucleic Acid)
 m-RNA
3-5% of RNA population
Molecular weight- 500 KD
Initiation Codon Termination Codon

AUG U A A
5’ 3’
Met AA2 AA3 AA4 AA5 AA6 AA7
 m-RNA
3-5% of RNA population
Molecular weight- 500 KD
Initiation Codon Termination Codon

A UGG GG C C A A A G G U U U U U C A C U A A
5’ 3’
Met Gly Pro Lys Val Phe His

UAG- Amber
UAA- Ochre
UGA - Opal
George Gamow , 1954 & Crick 1961

UAG- Amber
UAA- Ochre
UGA - Opal
 r-RNA
50-60% part of ribosomes
80% of RNA population
Molecular weight: 40-100 KD
 t-RNA
10-20% of RNA population
Molecular weight: *23-30 KD.
73-93 nucleotides

1. Hair Pin Model (Hoagland Model)

Anti-codon loop
 t-RNA
10-20% of RNA population
Molecular weight: *23-30 KD.
73-93 nucleotides

2. Clover Leaf Model (Holley Model)

DHU or D arm :

✓ This arm consists of stem & loop with unusual

pyrimidine – Dihydrouracil

✓ 4 base pair with a loop contain dihydrouridine

✓ Recognition site for specific enzyme aminoacyl

t-RNA synthetase (Needed to activate the
amino acid) DHU or D- Arm or
Amino Acyl Binding Loop
✓ Plays a important role in stabilization of t-RNA
tertiary structure.
Anti-codon loop:

✓ This arm also consists of stem & loop.

✓ Stem consists of 5 base pairs & loop (Called as

anti-codon loop) contains 7 unpaired
nucleotides.

✓ Out of these 7 unpaired nucleotides, the

middle 3 form - ANTICODON

✓ ANTI-CODON recognises , the codon on m-RNA

and binds to it
T –Phi –C loop:

✓ T-Phi- C is named of the sequence (Thymine –

Psudeo uridine – Cytosine) where Pseudo
uridine is unusual base.

✓ This arm also consists of stem & loop.

✓ Stem consists of 5 base pairs ; outermost of

these pairs is C-G.
T-phi-C or
✓ Loop contains 7 unpaired nucleotides. Ribosomal Binding Loop

✓ This loop contains a ribosome recognition

sequence,
 CUU
3’ 5’
• The protein part of the enzymes on its own, is not always adequate
to bring about the catalytic activity.

• Many enzymes require certain non-protein, small additional factors

collectively referred to as CO-FACTORS for catalysis.

• The CO-FACTORS may be:

✓ Organic or
✓ Inorganic in nature.
✓ The non-protein, organic, low molecular weight substance, loosely bound
& dialysable associated with enzyme function is known as CO-ENZYME.

✓ The functional enzyme is referred to as HOLOENZYME which is made up of

protein part (APOENZYME) and a non-protein part (CO-ENZYME).

✓ Some of the organic co-enzymes are nicotinamide-adenine-dinucleotide

(NAD) (contains Vit B3 Niacin) and flavin mononucleotide (FMN)
(contains Vit B2 Riboflavin).
• The term PROSTHETIC GROUP is used when non-protein moiety is
bound tightly to the enzyme which is not easily separable by
dialysis.

• The term ACTIVATOR is referred to the inorganic co-factors (like

Ca2+, Mg2+, Mn2+, etc) necessary to enhance enzyme activity.

• Iron (Fe2+) is a co-factor of enzyme catalase, manganese is a co-

factor of peptidases
Prosthetic
Group Co-enzymes Activators
Properties of Enzymes :

[Link] Property:
Properties of Enzymes :
[Link] Property:
Properties of Enzymes :

2. Specificity of Enzymes:
Properties of Enzymes :

3. Optimum Ph & Temp:

A. pH :
Ex: Pepsin in stomach : Optimum pH= 2 (Acidic range)
Trypsin in duodenum : Optimum pH= 9.5 (Alkaline range)

B. Temperature :
Optimum = 200 - 35 0C
Above 60-70 0C they become inactive.
CLASSIFICATION OF ENZYMES :

1. OXIDO-REDUCTASES.

2. TRANSFERASES

3. HYDROLASES

4. LYASES

5. ISOMERASES

6. LIGASES / SYNTHETASE.
Mechanism of enzyme action :
✓ The basic mechanism by which enzymes catalyze chemical reactions
begins with the binding of the substrate (or substrates) to the
active site on the enzyme.
✓ The ACTIVE SITE is the specific region of the enzyme which
combines with the substrate.
✓ The binding of the substrate to the enzyme causes changes in the
distribution of electrons in the chemical bonds of the substrate
and ultimately causes the reactions that lead to the formation of
products.
✓ The products are released from the enzyme surface to regenerate
the enzyme for another reaction cycle.
✓ There are two models to explain the mechanism of forming
Enzyme-Substrate complex, as described below:
 Lock & Key Model- Emil Fischer
Only the correctly sized key (substrate) fits into the key hole
(active site) of the lock (enzyme).
Induced Fit Model- Koshland

✓ It states that approach of a substrate induces a conformational

change in the enzyme.
✓ Unlike the lock-and-key model, the induced fit model shows that
enzymes are rather flexible structures in which the active site
continually reshapes by its interactions with the substrate until the
time the substrate is completely bound to it (it is also the point at
which the final form and shape of the enzyme is determined).
Factors affecting Enzyme Activity :

1. Substrate Conc.

2. Enzyme Conc.

3. Temperature.

4. pH

5. Other substances
 SUBSTRATE CONCENTRATION (RECTANGULAR HYPERBOLA)
The rate of enzymatic reaction is directly proportional to conc. Of substrate
C

A Km = 10 -5 to 10-2 moles

(moles/liter)
 ENZYME CONCENTRATION
The rate of enzymatic reaction is directly proportional to square root of conc. Of enzyme

2X Enzyme

Product Concentration
1X Enzyme

No Enzyme

Time
 TEMPERATURE
(Bell –shaped curve)
 pH
Bell –shaped curve)
SECONDARY METABOLITES:
✓ Are small organic molecules produced by organisms that are not
essential for their growth, development & reproduction.
✓ Several types of bacteria, fungi & plants produce secondary
metabolites.

They can be classified bases on different criteria’s:

1. Chemical structure ( containing small rings or sugars)

2. Composition (with or without N)

3. Solubility in various solvents

4. Pathway by which they are synthesized.

SECONDARY METABOLITES:

They can be classified into three main groups:

1. Terpenes :
Made from mevalonic acid that is composed of mainly carbon &
hydrogen.

2. Phenolics :
Made from simple sugars containing benzene rings, hydrogen &
oxygen.

3. Nitrogen containing compounds :

Extremely diverse class may also contain sulphur.
Papaver somniferum (Opium) – Morphine.
PAIN RELIVER AND COUGH SUPPRESANT