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CHEMISTRY
Aakash
ORGANIC CHEMISTRY
For – JEE/NEET
 Biomolecules
JEE Syllabus
General introduction and importance of biomolecules.
CARBOHYDRATES - Classification: aldoses and ketoses; monosaccharides
CHAPTER
8
(glucose and fructose), constituent monosaccharides of oligosacchorides
(sucrose, lactose, maltose) and polysaccharides (starch, cellulose, glycogen).
PROTEINS - Elemen tary I dea of ? - amino a cids, peptide bond,
polypeptides; Proteins: primary, secondary, tertiary and quaternary structure
(qualitative idea only), denaturation of proteins, enzymes.
VITAMINS - Classification and functions.
NUCLEIC ACIDS - Chemical constitution of DNA and RNA.
Biological functions of nucleic acids.

All living organisms are made of one or more cells which are considered as
the smallest units of life. Thus cell is a fundamental structural and functional unit THIS CHAPTER
of living organisms. INCLUDES
All the carbon compounds associated with cells are classified as
(i) Carbohydrates  Carbohydrates
(ii) Amino Acids and Proteins
(iii) Nucleic Acids  Monosaccharides
(iv) Lipids
 Disaccharides
CARBOHYDRATES
Oligosaccharides
1. Carbohydrates are mainly compounds of carbon, hydrogen and oxygen.
2. General formula initially considered was Cx(H2O)y
 Polysaccharides
e.g., glucose – C6H12O6, sucrose C12H22O11 etc.
But many of the compounds behave as carbohydrates but do not follow  Glucose
the Cx(H2O)y formula.
3. Thus carbohydrates are the class of compounds that include polyhydroxy  Preparation and
aldehydes or polyhydroxy ketones. Properties
4. Carbohydrates are also known as saccharides.
 Amino Acids
Classification
The carbohydrates are classified into three major classes  Proteins
(i) Monosaccharides
(ii) Oligosaccharides  Enzymes
(iii) Polysaccharides
 Nucleic Acids
Monosaccharides
(i) Monosaccharides are simple sugars with single unit of polyhydroxy  Vitamins
aldehyde or polyhydroxy ketones.
(ii) General formula CnH2nOn (with some exceptions).

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Oligosaccharides
(i) Oligosaccharides are made up of 2-9 units of monosaccharides or simple sugars.
(ii) Oligosaccharides with two, three, four monosaccharides respectively known as disaccharides, trisaccharides,
tetrasaccharides.
(iii) Sucrose is the example of this class

H
C12H22 O11  H2O 
 C 6H12 O 6  C 6H12O 6
(sucrose) (glucose) (fructose)

Polysaccharides
(i) Polysaccharides are made up of 'n' number of monosaccharide units (above 10 carbon atoms).
(ii) Starch, cellulose, glycogen are the examples of this class.
nH2 O
(iii) (C6H10 O 5 )n   nC 6H12 O 6
starch H glucose

(iv) Homopolysaccharides are made up of single type of monosaccharides. Heteropolysaccharide is made up

of two or more different types of monosaccharides.

Note : Monosaccharides and oligosaccharides are collectively known as Sugars as they are
soluble in water and sweet to taste. Whereas polysaccharides on other hand are known
as Non-sugars.

Monosaccharide-Glucose
Glucose is known as dextrose and also known as grape sugar.

Preparation
Acid hydrolysis of cane sugar in presence of alcohol gives glucose (along with fructose).
C12H22 O11  H2 O  C 6H12O 6  C6H12 O 6
sugar glucose fructose

Chemical Properties
(i) Reaction with PCl5 :

CHO CHO
(CHOH)4 + 5PCl5 (CHCl)4 + 5POCl3 + 5HCl

CH2OH CH2Cl
Glucose Penta-chloroglucose

(ii) Reaction with acetic anhydride :

CHO CHO
(CHOH)4 + (CH3CO)2O (CHOCOCH3)4

CH2OH CH2OOCCH3
Penta-acetate glucose

(iii) Reduction :
CHO CH2OH
Na-Hg
(CHOH)4 + 2H (CHOH)4
H2O
CH2OH CH2OH
Sorbitol

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(iv) Reaction with Fehling's solution :

CHO COOH
(CHOH)4 + 2CuO (CHOH)4 + Cu2O
CH2OH CH2OH
Gluconic acid red ppt.

(v) Reaction with Tollen's reagent :

CHO COOH
(CHOH)4 + Ag2O (CHOH)4 + 2Ag (mirror)
CH2OH CH2OH
Gluconic acid
(vi) Reaction with HNO3 :

CHO COOH
HNO3
(CHOH)4 + 3[O] (CHOH)4
CH2OH COOH
Saccharic acid
(Glucaric acid)

(vii) Reaction with phenylhydrazine :

CHO + H2NNHC6H5 CH NNHC6H5

(Phenylyhydrazine)
CHOH CHOH
(CHOH)3 (CHOH)3
CH2OH CH2OH
D-glucose D-glucose phenylhydrazone

H2NNHC6H5

CH NNHC6H5 CH NNHC6H5
C NNHC6H5 C O
H2NNHC6H5
(CHOH)3
CH2OH

(viii) Lobry de Bruyn-van Ekenstein rearrangement reaction :

Glucose on reaction with dilute NaOH undergoes a reversible isomerisation and is converted into a mixture
of D-Glucose, D-Mannose and D-Fructose.
D-Glucose D-Mannose D-Fructose.

Note : Due to this isomerisation fructose even it does not contain – CHO group reduces Fehling's
solution and Tollen's reagent in alkaline medium.

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Structure of D-Glucose
(i) Open chain structure :
The reaction of glucose with
(a) HI to give hexane
(b) Hydroxylamine to form monoxime
(c) HCN to form cyanohydrin gives the existence to the open chain structure of glucose
(ii) Cyclic structure of glucose :
The open chain structure of glucose fails to explain
(a) No reaction with NaHSO3 and NH3 – even though – CHO is present.
(b) Glucose does not react with Grignard reagent.
(c) Negative test (for aldehydes) with Schiff's base.
All the above observation indicates that free aldehydic group is not present.

H O H O H OH HO H
1 1 1 1
C C C C

CHOH CHOH CHOH CHOH

+ +
CHOH –H CHOH H CHOH CHOH
or
CHOH CHOH CHOH CHOH

CHOH CH O CH O CH O

CH2OH CH2OH CH2OH CH2OH

D-glucose -D-glucose -D-glucose
-D-glucose and -D-glucose are anomers of each other.

CH2OH CH2OH
O O
H H H OH
H H
1
OH H OH H
OH OH OH H

H OH H OH
-D-glucose -D-glucose

-D-glucose and -D-glucose on treatment with CH3OH in presence of dry HCl gas forms
methyl -D-glucoside and methyl -D-glucoside.

CHO H C OCH3 H3CO C H

H C OH H C OH H C OH
CH3OH
HO C H HO C H & HO C H
HCl
H C OH H C OH H C OH O
O
H C OH H C H C

CH2OH CH2OH CH2OH

Methyl -D-glucoside Methyl -D-glucoside

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Glucose ring can be easily broken up by strong reagents like HCN, NH2OH and C6H5NHNH2.
Mutarotation : The and anomers of glucose are obtained from crystallisation at 30°C and 98°C
respectively. If either of the two forms are allowed to stand, the specific rotation of the solution changes
slowly and reaches a constant value.
The spontaneous change is specific rotation of an optically active compound is called mutarotation.
-D-glucose Eq. mixture -D-glucose
+111° +52.5° +19°
Disaccharides
(i) Disaccharides are composed of two molecules of monosaccharides linked by glycosidic linkage.
(ii) The disaccharides may be reducing or non reducing in nature depending upon linkage.
+
H2O/H
Sucrose (C12H22O11) Glucose + Fructose
+
H2O/H
Lactose (C12H22O11) +
Glucose + Galactose
H2O/H
Maltose (C12H22O11) Glucose + Glucose

Structure of Sucrose, Lactose and Maltose

(i) Sucrose

6 CH2OH
-linkage
5 O
H H O O CH2OH
H 2
4 OH H 1 OH H
HO -linkage
H
3 2 HOH2C
H OH H OH
Glucose unit Fructose unit

(ii) Lactose

-linkage
CH2OH H OH
O 3 2
HO O
OH
H OH H
1
OH H 4
1
H H H O H
5
H OH CH2OH
6

(iii) Maltose

CH2OH CH2OH
O H H O
H H
H H
1 1
OH H OH H
HO O OH

H OH -linkage H OH

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Polysaccharides :
(i) In polysaccharides thousands of monosaccharide units are joined together by glycosidic linkage.
Starch : (C6H10O5)n
+
H /H2O
(C6H10O5)n C12H22O11 C6H12O6
Starch Maltose D-glucose
(ii) Starch does not reduce Fehling’s solution or Tollen’s reagent.
(iii) Starch does not form an Osazone.
(iv) Starch is a mixture of two polysaccharides i.e., amylose and amylopectin.
Cellulose : (C6H10O5)n
(i) Cellulose is a straight chain polysaccharide composed of only D-glucose units.
(ii) Cellulose does not reduce Tollen’s reagent or Fehling’s solution.

AMINO ACIDS
Amino acids are small molecules made of carbon, hydrogen, oxygen and nitrogen and in some cases also
sulphur. A free amino group is basic, a free carboxyl group is acidic. Lysine and arginine are Basic Amino
Acids because they carry two amino groups and one carboxyl group is acidic. Glutamic acid (glutamate) and
aspartic acid (aspartate) contain one amino and two carboxyl groups each and are classified as Acidic Amino
Acids. Alanine, glycine, valine and phenylalanine are Neutral Amino Acids as these contain one amino and one
carboxyl group
R CH COOH

NH2
Amino acid (R = side chain)

COOH -C COOH

H2N — C — H H2N — C — H
CH2 CH2
CH2 COOH
CH2
Aspartic acid
H2C — NH2

Lysine Side chains

Side chain of a basic and an acidic amino acids

COOH COOH COOH

H2N — C — H H2N — C — H H2N — C — H

CH3 CH2 H2COH

Alanine Serine
(nonpolar) CH2 (polar)

COOH
Glutamic acid
(polar)

Examples of polar and nonpolar amino acids

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Amino Acids which occur in Proteins

Glycine, alanine, serine, cysteine, aspartic acid, glutamic acid, asparagine, glutamine, methionine, threonine,
valine, leucine, isoleucine, lysine, histidine, arginine phenylalanine, tyrosine, tryptophan and proline.

PROTEINS
Proteins are polyamides formed from amino acids. The -carbon atom of the amino acids is asymmetric
and show optical isomerism (stereo). Proteins consist mainly of l isomers of amino acids. These are 20
commonly occurring amino acids in proteins. Amino acids form zwitter ion. Lack of essential amino acids
in diet can cause diseases such as Kwashiorkar.

Peptide Bond and Structure of Proteins

Amino acids are joined together by an amide linkage called peptide bond.

Proteins are long polymers of amino acids linked by peptide bonds (polypeptides). The sequence in which
the amino acids are arranged in a protein is called the primary structure.

The secondary structure arises due to the regular folding of the backbone of the polypeptide chain due
to intramolecular hydrogen bonding between the carboxyl and amino groups.

The tertiary structure is the three-dimensional structure of globular proteins. It arises due to folding and
superimposition of various secondary structural elements.

ENZYMES
Enzymes are biological catalysts which increase the rate of biochemical reactions even under mild
conditions of temperature and pH of living organisms.

Properties of Enzymes :

(i) They speed up reactions up to ten million times compared to the uncatalyzed reactions.

(ii) They are very specific in their action on substrates and each enzyme catalyzes only specific type
of reaction.

(iii) They are active at moderate temperature and pH.

(iv) The action of enzymes are inhibited by various organic and inorganic molecules.

Enzymes and Diseases : Certain diseases are caused by enzyme deficiencies. The congenital disease
phenylketone urea, is due to a deficiency of the enzyme phenylanine hydroxylase. Albinism is another
disease caused due to deficiency of an enzyme tyrosinase. Many heart attacks are caused by blood clot
formation in a coronary artery. The enzyme streptokinase is used to dissolve the clot.

NUCLEIC ACIDS
1. Nucleic acids play an essential role in transmission of the hereditary characteristics and the
biosynthesis of proteins.

2. There are two classes of nucleic acids : DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).
Nucleic acids are the long polymers in which the monomeric units are nucleotides. The nucleotides
are made up of three chemical components; a nitrogen containing heterocyclic base, a five-carbon sugar
and a phosphoric acid.

3. In nucleic acids, the individual nucleotides are linked through phosphate groups to give rise to long
polynucleotide structures.

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Structure of DNA
DNA consists of two strands of polynucleotides coiled around each other in the form of a double helix.
Functions of Nucleic Acids
Replication : The genetic information for the cell is contained in the sequence of the bases A, T, G and
C in the DNA molecule.
The DNA sequence that codes for a specific protein or polypeptide is called a GENE and thus every
protein in a cell has a corresponding gene.The relation between the nucleotide triplets and the amino
acids is called the GENETIC CODE.

VITAMINS
Vitamins are organic compounds necessary for normal health but cannot be synthesised in human body.
Deficiency of vitamins causes many disorders and diseases. Vitamins B and C are water soluble while
vitamins A, D, K and E are fat soluble.

  

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