01

NOTE
B I O L O G Y

BIOMOLECULES
NUCLEIC ACIDS AND PROTEINS

Key Takeaways

Nucleic acids Proteins

• Nucleotides • Amino acids
♦ Types of nucleic acids • Polypeptides
♦ Structure of DNA • Structure of proteins

Prerequisites

• The building blocks of life

Amino acids Fatty acids Monosaccharides Nucleobases

Nucleotides

Complex
Proteins Lipids DNA/RNA
carbohydrates

• Some biomolecules are polymers that are made of long chains of repeating molecules known
as monomers.

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Nucleic Acids

• Nucleic acids have molecular weight above 1000 daltons

and hence are macromolecules.
• They form the genetic material in all the living organisms.
• They are made of carbon, hydrogen, oxygen, phosphorus,
and nitrogen.
• They are polymers with nucleotides as monomers.

Nucleotides

• They are the monomers of nucleic acids.

• Nucleotide = Phosphate group + Pentose sugar + Nitrogenous base

Phosphate group

• They have a phosphate group.

O
O P O
O Phosphate group

Nitrogenous base

• It is a nitrogen-containing compound with a ring structure.

• The five nitrogenous bases are as follows:
O NH2

N N
NH N

N N NH2 N N
H H
Guanine(G) Adenine(A)
Purines
They have a double-ringed structure.

O O NH2

H3C
NH NH N

N O N O N O
H H H
Cytosine(C) Thymine(T) Uracil(U)
Pyrimidines
They have a single-ringed structure.

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• Purines and pyrimidines can pair with each other by the formation of
hydrogen bonds.
♦A denine can pair with thymine (DNA) or uracil (RNA) with the
formation of two hydrogen bonds.

H
CH3
N N H O

N N H N
H N N
O H
Adenine pairs with thymine/uracil (Two hydrogen bonds)

♦ Guanine pairs with cytosine (both DNA and RNA) with the
formation of three hydrogen bonds.

H
N O H N

N N H N
H N N
N H O H
H
Guanines pairs with cytosine (Three hydrogen bonds)

Pentose sugar

• It is a 5-carbon monosaccharide or sugar.

• It is the central molecule in a nucleotide.
• A pentose sugar can be as follows:

Ribose in the nucleic acid - Deoxyribose in the nucleic acid -

Ribonucleic acid (RNA) Deoxyribonucleic acid (DNA)
5’ 5’
HOCH₂ O OH HOCH₂ O OH
4’C C 1’ 4’C C 1’
H H H H
3’ 2’ 3’ 2’
H C C H H C C H

OH OH OH H
Ribose Deoxyribose

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Nucleotides and Nucleosides

• Nucleoside = Nitrogenous base + Pentose sugar (Deoxyribose/Ribose)

• Nucleotide = Phosphate group + Nucleoside

Nucleotide

Phosphate group Sugar Base

Nucleoside

Phosphodiester bond

• Nucleotides are linked to each other by phosphodiester bonds.

• A phosphodiester bond is an ester bond between the following:
♦P hosphate group of nucleotide 2
♦H ydroxyl group of the pentose sugar of nucleotide 1
• Phosphate group links the following:
♦3 ’-carbon of pentose sugar of nucleotide 1
♦ 5’-carbon of pentose sugar of nucleotide 2

O
O P O
O O
CH2 Base O P O
O O
HC CH 5' CH Base
2
O
HC CH
HC CH
OH OH 3'
Ligase HC CH
O OH H2O
O P O
OH
O
O P O Base
5' CH2
O O
CH2 Base HC CH
O 3'
HC CH
HC CH
OH OH
HC CH
OH OH
Phosphodiester bond

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Types of nucleic acids

Nucleic acids

Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA)

It is double stranded. It is generally single stranded.

Deoxyribose sugar Ribose sugar

5’
HOCH₂ O OH
5’
O
HOCH₂ OH
4’C C 1’
H H 4’C C 1’
H H
3’ 2’
H C C H H
3’ 2’
H
C C
OH H OH OH

• Bases present are: • Bases present are:

♦A denine (A) ♦ Adenine (A)
♦T
 hymine (T) ♦ Uracil (U)
♦G
 uanine (G) ♦ Guanine (G)
♦C
 ytosine (C) ♦ Cytosine (C)

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Structure of DNA

Double stranded DNA

Polynucleotide chain 1 Polynucleotide chain 2

5’ end
O O
P 3’ end
Hydrogen bond
O O OH
5’
H₂C 2’ 3’
4’ T A 1’
1’ 4’
O O 3’ 2’ 5’ CH₂
P O O
O O Purines P
H₂C O O
G C
Antiparallel

Antiparallel
O O
CH₂
P Pyrimidines O O
O O P
H₂C O O
C G
O O CH₂
P O O
O O P
H₂C O O
A T
CH₂
OH
O O
3’ end
Deoxyribose P
OH O

Sugar-phosphate 5’ end
backbone
Sugar-phosphate
backbone

• Two polynucleotide (polynucleotide is a polymer of nucleotides joined by phosphodiester

bonds) strands are joined together by hydrogen bonds between purines and pyrimidines.
• The sugar and phosphate make up the backbone, while the nitrogen bases are found in the
centre and hold the two strands together.
• The two strands are antiparallel to each other: the 5′ carbon end of one strand faces the
3′ carbon end of its matching strand.

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Pairing of nitrogenous bases and phosphodiester bond formation

Formation of GC bond Formation of AT bond

P P P P P P
5’
5’
dR dR
P P P
dR dR dR
C T

A C A

T G C A G T T G C A G T
1. Formation of hydrogen bond

dR dR dR dR dR dR dR dR dR dR dR dR dR dR
5’ 3’ 5’ 3’
P P P P P P P P P P P P

Unwound parent DNA Unwound parent DNA

5’
P P P P P
5’
P P P P dR dR dR
dR dR
T C A
C A
H bonds A
T G C G T
T G C A G T
dR dR dR dR dR dR dR
dR dR dR dR dR dR dR 5’ P P P P P P 3’
5’ 3’
P P P P P P

Unwound parent DNA Unwound parent DNA

2. Formation of phosphodiester bond

P P phosphodiester P P phosphodiester
bond 5’ bond 5’
P P P P P
dR dR dR dR dR

C A T C A

T G C A G T T G C A G T

dR dR dR dR dR dR dR dR dR dR dR dR dR dR
5’ 3’ 3’
P P P P P P 5’ P P P P P P

Unwound parent DNA Unwound parent DNA

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Structure of B-DNA (Watson and Crick model)

• B-DNA is the form of DNA which has right-handed double helical structure.
•T  his structure was proposed by James Watson and Francis Crick.
• It is made up of two polynucleotide chains existing as a double helix.
•T  he double helical structure of DNA resembles a staircase.
•E  ach step of the ladder is represented by a base pair.

Features of B-DNA

5’ 3’

Sugar-phosphate
backbone

G C

A T

A T

G C

10
9 C G

8 T A

7 C G 10 Base pairs = Pitch

6 C G Distance = 3.4 x 10 = 34 Å
5
Turn of the strand = 36° x 10 = 360°
4 G C
= 1 full turn
3 A T

2 A T

Between successive base pairs 1 G C

Distance = 3.4 Å
Turn of the strand = 36°
3’ 5’

Diameter = 20 Å

Proteins

• Proteins are the most abundant biomolecules.

• They play a major role in most body processes.
• At 10–15% of total cellular mass, proteins are the most abundant biomolecules in the cells.

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Component % of total cellular mass

Water 70–90

Protein 10–15

Nucleic acids 5–7

Carbohydrates 3

Lipids 2

Ions 1

• They are polymers made up of monomers, i.e., amino acids.

Amino acids

• Amino acids are the building blocks of protein.

Amino acids Chain of amino acids Protein

• The sequence and number of amino acids vary a lot between different proteins.
•2  0 amino acids have been found in most living organisms.

Amino acids

Threonine (Thr) Alanine (Ala) Tyrosine (Tyr) Cysteine (Cys)

Histidine (His) Aspartic acid (Asp) Isoleucine (Ile) Leucine (Leu)

Tryptophan (Trp) Glycine (Gly) Glutamine (Gln) Arginine (Arg)

Methionine (Met) Asparagine (Asn) Valine (Val) Glutamic acid (Glu)

Phenylalanine (Phe) Serine (Ser) Lysine (Lys) Proline (Pro)

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Essential and non-essential amino acids

Amino acids

Essential amino acids Non-essential amino acids

They are obtained through diet. The body They are synthesised by the body.
does not synthesise them.

Threonine, Histidine*, Tryptophan, Alanine, Aspartic acid, Glycine, Asparagine,

Methionine, Phenylalanine, Lysine, Valine, Serine, Proline,
Leucine, Isoleucine Glutamic acid, Arginine**, Glutamine,
Cysteine, Tyrosine

*, **: Histidine and arginine are also known as semi-essential amino acids as they have to be
consumed in extra amounts under certain conditions like the ill, pregnant females or lactating
mothers, and even children.

Essential amino acids

PVT TIM HALL

Phenylalanine Tryptophan Histidine

Arginine
Valine Isoleucine

Lysine
Threonine Methionine
Leucine

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Non-essential amino acids

Almost All Guys Get Cut After Going To Play Sports

Aspartic Acid Asparagine

Alanine Glutamine

Glycine Tyrosine

Glutamic acid Proline

Cysteine Serine

General structure of amino acids

• Amino acids are organic compounds containing the following on the same Carbon atom
(α-Carbon),
♦A
 mine group (-NH2)
♦C
 arboxyl group (-COOH)

H
Amine Carboxyl
H2N C COOH
group group
R

• Amino acids are known as substituted methanes.

This is because the three hydrogens of the central C-atom (α-Carbon) of methane are
substituted by other functional groups (carboxyl group, amino group, and a variable R group).

H H

H C H H2N C COOH

H R
Methane Amino acid

• The variable R group can be H as in glycine, CH3 as in alanine, CH2OH as in serine, and so on.

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R=H R = CH3 R = CH2OH

H H H

H2N C COOH H2N C COOH H2N C COOH

H CH3 CH2

OH

Glycine Alanine Serine

• Some amino acids like methionine and cysteine have sulphur.

H H

H2N C COOH H2N C COOH

CH2 CH2

SH CH2
Cysteine
SH

CH3
Methionine

Classification of amino acids

Amino acids (Based on number

of amine and carboxyl groups)

Acidic amino acids Basic amino acids Neutral amino acids

Acidic Basic Neutral

They have one carboxyl They have one amine group They have only one amine
group in the variable R in the variable R group. group and one carboxyl
group. This is in addition to This is in addition to the group.
the one carboxyl group in one amine group in the
the backbone, backbone,
one carboxyl groups, and one amine groups, and one
one amine group. carboxyl group.

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O H H

H2N CH C OH H2N C COOH H2N C COOH

CH2 CH2 H

C O CH2

OH CH2

CH2

NH2
Aspartic acid Lysine Glycine

Examples: Aspartic acid Examples: Lysine, arginine, Examples: Glycine, alanine,

and glutamic acid and histidine serine, methionine, aspar-
agine, cysteine, glutamine,
isoleucine, leucine, proline,
threonine, phenylalanine,
tyrosine, tryptophan, valine,
and more.

Amino acids (Based on the

presence of aromatic ring)

Non-aromatic amino acids Aromatic amino acids

They have straight chains and no aromatic They have aromatic (benzene) rings.
rings.
H O O H
O
H H H₂N C C OH
H₂N C C OH H₂N C C OH
CH₂
H2N C COOH CH₂ CH₂

H HN
OH

Glycine Phenylalanine Tryptophan Tyrosine

Glycine, valine, and more Phenylalanine, tyrosine, and tryptophan

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Amino acids as zwitterions

•T  he amine group (-NH2) is a strong base and can pick up protons (H+) from the carboxyl group
(-COOH).
•T  hus, (-NH2) acquires a positive charge to become (-NH3+) and (-COOH) acquires negative
charge to become (-COO-).
• Zwitterion: It is a molecule with one functional group having positive charge and the other
functional group having negative charge but the net charge is zero.

H H H H
N N

H C H H C H

C C
O O H O O

Ionisable nature of amino acids

Low pH High pH

NH3 NH3 NH2

R C COOH R C COO R C COO

H H H

Cation Zwitterion Anion

As pH decreases (low pH), At a particular pH, amino As pH increases (high pH),

-COO- picks up H+ and no
longer exists as zwitterion
and amino acid acts as a
cation (positively charged
ion).
acids exist as zwitterions
and this form is known as
zwitterionic form.
H+ is removed from -NH3+
and it no longer exists as
zwitterion and acts as an
anion (negatively charged
ion).

Polypeptides
GLN ASP
MET LEU SER MET
• Polypeptides are linear chains of different LYS
ASP GLU HIS
amino acids linked by peptide bonds. THR LEU
ALA
ILE LEU TRP
•P  roteins are heteropolymers since they have GLN LYS GLY
PRO PRO THR
different amino acids.
Peptide bond

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Formation of the peptide bond

• The carboxyl group of one amino acid reacts with the amine group of another amino acid
undergoing condensation reaction to form a peptide bond with the removal of a
water molecule.

Amino acid 1 Amino acid 2

H O H O

N C H N C H
H C O H C O

H H
R R

Carboxyl group Amine group

Amino acid 1 Amino acid 2

H O H O

N C H N C H
H C O H C O

H H
R R

H2O

Amino acid 1 Amino acid 2

H O H O

N C N C H
H C C O

H H
R R

Peptide bond

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Biuret test

• It is a test for the presence of proteins containing two or more peptide bonds.

Sample + NaOH + Biuret reagent

Negative result Positive result

Bluish colour - Absence of protein Violet-pinkish colour - Presence of protein

Structure of Proteins

• Polypeptides undergo modifications to form four levels of protein structure.

Four levels of protein structure

Primary structure

• It represents the linear arrangement of amino acids in a sequence.

Amino acid 1 Amino acid 2 Amino acid 3 Amino acid 4

H O H O H O H O

N C N C N C N C H
H C C C C O

H H H H
R R R R

N-terminal amino acid C-terminal amino acid

(Free amine group with alpha carbon) (Free carboxyl group
with alpha carbon)

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Secondary structure

• Proteins do not exist in their primary structure. They take up a secondary structure.
• It is formed by folding of the polypeptide chain due to interactions between amino acids by
H-bonds.

Secondary structure

Alpha-helix Beta-pleated

•P  olypeptide chain folds in the form of • The segments of polypeptide chain

helix, resembling a spring. line up next to each other, resembling
• In proteins, only right-handed helices pleated paper.
are observed. •T  he two parallel chains are held
•E  xample: Keratin together by hydrogen bonds.
•E  xample: Fibroin

Disulfide Bond

• It is the bond formed between -SH groups.

• Tertiary and quaternary structure of proteins are mainly held together by disulfide bonds.

Cys Cys
Disulfide bridge

SH S
SH S

Cys Cys

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Tertiary structure

• The interactions (hydrogen bonds) make the

protein fold into a 3D structure resembling a
hollow ball.
•T  ertiary structure is required for biological
activities of many proteins.
• Example: Enzymes

Quaternary structure

• It has two or more polypeptide chains known as

subunits.
• It is an arrangement of folded polypeptide chains with
respect to each other.
•T  he subunits are held together by H-bonds, disulfide
bonds, and van der Waals forces.
•E  xample: Haemoglobin
Haemoglobin β β
• It is made up of four polypeptide chains, - two
identical alpha chains, and two identical beta
chains. Heme
group α
α

Denaturation

Denaturation

Denaturation is a process in which

proteins lose the quaternary
structure, tertiary structure, and
Normal secondary structure, that is Denatured
protein present in their native state, by an protein
application of some external stress
like heat, acid or base, and more.

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Did you know?

• All hormones in the body are proteins.

• Majority of the enzymes are proteins.

RuBisCO (Ribulose bisphosphate Collagen

Carboxylase-Oxygenase) Most abundant animal protein
Most abundant protein in the biosphere.

Summary Sheet

Nucleotide

Phosphate group Sugar Base

•P
 O4 group at 5’C of pentose
sugar
•P
 hosphodiester bond: It is
an ester bond between 5’
PO4 group and 3’ OH group.
• Ribose in RNA
• Deoxyribose in DNA
• Purines (G and A): They
have a double-ringed
structure.
• Pyrimidines (C, U, and T):
They have a single-ringed
structure.

Types of nucleic acids

DNA RNA

• Double stranded, deoxyribose sugar • Single stranded, ribose sugar

• Bases present: T, C, A, G • Bases present: U, C, A, G

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Structure of DNA

Double stranded DNA

Polynucleotide chain 1 Polynucleotide chain 2

5’ end
O O
P 3’ end
Hydrogen bond
O O OH
5’
H₂C 2’ 3’
4’ T A 1’
1’ 4’
O O 3’ 2’ 5’ CH₂
P O O
O O Purines P
H₂C O O
G C
Antiparallel

Antiparallel
O O
CH₂
P Pyrimidines O O
O O P
H₂C O O
C G
O O CH₂
P O O
O O P
H₂C O O
A T
CH₂
OH
O O
3’ end
Deoxyribose P
OH O

Sugar-phosphate 5’ end
backbone
Sugar-phosphate
backbone

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Diameter
20 Å

Minor groove

One complete
turn 34 Å

Sugar-phosphate
backbone

Major groove

Nitogenous base pair

3.4 Å

Proteins

Amino acids

H H O

H N C C OH
Structure

Amino group R Carboxylic acid

group
Variable side
chain α-carbon

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Cation Zwitterion Anion

NH3 NH3 NH2

R C COOH R C COO R C COO

Charges
H H H

Low pH High pH
pH scale

Essential amino acid: They are Non-essential amino acid: They

obtained through diet. The body are synthesised by the body.
does not synthesise them.

Based on the number of amine and carboxyl groups in amino acids:

Acidic Basic Neutral
•T
 wo carboxyl and •T
 wo amine and one •O
 ne amine and one
one amine group carboxylic group carboxylic group
Classification •A
 spartic acid and •L
 ysine, arginine, and •G
 lycine, alanine,
glutamic acid histidine glutamine, and more.

Based on the presence of aromatic ring:

Aromatic Non-aromatic
•T
 hey have aromatic (benzene) •T
 hey have straight chains and no
ring(s). aromatic rings.
•E
 xample: Phenylalanine, •E
 xample: G
 lycine, valine, lysine,
tyrosine, tryptophan and more.

Structure of Proteins

• Positional information: Sequence of amino acids

Amino acid 1 Amino acid 2 Amino acid 3 Amino acid 4

H O H O H O H O
Primary
N C N C N C N C H
H C C C C O

H H H H
R R R R

N-terminal amino acid C-terminal amino acid

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Alpha-helix Beta-pleated

Secondary

•T
 hey are held together by •T
 hey are held together by
hydrogen bonds. hydrogen bonds.
•E
 xample: Keratin •E
 xample: Fibroin

•F
 olded into a 3D structure
•R
 equired for many biological activities of
proteins
Tertiary •H
 eld together by disulfide bonds
•E
 xample: Enzymes

•A
 rrangement of polypeptide chains β β
(subunits)
•T
 he subunits are held together
Quaternary by H-bonds, disulfide bonds, and
van der Waals forces. Heme
group α
•E
 xample: Haemoglobin
α

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