Stereochemistry

Nature’s Molecular Palette

Submitted by: Umm e Kalsoom (bsf2101962)

Javeria Tariq (bsf2102117)

Ayesha (bsf2102148)

Ayesha Amjad (bsf2102499)

Kalsoom Shehzadi (bsf2102437)
 Table of Content

1 01
Introduction of Biomolecules
2 Properties 01

3 Categories of Biomolecules 01

3.1 Carbohydrates 02

3.2 Amino acids and Proteins 03

3.3 Lipids 03

3.4 Nucleotides and Nucleic Acids 04

4 Introduction of Carbohydrates 05

5 Features of carbohydrates 05

6 Classification of carbohydrates 06

7 Monosaccharides 06

8 Classification of Monosaccharides 07

9 Biological Functions 09

10 Metabolic Pathways Involving Monosaccharides 10

11 Introduction of Disaccharides 11

12 Classification of Disaccharides 12

13 Examples of Disaccharides 13

14 Oligosaccharides 16

15 Characteristics of Oligosaccharides 17

16 Classification of Oligosaccharides 18
16.1 N-linked Oligosaccharides 20

16.2 O-linked Oligosaccharides 21

17 Glycosylated Biomolecules 22

18 Polysaccharides 23

19 Characteristics of Polysaccharides 25

20 Types of Polysaccharides 26

21 Function of Polysaccharides 28

22 Introduction of Proteins 29

23 Properties of Proteins 29

24 Amino Acids 30

24.1 Properties of Amino Acids 31

25 Types of Amino Acids 31

26 Function of Amino Acids 32

27 Structure of Proteins 33

28 Classification of Proteins 34

29 Protein Synthesis 35

30 Transcription 36

30.1 Stages of Transcription 37

32 Translation 38

32.1 Steps of Translation 39

33 Functions of Proteins 40

34 Introduction of Lipids 41

35 Importance of Lipids 42
36 Classification of Lipids 43

37 Chemical structure of Lipids 45

37.1 Hydrogen chain of Lipids 45

37.2 Functional group of Lipids 45

38 Saturation and Unsaturation of Lipids 46

39 Properties of Lipids 47

40 History and Introduction of Nucleic Acids 49

41 Nucleotides and its basic structure 50

42 Introduction of DNA 53

42.1 Chemical structure of DNA 53

43 Biochemical Properties 55

44 Structure of RNA 56

45 Types of RNA 57

46 Functions of Nucleic Acid 60

47 References 62
Submitted by: Umm e Kalsoom
Student ID: bsf2101962

Nature’s molecular palette

Introduction:
Nature’s molecular palette means the molecules present in living organisms
made by nature. We often called them Biomolecules.
A biomolecule, often known as a biological molecule, is a phrase used to describe
compounds present in living things that are necessary for one or more biological
processes, such as cell division, morphogenesis or development. Large
macromolecules like proteins, carbohydrates, lipids and nucleic acids, as well as
tiny primary metabolites, secondary metabolites are all biomolecules. Biological
materials are the name for this type of substance. Biomolecules are vital
components of all living things. While endogenous biomolecules are produced
within the organism. Organisms often require the presence of exogenous
biomolecules, such as certain nutrients.

Properties:
Composition and Structure
Carbon is the most abundant element in biomolecules and it operates the same way
it does in organic compounds, creating four bonds in a tetrahedral structure, linear,
branching, cyclic or aromatic carbon skeletons are all possible. H, O, N, P and S
are also essential elements. Biological systems require about 30 elements,
including iodine and numerous metals, albeit most of these are required in trace
amounts. Biomolecules have the same types of functional groups as organic
molecules, such as hydroxyl, amino, carbonyl and carboxyl groups, among others.
Many biomolecules are polyfunctional, meaning they contain two or more
functional groups that can impact the reactivity of each other.
Categories:
Biomolecules have two categories based on molecular weight and solubility .
Micromolecules or biomicromolecules: are typically smaller . They have
molecular weights of 18 to 800 Da(Dalton) and high solubility. Micromolecule
may be inorganic or organic compound (minerals, amino acid and nucleotides
etc.)

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Macromolecules or biomicromolecules: are large sized. They have high
molecular weight ( 800- 1000 Dalton except lipids ) and low solubility.
Macromolecules are carbohydrates, proteins, nucleic acid and lipids.
The majority of biomolecules have distinct 3-dimensional forms due to their vast
size. Numerous non-covalent connections between atoms in the molecule keep the
molecule’s three-dimensional shape and so on.

Major Biomolecules:
There are four major types of biomolecules:
 Carbohydrates
 Proteins
 Lipids
 Nucleic acid

Carbohydrates (sugar & starch)

 Carbohydrates are polyhydroxy aldoses,
ketoses and their condensation products.
 They provide a significant amount of energy to biological systems.
 Polysaccharides are monosaccharide polymers. Polysaccharides used as
structural elements or as a source of metabolic energy.
 The monosaccharide includes almost 1 unit, where the Oligosaccharides with
2-10 units and the polysaccharides include more than 10 units.

Figure: different carbohydrates (monosaccharide’s)

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Amino Acids and Proteins:
 Amino acids are tiny molecules.
 They are organic acids with carboxylic acid having an amino group, generally
attached to carbon next to the carboxylic group.
 They are utilized to build proteins, produce energy and synthesize other
compounds such as hormones.
 Proteins are amino acid polymers. They have molecular weights ranging from
a few thousand to over a million and fold into precise shapes.
 Proteins serve as enzymes (reaction catalysts), structural elements, transport
molecules, antibodies and
other functions

Lipids (fats & oils)

 Lipids are fatty acid esters of alcohols and related substances.
 Lipids are water-insoluble compounds.
 Chemically, they differ from one another kinds of biomolecules, with around a
half-dozen primary varieties identified by their water insolubility.
 Lipids are employed in the generation and storage of energy, as well as
hormones, cell membrane structural elements and vitamins.
 Although lipids cannot polymerize to create macromolecules, they can
assemble non-covalently to form massive structures.

Figure: structure of lipids

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Nucleotides and Nucleic Acids
 Nucleotides are tiny molecules with molecular weights in the hundreds of
thousands.
 They help enzymes catalyze processes by transferring energy and assisting
them.
 Large polymers of nucleotides are nucleic acids (DNA and RNA).
 They take the shape of a double helix structure and are responsible for storing,
conveying and utilizing genetic information.

Small Organic Molecules

In addition to the primary classes of biomolecules, cells require a large number of
relatively small organic molecules for extremely particular tasks; many molecules
do not cleanly fit into one of the broad groups listed above
These molecules can be precursors to macromolecules that aid enzyme function
(typically linked to vitamins) or intermediates in metabolic processes, among other
things

Inorganic Ions
 Many inorganic ions are required by cells, even though they are not
biomolecules
 They are often required at microscopic levels (as a trace element).
 Calcium, sodium, iron, magnesium, potassium, chlorine, and other minerals are
among them. Inorganic ions serve as structural elements (calcium in bone),
osmotic pressure and transport regulators (sodium), and components of
proteins and enzymes, among other things (iron).

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 Combinations of Biomolecules
 A lipoprotein (lipid plus protein) or a glycoprotein is
examples of biomolecules that comprise components from
two of the major types (carbohydrate plus protein).

Carbohydrates:
What are carbohydrates?
Carbohydrates, or carbs, are sugar molecules. Along with proteins and fats,
carbohydrates are one of three main nutrients found in foods and drinks. Your
body breaks down carbohydrates into glucose. Glucose, or blood sugar, is the main
source of energy for your body's cells, tissues, and organs.

Features:
 Carbohydrates are “hydrates of carbon” and have the generic structure of
C(n)H(2n)O(n).
 A single sugar unit is a monosaccharide. These can consist of 3-carbon
moieties (triose), 4-carbon units (tetrose), 5-carbon moieties (pentose), and
6-carbon moieties (hexose).
 Nutritionally important sugars are of the D-form (not the L-form). D and L
refer to stereo-orientation at asymmetric carbon position 5 in a hexose or
carbon position 4 in a pentose.
 Sugars link together via a glycosidic bond to form di- (two
monosaccharides) or oligo- (3 to 15 monosaccharides), and polysaccharides.
 The nature of glycosidic bonds influences the structural and chemical
properties of the sugars and influences their ease of digestion. Sugars that
bond via an alpha 1, 4 linkages may be digested by mammalian enzymes.
Sugars that are linked via the beta 1, 4 linkages are resistant to digestion.
 Nutritionally significant disaccharides are sucrose and lactose.
 Starch from plants serves as a major energy source in animal diets. Starch
consists of two types of molecules: amylose (alpha 1, 4 linked glucose) and
amylopectin (alpha 1, 4 and alpha 1, 6 linked glucose).
 Glycogen, a storage form of carbohydrates in the liver and muscles, is very
similar to starch also called animal starch.
 Plant polysaccharides also include cellulose and hemicellulose and pectin
(no starch polysaccharides). Mammalian enzymes cannot degrade these
polysaccharides to free sugars, but microbial enzymes can handle them.

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Classification:
They are classified into four categories:

 Monosaccharide
 Disaccharide
 Oligosaccharide
 Polysaccharide

Monosaccharides:
Characteristics:
 The most fundamental type is the simple sugars called monosaccharides.
This means that they cannot be broken down any further into
simpler sugars by hydrolysis.
 Glycosidic bonds (also called glycosidic linkages) are the covalent bonds
that join monosaccharides. The combination of two simple sugars is called
a disaccharide whereas carbohydrates consisting of three to ten simple
sugars are called oligosaccharides, and those with a larger number of
monosaccharide units are called polysaccharides.
 The chemical process of joining monosaccharide units is referred to
as dehydration synthesis since it results in the release of water as a
byproduct.
 A monosaccharide has a general chemical formula of CnH2nOn and its
chemical structure is H (CHOH) nC=O (CHOH) mH. The ratio of hydrogen
atoms to oxygen atoms is often 2:1.
 Monosaccharides are often colorless, crystalline solids, and sweet-tasting.
They can be dissolved in water and occur as syrups or liquid sugar.

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Classification:
No. of carbons Type of sugar Aldoses Ketoses
3 Trioses Glyceraldehyde Dihydroxyacetone
4 Tetrose Erythrose Erythrulose
5 Pentoses Ribose, Xylose Ribulose, Xylulose
6 Hexoses Glucose, Fructose
Galactose
7 Heptoses Glucoheptose Sedoheptulose

Trioses: is a three-carbon monosaccharide. An example is glyceraldehyde-3-

phosphate (C3H7O6P). It is a triose that serves as an intermediate in different
carbohydrate metabolic pathways.

Tetrose: is a monosaccharide with four carbon atoms. Some of the

naturally-occurring tetroses are D-erythrose, D-threose, and D-erythrulose.
The erythrose, C4H8O4, is a tetrose with one aldehyde group. It has chemical
formula: C 4 H 8 O 4 . Nevertheless, erythrulose is a ketotetrose for having a
ketone group in its structure.

7
 Pentoses: is a five-carbon monosaccharide. Examples of pentoses
are ribose, deoxyribose, xylose, ribulose, and xylulose. Ribose (chemical
formula C5H10O5) and deoxyribose (chemical formula C5H10O4) are
constituents of nucleotides and nucleic acids. In particular, ribose is the
pentose sugar component of the nucleotides of RNA whereas deoxyribose is
the sugar component of the nucleotides of DNA.

Hexoses: is a six-carbon monosaccharide. Examples of hexoses

are glucose, mannose, and galactose. Glucose, in particular, is the most
common hexose that serves as a metabolic intermediate of cellular
respiration. Excess glucose is stored as glycogen in animals and as starch in
plants.

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 Heptoses: is a seven-carbon monosaccharide. Examples of naturally-
occurring heptoses are L-glycero-D-manno-heptose and sedoheptulose.
Their chemical formula is C7H14O7. They are early intermediates in lipid A
biosynthesis.

Biological Functions
Monosaccharides perform vital biological roles. One of their major functions
is to serve as a structural unit for multifarious biological compounds. Through
glycosidic bonds, they join together to form disaccharides, oligosaccharides, and
polymers (e.g. cellulose, starch, and glycogen). They may also serve as a precursor
or a constituent of other compounds, such as galactosamine, glucosamine, sialic
acid, N-Acetylglucosamine, sulfoquinovose, ascorbic acid, mannitol, glucuronic
acid, etc. Many of these compounds have a monosaccharide component that is
involved in various biological functions.

Some common monosaccharides:

Glucose: is a monosaccharide that occurs naturally. It can join with
other monosaccharide units to form disaccharides: maltose (i.e. two glucose
molecules), lactose (i.e. glucose and galactose molecules), and sucrose (i.e.
glucose and fructose molecules).

Galactose: is similar to glucose in terms of chemical structure. However, the

orientations of H and OH on carbon 4 are exchanged. Unlike glucose, galactose
generally does not occur in a free state. It usually is a constituent of complex
biomolecules. For instance, galactose together with glucose forms lactose (milk
sugar), which is a disaccharide.
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Fructose: is regarded as the sweetest naturally-occurring carbohydrate. Some of
the natural sources of fructose are honey, fruits, and sugar cane. It is a ketonic
monosaccharide since it has a reducing group (carbonyl) at carbon 2. This is in
contrast to glucose (which is an aldose) that has its carbonyl group at carbon 1.
Fructose occurs naturally in plants, particularly in fruits, root vegetables, etc. It
occurs freely or bonded to glucose to form sucrose.

Metabolic Pathways Involving Monosaccharides

Monosaccharides are involved in many important metabolic pathways. Some of
these metabolic pathways are:

 Glycolysis: the conversion of a monosaccharide into pyruvate, with the

concomitant production of high-energy biomolecules
 Pentose phosphate pathway: an alternative metabolic route in breaking
down glucose
 Gluconeogenesis: the conversion of non-carbohydrate precursors into a
monosaccharide
 Glycogenolysis: the breaking down of stored glycogen into monosaccharide
units
 Glycogenesis: the conversion of glucose into glycogen
 Fructose metabolism : where fructose, instead of glucose, enters the
glycolytic pathway
 Galactose metabolism: where galactose enters the glycolytic pathway by
first being phosphorylated and then converted into glucose-6-phosphate

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Name: Javeria Tariq

Roll no: bsf2102117

Disaccharides

A disaccharide (also called a double sugar ) is the sugar formed when two
monosaccharides (simple sugars) are joined by glycosidic linkage. Like
monosaccharides, disaccharides are soluble in water. Three common examples
are sucrose, lactose, and maltose.

What are Disaccharides?

Disaccharides are those carbohydrates that on hydrolysis with acids or enzymes
give two molecules of monosaccharides which can either be the same or
different.

Disaccharides are one of the four chemical groupings of carbohydrates

(monosaccharides, disaccharides, oligosaccharides, and polysaccharides). The
most common types of disaccharides sucrose, lactose, and maltose have 12 carbon
atoms, with the general formula C12H22O11. The differences in these
disaccharides are due to atomic arrangements within the molecule.

The joining of monosaccharides into a double sugar happens by a condensation

reaction, which involves the elimination of a water molecule from the functional
groups only. Breaking apart a double sugar into its two monosaccharides is
accomplished by hydrolysis with the help of a type of enzyme called a
disaccharidase.

As building the larger sugar ejects a water molecule, breaking it down consumes a
water molecule. These reactions are vital in metabolism. Each disaccharide is

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broken down with the help of a corresponding disaccharidase (sucrase, lactase, and
maltase).

The oxide linkage is formed after the loss of the water molecule and then the two
monosaccharides are formed by that linkage. When two monosaccharide units are
joined via the oxygen atom then that linkage is called a glycosidic linkage.

Classification
There are two functionally different classes of disaccharides:

Reducing disaccharides

Reducing disaccharides, in which one monosaccharide, the reducing sugar of the

pair, still has a free hemiacetal unit that can perform as a reducing aldehyde group;
lactose, maltose and cellobiose are examples of reducing disaccharides, each with
one hemiacetal unit, the other occupied by the glycosidic bond, which prevents it
from acting as a reducing agent. They can easily be detected by the Woehlk test or
Fearon's test on methylamine.

Non-reducing disaccharides

Non-reducing disaccharides, in which the component monosaccharides bond

through an acetal linkage between their anomeric centers. This results in neither
monosaccharide being left with a hemiacetal unit that is free to act as a reducing
agent.

Sucrose and trehalose are examples of non-reducing disaccharides because their

glycosidic bond is between their respective hemiacetal carbon atoms. The reduced

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chemical reactivity of the non-reducing sugars, in comparison to reducing sugars,
may be an advantage where stability in storage is important.

Common disaccharides

Disaccharide Unit 1 Unit 2 Bond

Sucrose (table sugar, cane sugar, beet sugar, or α(1→2)

Glucose Fructose
saccharose) β

Lactose (milk sugar) Galactose Glucose β(1→4)

Maltose (malt sugar) Glucose Glucose α(1→4)

α(1→1)
Trehalose Glucose Glucose
α

Cellobiose Glucose Glucose β(1→4)

Glucosami Glucosami
Chitobiose β(1→4)
ne ne

Examples of Disaccharides

1. Sucrose
Sucrose being dextrorotatory in nature gives dextrorotatory glucose as well as
levorotatory fructose on hydrolysis. The overall mixture is levorotatory and this is
because the levorotation of fructose (-92.4) is more than the dextrorotation of
glucose (+52.5).

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 Figure 01: Structure of Sucrose

2. Maltose
Maltose is also one of the disaccharides which have two α -D-glucose units which
are connected by the first carbon of the glucose and also linked to the fourth carbon
of another glucose unit. In the solution, a free aldehyde can be produced at the first
carbon of the second glucose of the solution and it is a reducing sugar as it shows
reducing properties.

14
 Figure 02: Structure of Maltose

3. Lactose
Commonly it is called milk sugar as this disaccharide is found in milk. It is made
up of Beta-D-galactose and β-D-glucose. The bond is between the first carbon of
galactose and the fourth carbon of glucose. This is also a reducing sugar.

Figure 03: Structure of Lactose

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Some More Types of Disaccharides
There few more types which are not that popular, such as:

Trehalose
It is made up of 2 molecules of glucose which are linked differently. This can be
found in fungi, plants, and insects.

Lactulose
It is formed from galactose and fructose. It is helpful for the treatment of
constipation and liver diseases.

Cellobiose
It is also made up of two glucose molecules which are also arranged differently.
These can be seen bacteriology which is a form of chemical analysis.

Chitobiose
It comprises two glucosamine molecules which are linked. It is seen in some
bacteria, exoskeletons of insects and is also found in fish, octopus, and squid.

Oligosaccharides

An oligosaccharide is a saccharide polymer containing a small number (typically

three to ten of monosaccharides (simple sugars). Oligosaccharides can have
many functions including cell recognition and cell adhesion.

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They are normally present as glycans: oligosaccharide chains are linked to lipids
or to compatible amino acid side chains in proteins, by N- or O-glycosidic bonds.
N-Linked oligosaccharides are always pentasaccharides attached to asparagine via
a beta linkage to the amine nitrogen of the side chain. Alternately, O-linked
oligosaccharides are generally attached to threonine or serine on the alcohol group
of the side chain.

Not all natural oligosaccharides occur as components of glycoproteins or

glycolipids. Some, such as the raffinose series, occur as storage or transport
carbohydrates in plants. Others, such as maltodextrins or cellodextrins, result from
the microbial breakdown of larger polysaccharides such as starch or cellulose.

Characteristics of Oligosaccharides

 Complex Carbohydrates: Oligosaccharides are complex carbohydrates

composed of 3 to 10 simple sugars (monosaccharides) linked together.

 Diverse Structures: They exhibit diverse structural arrangements due to

different combinations and linkages of monosaccharides, such as glucose,
fructose, and galactose.

 Digestion: Oligosaccharides are not easily digested by human enzymes,

passing through the small intestine undigested and reaching the colon, where
they can be fermented by gut bacteria.

 Prebiotic Properties: They serve as prebiotics, promoting the growth and

activity of beneficial gut bacteria. This contributes to a healthy gut microbiota.

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 Found in Foods: Oligosaccharides are naturally present in various foods,
including legumes, onions, garlic, and certain grains. They are also added to
processed foods as sweeteners and thickeners.

 Health Benefits: Some oligosaccharides, like inulin and

fructooligosaccharides (FOS), are associated with health benefits such as
improved digestion, enhanced mineral absorption, and potential immune
system support.

 Sweetness: While not as sweet as monosaccharides like glucose or fructose,

oligosaccharides can impart a slightly sweet taste to foods and beverages.

Classifications of Oligosaccharides
Oligosaccharides may be classified based on the number of monosaccharides they
contain. Some of them are described below.

Trisaccharides
Trisaccharides are oligosaccharides comprised of three monosaccharides.
Examples include:

 nigerotriose – 3 glucose units joined by α(1→3) glycosidic linkage

 maltotriose – 3 glucose units joined by (1→4) glycosidic linkage
 melezitose (glucose-fructose-glucose)
 maltotriulose (glucose-glucose-fructose)
 raffinose (galactose-glucose-fructose)
 kestose (glucose-fructose-fructose).

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Tetrasaccharides
Tetrasaccharides are oligosaccharides comprised of four monosaccharides.
Examples are:

 nigerotetraose 4 glucose units joined by α(1→3) glycosidic linkage

 maltotetraose 4 glucose units joined by (1→4) glycosidic linkage
 lychnose (galactose-glucose-fructose-galactose)
 nystose (glucose-fructose-fructose-fructose)
 sesamose (galactose-galactose-fructose-glucose)
 stachyose (galactose-galactose-glucose-fructose)

Pentasaccharides
Pentasaccharides are those comprised of five sugar units. N-linked
oligosaccharides are mostly pentasaccharide.

Hexasaccharides
Hexasaccharides are oligosaccharides comprised of six sugar units. α-Cyclodextrin
is an example. It consists of six glucose units linked via α-1, 4 linkages.

Heptasaccharides
Heptasaccharides are oligosaccharides containing seven sugar units,
octasaccharides contain eight, nonasaccharides have nine, decasaccharides have
ten, and so on.

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Glycosylation
glycosylation is the process by which a carbohydrate is covalently attached to an
organic molecule, creating structures such as glycoproteins and glycolipids.

N-Linked Oligosaccharides
An example of an N-linked Oligosaccharide, shown here with GlcNAc. X is any
amino acid except proline.

Figure 04: Structure of N-Linked Oligosacchrides

N-Linked glycosylation involves oligosaccharide attachment to asparagine via a

beta linkage to the amine nitrogen of the side chain.The process of N-linked
glycosylation occurs cotranslationally, or concurrently while the proteins are being
translated. Since it is added cotranslationally, it is believed that N-linked
glycosylation helps determine the folding of polypeptides due to the hydrophilic
nature of sugars. All N-linked oligosaccharides are pentasaccharides: five
monosaccharides long.

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In N-glycosylation for eukaryotes, the oligosaccharide substrate is assembled right
at the membrane of the endoplasmatic reticulum. For prokaryotes, this process
occurs at the plasma membrane. In both cases, the acceptor substrate is an
asparagine residue. The asparagine residue linked to an N-linked oligosaccharide
usually occurs in the sequence Asn-X-Ser/Thr, where X can be any amino acid
except for proline, although it is rare to see Asp, Glu, Leu, or Trp in this position.

O-Linked oligosaccharides
An example of an O-linked oligosaccharide with β-Galactosyl-(1n3)-α-N-
acetylgalactosaminyl-Ser/Thr.

Oligosaccharides that participate in O-linked glycosylation are attached to

threonine or serine on the hydroxyl group of the side chain. O-linked glycosylation
occurs in the Golgi apparatus, where monosaccharide units are added to a complete
polypeptide chain.

Cell surface proteins and extracellular proteins are O-glycosylated. Glycosylation

sites in O-linked oligosaccharides are determined by the secondary and tertiary
structures of the polypeptide, which dictate where glycosyltransferases will add
sugars.

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 Figure 05: Structure of O-Linked Oligosacchrides

Glycosylated biomolecules
Glycoproteins and glycolipids are by definition covalently bonded to
carbohydrates. They are very abundant on the surface of the cell, and their
interactions contribute to the overall stability of the cell.

Glycoproteins
Glycoproteins have distinct Oligosaccharide structures which have significant
effects on many of their properties, affecting critical functions such as antigenicity,
solubility, and resistance to proteases. Glycoproteins are relevant as cell-surface
receptors, cell-adhesion molecules, immunoglobulins, and tumor antigens.

Glycolipids
Glycolipids are important for cell recognition, and are important for modulating
the function of membrane proteins that act as receptors. Glycolipids are lipid
molecules bound to oligosaccharides, generally present in the lipid bilayer.
Additionally, they can serve as receptors for cellular recognition and cell signaling.
The head of the oligosaccharide serves as a binding partner in receptor activity.

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The binding mechanisms of receptors to the oligosaccharides depends on the
composition of the oligosaccharides that are exposed or presented above the
surface of the membrane.

There is great diversity in the binding mechanisms of glycolipids, which is what

makes them such an important target for pathogens as a site for interaction and
entrance. For example, the chaperone activity of glycolipids has been studied for
its relevance to HIV infection.

Polysaccharides

Polysaccharides are major classes of biomolecules. They are long chains of

carbohydrate molecules, composed of several smaller monosaccharides. These
complex bio-macromolecules functions as an important source of energy in animal
cell and form a structural component of a plant cell. It can be a
homopolysaccharide or a heteropolysaccharide depending upon the type of the
monosaccharides.

Polysaccharides can be a straight chain of monosaccharides known as linear

polysaccharides, or it can be branched known as a branched polysaccharide.

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 Figure 06: Structure of Polysacchrides

Cellulose and chitin are examples of structural polysaccharides. Cellulose is used

in the cell walls of plants and other organisms and is said to be the most abundant
organic molecule on Earth.[6] It has many uses such as a significant role in the
paper and textile industries and is used as a feedstock for the production of rayon
(via the viscose process), cellulose acetate, celluloid, and nitrocellulose.

Chitin has a similar structure but has nitrogen-containing side branches, increasing
its strength. It is found in arthropod exoskeletons and in the cell walls of some
fungi. It also has multiple uses, including surgical threads. Polysaccharides also
include callose or laminarin, chrysolaminarin, xylan, arabinoxylan, mannan,
fucoidan and galactomannan.

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 Figure 07: Types of Polysacchrides

Characteristics Of Polysaccharides
Polysaccharides have the following properties:

 They are not sweet in taste.

 Many are insoluble in water.
 They are hydrophobic in nature.
 They do not form crystals on desiccation.
 Can be extracted to form a white powder.
 They are high molecular weight carbohydrates.
 Inside the cells, they are compact and osmotically inactive.
 They consist of hydrogen, carbon, and oxygen. The hydrogen to oxygen ratio
being 2:1.

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Types Of Polysaccharides
Polysaccharides are categorized into two types:

 Homopolysaccharides.
 Heteropolysaccharides.

Homopolysaccharidesn
A polysaccharide that contains the same type of monosaccharides is known as a
homopolysaccharide. Some of the important homopolysaccharides are:

Glycogen: It is made up of a large chain of molecules. It is found in animals and

fungi.

Cellulose: The cell wall of the plants is made up of cellulose. It comprises long
chains of ꞵ-glycosides.

Starch: It is formed by the condensation of amylose and amylopectin. It is found

largely in plants, fruits, seeds, etc.

Inulin: It is made up of a number of fructofuranose molecules linked together in

chains. It is found in the tubers of dahlia, artichoke, etc.

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 Figure 08: Polysacchrides Structures

Heteropolysaccharides
A polysaccharide that contains different types of monosaccharides is known as a
heteropolysaccharide. Some of the important heteropolysaccharides are:

Hyaluronic Acid: It is made up of D-glucuronic acid and N-acetyl-glucosamine. It

is found in connective tissues and skin.

Heparin: It is made up of D-glucuronic acid, L-iduronic acid, N-sulfo-D-

glucosamine and is largely distributed in mast cells and blood.

Chondroitin-4-sulfate: Its component sugars are D-glucuronic acid and N-acetyl-

D-galactosamine-4-O-sulfate. It is present in the cartilages.

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Gamma globulin: N-acetyl-hexosamine, D-mannose, D-galactose are the
component sugars of this polysaccharide. It is found in the blood.

Functions Of Polysaccharides
The polysaccharides serve as a structural organization in animals and plants. Other
functions of polysaccharides include:

 They store energy in organisms.

 Due to the presence of multiple hydrogen bonds, the water cannot invade the
molecules making them hydrophobic.
 They allow for changes in the concentration gradient which influences the
uptake of nutrients and water by the cells.
 Many polysaccharides become covalently bonded with lipids and proteins to
form glycolipids and glycoproteins. These glycolipids and glycoproteins are
used to send messages or signals between and within the cells.
 They provide support to the cells. The cell wall of plants is made up of
polysaccharide cellulose, which provides support to the cell wall of the plant.
In insects and fungi, chitin plays an important role in providing support to the
extracellular matrix around the cells.

28
Submitted by: Ayesha

Student ID: bsf2102148

Protein: An Essential Bio-molecule

Introduction:
Proteins are very large molecules composed of basic units called amino acids.
Proteins contain carbon, hydrogen, oxygen, nitrogen, and sulphur. Protein
molecules are large, complex molecules formed by one or more twisted and folded
strands of amino acids.

Proteins are highly complex molecules that are actively involved in the most basic
and important aspects of life. These include metabolism, movement, defense,
cellular communication, and molecular recognition.

Properties of Proteins:
Proteins are a diverse group of biomolecules that are essential for life. They
are made up of long chains of amino acids and perform a wide range of
functions in the body, including structural support, transport, signaling, and
catalysis. Here are some properties of proteins:

Size: Proteins can range in size from small peptides to large multi-subunit
complexes.

Structure: Proteins have a complex three-dimensional structure that is critical to

their function.

The structure of a protein can be described at four different levels:

 Primary
 Secondary
 Tertiary
 Quaternary

29
 Fig: Proteins Structural Analysis

Function: Proteins have a wide range of functions in the body. They can act as
enzymes, antibodies, transporters, and receptors.

Flexibility: Proteins can be flexible and adopt different conformations to carry out
their functions.

Stability: Proteins must be stable under physiological conditions to function

properly. Factors such as pH, temperature, and ionic strength can affect protein
stability.

What is an Amino acid?

Amino Acids are the organic compounds that combine to form proteins, hence
they are referred to as the building components of proteins.

Amino acids are organic compounds containing the basic amino groups (NH2) and
carboxyl groups (-COOH). The ingredients present in proteins are amino acids.
Both peptides and proteins are long chains of amino acids.

Structure of Amino Acids:

The general structure of Amino acids is H2NCH RCOOH, and it can be written as:

30
 COOH

H2N – C – H

There are 20 naturally occurring amino acids and all have common structural
features – an amino group (-NH3+), a carboxylate (-COO-) group and a hydrogen-
bonded to the same carbon atom.

They differ from each other in their side-chain called the R group. Each amino
acid has 4 different groups attached to α- carbon.

General properties of Amino acids:

1. They have a very high melting and boiling point.
2. Amino acids are white crystalline solid substances.
3. In taste, few Amino acids are sweet, tasteless, and bitter.
4. Most of the amino acids are soluble in water and are insoluble in organic
solvents.

Essential and Non-essential Amino acids:

Out of 20 amino acids, the amino acids which can easily synthesize by our body
are called non-essential amino acids. These include alanine, asparagine, arginine,
aspartic acid, glutamic acid, cysteine, glutamine, proline, glycine, serine, and
tyrosine.

The amino acids which cannot be synthesized by our body. They are called
essential amino acids, and they include isoleucine, histidine, lysine, leucine,
phenylalanine, tryptophan, methionine, threonine, and valine.

31
 Fig: Structures of Essential and Non-essential amino acids

Functions of Amino acids:

Functions of Essential Amino acids:
 Phenylalanine helps in maintaining a healthy nervous system and in boosting
memory power.
 Valine acts as an important component in promoting muscle growth. 
Threonine helps in promoting the functions of the immune system.
 Methionine is used in the treatment of kidney stones, maintaining healthy skin
and also used in controlling invade of pathogenic bacteria.
 Leucine is involved in promoting protein synthesis and growth hormones.

Functions of Non-Essential Amino acids:

 Alanine functions by removing toxins from our body and in the production of
glucose and other amino acids.
 Glutamine promotes a healthy brain function and is necessary for the synthesis
of nucleic acids – DNA and RNA.
 Glycine is helpful in maintaining the proper cell growth, and its function, and
it also plays a vital role in healing wounds.

32
Structure of Proteins:
Protein molecules are large, complex molecules formed by one or more twisted
and folded strands of amino acids. Each amino acid is connected to the next amino
acid by covalent bonds.

Primary (first level) – Protein structure is a sequence of amino acids in a chain.

Secondary (secondary level) – Protein structure is formed by folding and twisting

of the amino acid chain.

Tertiary (third level) – Protein structure is formed when the twists and folds of
the secondary structure fold again to form a larger three dimensional structure.

Quaternary (fourth level) – Protein structure is a protein consisting of more than

one folded amino acid chain.

Proteins can bond with other organic compounds and form “mixed” molecules.
For example, glycoproteins embedded in cell membranes are proteins with sugars
attached. Lipoproteins are lipid-protein combinations.

Fig: Structure of Proteins

33
Classification of Proteins:
Classification of proteins is done on the basis of the following:

 Shape
 Constitution
 Nature of molecules

On the basis of shape:

Fibrous protein(Scleroprotein): We can find these proteins in animals and are
insoluble in water. Fibrous proteins are resistant to
proteolytic enzymes and are coiled and exist in threadlike structures to form fibres.

Examples:

Actin, and myosin, keratin in hair, claws, feathers, etc.

Globular proteins: These proteins, unlike fibrous proteins are soluble in water.
They are made up of polypeptides that are coiled about themselves to form oval or
spherical molecules.

Examples:

Albumin, insulin, and hormones like oxytocin, etc.

Fig: Structure of fibrous and globular protein

34
On the basis of Constitution:
Simple proteins: These proteins are made up of amino acids only. e.g. albumins,
globulins, prolamins, etc.

Conjugated proteins: These are complex proteins that are combined with the
characteristic of non–amino acid substance called as a prosthetic group. These are
of following types:–

Nucleoproteins: Combination of protein and nucleic acid

Mucoproteins: Combination of proteins and carbohydrates

Glycoproteins: Combination of proteins and carbohydrates Chromoproteins:

Combination of proteins and coloured pigments.

Lipoproteins: Combination of proteins and lipids.

Metalloprotein: Combination of proteins and metal ions.

Phosphoprotein: Combination of proteins and phosphate group.

Derived proteins: When proteins are hydrolyzed by acids, alkalies or enzymes,

the degradation products obtained from them are called derived proteins.

On the basis of nature of Molecules:

Acidic proteins: They exist as anion and contain acidic amino acids. e.g. blood
groups.

Basic proteins: They exist as cations and are rich in basic amino acids e.g. lysine,
arginine etc.

Protein Synthesis – Central Dogma

The central dogma describes how the DNA makes its own copies by DNA
replication, then codes for the RNA by means of a transcription and RNA codes
for the proteins by translation.

35
Transcription:
Transcription is the first step of gene expression that involves the formation of
RNA molecule from DNA.

It is one of the first processes in gene expression. The genetic information flows
from DNA to protein and this flow of information takes place in a sequential
process of transcription and translation. Only one strand of DNA is copied during
the process of transcription known as the template strand and the RNA synthesized
is called the mRNA.

The main motive of transcription is RNA synthesis from the DNA sequence. The
RNA transcript carries the information used to encode a protein.

Fig: Transcription

RNA Polymerase:
The RNA polymerase is the main enzyme involved in transcription. It uses single-
strand DNA to synthesize a complementary RNA strand. The DNA-dependent
RNA polymerase binds to the promoter and catalyses the polymerization in the 5’
to 3’ direction on the template strand.

Once it reaches the terminator sequence, the process terminates and the newly
synthesized RNA strand is released.

36
Stages of Transcription: Transcription proceeds in enzymatically
catalysed steps i.e.

 Initiation
 Elongation
 Termination

Initiation:
RNA polymerase attaches to the DNA molecule and moves along the DNA strand
until it recognizes a promoter sequence. These are known as the transcription start
sites.

The DNA double helix then unwinds and all the bases on each of the DNA strands
are exposed. This acts as a template for a new mRNA strand.

Elongation:
Ribonucleotides are added to the template strand that enables the growth of mRNA
growth.

Termination:
RNA polymerase encounters a terminator sequence and the transcription stops.
RNA polymerase then releases the DNA template.

Fig: Stages of Transcription RNA Processing:

37
The transcribed RNA is known as the pre-mRNA. It is processed further to convert
it into mature RNA. RNA processing include:

 Capping:
 Polyadenylation
 Splicing

Capping:
 A methylated guanine cap is added to protect the mRNA. It involves:
 Addition of methylated guanine
 It occurs at 5′ end of mRNA transcript  It protects the mRNA from
degradation

Polyadenylation:
 The poly-A tail also protects the mRNA from degradation. It involves:  The
endonucleases cleave the mRNA at a specific sequence.
 The enzyme polyA polymerase facilitates the addition of several adenine
nucleotides.

Splicing:
 The non-coding sequences, i.e., the introns are removed
by spliceosome excision.
 The coding sequences or the exons join together by ligation.
 Thus several proteins can be made from a single pre-mRNA. A mature
mRNA is obtained at the end of transcription.

Translation:
The process by which the mRNA codes for a particular protein is known as
Translation. In the process, the ribosome translates the mRNA produced from
DNA into a chain of specific amino acids. This chain of amino acids leads to
protein synthesis.

38
It is a process where the expense of ATP is required and this energy is given by
the charged tRNA. The whole machinery of translation is present in the ribosomes.
Steps of Translation: tRNA charging:
The process of attaching an amino acid to its respective transfer RNA (tRNA) is
known as amino acid activation, also known as aminoacylation or tRNA charging
Initiation:
In the initiation step, the charged tRNA attaches to the start codon (AUG), the
small subunit of ribosome binds to the mRNA, and finally, the large ribosomal
subunit binds to create the initiation complex.

Elongation:
According to the codons found in the mRNA, the polypeptide chain keeps
growing.

Each amino acid has a peptide bond attaching it to the growing chain.

Elongation continues till the whole gene is translated.

Termination:
When the ribosome reaches a stop codon, such as UAA, UAG, or UGA,
translation is finished since these codons lack tRNAs.

When this happens, the translation stops, and the newly produced polypeptide
chain is released.

39
 Fig: Process of Translation Functions

Function of Proteins:
 The digestive enzymes are made up of proteins that are useful in carrying out
digestion.
 The protein acts as a chemical messenger for the interaction between cells,
tissues, and organs.
 Regeneration and creation of DNA molecules are done with the help of
proteins.
 Receptors are made up of proteins that help in the interaction of a cell with
other cells and the external environment.
 The immune system uses antibodies for repairing body cells which are mainly
made up of proteins.

40
Ayesha Amjad
Bsf2102499

Biomolecules (Lipids)
Lipids as organic molecules
Introduction:
Lipids are a diverse class of organic molecules that play essential roles in the
human body and in biology as a whole. They are hydrophobic compounds,
meaning they don't mix well with water. Lipids serve various functions, including
energy storage, structural components of cell membranes, insulation, and
protection. Major types of lipids include triglycerides (fats and oils),
phospholipids, and sterols. Triglycerides store energy, phospholipids form cell
membranes, and sterols like cholesterol are essential for various bodily functions.
Lipids are crucial for overall health but can also contribute to health issues when
imbalanced in the diet.

41
1.Definition:
Lipids are a diverse group of organic molecules that are insoluble in water. They
include fats, oils, phospholipids, and steroids. Lipids serve various functions in
living organisms, such as energy storage, insulation, and as structural components
of cell membranes.

2.Importance of lipids in biological systems:

Lipids play several crucial roles in biological systems:
1.Energy Storage:
Lipids, particularly triglycerides, serve as an efficient energy storage mechanism.
They can be broken down to release energy when needed.
2. Cell Membranes:
Phospholipids are fundamental components of cell membranes, forming a lipid
bilayer that controls the passage of substances in and out of cells.
3.Insulation:
Lipids can act as insulators, helping organisms maintain body temperature. For
example, adipose tissue stores fat for insulation.
4. Protection:
Lipids are found around vital organs, offering protection. They also play a role in
cushioning and shock absorption.
5.Hormone Production:
Steroid hormones, derived from cholesterol, regulate various physiological
processes, such as growth, metabolism, and reproduction.
6. Vitamin Transport:
Fat-soluble vitamins (A, D, E, and K) are transported and stored in the body via
lipids.
7. Cell Signaling:
Lipids can serve as signaling molecules and are involved in intracellular and
intercellular signaling processes.

42
8. Buoyancy:
Lipids in some aquatic organisms help them stay buoyant, facilitating their
movement and survival.
9. Structural Support:
Lipids, like waxes, can provide structural support in some organisms, such as
plants with waxy cuticles.
Overall, lipids are essential for the structure, function, and regulation of biological
systems.
3.Classification of lipids:
Lipids are classified into several main categories:
1.Fatty Acids:
These are the building blocks of many lipids. They can be saturated (no double
bonds) or unsaturated (one or more double bonds).
2. Triglycerides:
These are fats and oils. They consist of three fatty acids attached to a glycerol
molecule. They are a major energy storage form in the body.
3. Phospholipids:
These are major components of cell membranes. They consist of a glycerol
molecule, two fatty acids, a phosphate group, and a polar head group.
4. Steroids:
Includes cholesterol and hormones like estrogen and testosterone.
They have a characteristic ring structure.
5. Waxes:
These are long-chain fatty acids esterified to long-chain alcohols. They serve as
protective coatings in plants and animals.

43
6. Sphingolipids:
These are based on the amino alcohol sphingosine and are important components
of cell membranes.
7. Lipoproteins:
These are complexes of lipids and proteins. They transport lipids in the
bloodstream, including HDL (high-density lipoprotein) and LDL (low-density
lipoprotein).
8. Isoprenoids:
Also known as terpenoids, they include compounds like vitamin A, carotenoids,
and many natural rubber products.
9. Eicosanoids:
These are signaling molecules that include prostaglandins and leukotrienes, which
are involved in inflammation and other cellular processes.

44
4.Chemical structure of lipids:
Lipids are a diverse group of organic compounds, and their general chemical
structure consists of long hydrocarbon chains or rings. The
main types of lipids include triglycerides (fats and oils), phospholipids, and
steroids. Here are their basic structures:
1. Triglycerides:
- General Formula: C55H98O6
- Structure: Three fatty acid chains (hydrocarbon tails) attached to a
glycerol molecule.
2. Phospholipids:
- General Formula: Varies, but one common example is C42H80NO8P
- Structure: Two fatty acid chains, a glycerol molecule, a phosphate group,
and a polar head group. The specific structures can vary.
3. Steroids (e.g., cholesterol):
- General Formula: Varies, but cholesterol's molecular formula is
C27H46O
- Structure: A four-ring structure with a hydrocarbon tail in the case of
cholesterol.
(a) Hydrogen chains of lipids:
Hydrogen chains of lipids refer to the hydrocarbon chains found in the structure of
lipids, particularly in fatty acids and triglycerides. These hydrocarbon chains
consist of carbon atoms bonded to each other, with hydrogen atoms saturating the
remaining bonding sites on the carbon atoms. The length and saturation of these
hydrocarbon chains play a significant role in the properties and functions of lipids,
such as their role in cell membranes and energy storage. Longer and more saturated
chains tend to be solid at room temperature, as seen in fats, while shorter and more
unsaturated chains are often liquid, as seen in oils.
(b) Functional groups of lipids:
Lipids are a diverse group of organic molecules, and they can be categorized into
several functional groups. The main functional groups of lipids include:
1. Fatty Acids: These are the building blocks of many lipids. They consist of a
long hydrocarbon chain with a carboxylic acid group (COOH) at one end.

45
 2. Triglycerides: These are the most common dietary fats and oils, consisting of
three fatty acid chains esterified to a glycerol molecule.
3. Phospholipids: These are a major component of cell membranes, with two fatty
acid chains and a phosphate group attached to glycerol.
4. Steroids: These lipids have a characteristic four-ring structure.
Cholesterol is a well-known example.
5. Waxes: Waxes consist of long-chain fatty acids esterified to longchain alcohols.
They serve as protective coatings in many organisms.
6. Glycolipids: These lipids have a carbohydrate group attached to the
hydrophobic lipid tail. They play a role in cell recognition and adhesion.
These functional groups give lipids their diverse properties and enable them to
perform various biological functions in living organisms.

5.Saturation and unsaturation of lipids:

The terms "saturation" and "unsaturation" are commonly used to describe the
structure of fatty acids, which are a key component of lipids.

1. Saturated Fatty Acids:

These fatty acids have no double bonds between the carbon atoms in their
hydrocarbon chain. As a result, they are fully saturated with hydrogen atoms.
Saturated fats tend to be solid at room temperature and are often found in
animal products like butter and lard. They are associated with an increased risk
of cardiovascular disease when consumed in excess.
2.Unsaturated Fatty Acids:
These fatty acids have one or more double bonds between the carbon atoms in their
hydrocarbon chain. Unsaturated fats can be further divided into:
- Monounsaturated Fatty Acids: These contain one double bond. Foods rich in
monounsaturated fats include olive oil, avocados, and nuts. They are considered
heart-healthy.
- Polyunsaturated Fatty Acids: These contain multiple double bonds. Two
common types are omega-3 and omega-6 fatty acids. Sources of polyunsaturated
fats include fatty fish (for omega-3) and vegetable oils (for omega-6). They are
also considered beneficial for health.

46
The degree of saturation affects the physical properties of lipids. Saturated fats are
typically solid at room temperature, while unsaturated fats are usually liquid. This
is why saturated fats are often referred to as "bad" fats in excessive amounts, as
they are associated with health issues, whereas unsaturated fats, particularly the
monounsaturated and polyunsaturated types, are considered "good" fats and are
part of a healthy diet.

6.Properties of lipids:
Lipids are diverse organic molecules with several important properties in
chemistry:

1. Hydrophobic:
Lipids are generally nonpolar and hydrophobic, meaning they don't mix well
with water due to their long hydrocarbon chains.

2. Fats and Oils:

Common lipid examples include triglycerides, which can be solid fats
(saturated) or liquid oils (unsaturated) at room temperature.
3. Energy Storage:
Lipids are a primary energy storage molecule in organisms, providing more
energy per gram than carbohydrates or proteins.
4. Structure:
Phospholipids are vital components of cell membranes, forming a lipid bilayer
that separates the internal and external environments of cells.
5.Steroids:
Steroids are another class of lipids, including cholesterol and hormones like
testosterone and estrogen.
6.Insulation:
Lipids can serve as insulators, helping to retain heat in organisms.
7. Protection:

47
 In some organisms, lipids, like waxes, serve as protective coatings or barriers.
8. Lipid Reactions:
Lipids can undergo various chemical reactions, including hydrolysis to release fatty
acids or esterification to form triglycerides.
These properties make lipids essential for various biological functions and
chemical processes.
7.Significance of lipids
Lipids have several significant roles in the human body:
1. Energy Storage: They are a dense source of energy and serve as long-term energy
storage in the form of triglycerides.
2. Structural Components: Lipids are vital for cell membrane structure, providing
fluidity and maintaining the integrity of cell membranes.
3. Insulation: Adipose tissue, a type of lipid, acts as insulation and helps regulate
body temperature.
4. Hormone Production: Lipids are essential for the synthesis of steroid hormones,
such as testosterone and estrogen.
5. Brain Function: Lipids, including essential fatty acids, play a crucial role in brain
development and function.
6. Absorption of Fat-Soluble Vitamins: They aid in the absorption of fat-soluble
vitamins (A, D, E, and K) in the digestive system.
7. Protection: Lipids can provide cushioning and protection to vital organs, such as
the heart and kidneys.
8. Long-term Satiety: Dietary fats help regulate appetite and provide a sense of
fullness.
9. Cellular Signaling: Some lipids act as signaling molecules in cell communication.
Overall, lipids are essential for various physiological processes and are a
fundamental component of a balanced diet.

48
Kalsoom Shahzadi

Bsf2102457

Nucleic Acid
History
Nucleic acid was first discovered by Friedrich Miescher in 1869 at the
University of Tübingen, Germany. He gave its first name as nuclein.

Fig. Friedrich Miescher

In the early 1880s Albrecht Kossel further purified the substance and discovered
its highly acidic properties. He later also identified the nucleobases. In 1889
Richard Altmann created the term nucleic acid – at that time DNA and RNA were
not differentiated. In 1938 Astbury and Bell published the first X-ray diffraction
pattern of DNA.

Introduction

Nucleic acids are biopolymers, macromolecules, essential to all known forms of life.
They are composed of nucleotides, which are the monomer components: 5-
carbon sugar, phosphate group and nitrogenous base

49
Nucleic acid, naturally occurring chemical compound that is capable of being
broken down to yield phosphoric acid, sugars, and a mixture of organic bases
(purines and pyrimidines). Nucleic acids are the main information-carrying
molecules of the cell, and, by directing the process of protein synthesis, they
determine the inherited characteristics of every living thing.

Nomenclature
The term nucleic acid is the overall name for DNA and RNA, members of a
family of biopolymers, and is synonymous with polynucleotide. Nucleic acids
were named for their initial discovery within the nucleus, and for the presence of
phosphate groups (related to phosphoric acid). Although first discovered within
the nucleus of eukaryotic cells, nucleic acids are now known to be found in all life
forms including within bacteria, archaea, mitochondria, chloroplasts, and viruses
(There is debate as to whether viruses are living or non-living).

Nucleotides: Building blocks of nucleic acids

The repeating, or monomer, units that are linked together to form nucleic acids are known
as nucleotides.

The deoxyribonucleic acid (DNA) of a typical mammalian cell contains about 3 ×

109 nucleotides. Nucleotides can be further broken down to a phosphate group
(PO4-3) and a nucleoside which is composed of a aldopentose sugar (a sugar with
five carbon atoms), and a heterocyclic purine or pyrimidine base (a base
containing nitrogen atoms).

Basic structure
➢ Each nucleotide consists of a nitrogen-containing aromatic base attached
to a pentose (five-carbon) sugar, which is in turn attached to a phosphate
group.  Each nucleic acid contains four of five possible
nitrogencontaining bases: adenine (A), guanine (G), cytosine (C), thymine

50
 (T), and uracil (U). A and G are categorized as purines, and C, T, and U
are collectively called pyrimidines.
➢ All nucleic acids contain the bases A, C, and G; T, however, is found only
in DNA, while U is found in RNA.

Fig. Structure of Purines and Pyrimidines Classification

➢The pentose sugar in DNA (2′-deoxyribose) differs from the sugar in RNA
(ribose) by the absence of a hydroxyl group (―OH) on the 2′ carbon of the
sugar ring. Without an attached phosphate group, the sugar attached to one of
the bases is known as a nucleoside.
➢The phosphate group connects successive sugar residues by bridging the
5′hydroxyl group on one sugar to the 3′-hydroxyl group of the next sugar in
the chain. These nucleoside linkages are called phosphodiester bonds and are
the same in RNA and DNA.

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 Fig. Phosphodiester Bond

The two main classes of nucleic acids are

1. Deoxyribonucleic acid (DNA)
2. Ribonucleic acid (RNA)
If the sugar is ribose, the polymer is RNA; if the sugar is deoxyribose, a
version of ribose, the polymer is DNA.

Fig. Deoxyribose and Ribose Sugar

52
1.DNA (Deoxyribonucleic Acid)
DNA is a polymer of the four nucleotides A, C, G, and T, which are joined
through a backbone of alternating phosphate and deoxyribose sugar residues.
These nitrogen-containing bases occur in complementary pairs as determined by
their ability to form hydrogen bonds between them.
A always pairs with T through two hydrogen bonds, and G always pairs with C
through three hydrogen bonds. The spans of A:T and G:C hydrogen-bonded
pairs are nearly identical, allowing them to bridge the sugar-phosphate chains
uniformly. This structure, along with the molecule’s chemical stability, makes
DNA the ideal genetic material. The bonding between complementary bases
also provides a mechanism for the replication of DNA and the transmission of
genetic information.

Fig. Structure of DNA

Chemical Structure

In 1953 James D. Watson and Francis H.C. Crick proposed a three-dimensional

structure for DNA based on low-resolution X-ray crystallographic data and on Erwin
Chargaff’s observation that, in naturally occurring DNA, the amount of T equals the
amount of A and the amount of G equals the amount of C.

53
Watson and Crick, who shared a Nobel Prize in 1962 for their efforts,
postulated that two strands of polynucleotides coil around each other, forming a
double helix. The two strands, though identical, run in opposite directions as
determined by the orientation of the 5′ to 3′ phosphodiester bond. The sugar-
phosphate chains run along the outside of the helix, and the bases lie on the
inside, where they are linked to complementary bases on the other strand through
hydrogen bonds.

Fig. Major and Minor Grooves of DNA

➢ The double helical structure of normal DNA takes a right-handed form

called the B-helix. The helix makes one complete turn approximately every
10 base pairs.
➢ B-DNA has two principal grooves, a wide major groove and a narrow
minor groove. Many proteins interact in the space of the major groove,
where they make sequence-specific contacts with the bases. In addition, a
few proteins are known to make contacts via the minor groove.
➢ Several structural variants of DNA are known. In A-DNA, which forms
under conditions of high salt concentration and minimal water, the base
pairs are tilted and displaced toward the minor groove.

54
 ➢ Left-handed Z-DNA forms most readily in strands that contain sequences
with alternating purines and pyrimidines. DNA can form triple helices
when two strands containing runs of pyrimidines interact with a third
strand containing a run of purines.
➢ B-DNA is generally depicted as a smooth helix; however, specific
sequences of bases can distort the otherwise regular structure. For example,
short tracts of A residues interspersed with short sections of general
sequence result in a bent DNA molecule.
Biochemical properties
I. Denaturation
The strands of the DNA double helix are held together by hydrogen bonding
interactions between the complementary base pairs. Heating DNA in solution
easily breaks these hydrogen bonds, allowing the two strands to separate—a
process called denaturation or melting. The two strands may reassociate when
the solution cools, reforming the starting DNA duplex—a process called
renaturation or hybridization.

II. Ultraviolet absorption

DNA melting and reassociation can be monitored by measuring the absorption of
ultraviolet (UV) light at a wavelength of 260 nanometres (billionths of a metre).
When DNA is in a double-stranded conformation, absorption is fairly weak, but
when DNA is single-stranded, the unstacking of the bases leads to an
enhancement of absorption called hyperchromicity. Therefore, the extent to
which DNA is single-stranded or double-stranded can be determined by
monitoring UV absorption.

III. Chemical modification

After a DNA molecule has been assembled, it may be chemically modified—
sometimes deliberately by special enzymes called DNA methyltransferases and
sometimes accidentally by oxidation, ionizing radiation, or the action of chemical

55
IV. Nucleases
Nucleases are enzymes that hydrolytically cleave the phosphodiester backbone of
DNA. Endonucleases cleave in the middle of chains, while exonucleases operate
selectively by degrading from the end of the chain. Nucleases that act on both
single- and double-stranded DNA are known.

V. Restriction endonucleases
Restriction endonucleases are a special class that recognize and cleave specific
sequences in DNA. Type II restriction endonucleases always cleave at or near
their recognition sites. They produce small, well-defined fragments of DNA that
help to characterize genes and genomes and that produce recombinant DNAs.
Fragments of DNA produced by restriction endonucleases can be moved from
one organism to another. In this way it has been possible to express proteins such
as human insulin in bacteria.
2.RNA (Ribonucleic Acid)

Chemically RNA is similar to DNA, it is a chain of similar monomers. The

building blocks are nucleotides containing the 5-carbon sugar ribose, a phosphate
and a nitrogenous base. The phosphate is attached to the 5′ carbon of the ribose
and the nitrogenous base to the 1′ carbon. RNA contains four bases adenine,
guanine, cytosine and uracil. RNA is more labile (easily broken down) than DNA
and most RNA molecules do not form stable secondary structures, some notable
exceptions will be discussed below. The properties of RNA make it ideal as a
genetic messenger during protein synthesis, the idea of this genetic messenger,
mRNA, was proposed by François Jacob and Jacques Monod.

The structure of RNA

An RNA strand containing the four nucleotides with the nitrogenous bases:
adenine (A), cytosine (C), guanine (G) and uracil (U) respectively. The 3′ carbon
of the ribose of one nucleotide is linked to the 5′ carbon of the next via a
phosphodiester bond. The 5′ end on the left and the 3′ end on the right.

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 Fig. Structure of RNA

RNA Types
There are various types of RNA, out which most well-known and most
commonly studied in the human body are :

I.Transfer RNA
The transfer RNA is held responsible for choosing the correct protein or the
amino acids required by the body in-turn helping the ribosomes. It is located at
the endpoints of each amino acid. This is also called as soluble RNA and it forms
a link between the messenger RNA and the amino acid.

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 Fig. Transfer RNA
tRNAs are RNA molecules that translate mRNA into proteins. They have a
cloverleaf structure that consists of a 3’ acceptor site, 5’ terminal phosphate, D
arm, T arm, and anticodon arm. The primary function of a tRNA is to carry
amino acids on its 3’ acceptor site to a ribosome complex with the help of
aminoacyltRNA synthetase. Aminoacyl-tRNA synthetases are enzymes that load
the appropriate amino acid onto a free tRNA to synthesize proteins. Once an
amino acid is bound to tRNA, the tRNA is considered an aminoacyl-tRNA. The
type of amino acid on a tRNA is dependent on the mRNA codon, which is a
sequence of three nucleotides that codes for an amino acid. The anticodon arm of
the tRNA is the site of the anticodon, which is complementary to an mRNA
codon and dictates which amino acid to carry. tRNAs also regulate apoptosis by
acting as a cytochrome c scavenger.
II. Ribosomal RNA
The rRNA is the component of the ribosome and are located within the in the
cytoplasm of a cell, where ribosomes are found. In all living cells, the ribosomal
RNA plays a fundamental role in the synthesis and translation of mRNA into
proteins. The rRNA is mainly composed of cellular RNA and are the most
predominant RNA within the cells of all living beings.

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 Fig. rRNA

rRNA forms ribosomes, which are essential in protein synthesis. A ribosome

contains a large and small ribosomal subunit. In prokaryotes, a small 30S and
large 50S ribosomal subunit make up a 70S ribosome. In eukaryotes, the 40S and
60S subunit form an 80S ribosome. The ribosomes contain an exit (E), peptidyl
(P), and acceptor (A) site to bind aminoacyl-tRNAs and link amino acids together
to create polypeptides.
III. Messenger RNA
This type of RNA functions by transferring the genetic material into the
ribosomes and pass the instructions about the type of proteins, required by the
body cells. Based on the functions, these types of RNA is called the messenger
RNA.
Therefore, the mRNA plays a vital role in the process of transcription or during
the protein synthesis process.

Prokaryotic mRNA does not need to be processed and can proceed to synthesize
proteins immediately.

In eukaryotes, a freshly transcribed RNA transcript is considered a pre-mRNA

and needs to undergo maturation to form mRNA. A pre-mRNA contains non-
coding and coding regions known as introns and exons, respectively. During pre-
mRNA processing, the introns are spliced, and the exons are joined together. A
5’ cap known as 7-methylguanosine is added to the 5’ end of the RNA transcript,

59
and the 3’ end is polyadenylated. Polyadenylation refers to the process where a
poly(A) tail, which is a sequence of adenine nucleotides, is added to the
transcript. The 5’ cap protects the mRNA from degradation, and the 3’ poly(A)
tail contributes to the stability of mRNA and aids it in transport. Researchers are
also studying mRNA as an anti-cancer treatment due to its ability to modify cells.

Fig. RNA processing in eukaryotes

Functions of Nucleic Acid
➢ Nucleic acids are responsible for the transmission of inherent characters
from parent to offspring.
➢ They are responsible for the synthesis of protein in our body.
➢ DNA fingerprinting is a method used by forensic experts to determine
paternity. It is also used for the identification of criminals. It has also
played a major role in studies regarding biological evolution and genetics.
➢ Loss of DNA content is linked to many diseases.
➢ DNA is an essential component required for transferring genes from
parents to offspring.
➢ All the information of a cell is stored in DNA.

The primary functions of RNA:

➢ Facilitate the translation of DNA into proteins

➢ Functions as an adapter molecule in protein synthesis  Serves as a
messenger between the DNA and the ribosomes.

60
➢ They are the carrier of genetic information in all living cells
➢ Promotes the ribosomes to choose the right amino acid which is required in
building up of new proteins in the body.

61
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