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❖Bio molecules are the molecules present in a
living organism. These bio molecules are
fundamental building blocks of living organisms.
❖They support the biological processes essential
for life. Ex: carbohydrates, proteins, nucleic-acids,
lipids, enzymes, vitamins, etc.
Carbohydrates are involved in energy storage; the
hormones catalyse the biochemical reactions;
DNA/RNA store/transmit the genetic codes of a
living being.
 Proteins are polymers of α-amino acids. They are essential for
growth and maintenance of a living being’s. They occur naturally
in milk, cheese, pulses, peanuts, fish, meat, etc.
 Amino acids contain an amino (–NH2) and carboxyl (–COOH)
functional groups. The amino acids can be classified as α, β, γ, δ
and so on, on the basis of the relative position of the amino group
with respect to the carboxyl group.
 The linkage/bond between molecules of amino acids is known as
Peptide bond.
 Change in the biological activity of a protein due to change in the
ambient temperature or pH level denaturizes proteins.
 Curdling of milk or coagulation of egg white on boiling is an
example of denaturation of Proteins.
 The structure of protein sets the foundation for its interaction with
other molecules in the body and, therefore, determines its
function.
❖ Proteins are made up of a long chain of amino acids. Even with a
limited number of amino acid monomers – there are only 20 amino
acids commonly seen in the human body – they can be arranged in a
vast number of ways to alter the three-dimensional structure and
function of the protein. The simple sequencing of the protein is known
as its primary structure.
❖ The secondary protein structure depends on the local interactions
between parts of a protein chain, which can affect the folding and
three-dimensional shape of the protein. There are two main things
that can alter the secondary structure:
❖ α-helix: N-H groups in the backbone form a hydrogen bond with
the C=O group of the amino acid 4 residues earlier in the helix.
❖ β-pleated sheet: N-H groups in the backbone of one strand form
hydrogen bonds with C=O groups in the backbone of a fully extended
strand next to it.
❖ There can also be a several functional groups such as alcohols,
carboxamines, carboxylic acids, thioesters, thiols, and other basic
groups linked to each protein. These functional groups also affect the
folding of the proteins and, hence, its function in the body.
Tertiary structure
❖ The tertiary structure of proteins
refers to the overall three-
dimensional shape, after the
secondary interactions. These
include the influence of polar,
nonpolar, acidic, and basic R groups
that exist on the protein.
Quaternary protein
 The quaternary protein structure refers to the orientation and
arrangement of subunits in proteins with multi-subunits. This is
only relevant for proteins with multiple polypeptide chains.
 Proteins fold up into specific shapes according to the sequence of
amino acids in the polymer, and the protein function is directly
related to the resulting 3D structure.
 Proteins may also interact with each other or other
macromolecules in the body to create complex assemblies. In these
assemblies, proteins can develop functions that were not possible
in the standalone protein, such as carrying out DNA replication
and the transmission of cell signals.
 The nature of proteins is also highly variable.
 For example, some are quite rigid, whereas other are somewhat
flexible. These characteristics also fit the function of the protein.
For example, more rigid proteins may play a role in the structure
of the cytoskeleton or connective tissues. On the other hand, those
with some flexibility may act as hinges, springs, or levers to assist
in the function of other proteins.
Proteins play an important role in many crucial
biological processes and functions. They are very
versatile and have many different functions in the
body, as listed below:
 Act as catalysts
 Transport other molecules
 Store other molecules
 Provide mechanical support
 Provide immune protection
 Generate movement
 Transmit nerve impulses
 Control cell growth and differentiation
Haemoglobin is the red colouring matter of blood which is present in the red
blood cells. It is a conjugated protein consisting of haeme and the protein
globin. ❖ The structure of Haemoglobin can be classified as
a. Structure of Haeme, the prosthetic group.
b. Structure of Globin, the protein part— apo-protein.
Structure of Heme:
❖ It is an iron porphyrin. The porphyrins are cyclic compounds with “tetra
pyrrole” structure.
❖ Four pyrrole rings called I to IV are linked through methylene bridges.
❖ The outer carbon atoms, which are not linked with the methylene bridges,
are numbered 1 to 8.
❖ The methylidene bridges are designated as α, β, γ, δ, respectively.
❖ Iron in the ferrous state is bound to the nitrogen atom of the pyrrole rings.
❖ Iron is also linked internally (5th linkage) to the nitrogen of the imidazole
ring of Histidine of the polypeptide chains.
❖ The propionic acid of 6th and 7th position of haeme of III and IV pyrroles
are also linked to the amino acids Arg and Lys of the polypeptide chain,
respectively.
 Nucleic Acid: Nucleic acids are polymers of nucleotides present in
the nucleus of all living cells. They play an important role in the
biosynthesis of proteins. Also, they store and transmit the genetic
codes of a living being from the parent to its offspring.
 Mainly, there are two types of nucleic acids - deoxyribonucleic
acid (DNA) and ribonucleic acid (RNA).
 DNA contains the deoxyribose sugar, while RNA contains the
ribose sugar. The main and only difference between ribose and
deoxyribose sugar is that ribose has one more -OH group than
deoxyribose, which has -H attached to the second carbon in the
ring.
 DNA is double-stranded and RNA is a single-stranded molecule.
 Base pairing in DNA and RNA is slightly different as DNA uses
the bases adenine, thymine, cytosine, and guanine and RNA uses
the bases adenine, uracil, cytosine, and guanine.
 DNA is made up of molecules called nucleotides. Each nucleotide contains a
phosphate group, a sugar group and a nitrogen base.
 The four types of nitrogen bases are adenine (A), thymine (T), guanine (G) and
cytosine (C).
 The order of these bases is that determines DNA's instructions or genetic code.
 Human DNA has around 3 billion bases, and more than 99 % of those bases
are the same in all people, according to the U.S. National Library of Medic
 Watson, Crick, and Wilkins proposed in the early 1950s a model of a
doublestranded DNA molecule.
 The two strands of this double-stranded helix are held by hydrogen bonds
between the purine and pyrimidine bases of the respective linear molecules.
The pairing between purine and pyrimidine nucleotides on the opposite
strands are very specific and are dependent upon hydrogen bonding of A
with T and G with C.
 This common form of DNA is said to be right handed. A to pair only with T
by two hydrogen bonds and G only with C by three hydrogen bonds .
 Thus, the G–C bonds are much more resistant to denaturation than A–T rich
regions.
 DNA is the information molecule. It stores instructions for making other
large molecules, called proteins. These instructions are stored inside each
cells and distributed among 46 long structures called chromosomes.
 These chromosomes are made up of thousands of shorter segments of
DNA, called genes. Each gene stores the directions for making protein
fragments.
 DNA is well-suited to perform biological function because of its
molecular structure and the development of a series of high performance
enzymes.
 The match between DNA structure and the activities of these enzymes is
so effective and well-defined that DNA has become, over evolutionary
time, the universal informationstorage molecule for all forms of life.
 Nature has yet to find a better solution than DNA for storing, expressing,
and passing along instructions for making proteins.
 A person's DNA contains information about their heritage, and can
sometimes reveal whether they are at risk for certain diseases.
 DNA tests, or genetic tests, are used for a variety of reasons, including to
diagnose genetic disorders, to determine whether a person is a carrier of a
genetic mutation that they could pass on to their children, and to examine
whether a person is at risk for a genetic disease.
 RNA is typically single stranded and is made of ribo-nucleotide
that are linked by phospho-di-ester bonds. A ribo-nucleotide in
the RNA chain contains ribose sugar, one of the four nitrogenous
bases (A,U,G and C), and a phosphate group.
 The relative instability of RNA makes it more suitable for its more
short-term functions. The RNA-specific pyrimidine uracil forms a
complementary base pair with adenine and is used instead of the
thymine used in DNA. Even though RNA is single stranded, most
types of RNA molecules show extensive intra-molecular base
pairing between complementary sequences within the RNA
strand.
 Based on the role in protein synthesis, RNA‘s are of three types. They
are messenger RNA(mRNA), transfer RNA(tRNA), and ribosomal
RNA(rRNA), which are present in all organisms. These RNA
primarily carry out biochemical reactions, similar to enzymes and
play an important role in both normal cellular processes and diseases.
 In protein synthesis, mRNA carries genetic codes from the DNA in
the nucleus to ribosomes.
 Ribosomes are composed of rRNA and protein. The ribosome protein
subunits are encoded by rRNA and are synthesized in the nucleolus.
❖ Once fully assembled, they move to the cytoplasm, where they act
as key regulators of translation, they “read” the code carried by
mRNA.
 A sequence of three nitrogenous bases in mRNA specifies
incorporation of a specific amino acid in the sequence that makes up
the protein.
 Molecules of tRNA which contain fewer than 100 nucleotides, bring
the specified amino acids to the ribosomes, where they are linked to
form proteins.
Carbohydrates are defined as biomolecules
containing a group of naturally occurring carbonyl
compounds (aldehydes or ketones) and several
hydroxyl groups. It consists of carbon (C), hydrogen
(H), and oxygen (O) atoms, usually with a hydrogen-
oxygen atom ratio of 2:1 (as in water). It’s represented
with the empirical formula Cm(H2O)n (where m and
n may or may not be different) or (CH2O)n
Classification of Carbohydrates
Carbohydrates are divided into four major groups
based on the degree of polymerization:
monosaccharides, disaccharides, oligosaccharides,
and polysaccharides.
 Monosaccharides are the simplest carbohydrates and cannot be
hydrolyzed into other smaller carbohydrates. The “mono” in
monosaccharides means one, which shows the presence of only
one sugar unit.
 They are the building blocks of disaccharides and
polysaccharides. For this reason, they are also known as simple
sugars. These simple sugars are colorless, crystalline solids that
are soluble in water and insoluble in a nonpolar solvent.
The general formula representing monosaccharide structure is
Cn(H2O)n
The monosaccharides containing the aldehyde group (the functional
group with the structure, R-CHO) are known as aldolases and the one
containing ketone groups is called ketoses (the functional group with
the structure RC(=O)R′). Some examples of monosaccharides are
glucose, fructose, erythrulose, and ribulose.
 Monosaccharides are either present as linear chains or ring-
shaped molecules. In a ring form, glucose’s hydroxyl group (-OH)
can have two different arrangements around the anomeric carbon
(carbon-1 that becomes asymmetric in the process of ring
formation).
 If the hydroxyl group is below carbon number 1 in the sugar, it is
said to be in the alpha (α) position, and if it is above the plane, it is
said to be in the beta (β) position
 Glucose (C6H12O6) is an important source of energy in
humans and plants. Plants synthesize glucose using
carbon dioxide and water, which in turn is used for
their energy requirements. They store the excess
glucose as starch which humans and herbivores
consume.
 The presence of galactose is in milk sugar (lactose), and
fructose in fruits and honey makes these foods sweet.
 Ribose is a structural element of nucleic acids and some
coenzymes.
 Mannose is a constituent of mucoproteins and
glycoproteins required for the proper functioning of
the body
 Disaccharides consist of two sugar units. When subjected to a
dehydration reaction (condensation reaction or dehydration
synthesis), they release two monosaccharide units.
 In this process, the hydroxyl group of one monosaccharide
combines with the hydrogen of another monosaccharide through
a covalent bond, releasing a molecule of water. The covalent bond
formed between the two sugar molecules is known as a glycosidic
bond.
 The glycosidic bond or glycosidic linkage can be alpha or beta
type. The alpha bond is formed when the OH group on the
carbon-1 of the first glucose is below the ring plane, and a beta
bond is formed when the OH group on the carbon-1 is above the
ring plane.
Reducing sugar: A disaccharide in which the reducing sugar has a free
hemiacetal unit serving as a reducing aldehyde group. Examples
include maltose and cellobiose.
Non-reducing Sugar: Disaccharides that do not have a free hemiacetal
because they bond through an acetal linkage between their anomeric
centers. Examples are sucrose and trehalose.
 Sucrose is a product of photosynthesis, which
functions as a major source of carbon and energy
in plants.
 Lactose is a major source of energy in animals.
 Maltose is an important intermediate in starch and
glycogen digestion.
 Trehalose is an essential energy source for insects.
 Cellobiose is essential in carbohydrate metabolism.
 Gentiobiose is a constituent of plant glycosides and
some polysaccharides.
 Oligosaccharides are compounds that yield 3 to 10 molecules of the same
or different monosaccharides on hydrolysis. All the monosaccharides are
joined through glycosidic linkage. And based on the number of
monosaccharides attached, the oligosaccharides are classified as
trisaccharides, tetrasaccharides, pentasaccharides, and so on.
 The general formula of trisaccharides is Cn(H2O)n-2, and that of
tetrasaccharides is Cn(H2O)n-3, and so on. The oligosaccharides are
normally present as glycans. They are linked to either lipids or amino
acid side chains in proteins by N- or O-glycosidic bonds known as
glycolipids or glycoproteins.
 The glycosidic bonds are formed in the process of glycosylation, in which
a carbohydrate is covalently attached to an organic molecule, creating
structures such as glycoproteins and glycolipids
N-Linked Oligosaccharides: It involves the attachment of
oligosaccharides to asparagine via a beta linkage to the amine nitrogen of the
side chain. In eukaryotes, this process occurs at the membrane of the
endoplasmic reticulum. Whereas in prokaryotes, it occurs at the plasma
membrane.
O-Linked Oligosaccharides: It involves the attachment of
oligosaccharides to threonine or serine on the hydroxyl
group of the side chain. It occurs in the Golgi apparatus,
where monosaccharide units are added to a complete
polypeptide chain.
Functions of Oligosaccharides
 Glycoproteins are carbohydrates attached to proteins
involved in 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 are carbohydrates attached to lipids that
are important for cell recognition and modulate
membrane proteins that act as receptors.
 Cells produce specific carbohydrate-binding proteins
known as lectins, which mediate cell adhesion with
oligosaccharides.
 Oligosaccharides are a component of fiber from plant
tissues.
 Polysaccharides are a chain of more than 10 carbohydrates joined
together through glycosidic bond formation. They are ubiquitous and
mainly involved in the structural or storage functions of organisms. They
are also known as glycans.
 These compounds’ physical and biological properties depend on the
components & the architecture of their binding or reacting molecules and
their interaction with the enzymatic machinery.
 Polysaccharides are classified based on their functions, the type of
monosaccharide units they contain, or their origin.
 Based on the type of monosaccharides involved in the formation of
polysaccharide structures, they are classified into two groups:
homopolysaccharides and heteropolysaccharides.
Homopolysaccharides:
 They are composed of repeating units of only one type of monomer. A
few examples of homopolysaccharides include cellulose, chitin, starches
(amylose and amylopectin), glycogen, and xylans. And based on their
functional roles, these compounds are classified into structural
polysaccharides and storage polysaccharides
 Cellulose is a linear, unbranched polymer of glucose units joined
by beta 1-4 linkages. It’s one of the most abundant organic
compounds in the biosphere.
 Chitin is a linear, long-chain polymer of N-acetyl-D-glucosamine
(a derivative of glucose) residues/units, joined by beta 1-4
glycosidic linkages. It’s the second most abundant natural
biopolymer after cellulose.
 Starch is made of repeating units of D-glucose that are joined
together by alpha-linkages. It’s one of the most abundant
polysaccharides found in plants and is composed of a mixture of
amylose (15-20%) and amylopectin (80-85%)
 They are composed of two or more repeating units of different
types of monomers. Examples include glycosaminoglycans,
agarose, and peptidoglycans. In natural systems, they are linked
to proteins, lipids, and peptides.
 Glycosaminoglycans (GAG) are negatively charged unbranched
heteropolysaccharides. They are composed of repeating units of
disaccharides with the general structural formula n. Amino acids
like N-acetylglucosamine or N-acetylgalactosamine and uronic
acid (like glucuronic acid) are normally present in the GAG
structure.
 Peptidoglycan is a heteropolymer of alternating units of N-
acetylglucosamine (NAG) and N-acetylmuramic acids (NAM),
linked together by beta-1,4-glycosidic linkage.
 Agarose is a polysaccharide composed of repeating units of a
disaccharide, agarobiose, consisting of D-galactose and 3,6-
anhydro-L-galactopyranose.
 Structural polysaccharide: They provide mechanical stability to cells,
organs, and organisms. Examples include chitin and cellulose. Chitin is
involved in the synthesis of fungal cell walls, while cellulose is an
important constituent of diet for ruminants.
 Storage polysaccharides: They are carbohydrate storage reserves that
release sugar monomers when required by the body. Examples include
starch, glycogen, and inulin. Starch stores energy for plants, and in
animals, it is catalyzed by the enzyme amylase (found in saliva) to fulfill
the energy requirement. Glycogen is a polysaccharide food reserve of
animals, bacteria, and fungi, while inulin is a storage reserve in plants
 Agarose provides a supporting structure in the cell wall of marine algae.
 Peptidoglycan is an essential component of bacterial cell walls. It
provides strength to the cell wall and participates in binary fission during
bacterial reproduction.
 Peptidoglycan protects bacterial cells from bursting by counteracting the
osmotic pressure of the cytoplasm.
Lipids differ from the other classes of naturally occurring biomolecules
(carbohydrates, proteins, and nucleic acids)
Lipids are more soluble in non-to-weakly polar solvents (diethyl ether,
hexane, dichloromethane) than they are in water.
Lipids include a variety of structural types, a collection of which is
introduced in this chapter.
In spite of the number of different structural types, Lipids share a
common biosynthetic origin in that they are ultimately derived from
glucose.
During one stage of carbohydrate metabolism, called glycolysis, glucose is
converted to lactic acid. Pyruvic acid is an intermediate
L IPI D
L IPI D
1. FATS, OILS, AND FATTY ACIDS
Fats and oils are naturally occurring mixtures of triacylglycerols, also
called triglycerides. They differ in that fats are solids at room temperature
and oils are liquids. We generally ignore this distinction and refer to both
groups as fats.
Triacylglycerols are built on a glycerol framework
All three acyl groups in a triacylglycerol may be the same, all three
may be different, or one may be different from the other two.
The structures of two typical triacylglycerols, 2-oleyl-1,3-distearylglycerol
and tristearin. Both occur naturally—in cocoa butter, for example.
All three acyl groups in tristearin are stearyl (octadecanoyl) groups.
In 2-oleyl-1,3-distearylglycerol, two of the acyl groups are stearyl, but the
one in the middle is oleyl (cis-9-octadecenoyl).
L IPI D
1. FATS, OILS, AND FATTY ACIDS
Hydrolysis of fats yields glycerol and long-chain fatty acids. Thus,
tristearin gives glycerol and three molecules of stearic acid on
hydrolysis. Table 1 lists a few representative fatty acids. As these
examples indicate, most naturally occurring fatty acids possess an even
number of carbon atoms and an unbranched carbon chain. The carbon
chain may be saturated or it can contain one or more double bonds.
When double bonds are present, they are almost always cis. Acyl groups
containing 14–20 carbon atoms are the most abundant in
triacylglycerols.
L IPI D
1. FATS, OILS, AND FATTY ACIDS
Table 1. Some Representative Fatty Acids
L IPI D
1. FATS, OILS, AND FATTY ACIDS
A few fatty acids with trans double bonds (trans fatty acids) occur
naturally, but the major source of trans fats comes from the
processing of natural fats and oils.
Furthermore, the same catalysts that promote hydrogenation
promote the reverse process—dehydrogenation—by which new
double bonds, usually trans, are introduced in the acyl group.
Fatty acids occur naturally in forms other than as glyceryl triesters,
and we’ll see numerous examples as we go through the chapter.
One recently discovered fatty acid derivative is anandamide.
Fatty acids are biosynthesized by way of acetyl coenzyme A. The
following section outlines the mechanism of fatty acid biosynthesis.
L IPI D
2. FATTY ACID BIOSYNTHESIS
We can describe the major elements of fatty acid biosynthesis by
considering the formation of butanoic acid from two molecules of acetyl
coenzyme A. The “machinery” responsible for accomplishing this
conversion is a complex of enzymes known as fatty acid synthetase.
L IPI D
2. FATTY ACID BIOSYNTHESIS
This phase of fatty acid biosynthesis concludes with the transfer of the acyl group
from acyl carrier protein to coenzyme A. The resulting acyl coenzyme A molecules
can then undergo a number of subsequent biological transformations. One such
transformation is chain extension, leading to acyl groups with more than 16
carbons. Another is the introduction of one or more carbon–carbon double bonds.
A third is acyl transfer from sulfur to oxygen to form esters such as triacylglycerols.
The process by which acyl coenzyme A molecules are converted to triacylglycerols
involves a type of intermediate called a phospholipid
L IPI D
3. PHOSPHOLIPIDS
L IPI D
4. WAXES
Waxes are water-repelling solids that are part of the protective
coatings of a number of living things, including the leaves of plants, the
fur of animals, and the feathers of birds.
Waxes are usually mixtures of esters in which both the alkyl and acyl
group are unbranched and contain a dozen or more carbon atoms.
Beeswax, for example, contains the ester triacontyl hexadecanoate as
one component of a complex mixture of hydrocarbons, alcohols, and
esters.
Fatty acids normally occur naturally as esters; fats, oils, phospholipids,
and waxes all are unique types of fatty acid esters. There is, however,
an important class of fatty acid derivatives that exists and carries out its
biological role in the form of the free acid. This class of fatty acid
derivatives
L IPI D
5. PROSTAGLANDINS
Sheep prostate glands proved to be a convenient source of this material
and yielded a mixture of structurally related substances referred to
collectively as prostaglandins.
We now know that prostaglandins are present in almost all animal tissues,
where they carry out a variety of regulatory functions.
Prostaglandins are extremely potent substances and exert their
physiological effects at very small concentrations. Because of this, their
isolation was difficult, and it was not until 1960 that the first members of
this class, designated PGE1 and PGF1’
L IPI D
6. TERPENES : THE ISOPRENE RULE
The word “essential” as applied to naturally occurring organic
substances can have two different meanings. For example, as used in
the previous section with respect to fatty acids, essential means
“necessary.”
Linoleic acid is an “essential” fatty acid; it must be included in the diet in
order for animals to grow properly because they lack the ability to
biosynthesize it directly.
“Essential” is also used as the adjective form of the noun “essence.” The
mixtures of substances that make up the fragrant material of plants are
called essential oils because they contain the essence, that is, the odor,
of the plant.
The study of the composition of essential oils ranks as one of the oldest
areas of organic chemical research. Very often, the principal volatile
component of an essential oil belongs to a class of chemical substances
called the terpenes.
L IPI D
6. TERPENES : THE ISOPRENE RULE
The structural feature that distinguishes terpenes from other natural
products is the isoprene unit. The carbon skeleton of myrcene
(exclusive of its double bonds) corresponds to the head-to-tail union of
two isoprene units.
Terpenes are often referred to as isoprenoid compounds.
L IPI D
6. TERPENES : THE ISOPRENE RULE
Table 2. Classification of Terpenes
Tail-to-tail linkages of isoprene units sometimes occur, especially in the
higher terpenes. The C(12)±C(13) bond of squalene unites two C15 units
in a tail-to-tail manner. Notice, however, that isoprene units are joined
head to tail within each C15 unit of squalene
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Biomolecules ARE DSCUSES IN THSI KSJDIFN

  • 1. ❖Bio molecules are the molecules present in a living organism. These bio molecules are fundamental building blocks of living organisms. ❖They support the biological processes essential for life. Ex: carbohydrates, proteins, nucleic-acids, lipids, enzymes, vitamins, etc. Carbohydrates are involved in energy storage; the hormones catalyse the biochemical reactions; DNA/RNA store/transmit the genetic codes of a living being.
  • 2.
  • 3.  Proteins are polymers of α-amino acids. They are essential for growth and maintenance of a living being’s. They occur naturally in milk, cheese, pulses, peanuts, fish, meat, etc.  Amino acids contain an amino (–NH2) and carboxyl (–COOH) functional groups. The amino acids can be classified as α, β, γ, δ and so on, on the basis of the relative position of the amino group with respect to the carboxyl group.  The linkage/bond between molecules of amino acids is known as Peptide bond.  Change in the biological activity of a protein due to change in the ambient temperature or pH level denaturizes proteins.  Curdling of milk or coagulation of egg white on boiling is an example of denaturation of Proteins.  The structure of protein sets the foundation for its interaction with other molecules in the body and, therefore, determines its function.
  • 4. ❖ Proteins are made up of a long chain of amino acids. Even with a limited number of amino acid monomers – there are only 20 amino acids commonly seen in the human body – they can be arranged in a vast number of ways to alter the three-dimensional structure and function of the protein. The simple sequencing of the protein is known as its primary structure.
  • 5. ❖ The secondary protein structure depends on the local interactions between parts of a protein chain, which can affect the folding and three-dimensional shape of the protein. There are two main things that can alter the secondary structure: ❖ α-helix: N-H groups in the backbone form a hydrogen bond with the C=O group of the amino acid 4 residues earlier in the helix. ❖ β-pleated sheet: N-H groups in the backbone of one strand form hydrogen bonds with C=O groups in the backbone of a fully extended strand next to it. ❖ There can also be a several functional groups such as alcohols, carboxamines, carboxylic acids, thioesters, thiols, and other basic groups linked to each protein. These functional groups also affect the folding of the proteins and, hence, its function in the body.
  • 6. Tertiary structure ❖ The tertiary structure of proteins refers to the overall three- dimensional shape, after the secondary interactions. These include the influence of polar, nonpolar, acidic, and basic R groups that exist on the protein.
  • 7. Quaternary protein  The quaternary protein structure refers to the orientation and arrangement of subunits in proteins with multi-subunits. This is only relevant for proteins with multiple polypeptide chains.  Proteins fold up into specific shapes according to the sequence of amino acids in the polymer, and the protein function is directly related to the resulting 3D structure.  Proteins may also interact with each other or other macromolecules in the body to create complex assemblies. In these assemblies, proteins can develop functions that were not possible in the standalone protein, such as carrying out DNA replication and the transmission of cell signals.  The nature of proteins is also highly variable.  For example, some are quite rigid, whereas other are somewhat flexible. These characteristics also fit the function of the protein. For example, more rigid proteins may play a role in the structure of the cytoskeleton or connective tissues. On the other hand, those with some flexibility may act as hinges, springs, or levers to assist in the function of other proteins.
  • 8. Proteins play an important role in many crucial biological processes and functions. They are very versatile and have many different functions in the body, as listed below:  Act as catalysts  Transport other molecules  Store other molecules  Provide mechanical support  Provide immune protection  Generate movement  Transmit nerve impulses  Control cell growth and differentiation
  • 9. Haemoglobin is the red colouring matter of blood which is present in the red blood cells. It is a conjugated protein consisting of haeme and the protein globin. ❖ The structure of Haemoglobin can be classified as a. Structure of Haeme, the prosthetic group. b. Structure of Globin, the protein part— apo-protein. Structure of Heme: ❖ It is an iron porphyrin. The porphyrins are cyclic compounds with “tetra pyrrole” structure. ❖ Four pyrrole rings called I to IV are linked through methylene bridges. ❖ The outer carbon atoms, which are not linked with the methylene bridges, are numbered 1 to 8. ❖ The methylidene bridges are designated as α, β, γ, δ, respectively. ❖ Iron in the ferrous state is bound to the nitrogen atom of the pyrrole rings. ❖ Iron is also linked internally (5th linkage) to the nitrogen of the imidazole ring of Histidine of the polypeptide chains. ❖ The propionic acid of 6th and 7th position of haeme of III and IV pyrroles are also linked to the amino acids Arg and Lys of the polypeptide chain, respectively.
  • 10.
  • 11.  Nucleic Acid: Nucleic acids are polymers of nucleotides present in the nucleus of all living cells. They play an important role in the biosynthesis of proteins. Also, they store and transmit the genetic codes of a living being from the parent to its offspring.  Mainly, there are two types of nucleic acids - deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).  DNA contains the deoxyribose sugar, while RNA contains the ribose sugar. The main and only difference between ribose and deoxyribose sugar is that ribose has one more -OH group than deoxyribose, which has -H attached to the second carbon in the ring.  DNA is double-stranded and RNA is a single-stranded molecule.  Base pairing in DNA and RNA is slightly different as DNA uses the bases adenine, thymine, cytosine, and guanine and RNA uses the bases adenine, uracil, cytosine, and guanine.
  • 12.
  • 13.  DNA is made up of molecules called nucleotides. Each nucleotide contains a phosphate group, a sugar group and a nitrogen base.  The four types of nitrogen bases are adenine (A), thymine (T), guanine (G) and cytosine (C).  The order of these bases is that determines DNA's instructions or genetic code.  Human DNA has around 3 billion bases, and more than 99 % of those bases are the same in all people, according to the U.S. National Library of Medic  Watson, Crick, and Wilkins proposed in the early 1950s a model of a doublestranded DNA molecule.  The two strands of this double-stranded helix are held by hydrogen bonds between the purine and pyrimidine bases of the respective linear molecules. The pairing between purine and pyrimidine nucleotides on the opposite strands are very specific and are dependent upon hydrogen bonding of A with T and G with C.  This common form of DNA is said to be right handed. A to pair only with T by two hydrogen bonds and G only with C by three hydrogen bonds .  Thus, the G–C bonds are much more resistant to denaturation than A–T rich regions.
  • 14.  DNA is the information molecule. It stores instructions for making other large molecules, called proteins. These instructions are stored inside each cells and distributed among 46 long structures called chromosomes.  These chromosomes are made up of thousands of shorter segments of DNA, called genes. Each gene stores the directions for making protein fragments.  DNA is well-suited to perform biological function because of its molecular structure and the development of a series of high performance enzymes.  The match between DNA structure and the activities of these enzymes is so effective and well-defined that DNA has become, over evolutionary time, the universal informationstorage molecule for all forms of life.  Nature has yet to find a better solution than DNA for storing, expressing, and passing along instructions for making proteins.  A person's DNA contains information about their heritage, and can sometimes reveal whether they are at risk for certain diseases.  DNA tests, or genetic tests, are used for a variety of reasons, including to diagnose genetic disorders, to determine whether a person is a carrier of a genetic mutation that they could pass on to their children, and to examine whether a person is at risk for a genetic disease.
  • 15.  RNA is typically single stranded and is made of ribo-nucleotide that are linked by phospho-di-ester bonds. A ribo-nucleotide in the RNA chain contains ribose sugar, one of the four nitrogenous bases (A,U,G and C), and a phosphate group.  The relative instability of RNA makes it more suitable for its more short-term functions. The RNA-specific pyrimidine uracil forms a complementary base pair with adenine and is used instead of the thymine used in DNA. Even though RNA is single stranded, most types of RNA molecules show extensive intra-molecular base pairing between complementary sequences within the RNA strand.
  • 16.  Based on the role in protein synthesis, RNA‘s are of three types. They are messenger RNA(mRNA), transfer RNA(tRNA), and ribosomal RNA(rRNA), which are present in all organisms. These RNA primarily carry out biochemical reactions, similar to enzymes and play an important role in both normal cellular processes and diseases.  In protein synthesis, mRNA carries genetic codes from the DNA in the nucleus to ribosomes.  Ribosomes are composed of rRNA and protein. The ribosome protein subunits are encoded by rRNA and are synthesized in the nucleolus. ❖ Once fully assembled, they move to the cytoplasm, where they act as key regulators of translation, they “read” the code carried by mRNA.  A sequence of three nitrogenous bases in mRNA specifies incorporation of a specific amino acid in the sequence that makes up the protein.  Molecules of tRNA which contain fewer than 100 nucleotides, bring the specified amino acids to the ribosomes, where they are linked to form proteins.
  • 17.
  • 18. Carbohydrates are defined as biomolecules containing a group of naturally occurring carbonyl compounds (aldehydes or ketones) and several hydroxyl groups. It consists of carbon (C), hydrogen (H), and oxygen (O) atoms, usually with a hydrogen- oxygen atom ratio of 2:1 (as in water). It’s represented with the empirical formula Cm(H2O)n (where m and n may or may not be different) or (CH2O)n Classification of Carbohydrates Carbohydrates are divided into four major groups based on the degree of polymerization: monosaccharides, disaccharides, oligosaccharides, and polysaccharides.
  • 19.  Monosaccharides are the simplest carbohydrates and cannot be hydrolyzed into other smaller carbohydrates. The “mono” in monosaccharides means one, which shows the presence of only one sugar unit.  They are the building blocks of disaccharides and polysaccharides. For this reason, they are also known as simple sugars. These simple sugars are colorless, crystalline solids that are soluble in water and insoluble in a nonpolar solvent. The general formula representing monosaccharide structure is Cn(H2O)n The monosaccharides containing the aldehyde group (the functional group with the structure, R-CHO) are known as aldolases and the one containing ketone groups is called ketoses (the functional group with the structure RC(=O)R′). Some examples of monosaccharides are glucose, fructose, erythrulose, and ribulose.
  • 20.  Monosaccharides are either present as linear chains or ring- shaped molecules. In a ring form, glucose’s hydroxyl group (-OH) can have two different arrangements around the anomeric carbon (carbon-1 that becomes asymmetric in the process of ring formation).  If the hydroxyl group is below carbon number 1 in the sugar, it is said to be in the alpha (α) position, and if it is above the plane, it is said to be in the beta (β) position
  • 21.
  • 22.  Glucose (C6H12O6) is an important source of energy in humans and plants. Plants synthesize glucose using carbon dioxide and water, which in turn is used for their energy requirements. They store the excess glucose as starch which humans and herbivores consume.  The presence of galactose is in milk sugar (lactose), and fructose in fruits and honey makes these foods sweet.  Ribose is a structural element of nucleic acids and some coenzymes.  Mannose is a constituent of mucoproteins and glycoproteins required for the proper functioning of the body
  • 23.  Disaccharides consist of two sugar units. When subjected to a dehydration reaction (condensation reaction or dehydration synthesis), they release two monosaccharide units.  In this process, the hydroxyl group of one monosaccharide combines with the hydrogen of another monosaccharide through a covalent bond, releasing a molecule of water. The covalent bond formed between the two sugar molecules is known as a glycosidic bond.  The glycosidic bond or glycosidic linkage can be alpha or beta type. The alpha bond is formed when the OH group on the carbon-1 of the first glucose is below the ring plane, and a beta bond is formed when the OH group on the carbon-1 is above the ring plane.
  • 24. Reducing sugar: A disaccharide in which the reducing sugar has a free hemiacetal unit serving as a reducing aldehyde group. Examples include maltose and cellobiose. Non-reducing Sugar: Disaccharides that do not have a free hemiacetal because they bond through an acetal linkage between their anomeric centers. Examples are sucrose and trehalose.
  • 25.  Sucrose is a product of photosynthesis, which functions as a major source of carbon and energy in plants.  Lactose is a major source of energy in animals.  Maltose is an important intermediate in starch and glycogen digestion.  Trehalose is an essential energy source for insects.  Cellobiose is essential in carbohydrate metabolism.  Gentiobiose is a constituent of plant glycosides and some polysaccharides.
  • 26.  Oligosaccharides are compounds that yield 3 to 10 molecules of the same or different monosaccharides on hydrolysis. All the monosaccharides are joined through glycosidic linkage. And based on the number of monosaccharides attached, the oligosaccharides are classified as trisaccharides, tetrasaccharides, pentasaccharides, and so on.  The general formula of trisaccharides is Cn(H2O)n-2, and that of tetrasaccharides is Cn(H2O)n-3, and so on. The oligosaccharides are normally present as glycans. They are linked to either lipids or amino acid side chains in proteins by N- or O-glycosidic bonds known as glycolipids or glycoproteins.  The glycosidic bonds are formed in the process of glycosylation, in which a carbohydrate is covalently attached to an organic molecule, creating structures such as glycoproteins and glycolipids N-Linked Oligosaccharides: It involves the attachment of oligosaccharides to asparagine via a beta linkage to the amine nitrogen of the side chain. In eukaryotes, this process occurs at the membrane of the endoplasmic reticulum. Whereas in prokaryotes, it occurs at the plasma membrane.
  • 27. O-Linked Oligosaccharides: It involves the attachment of oligosaccharides to threonine or serine on the hydroxyl group of the side chain. It occurs in the Golgi apparatus, where monosaccharide units are added to a complete polypeptide chain. Functions of Oligosaccharides  Glycoproteins are carbohydrates attached to proteins involved in 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 are carbohydrates attached to lipids that are important for cell recognition and modulate membrane proteins that act as receptors.  Cells produce specific carbohydrate-binding proteins known as lectins, which mediate cell adhesion with oligosaccharides.  Oligosaccharides are a component of fiber from plant tissues.
  • 28.  Polysaccharides are a chain of more than 10 carbohydrates joined together through glycosidic bond formation. They are ubiquitous and mainly involved in the structural or storage functions of organisms. They are also known as glycans.  These compounds’ physical and biological properties depend on the components & the architecture of their binding or reacting molecules and their interaction with the enzymatic machinery.  Polysaccharides are classified based on their functions, the type of monosaccharide units they contain, or their origin.  Based on the type of monosaccharides involved in the formation of polysaccharide structures, they are classified into two groups: homopolysaccharides and heteropolysaccharides. Homopolysaccharides:  They are composed of repeating units of only one type of monomer. A few examples of homopolysaccharides include cellulose, chitin, starches (amylose and amylopectin), glycogen, and xylans. And based on their functional roles, these compounds are classified into structural polysaccharides and storage polysaccharides
  • 29.  Cellulose is a linear, unbranched polymer of glucose units joined by beta 1-4 linkages. It’s one of the most abundant organic compounds in the biosphere.  Chitin is a linear, long-chain polymer of N-acetyl-D-glucosamine (a derivative of glucose) residues/units, joined by beta 1-4 glycosidic linkages. It’s the second most abundant natural biopolymer after cellulose.  Starch is made of repeating units of D-glucose that are joined together by alpha-linkages. It’s one of the most abundant polysaccharides found in plants and is composed of a mixture of amylose (15-20%) and amylopectin (80-85%)
  • 30.  They are composed of two or more repeating units of different types of monomers. Examples include glycosaminoglycans, agarose, and peptidoglycans. In natural systems, they are linked to proteins, lipids, and peptides.  Glycosaminoglycans (GAG) are negatively charged unbranched heteropolysaccharides. They are composed of repeating units of disaccharides with the general structural formula n. Amino acids like N-acetylglucosamine or N-acetylgalactosamine and uronic acid (like glucuronic acid) are normally present in the GAG structure.  Peptidoglycan is a heteropolymer of alternating units of N- acetylglucosamine (NAG) and N-acetylmuramic acids (NAM), linked together by beta-1,4-glycosidic linkage.  Agarose is a polysaccharide composed of repeating units of a disaccharide, agarobiose, consisting of D-galactose and 3,6- anhydro-L-galactopyranose.
  • 31.  Structural polysaccharide: They provide mechanical stability to cells, organs, and organisms. Examples include chitin and cellulose. Chitin is involved in the synthesis of fungal cell walls, while cellulose is an important constituent of diet for ruminants.  Storage polysaccharides: They are carbohydrate storage reserves that release sugar monomers when required by the body. Examples include starch, glycogen, and inulin. Starch stores energy for plants, and in animals, it is catalyzed by the enzyme amylase (found in saliva) to fulfill the energy requirement. Glycogen is a polysaccharide food reserve of animals, bacteria, and fungi, while inulin is a storage reserve in plants  Agarose provides a supporting structure in the cell wall of marine algae.  Peptidoglycan is an essential component of bacterial cell walls. It provides strength to the cell wall and participates in binary fission during bacterial reproduction.  Peptidoglycan protects bacterial cells from bursting by counteracting the osmotic pressure of the cytoplasm.
  • 32. Lipids differ from the other classes of naturally occurring biomolecules (carbohydrates, proteins, and nucleic acids) Lipids are more soluble in non-to-weakly polar solvents (diethyl ether, hexane, dichloromethane) than they are in water. Lipids include a variety of structural types, a collection of which is introduced in this chapter. In spite of the number of different structural types, Lipids share a common biosynthetic origin in that they are ultimately derived from glucose. During one stage of carbohydrate metabolism, called glycolysis, glucose is converted to lactic acid. Pyruvic acid is an intermediate L IPI D
  • 33. L IPI D 1. FATS, OILS, AND FATTY ACIDS Fats and oils are naturally occurring mixtures of triacylglycerols, also called triglycerides. They differ in that fats are solids at room temperature and oils are liquids. We generally ignore this distinction and refer to both groups as fats. Triacylglycerols are built on a glycerol framework All three acyl groups in a triacylglycerol may be the same, all three may be different, or one may be different from the other two. The structures of two typical triacylglycerols, 2-oleyl-1,3-distearylglycerol and tristearin. Both occur naturally—in cocoa butter, for example. All three acyl groups in tristearin are stearyl (octadecanoyl) groups. In 2-oleyl-1,3-distearylglycerol, two of the acyl groups are stearyl, but the one in the middle is oleyl (cis-9-octadecenoyl).
  • 34. L IPI D 1. FATS, OILS, AND FATTY ACIDS Hydrolysis of fats yields glycerol and long-chain fatty acids. Thus, tristearin gives glycerol and three molecules of stearic acid on hydrolysis. Table 1 lists a few representative fatty acids. As these examples indicate, most naturally occurring fatty acids possess an even number of carbon atoms and an unbranched carbon chain. The carbon chain may be saturated or it can contain one or more double bonds. When double bonds are present, they are almost always cis. Acyl groups containing 14–20 carbon atoms are the most abundant in triacylglycerols.
  • 35. L IPI D 1. FATS, OILS, AND FATTY ACIDS Table 1. Some Representative Fatty Acids
  • 36. L IPI D 1. FATS, OILS, AND FATTY ACIDS A few fatty acids with trans double bonds (trans fatty acids) occur naturally, but the major source of trans fats comes from the processing of natural fats and oils. Furthermore, the same catalysts that promote hydrogenation promote the reverse process—dehydrogenation—by which new double bonds, usually trans, are introduced in the acyl group. Fatty acids occur naturally in forms other than as glyceryl triesters, and we’ll see numerous examples as we go through the chapter. One recently discovered fatty acid derivative is anandamide. Fatty acids are biosynthesized by way of acetyl coenzyme A. The following section outlines the mechanism of fatty acid biosynthesis.
  • 37. L IPI D 2. FATTY ACID BIOSYNTHESIS We can describe the major elements of fatty acid biosynthesis by considering the formation of butanoic acid from two molecules of acetyl coenzyme A. The “machinery” responsible for accomplishing this conversion is a complex of enzymes known as fatty acid synthetase.
  • 38. L IPI D 2. FATTY ACID BIOSYNTHESIS This phase of fatty acid biosynthesis concludes with the transfer of the acyl group from acyl carrier protein to coenzyme A. The resulting acyl coenzyme A molecules can then undergo a number of subsequent biological transformations. One such transformation is chain extension, leading to acyl groups with more than 16 carbons. Another is the introduction of one or more carbon–carbon double bonds. A third is acyl transfer from sulfur to oxygen to form esters such as triacylglycerols. The process by which acyl coenzyme A molecules are converted to triacylglycerols involves a type of intermediate called a phospholipid
  • 39. L IPI D 3. PHOSPHOLIPIDS
  • 40. L IPI D 4. WAXES Waxes are water-repelling solids that are part of the protective coatings of a number of living things, including the leaves of plants, the fur of animals, and the feathers of birds. Waxes are usually mixtures of esters in which both the alkyl and acyl group are unbranched and contain a dozen or more carbon atoms. Beeswax, for example, contains the ester triacontyl hexadecanoate as one component of a complex mixture of hydrocarbons, alcohols, and esters. Fatty acids normally occur naturally as esters; fats, oils, phospholipids, and waxes all are unique types of fatty acid esters. There is, however, an important class of fatty acid derivatives that exists and carries out its biological role in the form of the free acid. This class of fatty acid derivatives
  • 41. L IPI D 5. PROSTAGLANDINS Sheep prostate glands proved to be a convenient source of this material and yielded a mixture of structurally related substances referred to collectively as prostaglandins. We now know that prostaglandins are present in almost all animal tissues, where they carry out a variety of regulatory functions. Prostaglandins are extremely potent substances and exert their physiological effects at very small concentrations. Because of this, their isolation was difficult, and it was not until 1960 that the first members of this class, designated PGE1 and PGF1’
  • 42. L IPI D 6. TERPENES : THE ISOPRENE RULE The word “essential” as applied to naturally occurring organic substances can have two different meanings. For example, as used in the previous section with respect to fatty acids, essential means “necessary.” Linoleic acid is an “essential” fatty acid; it must be included in the diet in order for animals to grow properly because they lack the ability to biosynthesize it directly. “Essential” is also used as the adjective form of the noun “essence.” The mixtures of substances that make up the fragrant material of plants are called essential oils because they contain the essence, that is, the odor, of the plant. The study of the composition of essential oils ranks as one of the oldest areas of organic chemical research. Very often, the principal volatile component of an essential oil belongs to a class of chemical substances called the terpenes.
  • 43. L IPI D 6. TERPENES : THE ISOPRENE RULE The structural feature that distinguishes terpenes from other natural products is the isoprene unit. The carbon skeleton of myrcene (exclusive of its double bonds) corresponds to the head-to-tail union of two isoprene units. Terpenes are often referred to as isoprenoid compounds.
  • 44. L IPI D 6. TERPENES : THE ISOPRENE RULE Table 2. Classification of Terpenes Tail-to-tail linkages of isoprene units sometimes occur, especially in the higher terpenes. The C(12)±C(13) bond of squalene unites two C15 units in a tail-to-tail manner. Notice, however, that isoprene units are joined head to tail within each C15 unit of squalene