introduction about biochemistry basic concepts of atoms and molecules types of bonding isomerism and their structure

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CHAPTER - I
BIOCHEMISTRY
-Fathima Hameed
CONTENTS
definition of biochemistry
scope of biochemistry
concepts of atoms and molecules
types of bonding
isomerism
types of isomerism

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BIOCHEMISTRY
The branch of science dealing with the study of living organisms is known as
biochemistry. It combines elements from both biology and chemistry. Biochemistry became a
separate discipline in the early 20th
Century.
People who are in the field of Biochemistry are often referred to as Biochemists.
Biochemists study relatively large molecules like proteins, lipids, and carbohydrates, which are
important in metabolism and other cellular activities; they also study molecules like enzymes and
DNA. Biochemistry deals with the chemical combinations and reactions that take place because
of the biological processes such as growth, reproduction, metabolism, heredity, etc.
SCOPE OF BIOCHEMISTRY
 Modern Biochemistry has two branches; descriptive Biochemistry and dynamic
Biochemistry.
 Descriptive Biochemistry deals with the qualitative and quantitative characterization of
the various cell components. Dynamic Biochemistry deals with the elucidation of the
nature and the mechanism of the reactions involving these cell components.
OBJECTIVES OF BIOCHEMISTRY
The major objective of Biochemistry is the complete understanding of all the chemical processes
associated with living cells at the molecular level. To achieve this objective, biochemists have
attempted to isolate numerous molecules (Bio molecules) found in cells, to determine their
structures and to analyze how they function.
In brief the objectives can be listed as follows:
1. Isolation, structural elucidation and the determination of mode of action of biomolecules.
2. Identification of disease mechanism
3. Study of in born errors of metabolism
4. Study of oncogenes in cancer cells
5. The relationship of biochemistry with genetics, physiology, immunology, pharmacology
& toxology

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APPLICATION OF BIOCHEMISTRY
1. Drug Manufacturing Companies
2. Public Health Entities
3. Blood Service
4. Industrial Laboratories
5. Cancer research institutes
6. Research Departments
7. Educational Institutes
8. Environmental Pollution Control
9. Agriculture and fisheries
10. Forensic Science & Hospitals
11. Public Health Laboratories
12. Cosmetic Industries
ATOMS
 Atoms are the basic building blocks from which everything around us is built. All of
them are made up of atoms. Atoms are made up of three types of tiny particles;
1. Protons (or) positively charged particles
2. Neutrons (or) particles that contain no
Charges are found in the nucleus of an atom.
3. Electrons (or) negatively charged particles
are found outside the nucleus.

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 There are 118 elements, or substances composed of a single type of atom, on the periodic
table, including hydrogen, carbon, lead, gold, lithium, oxygen, and more.
 What makes each element different is the number of positively charged protons in the
nucleus of the atom. Typically, these elements have the same number of negatively
charged electrons orbiting around the outside of the nucleus. Ions are atoms that have lost
or gained electrons. The number of neutrons varies and is necessary for keeping an atom
stable.
 The atomic mass (atomic weight) is the sum of protons and neutrons in an atom. It is
expressed in atomic mass units (denoted by u).
MOLECULES
 It is made up of two or more atoms that are bound together by chemical bonding. If the
molecule contains atoms of different types bonded together, we call it a compound. For
example, two hydrogen atoms and one oxygen atom bonded together creates the
compound water.
 The molecular weight of a molecule is the sum of the atomic weights of its component
atoms.
 Molecules can be classified into two groups depending on the type the elemental atoms.
 Homoatomic Molecules - These are the molecules of elements and are made up of one
type of atoms only. Example; H2, O2, N2, S8
 Heteroatomic Molecules: These are the molecules of compounds and are made up of
more than one type of elements. Examples; NH3, H2O, CH4.

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TYPES OF BONDING IN BIOMOLECULES
 Biomolecules are molecules that occur in living organisms.
 The biological molecules are divided into four major categories; carbohydrates, lipids,
proteins, and nucleic acids. They are formed by polymerization of smaller units called as
monomers. These monomeric units are formed by chemical associations or linkages
between different atoms depend upon the chemical nature of monomeric unit.
 The chemical bonds in case of biological molecules can be divided into two categories;
 Primary Bonds
 Secondary Bonds
PRIMARY BONDS
 These are the covalent bonds formed as a result of electron sharing among two or more
atoms. They are formed as a result of a chemical reaction that may be reversible or
irreversible.
1. Glycosidic bond
2. Peptide bond
3. Ester bond
4. Phosphodiester bond
SECONDARY BONDS
 The secondary bonds in biological molecules are the temporary forces of attractions that
are developed when certain atoms or groups come close together. These bonds are mainly
involved in maintaining the secondary, tertiary or other higher structures of biological
molecules. They are most important in proteins and nucleic acids.
1. Hydrogen Bond
2. Disulfide Bond
1) Glycosidic bond
 These bonds are found in carbohydrates. When two adjacent monosaccharide units link to
form disaccharides or polysaccharides, a glycosidic bond is formed.

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 Whenever a glycosidic bond is formed, there is the elimination of a water molecule similar to
the formation of a peptide bond. These reactions are called dehydration or condensation
reactions. Glycosidic bonds are covalent chemical bonds that link ring-shaped sugar
molecules to other molecules.
 Example: 1, 4 glycosidic bonds are formed due to condensation reaction between a hydroxyl
residue on carbon-1 and the anomeric carbon-4 on two monosaccharide units to form
disaccharides.
2) Peptide bond
These bonds are found in proteins. Proteins are made up of amino acids that form
polypeptide chains. Each amino acid has two functional groups- amine (-NH2) group, and
the carboxylic acid (-COOH) group. A peptide bond is formed (-CONH) between the –
NH2 group and the –COOH group of any two adjacent amino acids and it leads to the
elimination of a water molecule. The resultant product formed is an amide.
3) Ester bond
 It is a covalent bond that is essential in various types of lipids. An ester bond or ester
linkage is formed between an acid and an alcohol.

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 An ester bond is formed when a molecule having the carboxylic group reacts with
another molecule having a hydroxyl group. The carboxylic group loses its hydrogen and
oxygen, while the alcohol loses hydrogen of its hydroxyl group. As a result, a water
molecule is released, and the two carbons are linked via an oxygen bridge forming a -
COC- linkage.
4) Phosphodiester bond
 It is the primary covalent bond that joins different nucleotides in a polynucleotide or
nucleic acids. It is also a type of ester bond but involves two ester linkages.
 A Phosphodiester bond is a double ester linkage formed when the phosphate group at the
5’ end of one nucleotide reacts with the free hydroxyl group at the 3’ end of another
nucleotide. A molecule of water is released, and two ester linkages are formed. In these
linkages, the oxygen bridge is used to connect a carbon atom with a phosphate group.
The two ester linkages are as follows;
a. One ester linkage attaches the phosphate group with the 5’ carbon of one nucleotide
b. The second ester linkage attaches the same phosphate to the 3’ carbon of the other
nucleotide
 The compound thus formed is called a dinucleotide. It can form additional
phosphodiester bonds at both ends because of having a free hydroxyl group at the 3’ end
and a free phosphate group at the 5’ end.

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1) Secondary- hydrogen bond
Once the nucleotides form nucleic acids, DNA and RNA formation occurs. DNA is double-
stranded whereas RNA is single stranded. The two strands of the DNA are held together by
weak hydrogen bonds that form between the nitrogen bases. The hydrogen bonds between
the nitrogen bases are very specific. Adenine bonds only with thymine in the opposite strand
by forming 2 hydrogen bonds, guanine forms 3 hydrogen bonds when it pairs with cytosine
of the opposite strand. Two bonded nitrogenous bases from opposite strands constitute a
base pair.

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2) Disulfide Bond
 It is involved in maintaining the higher structures of biological molecules.
 A disulfide bond is formed between the thiol groups present in the side chains of two
cysteine residues to form one cysteine residue. This bond brings the two cysteine residues
together that have been kept apart by the intervening amino acids.
 This bond is involved in stabilizing the tertiary structure of proteins and guiding the
protein folding.
ISOMERISM
 Isomerism is the phenomenon in which more than one compounds have the same
chemical formula but different chemical structures. Chemical compounds that have
identical chemical formulae but differ in properties and the arrangement of atoms in the
molecule are called isomers.
 The word “isomer” is derived from the Greek words “isos” and “meros”, which mean
“equal parts”. This term was coined by the Swedish chemist Jacob Berzelius in the year
1830.

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TYPES OF ISOMERISM
There are two primary types of isomerism, which can be further categorized into different
subtypes. These primary types are Structural Isomerism and Stereoisomerism. The
classification of different types of isomers is illustrated below.
STRUCTURAL ISOMERISM
Structural isomerism is commonly referred to as constitutional isomerism. The functional groups
and the atoms in the molecules of these isomers are linked in different ways. Different structural
isomers are assigned different IUPAC names since they may or may not contain the same
functional group. The different types of structural isomerism are discussed in this subsection.
1) Chain Isomerism
 It is also known as skeletal isomerism.
 The components of these isomers display differently branched structures.
 Commonly, chain isomers differ in the branching of carbon
 An example of chain isomerism can be observed in the compound C5H12, as illustrated
below.

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2) Position Isomerism
 The positions of the functional groups or substituent atoms are different in position
isomers.
 Typically, this isomerism involves the attachment of the functional groups to different
carbon atoms in the carbon chain.
 An example of this type of isomerism can be observed in the compounds having the
formula C3H7Cl.
3) Functional Isomerism
 It is also known as functional group isomerism.
 As the name suggests, it refers to the compounds that have the same chemical formula
but different functional groups attached to them.
 An example of functional isomerism can be observed in the compound C3H6O.

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4) Metamerism
 This type of isomerism arises due to the presence of different alkyl chains on each side of
the functional group.
 It is a rare type of isomerism and is generally limited to molecules that contain a divalent
atom (such as sulfur or oxygen), surrounded by alkyl groups.
 Example: C4H10O can be represented as ethoxyethane (C2H5OC2H5) and methoxy-
propane (CH3OC3H7).
5) Tautomerism
 A tautomer of a compound refers to the isomer of the compound which only differs in the
position of protons and electrons.
 Typically, the tautomers of a compound exist together in equilibrium and easily
interchange.
 It occurs via an intramolecular proton transfer.
 An important example of this phenomenon is Keto-enol tautomerism.

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6) Ring-Chain Isomerism
 In ring-chain isomerism, one of the isomers has an open-chain structure whereas the other
has a ring structure.
 They generally contain a different number of pi bonds.
 A great example of this type of isomerism can be observed in C3H6. Propene and
cyclopropane are the resulting isomers, as illustrated below.
STEREOISOMERISM
This type of isomerism arises in compounds having the same chemical formula but different
orientations of the atoms belonging to the molecule in three-dimensional space. The compounds
that exhibit stereoisomerism are often referred to as stereoisomers. This phenomenon can be
further categorized into two subtypes. Both these subtypes are briefly described in this
subsection.
1) Geometric Isomerism
 It is popularly known as cis-trans isomerism.
 These isomers have different spatial arrangements of atoms in three-dimensional space.
 An illustration describing the geometric isomerism observed in the acyclic But-2-ene
molecule is provided below.

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2) Optical Isomerism
 Compounds that exhibit optical isomerism feature similar bonds but different spatial
arrangements of atoms forming non-superimposable mirror images.
 These optical isomers are also known as enantiomers.
 Enantiomers differ from each other in their optical activities.
 Dextro enantiomers rotate the plane of polarized light to the right whereas laevo
enantiomers rotate it to the left, as illustrated below.

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REFERENCES
 https://biologydictionary.net/biochemistry/
 https://www.careerindia.com/courses/unique-courses/what-is-biochemistry-career-scope-
015218.html
 http://biogeny.net/view/Biochemistry,_Scope_and_Importance
 https://study.com/academy/lesson/what-are-atoms-molecules-definition-
differences.html#:~:text=The%20universe%20is%20made%20up,electrons%20(negativel
y%20charged%20particles).&text=Molecules%20are%20formed%20when%20two,is%2
0known%20as%20a%20compound.
 http://www2.estrellamountain.edu/faculty/farabee/biobk/biobookchem1.html
 https://www.askiitians.com/iit-jee-chemistry/physical-chemistry/some-basic-concept-of-
chemistry/atoms-and-molecules.html
 https://alevelbiology.co.uk/notes/types-of-bonds-in-biological-molecules/
 https://www.toppr.com/guides/biology/biomolecules/bond-linking-monomers/
 https://byjus.com/chemistry/isomerism/#:~:text=Isomerism%20is%20the%20phenomeno
n%20in,the%20molecule%20are%20called%20isomers.