Introduction to Biochemistry

“From Classical Concepts of

Matters to Modern Biochemistry”

Assoc. Prof. Dr. Atif Amin Baig,

Faculty of Medicine, Universiti Sultan Zainal Abidin,
Malaysia
 Learning Outcomes
 What is Mater?

 Basic characteristics of mater?

 Orbital hybridization & chemical bonding?

 Molecular forms of mater?

 Concepts of basic biological molecules?

 Isomerism?

 Types of isomerism?

 Functional Molecules in Organic compounds?

 Branches of Biochemistry?

 Used of Biochemistry in modern era?

 Recall (Level = C1)
• Basic knowledge
• About you?
• Why have you chosen this field?
• Method of Assessment
• Method of Teachings? Lectures, Seminars and CLA
• Discipline in the class?
 Matter

Matter is anything that has

1. Mass
2. Occupies Volume
Measure of amount of mass in a given Volume
Mass ?
Volume?

4
 Mass Vs Weight
Does it Mater to be a Matter?

 Is Mass and Weight changes the definition of Matter?

 Mass is the measure of amount of matter in a body and is

denoted by M.

 Weight is the amount of force acting on a mass due to the

acceleration due to gravity. It is denoted by W

W=Mxg

What it means?
Why We need to know the Mass of a Matter?

Law of Mass Action

When two reactants, A and B, react together at a given temperature in a "substitution reaction,"
the affinity, or chemical force between them, is proportional to the active masses, [A] and [B],
each raised to a particular power
Basic Definition
 States of a Matter

There are FOUR states of Matter

1. Solid
2. Liquid
3. Gases
4. Plasma
 Basis of States of Matter

 Based on particle arrangement

 Based on energy of particles

 Based on distance between particles

 Kinetics Theory of Matter

Matter is made up of particles which are in

continual random motion.
 Solids
Particles of solids are tightly packed
vibrate about a fixed position
Solids have a definite shape
Definite volume
 Liquids
 Particles of liquids are tightly packed
 But are far enough apart to slide over one another
 Liquids have an indefinite shape
 Liquids have a definite volume.
 Gases
 Particles of gases are very far apart and move
freely

 Gases have an indefinite shape and an indefinite

volume.
 PHASE CHANGES
Type of change Phenomenon of Movement of heat
change During the Phase
change
Solid  Liquid Melting Heat goes into the
solid as it melts
Liquid  Solids Freezing Heat Leaves the
liquid as it freezes
Liquid  Gas Vaporization Heat goes into the
liquid as it
vaporizes
Gas  Liquid Condensation Heat leaves the gas
as it condenses
Solid  Gas Sublimation Heat goes inside
the solid as it
sublimate
But what happens if you raise the temperature to super-high levels…
between
1000°C and 1,000,000,000°C ?

Will everything just

be a gas?
Plasma

http://www.terraplasma.com/plasma_action.html
 Plasma
 A plasma is an ionized gas.

 A plasma is a very good conductor

of electricity and is affected by
magnetic fields.

 Plasmas, like gases have an

indefinite shape and an indefinite
volume.

 Cold Plasma? What is new in field?

Where Plasma can be found?

Flames
 Where Plasma can be found?

2. Lightning
Lightning
Where Plasma can be found?

Aurora
Sun is an example of a Star in Plasma state
 STATES OF MATTER

SOLID LIQUID GAS PLASMA

Tightly packed, in Close together Well separated Has no definite

a regular pattern with no regular with no regular volume or shape
Vibrate, but do not arrangement. arrangement. and is composed
move from place Vibrate, move Vibrate and move of electrical
to place about, and slide freely at high charged particles
past each other speeds
 Periodic Table

Dmitri Mendeleev
 Orbital Hybridization
Definition of Orbital Hybridization?

Process of mixing of atomic orbitals of

nearly same energy to
Produce a set of entirely new orbitals
is known as hybridization.

The Orbital System

Atomic Orbits  Atomic Orbitals

The Solar System

 Molecular orbitals
When atomic orbitals overlap, they combine to form molecular orbitals.

Orbitals can be used to explain bonding between

atoms. Atomic orbitals are the volume of space that
the electrons of an atom are likely to be found in.

H H

1s atomic orbitals of hydrogen

The atomic orbitals containing the valence electrons

(outer electrons) are the ones that are important to us.
 Molecular orbitals
In the case of hydrogen, the overlap of two 1s atomic
orbitals results in the formation of a σ (sigma)
molecular orbital.
σ molecular orbital

H H H H

1s atomic orbitals of hydrogen

This molecular orbital is more stable than each of the

separate atomic orbitals and contributes to the shape
of the molecule.
Sigma(σ) and Pi (π )Bonds
Difference between Sigma(σ) and Pi (π )Bonds
 Chemical Bonding
Definition of Chemical Bond
Force that holds groups of two or more atoms together and
makes the atoms function as a unit.

Example: H-O-H Bond Energy

Ionic Bond is the bond

formed between two
oppositely charged ions
by transfer of electrons

eg: Na+Cl-

Ionic Compound
M+ + X-  MX
 Covalent and Polar Covalent Bonds

Polar Covalent Bond is

Covalent Bond is
formed by sharing of
formed by sharing of
electrons between two
electrons between
ions where one nuclei
two ions
share more electrons
than others
 Molecular Structures
 The chemical structure reflects the functional diversity of a molecule

 Molecular structures are represented and defined by

1. Molecular Illustrations

2. Bond Length & Angles

3. Bond Polarity

4. Hydrogen Bonds
 Molecular Illustrations
Structural Formula
 The molecular illustrations can explain:

1. structural prediction (size & shape) of a molecule

2. Chemical Reactivity of a molecule

 Types of Molecular Illustrations

Chiral Center

1. Structural Formula Chiral centers are tetrahedral atoms (usually

carbons) that have four different
substituents. Each chiral center in a molecule
2. Ball and Stick Models will be either R or S. .

3. Van der Waals Models

 Molecular Illustrations
Ball and Stick Models
 The molecular illustrations can explain:

1. structural prediction (size & shape) of a molecule

2. Chemical Reactivity of a molecule

 Types of Molecular Illustrations Colored balls & Cylinders

1. Structural Formula
Bond length & angles correspond
to the actual conditions
2. Ball and Stick Models
Size of atoms are represented to be very small
3. Van der Waals Models
Non-comprehensible
 Molecular Illustrations
Van der Waals Models
 The molecular illustrations can explain:
Truncated Balls

1. structural prediction (size & shape) of a molecule

2. Chemical Reactivity of a molecule

 Types of Molecular Illustrations Space Filling Van der Waals Model

1. Structural Formula
Actual Size and Shape of Molecules

2. Ball and Stick Models Their effective extent is determined

by Van der Waals radius

3. Van der Waals Models Calculated from the energetically most

favorable distance between atoms that are
Not chemically bonded
 Bond Length & Angles
Covalent bond distance is defined by
Van der Waals Radius is the internuclear distance between
always bigger than Covalent two covalently bonded atoms and is
denoted by d.
Radius
These distances are
usually expressed
in picometer

1 pm = 10-12

Old Angstrom Unit

(Å) = 100 pm

Covalent bond radius refers to half of

Double bonds are 10-20% Van der Waals Radius is defined the distance between two singly
shorter than single bonds as half of the internuclear bonded atoms of the same element
separation of two non-bonded
sp3-hybridization = 110o atoms of the same element on
sp2-hybridization = 120o their closest possible approach
 Bond Polarity

 Depending on the position of element in the periodic table, the electronegativity of an element can be known
 Most strongly electronegative  Oxygen
 Most polar bond C=O
 Hydrogen Bonds
 The bonding energies of hydrogen bonds are 10-40 KJ/mol
 The bonding energies of covalent bonds are approximately 400 KJ/mol
 Hydrogen bonds are special  ?
 Hydrogen atom of OH, NH, SH groups (H bond DONORS) interact with free electrons of ACCEPTORS atoms
 Example? Most important and numerous in DNA and Protein Structures and Functions
Basic Biological Molecules
 Isomerism
Isomerism are the
molecules with the

The image is Derived from cesar dogfood advertisments

same composition (i.e.
same molecular
formula) but with
different physical and
chemical properties.

Many things in nature try to look similar, but

they are completely different !
 Types of Isomerism
Examples of All ?
STRUCTURAL ISOMERISM
Same molecular formula but
different structural formulae
STEREOISOMERISM
Same molecular
formula but atoms
occupy different
positions in space.
CHAIN ISOMERISM
POSITION ISOMERISM
FUNCTIONAL GROUP
ISOMERISM
GEOMETRICAL ISOMERISM
Occurs due to the restricted
rotation of C=C double bonds...
two forms - CIS and TRANS
OPTICAL ISOMERISM
Occurs when molecules have a
chiral centre. Get two non-
superimposable mirror images.
 Chain Isomerism
 These isomers arise because of the possibility of branching in carbon chains.

Example:

There are two isomers of butane, C4H10

 In one of them, the carbon atoms lie in a "straight chain" whereas in the
other the chain is branched.

http://www.chemguide.co.uk/basicorg/isomerism/structural.html
 Position Isomerism
 Basic carbon skeleton remains unchanged, but important groups are
moved around on that skeleton.

Example:
 There are two structural isomers with the molecular formula C3H7Br. In
one of them the bromine atom is on the end of the chain, whereas in the
other it's attached in the middle.
Functional Group Isomerism
 Functional Group Isomerism
 These isomers contain different functional groups

 They belong to different families of compounds (different homologous series)

Example:
A molecular formula C3H6O could be either propanal (an aldehyde) or propanone
(a ketone)
 Geometrical Isomerism

 Found in some, but not all, alkenes occurs due to the RESTRICTED ROTATION OF
C=C bonds get two forms....

CIS TRANS
Groups/atoms are on the Groups/atoms are on OPPOSITE
SAME SIDE of the double bond SIDES across the double bond
 Geometrical Isomerism
RESTRICTED ROTATION OF C=C BONDS

Single covalent bonds can easily rotate. What appears to be a different structure in an
alkane is not. Due to the way structures are written out, they are the same.

ALL THESE STRUCTURES ARE THE SAME BECAUSE C-C BONDS HAVE ‘FREE’ ROTATION
 Geometrical Isomerism
RESTRICTED ROTATION OF C=C BONDS

C=C bonds have restricted rotation so the groups on either end of the bond are ‘frozen’ in one
position; it isn’t easy to flip between the two.

This produces two possibilities. The two structures cannot interchange easily
so the atoms in the two molecules occupy different positions in space.
 Optical Isomerism

 Another form of stereoisomerism occurs when compounds have non-

superimposable mirror images

 The two different forms are known as optical isomers or enantiomers

 Molecules have a chiral centre

 Chiral centre has a “asymmetrical carbon atom”

 An asymmetric carbon has four different atoms (or groups) arranged

tetrahedrally around it.
 SPOTTING CHIRAL CENTRES

Look at each carbon atom in the chain and see what is attached to it. For a chiral centre
you need an asymmetric carbon with four different atoms/groups) arranged tetrahedrally around it.
IF A CARBON HAS MORE THAN ONE OF ANY ATOM/GROUP ATTACHED, IT CAN’T BE CHIRAL

C 3 H’s around it NOT chiral

CH3CH2CH2CH2Cl
1-chlorobutane
C
C
2 H’s around it
2 H’s around it
NOT chiral
NOT chiral 
C 2 H’s around it NOT chiral

CH3CH2CHClCH3 C 3 H’s around it NOT chiral

2-chlorobutane
C
C
2 H’s around it
H, CH3, Cl,C2H5 around it
NOT chiral
CHIRAL 
C 3 H’s around it NOT chiral

C 3 H’s around it NOT chiral

(CH3)2CHCH2Cl
1-chloro-2-methylpropanane
C 2 CH3’s around it
C 2 H’s around it
NOT chiral
NOT chiral

(CH3)3CCl C 3 H’s around it NOT chiral
2-chloro-2-methylpropanane C 3 CH3’s around it NOT chiral 
 Optical Isomerism

CHIRAL CENTRES

There are four different colours 2-chlorobutane exhibits optical isomerism

arranged tetrahedrally about because the second carbon atom has four
the carbon atom different atoms/groups attached
 OPTICAL ISOMERISM
Spatial differences between isomers

• two forms exist which are NON-SUPERIMPOSABLE MIRROR IMAGES of each other
• non-superimposable means you you can’t stack one form exactly on top of the other

Some common objects are mirror images and superimposable spoons

superimposable but not mirror images books
non-superimposable mirror images hands

 For optical isomerism in molecules, both conditions must apply...

they must be mirror images AND be non-superimposable
 OPTICAL ISOMERISM
What is a non-superimposable mirror image?
Chemical Reactions

Zindagi kya hai anasir mein zahur-e tarteeb,

Maut kya hai ini ajza ka pareshan hona

(‫)برج نارائن چکبست‬

Brij Narayan Chakbast
1882–1926
 Biochemical Reactions
 Chemical reactions associated with biological processes

 Often involve a combination of more than one type of

reaction

 Four main types of reactions:

 Neutralization
 Oxidation-Reduction
 Condensation
 Hydrolysis
Neutralization Reactions
Neutralization Reactions
 Oxidation-Reduction Reactions
Involves the transfer of electrons
Oxidation: loss of electrons
Reduction: gain of electrons

Electrons are highly reactive and don’t exist on their

own in cells
If oxidation occurs to one molecule in the cell, reduction
must immediately to another molecule

The entire reaction is often called a redox reaction

Oxidation-Reduction Reactions
Oxidation-Reduction Reaction
 Condensation Reactions

 Involved in the assembly of all four

types of macromolecules

 An H atom is removed from a functional

group on one molecule, and an OH
group is removed from another
molecule

 Result: a larger molecule + water (water

out, monomer in)

 Also known as dehydration synthesis

 Hydrolysis Reactions

 Involved in the breakdown of

macromolecules into their
monomers

 Water is added to break the bonds

between monomers (water in,
monomer out)

 H from the water is added to one

molecule, and the OH group is
added to the adjacent monomer

 Covalent bond between monomers

breaks to form two smaller
molecules
Biochemistry Phenotype and
Physiology

Genes

Proteins
 Biochemistry

Definition
Branches of Biochemistry

SCOPE

FIELD
Use of Biochemistry in Modern Era
Thank you for Not Sleeping