BASIC CONCEPTS

OF CHEMISTRY
Dr. Muhammad Nabi
Doctor of Pharmacy,
M. Phil Biochemistry
M. Phil Pharmacology,
Ph. D Pharmacology
 Outlines
▶ Basic concepts of Chemistry
1. Importance of Chemistry in nursing
2. Matter
3. Elements Mixtures & Compound
4. Structure of Atom (Periodic Table)
5. Chemical formula
6. Chemical Reactions
7. Equations
8. Bonding
9. Redox Reaction
10. Acid Base
 What is Nursing?
Nursing is a healthcare profession focused on the care of
individuals, families and communities so they may attain,
maintain, or recover optimal health and quality of life from
conception to death.
(From Wikipedia)
Why is Chemistry Important to
Nursing?

A nurse should have basic knowledge of all the processes

that occur at the cellular level, e.g.
▶ actions of enzymes
▶ diffusion across cell membranes
▶ oxygen transport
▶ How pH of the blood is balanced
▶ glucose metabolism
▶ what goes wrong in patients with diabetes?

All these questions and many, many more all need a good
understanding of the basic concepts of chemistry.
Continued

▶ Your patient might have acidosis or alkalosis which may

be metabolic or respiratory in nature or both.

▶ you also need an understanding about electrolytes ( Na,

K, Ca etc).

▶ The nurse will be handling so many different fluids and

if he/she does not know what it is for, and how it will
affect the patient, the patients life will be in danger.
Continued

▶ You need to know the language of chemistry.

▶ If someone says that substace X is in millimoles, you

must know what it means.

▶ You must know how to prepare 5% solution of a

medicine etc.
Continued

▶ Also, you need to have a basic understanding of the

difference between a base and an acid

▶ It will also help you understand how it is that some

medications are more readily absorbed than others in
the body.

▶ pH is a concept that comes up in urinalysis, blood work

and blood gasses.
▶ Nurses must understand how particular medicines will react in different
patients. This helps to avoid wrong combinations of drugs that can lead to
adverse effects.

▶ Your patient is feeling giddy. If you don’t know chemistry you will not be
able to treat that.

▶ Your patient is vomiting and you don’t know chemistry then you cannot
treat him.

▶ Your patient have ingested a toxic chemical. If you don’t know the
formula of that chemical and its anti toxin then you are not able to treat
him.
2.Matter

▶ Matter is everything around . Atoms and molecules are all

composed of matter. Matter is anything that has mass and takes up
space.
▶ Matter can be classified on the basis of chemical and physical
properties. On the basis of physical properties matter can be
classified into solids, liquids and gasses. And on the basis of
chemical properties matter is classified as elements, mixtures and
compounds. We will study about the classification of matter on the
basis of physical properties.
States of Matter

Copied from: http://media-2.web.britannica.com/eb-media/65/63065-004-07B69F7B.jpg

Date: October 7, 2015
 Characteristics of Matter

• Particles of matter have spaces between them

• Particles of matter are constantly moving

• Particles of matter attract each other.

 States of matter
On the basis of physical states, all the matter
can be classified into three groups: Solids,
Liquids and Gasses. For example:

i) Sugar, Sand, Iron, Wood, Rocks etc.

ii) Water, Milk, Petrol, kerosene etc.

iii) Air, Oxygen, Steam etc.

 Properties Of
Solids

The solids have the following characteristic properties:

• Have a fixed shape and a fixed volume.
• Cannot be compressed much.
• Have high density.
 Properties Of
Liquids

The liquids have following characteristics properties:

• Have no fixed shape .
• Cannot be compressed.
• Generally flow easily.
 Properties Of
Gasses

The gasses have following characteristics properties:

• Have neither a fixed shape nor fixed volume.
• Gasses have very low density.
• Can be compressed easily.
1. Spaces between the particles . Spaces between the particles is
minimum in solids, maximum in gasses and intermediate in
liquids.
2.The force of attraction between particles. The forces of
attraction between the particles are the strongest in solids ,
less strong in liquids and negligible in gasses.
3. The amount of particles. The movement of particles is the
minimum in solids, intermediate in liquid an maximum in gasses
3.Elements
An element is a pure substancethat cannot be
separated into simpler substances by physical
or chemical means
Characteristic Properties
▫ Physical Properties
🞄 Boiling Point
🞄 Melting Point
🞄 Density

▫ Chemical Properties
🞄 Reactivity with different substances
Can you use: density, conductivity, reactivity,
melting point to identify each element?
Elements are grouped into
categories based on the
properties they share
🞄 Example: Iron, nickel, and cobalt are all shiny and conduct
heat and electrical current. They’ve been
placed into a large group called metals with similar
elements. If you know the category, you knowthe properties.
 Elements
are divided into

Metals Nonmetals Metalloids

Periodic Table
Major Categories of Elements

1. Metals: shiny, good conductors of

thermal energy and electric current,
malleable (can be hammered into
thing sheets) and ductile (can be
drawn into thin wires)

Elements in this category

Iron, Tin, Lead, Copper
2. Nonmetals: dull, poor conductors of
thermal energy and electric current,
brittle and unmalleable

Elements in this category

Neon, Bromine, Sulfur
▶3. Metalloids: have properties
of both metals and nonmetals,
some are shiny while others
are dull, some are good
conductors while others are not
▶Elements in this category
Silicon, Antimony, Boron
Compounds
Compounds
▫ Pure substance composed of two or
more elements that are chemically
combined.
▫ In order for elements to combine, they
must react, or undergo a chemical
change, with one another.
Familiar Compounds
▫ Table Salt: Sodium and Chlorine

▫ Water: Hydrogen and Oxygen

▫ Sugar: Carbon, Hydrogen, and Oxygen

▫ Carbon Dioxide: Carbon and Oxygen

▫ Baking Soda: Sodium, Hydrogen, Carbon,

and Oxygen
Compounds Have
Unique Sets of Properties
▫ Physical properties
▫ Chemical properties

▫ Compounds have different properties

from the elements that form it.
🞄 Ex: Table salt is made of sodium (which
reacts violently with water) and chlorine
(which is poisonous).
Compounds Can Be
Broken Down into Simpler Substances
▫ Either broken down into elements
through chemical changes…
▫ Or undergo chemical changes and form
simpler compounds
Compounds Cannot Be
Broken Down by Physical Changes

▫ Only way to break down a compound is

through a CHEMICAL change.
Mixtures
▶Mixture: combination of two or more
substances that are not chemically
combined

Two or more materials form a mixture if

they do not react to form a compound
Substance in a mixture keep their
identities.

Mixtures can be physically separated.

Solutions
▫ Solution: mixture that appears to be a
single substance but is composed of
particles of two or more substances that
are distributed evenly amongst each
other

▫ Also described as a homogenous

mixture
▫ Process in which particles separate and
spread evenly throughout a mixture is
known as dissolving.

▫ The solute is the substance that is

dissolved, and the solvent is the
substance in which the solute is
dissolved.
Salt water
Solute: Salt
Solvent:Water
Examples of Different
States in Solutions
Gas in gas Dry air (oxygen in nitrogen)

Gas in liquid Soft drinks (carbon dioxide in water)

Liquid in liquid Antifreeze (alcohol in water)

Solid in liquid Salt water (salt in water)

Solid in solid Brass (zinc in copper)

▶ Particles in solutions are so small that they never settle out, nor
can they be filtered out, and they don’t scatter or block light.
Concentration:
How much solute is dissolved?
▫ Concentration: measure of the amount of
solute dissolved in a solvent

▫ Knowing the exact concentration of a

solution is very important in chemistry
and medicine because using the wrong
concentration can be dangerous.
Suspensions
▫ Mixture in which particles of a material
are dispersed throughout a liquid or gas
but are large enough that they settle
out.

▫ A suspension can be separated by

passing it through a filter
Application
▫ Many medicines, such as remedies for
upset stomachs, are suspensions. The
directions on the label instruct you to
shake the bottle well before use.

▫ Why must you shake the bottle?

▫ What problem could arise if you don’t?

Biology Connection
▫ Blood is a suspension. The suspended
particles, mainly red blood cells, white
blood cells, and platelets, are actually
suspended in a solution called plasma.
Plasma is 90% water and 10%
dissolved solutes including sugar,
vitamins, and proteins.
S T R U C T U R E O F A N ATO M

CHEMISTRY GROUP WORK

 INTRODUCTION
Atom was discovered by John Dalton. He
proposed the famous atomic theory in
1807. Atoms are fundamental unit of
matter. The existence of different kinds of
matter is due to different atoms constituting
them.
A major challenge before the scientists at the
end of the 19th century was to reveal the
structure of the atom as well as to explain its
important properties. Many scientists worked
hard and proposed many models for the
atom, here we are going to learn about the
structure of an atom
NEUTRONS
What is in the structure of an
atom?
• Nucleus - center of the atom
 Home of Protons and Neutrons
 Has a positive charge
• Proton
 Has a relative mass of 1u
 Has a positive (+) charge
 Determines the atomic number
 Found inside the nucleus
What is in the structure of an
atom?
• Neutron
 Has no (0) charge
 Has a relative mass of 1u
 Found inside the nucleus
Structure of an atom

• Electron
 Has a negative (-) charge
 Found outside the nucleus
• Rutherford atom model - electrons are
around the nucleus
• Bohr model – electrons are in specific
energy levels called shells
 How are p, n, e
related?
• No. protons = No. electrons
• No. protons = atomic number
• No. protons + No.neutrons = mass number
• No. neutrons=mass no. - atomic no.
• The outermost shell of an atom is known as its
valence shell.
• The electrons present in the outermost shell
of an atom are known as the valence electrons
• The Valency of an element may be defined as
the combining capacity of its atoms with
atoms of other elements in order to acquire
octet configuration.
• For eg; The valency of hydrogen is 1.
• The number of protons in an atom is referred
to as its Atomic Number.
• It is denoted by the letter ‘ Z ’.
• Elements are defined by the number of
protons they posses.
• The atomic number of hydrogen is 1.
• The mass of an atom resides in its nucleus.
The mass of an atom is practically due to
protons and neutrons alone.
• Therefore, Mass Number of an atom is the
sum of neutrons and protons present in the
nucleus of an atom
• for hydrogen, its mass number is 1u.
• Isotopes are atoms of same element, which
have different mass numbers but same atomic
number.
• Their chemical properties are similar but
physical properties are different.
• An isotope of uranium is used as a fuel in
nuclear reactors.
• An isotopes of cobalt is used in the treatment
of cancer.
• An isotope of iodine is used in the treatment
of goitre.
• Atoms of different elements with different
atomic numbers ,which have the same mass
number are known as isobars.
• Examples of isobars are: calcium(z=20)and
argon(z=18).their mass number is 40 u.
BREAK TIME
Chemical Formula
Dictionary:

The chemical formula of a molecule shows the number

of atoms of each element in the molecule.

Formula consists of the symbols for the elements that

make up the molecule, each followed by a number.

Examples
oxygen molecule contains 2 atoms O2

bromine molecule contains 2 atoms Br2

nitrogen molecule contains2 atoms N2

If the formula contains only one atom of a particular type,

there is no need to put in ‘1’.
 Exercise:
🠜 Draw a target diagram for the following covalent compounds
🠜 Draw a diagram of the molecule using lines to represent the covalent
bonds
🠜 Write the formula for each compound under the target diagram

9. Hydrogen fluoride HF
10. Carbon chloride CCl4
11. Phosphorus hydride PH3
12. Sulphur oxide SO
 Valencies can be used to work out formula.

Step 1: Write down the symbols for the elements present

e.g. calcium cholride
Ca Cl

Step 2: write the valencies of the elements

present above each symbol

2 1
Ca Cl
 Step 3: Cross over the valencies

2 1
Ca Cl

Ca1Cl2

Step 4: if there are any common factors cancel them

out and omit any ‘1’ present

The formula of calcium chloride is: CaCl2

What about silicon oxide:
Step 1: Write down the symbols for the elements

present Si O

Step 2: write the valencies of the

elements present above each symbol

4 2
Si O
Step 3: Cross over the valencies

4 2
Si O

Si2O4

Step 4: if there are any common factors cancel them

out and omit any ‘1’ present

In this case both factors can be divided by 2.

The formula for silicon oxide is SiO2.

Examples:
• Phosphorus chloride PCl3
• Boron sulphide B2S3
• Silicon fluoride SiF4
• Sulphur chloride SCl2
• Phosphorus iodide
PI3
• Iodine bromide
• Boron chloride IBr
BCl3
The same method works for compounds containing
metals and non metals.

Try these examples:

• Magnesium oxide MgO

• Sodium chloride NaCl
• Aluminium iodide AlI3
• Potassium sulphide K2S
• Lithium oxide Li2O
Exercise

•Work out the formula for copper(I) chloride and

copper(II) chloride
•Work out the formula for the following transition
metal compounds:

1. Copper(I) oxide Cu2O

2. Tin(IV) chloride SnCl4
3. Iron(II) oxide FeO
4. Iron(III) sulphide Fe2O3
 Chemical Reaction

 A chemical reaction occurs when one or more

chemicals react to become different chemicals.
 A chemical reaction is characterized by the re-
arrangement of atoms from the reactant side of
the equation to the product side.

-: Example :-
Hydrogen gas burns in oxygen to make water.
2H2 + O2 2H2O
 Types of Chemical Reaction

 Decomposition Reactions

 Combination Reactions

 Single-Replacement Reactions

 Double-Replacement Reactions

 Combustion Reactions
 Decomposition Reaction

A decomposition reaction is a reaction in which

a single compound decomposes to two or more
other substances.
AB A+B
Where A and B can be elements or compounds.

Most compounds can be broken down into simpler

substances or decomposed.
 Decomposition Reaction

-: Example :-
The industrial preparation of calcium oxide (Lime)
involves the decomposition of calcium carbonate
by heating it.

CaCO3(s) CaO(s) + CO2(g)

 Combination Reaction

A combination reaction is a reaction in which

two substances combine to form a third.

A+B AB
Where A and B can be elements or compounds.

Decomposition and combination reactions can

be considered to be the reverse of each other.
 Combination Reaction

-: Example :-
The reaction of calcium oxide with sulfur dioxide
to form calcium sulfite

CaO(s) + SO2(g) CaSO3(s)

 Single-Replacement Reaction

A single-replacement reaction is a reaction in

which an element reacts with a compound and
replaces another element in the compound.

A + BC AB + C
Where A and C are elements and BC and AB are
compounds.
 Single-Replacement Reaction

-: Example :-
The reaction in which copper displaces silver
from an aqueous solution of silver nitrate

Cu(s) + 2AgNO3(aq) Cu(NO3)2(aq) + 2Ag(s)

 Double-Replacement Reaction
A double-replacement reaction is a reaction in
which there is an exchange of positive ions between
two compounds. These reactions generally take
place between two ionic compounds in aqueous
solution.
AB + CD AD + CB
Where A and C are cations and B and D are anions.
For a double-replacement reaction to occur, at least
one of the products must be a gas or water, or a
precipitate.
 Double-Replacement Reaction

-: Example :-
Precipitation reactions are one type of double-
replacement reaction.

AgNO3(aq) + NaCl(aq) AgCl(s) + NaNO3(aq)

Combustion Reaction
 A combustion reaction is a reaction in which a
substance reacts with oxygen, usually with the fast
release of heat and the production of a flame.

 Organic compounds usually burn in the oxygen in air

to produce carbon dioxide and if the compound
contains hydrogen, another product will be water.
 For example butane burns in air as follows.
Combustion Reaction
-: Example :-
In general:
CxHy + O2 CO2 + H2O
Products in combustion are ALWAYS carbon dioxide
And water.
Combustion is used to heat homes and run
automobiles (octane, as in gasoline, is C8H18).
 The simplest form of description of a
chemical reaction in a shorter form is by
writing it in the form of an equation.E.g.-

Mg + O 2 MgO
 The reactants are written on the left side
and product is written on the right side.
 An arrow is placed between them to
show the direction of reaction.
The equation must contain the correct
formulas for the reactants and products.

The law of conservation of mass must

be satisfied.
• According to the law of conservation of mass, total
mass must be equal on the both sides of the
equation.
• This type of equation is known as a balanced
chemical reaction. E.g.-
2Mg + O2 2MgO
• Here both sides have two atoms of Magnesium and
two atoms of Oxygen.
Unbalanced and Balanced Equations

Cl Cl H H
Cl H
H Cl Cl Cl
H
Cl
H

H2 + Cl2  HCl (unbalanced) H2 + Cl2  2 HCl (balanced)

reactants products reactants products

H 2 1 H 2 2
Cl 2 1 Cl 2 2
Reactants Products
1 C atom 1 C atom
4 H atoms 4 H atoms
4 O atoms 4 O atoms
Visualizing a Chemical Reaction
2 Na + Cl2 2 NaCl

_1_0_mole Na _5 mole Cl2 _1_?0_mole NaCl

1. Combination reaction A + B  AB

2. Decomposition reaction AB  A + B

3. Single-displacement reaction A + BC  AC + B

AB + CD  AD + CB
4. Double-displacement reaction

5. Redox reaction
 These type of reactions occur when two
reactants combine to form one or more
products. E.g. –

1. CaO + H2O Ca(OH)2

2. C + O2 CO2

 They are generally exothermic reactionswhich

involve evolution of heat during reaction.
 Decomposition Reaction
• The types of reaction in which a single reactant
breaks down to give simpler products are called
decomposition reaction. E.g.-
2 H2O 2 H2 + O2
• When a decomposition reaction is carried out by
heating, it is known as thermal decomposition.
Hydrogen Peroxide
2 H2O2 2 H2O + O2

Electrolysis of water
electricity
2 H2O 2 H2 + O2

Nitrogen triiodide
2 NI3 N2 + 3 I2

General Form
AB A + B
Single-replacement reaction

Mg + CuSO4  MgSO4 + Cu

General form:
A + BC  AC + B

Double-replacement reaction

CaCO3 + 2 HCl  CaCl2 + H2CO3

General form:
AB + CD  AD + CB
• If a substance gains oxygen during a reaction, it is
said to be oxidised.
• If a substance loses oxygen during a reaction, it is
said to be reduced.
• Reactions in which this type of change occurs is
known as Oxidation and Reduction reactions or
Redox reactions. E.g. –
CuO + H2 Cu +H2O
 Introduction

Chemical bonding provides the energy

necessary to hold two different atoms
together as part of a chemical compound.

Strength of the bond depends on the

molecules or atoms involved in the process
of bond formation.

© iTutor. 2000-2013. All Rights Reserved

 Types of Chemical Bonding

Ionic Bonds

Covalent Bonds

Hydrogen Bonds

Metallic Bonds

© iTutor. 2000-2013. All Rights Reserved

 Ionic Bonds

An Ionic bond is when an electron leaves

one atom and exothermically enters into
orbit around another. These to oppositely
charged ions now attract each other.

Ionic bonds are generally formed between

metals and nonmetals

© iTutor. 2000-2013. All Rights Reserved

 Example of Ionic Bond

A classic example of ionic bonding is between Na and Cl. Na is a

silvery metal. It has 1 valence electron. Cl is a yellow-green gas, and
it needs 1 electron to fill its valence shell. If you put the gas and
the metal together, then they will burn as electrons are exchanged.
The metal dissolves and the gas disappears. The ions now have
opposite charges and are attracted to each other by electrostatic
forces. They form a crystal with the rock salt structure.
© iTutor. 2000-2013. All Rights Reserved
 Covalent Bonds

A type of chemical bond in which there is

mutual sharing of electrons between two
atoms is called covalent bond. It is
further classified into single, double, and
triple covalent bond with respect to
mutual sharing of one, two, and three
bonds respectively.

© iTutor. 2000-2013. All Rights Reserved

 Example of Covalent Bond

when two hydrogen atoms get close enough together, the attraction
is balanced in both directions and they share the electrons
between them. A covalent bond is made and hydrogen gas (H2) is
formed.
In the hydrogen molecule (H2) the darker area between the two
nuclei shows where the two electrons, which are now shared, are
most likely to be.

© iTutor. 2000-2013. All Rights Reserved

 Hydrogen Bonds

A hydrogen bond is the attractive force

between the hydrogen attached to an
electronegative atom of one molecule and
an electronegative atom of a different
molecule.
Usually the electronegative atom is
oxygen, nitrogen, or fluorine, which has a
partial negative charge.

© iTutor. 2000-2013. All Rights Reserved

 Example of Hydrogen Bond

Each hydrogen atom is covalently bonded to the oxygen via a

shared pair of electrons. Oxygen also has two unshared pairs of
electrons. Thus there are 4 pairs of electrons surrounding the
oxygen atom, two pairs involved in covalent bonds with hydrogen,
and two unshared pairs on the opposite side of the oxygen atom.
Oxygen is an "electronegative“ atom compared with hydrogen.

© iTutor. 2000-2013. All Rights Reserved

 Metallic Bonds

Metallic bonding is the type of bonding

found in metallic elements. This is the
electrostatic force of attraction between
positively charged ions and delocalized
outer electrons.
Metallic bonding refers to the interaction
between the delocalized electrons and the
metal nuclei.

© iTutor. 2000-2013. All Rights Reserved

 Example of Metallic Bond

As the metal cations and the electrons are oppositely charged,

they will be attracted to each other, and also to other metal
cations. These electrostatic forces are called metallic bonds, and
these are what hold the particles together in metals.

© iTutor. 2000-2013. All Rights Reserved

 REDOX
REACTION
INTRODUCTION
Redox reaction include all chemical
reactions in which atoms have their
oxidation state changed; in general,
redox reactions involve the transfer of
electrons between species.
 The term "redox" comes from two concepts involved with electron transfer: reduction
and oxidation. It can be explained in simple terms:
• Oxidation is the loss of electrons or an increase in oxidation state by a molecule,
atom, or ion.
• Reduction is the gain of electrons or a decrease in oxidation state by a molecule,
atom, or ion.
 OXIDIZING AND REDUCING AGENT

 An oxidizing agent (also called an oxidant or oxidizer) is

a chemical compound that readily transfers oxygen atoms
or a substance that gains electrons in a redox chemical
reaction.
 An oxidizing agent oxidizes other substances
and gains electrons; therefore, its oxidation state
will decrease.
 An reducing agent (also called a reductant or reducer) is
the element or a compound in a redox reaction that
reduces another species. In doing so, it becomes oxidized,
and is therefore a electron donor in redox reaction.
 A reducing agent reduces other substances
and lose electrons; therefore, its oxidation state
will increase.
 In simple terms:
* The oxidizing agent is reduced.
* The reducing agent is oxidized.
*All atoms in a molecule can be assigned an
oxidation number. This number changes when an
oxidant acts on a substrate.
*Redox reactions occur when electrons are
exchanged.

 A mnemonic for differentiating the reactions is "OIL

RIG": Oxidation Is Loss, Reduction Is Gain (of
electrons) or "LEO the lion says GER" (Lose Electrons:
Oxidation, Gain Electrons: Reduction).
EXAMPLE
Ca0 + 2 H+1Cl-1  Ca+2Cl-1 + H 0
2 2
 Since Ca0 is being oxidized and H+1 is being reduced,
the electrons must be going from the Ca0 to the H+1.
 Since Ca0 would not lose electrons (be oxidized) if
H+1 weren’t there to gain them, H+1 is the cause, or
agent, of Ca0’s oxidation. H+1 is the oxidizing
agent.
 Since H+1 would not gain electrons (be reduced) if
Ca0 weren’t there to lose them, Ca0 is the cause, or
agent, of H+1’s reduction. Ca0 is the reducing
agent.
 BALANCING REDOX REACTIONS
 STEP 1. Split Reaction into 2 Half-Reactions
 STEP 2. Balance Elements Other than H & O
 STEP 3. Balance O by Inserting H2O into eqns. as
necessary
 STEP 4. Balance H with H+ or H2O (see 4a, 4b)
 STEP 5. Balance Charge by Inserting Electrons as
needed
 STEP 6. Multiply Each 1/2 Reaction by Factor needed
to make no. of Electrons in each 1/2 Reaction Equal
 STEP 7. Add Eqns. & Cancel Out Duplicate terms,
where possible
 STEP 4a. In ACID: Balance H by Inserting H+, as
needed
 STEP 4b. In BASE: Balance H by (i) inserting 1 H2O
for each missing H & (ii) inserting same no. of OH-
on OTHER SIDE OF REACTION as H2Os added in (i)
EXAMPLE
 Complete and Balance Following Reaction:
CuS (s) + NO3 - (aq) Cu2+(aq) + SO42- (aq) + NO (g)
 STEP1. Split into 2 Half-Reactions
a.1 CuS Cu2+ + SO42-
b.1 NO3 - NO
 STEP 2. Balance Elements Other than H & O (It is already balanced).
 STEP 3. Balance O by inserting H2O into equations as necessary.
a.3 CuS + 4H2O Cu2+ + SO42-
b.3 NO3- NO + 2H2O
 STEP 4. ACIDIC, so Balance H by inserting H+ as needed.
2- +
a4. CuS + 4H2O Cu2+ + SO4 + 8H
- +
b4. NO3 + 4H NO + 2H2O
Acids and Bases
 Acids
• An acid is a substance that releases H+ ions in
an aqueous solution
– Aqueous means water
• Example: when hydrochloric acid is dissolved
in water, the compound separates into
chlorine ions (Cl-) and hydrogen ions (H+)
 Strong Acids

• A strong acid breaks down completely in

water and gives off many H+ ions
 Weak Acid

• A weak acid only partially breaks down. It

gives off much less H+ than a strong acid.
 Characteristics of Acids

• Acids have a sour taste

• Acids react with metals & carbonates to
produce gas
• Acids contain hydrogen

H
Characteristics of Acids: Taste Sour

• Acids in foods taste sour and produce a

burning or prickling feeling on the skin
 Characteristics of Acids

• Since tasting or touching an unknown

chemical is extremely dangerous, other
methods are needed to tell whether a solution
is an acid
 Characteristics of Acids: Reacts
with Carbonate
• A safe way to test to see if a solution is an acid is
to place a few drops on a compound that
contains a carbonate (CO3)
• Example: limestone is a rock that contains
calcium carbonate (CaCO3) When an acid touches
a piece of limestone, a reaction occurs that
produces carbon dioxide gas
 Characteristics of Acids: Reacts
with Metal

• Acids also reacts with most

metals
• The reaction produces
hydrogen gas, which you
can see as bubbles
Characteristics of Acids:
Contain Hydrogen
 Bases

• A base is a substance that releases hydroxide

(OH-) ions in an aqueous solution
• Example: When sodium hydroxide (NaOH) is
dissolved in water, the compound separates
into sodium ions (Na+) and hydroxide ions
(OH-)
 Characteristics of Bases

• Bases usually taste bitter

• Bases feel slippery
• Bases contain hydroxide ions (OH-)
 Characteristics of Bases: Taste
Bitter
• Example: Baking soda
 Characteristics of Bases: Taste
Bitter
• Mild bases in foods taste bitter and feel
slippery, but as with acids, tasting and
touching are not safe ways of testing whether
a solution is a base
• In fact, some strong bases can burn the skin as
badly as strong acids
 Characteristics of Bases: Feel
Slippery
• Bases feel soapy or slippery because they
react with acid molecules in your skin called
fatty acids
 Characteristics of Bases: Feel
• InSfalicpt,ptheisryisexactly how soap is
made. Mixing base- usually
sodium hydroxide – with fatty
acids produces soap
• So when a base touches your
skin, the combination of the base
with your own fatty acids actually
makes a small amount of soap
Characteristics of Bases:
Contain Sodium
Hydroxide (OH-)
Strong Bases The Formulae

Lithium hydroxide LiOH

Sodium hydroxide NaOH
Potassium hydroxide KOH
Rubidium hydroxide RbOH
Caesium hydroxide CsOH
Barium hydroxide Ba(OH)2
Calcium hydroxide Ca(OH)2
Strontium hydroxide Sr(OH)2
Properties of Acids and Bases
 Properties of Acids & Bases

• Similarities between acids and bases

– Dissolve in water
– Conduct electricity in aqueous solution
– Can irritate or burn skin
Acid-Base Strength

• pH stands for “potential hydrogen” and is a

measure of how many H+ ions there are in
solution.
• The strength of an acid or base is usually
measured using a pH scale
• The more H+ there are, the lower the pH will
be
 Acid-Base Strength

High H+ concentration
Low H+ concentration
Acid-Base Strength

• The numbers of the pH scale usually range

from 0 – 14, but numbers outside this range
are possible
• The middle number, 7, represents a neutral
solution
• A neutral substance is neither an acid nor a
base. Pure water has a pH of 7
Acid-Base Strength

• pH < 7 indicate acidic solution

• pH = 7 indicate neutral solution
• pH > 7 indicate basic solution
Acid-Base Strength

• A concentrated strong acid has a low pH value

• A concentrated strong base has a high pH
value
 Acid-Base Indicators
• An acid-base indicator is a compound that will
change color in the presence of an acid or
base
• Litmus is a plant extract that can be blue or
red (pink)
– Litmus turns red/pink in an acidic solution
– Litmus turns blue in a basic solution
 Acid-Base Indicators

• The color of hydrangea flowers is dependent

upon the pH of soil
 Acid-Base Indicators

• It would be impossible to determine the pH of

all solutions using just one indicator, such as
litmus
• Several other acid-base indicators exist, each
producing a color change at a specific pH level
 Acid-Base Indicators

• A universal indicator is a mixture of chemicals

that changes color through a wide range of pH
values
 Acids and Bases Neutralize Each
Other
• The salts formed may be soluble in
water or can be insoluble
• If the salt is insoluble, a precipitate
will form
• Recall: a precipitate is a suspension
of a small, solid particles formed
during a chemical reaction
 Acids and Bases Neutralize Each
Other
• General formula for acid base reaction

Acid + Base → H2O + Salt

HCl + NaOH → H2O + NaCl

• Salt means any ionic compound formed
from an acid/base reaction NOT JUST
NaCl !!
 Acids and Bases Neutralize Each
•OAthcoemrmonexample of neutralization reaction occurs
when you swallow an antacid tablet to relieve an
upset stomach.
• The acid in your stomach has a pH of about 1.5 due
to mostly hydrochloric acid produced by the stomach
lining
 Acids and Bases Neutralize Each
•OAtnhaentracidtablet contains a base, such as sodium
bicarbonate, magnesium hydroxide or calcium
carbonate. The base reacts with the stomach acid
and produces a salt and water.
• This reaction lowers the acidity and raises to pH to its
normal value (about 2)
REFRENCES
1. Rayner- Canham, G. Descriptive Inorganic Chemistry;
Freeman:New York,1996; Chapter 9

2. Douglas, B; McDaniel, D.; Alexander, J. Concepts and Models of

Inorganic Chemistry, 3rd ed.; Wiley & Sons: New York, 1994;
Chapter 8.

3. J. Kotz, P.Treichel, J. Townsend, D. Treiche, Chemistry &

Chemical Reactivity, 9th ed. ; Cengage Learning.

4. J.E. Huheey, E.A. Keiter, R.L. Keiter, O.K. Medhi, Inorganic

Chemistry: Principles of Structure and Reactivity, 4th ed. ; Pearson
Education.

-THANK YOU
Basics of organic chemistry
 Classification of Organic Compounds

• I. Classification based on structures :

• (1) Acyclic compounds :- Atoms link together to form a chain (straight or branch) but
not rings.

• (2) Cyclic or closed chain compounds :- These are compounds with one or more
rings. Molecules with more than one ring are called polycyclic compounds. These
are further divided into
• (A) Carbocyclic compounds : with one or more rings solely of carbon. These are of two types.
• (i) Alicyclic compounds : Ring compounds composed of carbon atoms and resembling alphatic compounds in their properties.
• (ii) Aromatic compounds : The word ‘aromatic’ originated from the Greek word aroma meaning ‘fragrant smell.’ These are
unsaturated cyclic compounds containing alternate double bonds (conjugate) having minimum six p -electrons.
• In 1865, Kekule suggested that the actual structure of benzene is intermediate the below two structures. Double bonds are
not fixed but are in a state of oscillation.
 Heterocyclic compounds
• : These are cyclic compounds which in addition to carbon
atoms contain one or more heteroatoms (atoms other than
carbon) such as N, O, S in the ring. These are also of two types:
• (i) Non-aromatic
• (ii) Aromatic
 Classification based on functional groups

• Organic compounds can also be classified according to the nature

of the functional group present in them.
 Rules for Naming Alkanes

• The parent name, longest chain.

• If two chains have same length, chain with max substituents.
• number from the end nearest substituent.
• If same from both ends, number from the end nearest the next
substituent.
• for more substituent, Use di- for two, tri- for three, tetra- for
four, etc. and use the number assigned to the carbon to
indicate the position of each substituent.
 Branched Alkanes

• Branched substituents are numbered starting from the carbon of the

substituent attached to the parent chain. From this carbon, count the
number of carbons in the longest chain of the substituent. The substituent
is named as an alkyl group based on the number of carbons in this chain.
• Numbering of the substituent chain starts from the carbon attached to the
parent chain.
• The entire name of the branched substituent is placed in parentheses,
preceded by a number indicating which parent-chain carbon it joins.
• Substituents are listed in alphabetical order. To alphabetize, ignore
numerical (di-, tri-, tetra-) prefixes (e.g., ethyl would come before
dimethyl), but don't ignore don't ignore positional prefixes such as iso and
tert (e.g., triethyl comes before tertbutyl).
 Cyclic Alkanes

• The parent name=number of carbons in the largest ring (e.g.,

cycloalkane such as cyclohexane).
• if ring is attached to a chain, the ring is substituent on the
chain.
• When two rings are attached to each other, the larger ring is
the parent and the smaller is a cycloalkyl substituent.
• The carbons of the ring are numbered such that the
substituents are given the lowest possible numbers.
 Nomenclature of Alkenes
• a. -ene. The parent structure is the longest chain containing both carbon atoms of the double bond.

• b. Give the double bond the lowest possible numbers regardless of substituent placement.
•  Try to name the following compound...
•

• c. Common names that you should know are...

• vinyl substituent H2C=CH-
• allyl substituent H2C=CH-CH2-
• allene molecule H2C=C=CH2
• d. Endocyclic double bonds have both carbons in the ring and exocyclic double bonds have only one carbon as part of the ring.
• Cyclopentene is an example of an endocyclic double bond.

• Methylenecylopentane is an example of an exocyclic double bond.

• e. Double bonds can exist as geometric isomers and these isomers are designated by using either the cis / trans designation or the modern E / Z designation.
• cis...The two largest groups are on the same side of the double bond.
• trans...The two largest groups are on opposite sides of the double bond.
• E/Z nomenclature
• E = entgegan ("trans") Z = zusamen ("cis")
 Naming Alkynes

• Rule 1.
• Find the longest carbon chain that includes both carbons of the triple bond.
• Rule 2
• Number the longest chain starting at the end closest to the triple bond. A 1-alkyne is referred to as a terminal alkyne and alkynes at any other position are called internal alkynes.
• For example:
• 4-chloro-6-diiodo-7-methyl-2-nonyne
• Rule 3
• After numbering the longest chain with the lowest number assigned to the alkyne, label each of the substituents at its corresponding carbon. While writing out the name of the molecule, arrange the
substituents in alphabetical order. If there are more than one of the same substituent use the prefixes di, tri, and tetra for two, three, and four substituents respectively. These prefixes are not taken into
account in the alphabetical order.
• For example:
• 1-triiodo-4-dimethyl-2-nonyne
• If there is an alcohol present in the molecule, number the longest chain starting at the end closest to it, and follow the same rules. However, the suffix would be –ynol, because the alcohol group takes
priority over the triple bond.
• 5- methyl-7-octyn-3-ol
• When there are two triple bonds in the molecule, find the longest carbon chain including both the triple bonds. Number the longest chain starting at the end closest to the triple bond that appears first.
The suffix that would be used to name this molecule would be –diyne.
• For example:
• 4-methyl-1,5-octadiyne
• Rule 4
• Substituents containing a triple bond are called alkynyl.
• :
• Rule 5
• A molecule that contains both double and triple bonds is called an alkenyne. The chain can be numbered starting with the end closest to the functional group that appears first.
• The steps to naming an organic compound are:
1. Identify the parent hydrocarbon chain. This chain must follow the
following rules, in order of precedence:
1. It should have maximum substituents of the suffix functional group. By
suffix, it is meant that the parent functional group should have a suffix,
unlike halogen substituents. If more than one functional group is present,
use the one with highest precedence.
2. It should have maximum number of multiple bonds
3. It should have maximum number of double bonds.
4. It should have the maximum length.
1. Identify the parent functional group, if any, with the highest order of precedence.
2. Identify the side-chains. Side chains are the carbon chains that are not in the parent chain, but are branched off from it.
3. Identify the remaining functional groups, if any, and name them by the name of their ions (such as hydroxy for -OH, oxy for =O , oxyalkane for O-
R, etc.).
Different side-chains and functional groups will be grouped together in alphabetical order. (The prefixes di-, tri-, etc. are not taken into
consideration for grouping alphabetically. For example, ethyl comes before dihydroxy or dimethyl, as the "e" in "ethyl" precedes the "h" in
"dihydroxy" and the "m" in "dimethyl" alphabetically. The "di" is not considered in either case). In the case of there being both side chains and
secondary functional groups, they should be written mixed together in one group rather than in two separate groups.
4. Identify double/triple bonds.
5. Number the chain. To number the chain, first number in both directions (left to right and right to left), and then choose the numbering which
follows these rules, in order of precedence:
1. Has the lowest locant (or locants) for the suffix functional group. Locants are the numbers on the carbons to which the substituent is
directly attached.
2. Has the lowest locants for multiple bonds (The locant of a multiple bond is the number of the adjacent carbon with a lower number).
3. Has the lowest locants for double bonds
4. Has the lowest locants for prefixes.
1. Number the various substituents and bonds with their locants. If there is more than one of the same type of substituent/double bond, add the prefix (di-, tri-, etc.)
before it. The numbers for that type of side chain will be grouped in ascending order and written before the name of the side-chain. If there are two side-chains with the
same alpha carbon, the number will be written twice. Example: 2,2,3-trimethyl- . If there are both double bonds and triple bonds, write the "ene" before the "yne". In
case the main functional group is a terminal functional group (A group which can only exist at the end of a chain, like formyl and carboxyl groups), there is no need to
number it.
2. Arrange everything like this: Group of side chains and secondary functional groups with numbers made in step 3 + prefix of parent hydrocarbon chain (eth, meth) +
double/triple bonds with numbers (or "ane") + primary functional group suffix with numbers.
Wherever it says "with numbers", it is understood that between the word and the numbers, you use the prefix(di-, tri-)
3. Add punctuation:
1. Put commas between numbers (2 5 5 becomes 2,5,5)
2. Put a hyphen between a number and a letter (2 5 5 trimethylheptane becomes 2,5,5-trimethylheptane)
3. Successive words are merged into one word (trimethyl heptane becomes trimethylheptane)
Note: IUPAC uses one-word names throughout. This is why all parts are connected.
• The finalized name should look like this:
#,#-di<side chain>-#-<secondary functional group>-#-<side chain>-#,#,#-tri<secondary functional group><parent chain suffix><If all bonds are single bonds, use "ane">-
#,#-di<double bonds>-#-<triple bonds>-#-<primary functional group>
Note: # is used for a number. The group secondary functional groups and side chains may not look the same as shown here, as the side chains and secondary functional
groups are arranged alphabetically. The di- and tri- have been used just to show their usage. (di- after #,#, tri- after #,#,# , etc.)
Priority Functional group Formula Prefix Suffix
1 Cations -onio- -onium
e.g. Ammonium NH4+ ammonio- -ammonium
2 Carboxylic acids –COOH carboxy- -oic acid*
–COSH sulfanylcarbonyl- -thioic S-acid*
–COSeH selanylcarbonyl- -selenoic Se-acid*
Carbothioic S-acids
–SO3H sulfo- -sulfonic acid
–SO2H sulfino- -sulfinic acid
Carboselenoic Se-acids

Sulfonic acids

Sulfinic acids

3 Carboxylic acid derivatives

–COOR R-oxycarbonyl- -R-oate
–COX halocarbonyl- -oyl halide*
Esters
–CONH2 carbamoyl- -amide*
–CON=C< -imido- -imide*
Acyl halides –C(=NH)NH2 amidino- -amidine*

Amides

Imides

Amidines

4 Nitriles –CN cyano- -nitrile*

Isocyanides –NC isocyano- isocyanide
5 Aldehydes –CHO formyl- -al*
Thioaldehydes –CHS thioformyl- -thial*
6 Ketones =O oxo- -one
=S sulfanylidene- -thione
=Se selanylidene- -selone
Thiones
=Te tellanylidene- -tellone

Selones

Tellones

7 Alcohols –OH hydroxy- -ol

–SH sulfanyl- -thiol
–SeH selanyl- -selenol
Thiols
–TeH tellanyl- -tellurol

Selenols

Tellurols

8 Hydroperoxides
-OOH hydroperoxy- -peroxol
-SOH hydroxysulfanyl- -SO-thioperoxol
Peroxols
-SSH disulfanyl- -dithioperoxol

Thioperoxols (Sulfenic acid)

Dithioperoxols

9 Amines –NH2 amino- -amine

Imines =NH imino- -imine
Hydrazines –NHNH2 hydrazino- -hydrazine

10 Ethers –O– -oxy-

Thioethers –S– -thio-
Selenoethers –Se– -seleno-

11 Peroxides –OO– -peroxy-

Disulfides –SS– -disulfanyl-
Classification of Organic Compounds

Dr. Nabi
Classification of Organic Compounds
Organic compounds have been divided into
two categories depending upon the nature
of their carbon skeleton.

These are:
1. Acyclic Compound (Open chain)
2. Cyclic Compound (Closed chain)
 Acyclic (Or) Open Chain Compounds:
These compounds contain open chain of carbon atoms
in their molecules.
The terminal carbon atoms are completely free they are not
linked with each other.
The chain is open so ,it is called as open chain compound.

Eg1: CH₃-CH₂-CH₃ Propane

free terminal carbon atom -CH₃-CH₂-CH₃-

Free terminal carbon atom
Eg2 : CH₃-CH₂-CH₂-CH₂-CH₃ pentane
Eg3 : CH₃-COOH Acetic acid
 Acyclic (Or) Open Chain Compounds:
 The carbon atoms are present in the form of an open chain.
 This chain may either be a straight chain or a branched chain.
 These were initially known as Aliphatic compounds because the
 compounds of this class were derived from either animal or vegetable fats
Straight Chain Compounds:
The carbon skeleton is in the form of a straight chain.
Examples:
n-Propane CH3-CH2-CH3
Propene CH2=CH-CH3

Branched Chain Compounds

The carbon skeleton is in the form of a branched chain.
Examples: Isobutylene
 Cyclic(or)closed Chain Compounds:

These compounds contain one (or)more closed chains (or) rings of

atoms in their molecules.
In these case two terminal carbon atoms are linked with each
other.
In order to form a closed ring.
It can be either a three ,four, five membered rings.
Eg:
, , ,

They are divided into two types.

1) Homocyclic
2) Heterocyclic
1) Homocyclic (Or) Carbocyclic Compounds:
These compounds contain rings which are
made up of atoms of one kind (i.e., carbon
atoms only).
It is furtherly divided into 2 types.

1) Alicyclic Compounds
2) Aromatic Compounds
i) Alicyclic(Aliphatic+cyclic):
These are the carbocyclic compounds which
resembles aliphatic compounds in most of their
properties.
Eg: Cyclopropane ,Cyclobutane, Cyclopentane, Cyclohexane.

ii) Aromatic Compounds:

These are the carbocyclic compounds which
contain alternate double and single bonds
between the carbon atoms.
Eg: benzene
It is again divided into 2 types.
1)Benzenoid
2)Non-Benzenoid.
a) Benzenoid Compound:
Organic compounds containing one (or) more
fused benzene rings.

Eg: benzene -

Napthalene -

Anthrecene -
b) Non- Benenoid Compounds:
Aromatic compounds which donot have
contain a benzene ring.
Eg: Azulene and
Tropolone
2)Heterocyclic Compounds:

These compounds contain rings made up of one (or) more

atoms of nitrogen, oxygen, sulphur etc…, in addition to
carbon atoms.

It is again divided into 2 types.

i) Alicyclic Heterocyclic Compounds

ii)Aromatic Heterocyclic Compounds
i) Alicyclic Heterocyclic Compounds :
Aliphatic heterocyclic compounds containing one (or) more hetero
atoms in their rings.
Eg: Tetrahydrofuran,Tetrahydropyrole.

ii) Aromatic Heterocyclic Compounds:

Aromatic heterocyclic compounds containing one (or) more
heteroatoms in their molecule.
Eg: Furan, Pyrole, Thiopene, Pyridine etc…,
Thank you
Carbohydrate
By Dr. Muhammad Nabi
Pharm-D, R.Ph,
M.Phil Biochemistry
M.Phil Pharmacology
Ph.D Pharmacology
 Carbohydrates
Carbohydrates are polyhydroxy aldehydes or ketones, or substances that
yield such compounds on hydrolysis.
▶ The name carbohydrate which is signifies as hydrate of carbon.
▶ Most abundant bio-molecules on Earth.
▶ Photosynthesis converts more than 100 billion metric tons of CO2 and H2O
into cellulose and other plant products/ year.
▶ Sugar and starch are a dietary staple in most parts of the world
▶ The oxidation of carbohydrates is the central energy-yielding pathway in
most non-photosynthetic cells.
▶ Insoluble carbohydrate polymers serve as structural and protective
elements in the cell walls of bacteria and plants and in the connective
tissues of animals.
▶ Many, but not all, carbohydrates have the empirical formula (CH2O)n
▶ Some also contain nitrogen, phosphorus, or sulphur. Carbs includes sugars
are also called saccharides.(saccharides = sugar)
Foods high in carbohydrates

▶ Sweets
▶ Soft drinks
▶ Breads
▶ Beans, peas
▶ Cereals, Rice, maize, barley, wheat, corn
▶ apricot, dates, blueberry, banana, grapes, apple, orange, pineapple,
strawberry and watermelon etc
▶ macaroni, spaghetti, potato, carrot
Examples of Carbohydrates
▶ Glucose: major metabolic fuel of mammals
▶ Glycogen: storage; in animals
▶ Starch: Storage; in plants
▶ Cellulose: structure; in plants; in paper
▶ Chitin: stucture; in Arthropods
▶ Ribose: RNA, ATP, NAD
▶ Deoxyribose: DNA
▶ lactose: Milk
Functions

▶ Carbohydrates have six major functions within the body:

▶ Providing energy and regulation of blood glucose

▶ Sparing the use of proteins for energy
▶ Breakdown of fatty acids
▶ Biological recognition processes
▶ Flavor and Sweeteners
▶ Dietary fiber
▶ Carbohydrate is necessary for the regulation of nerve tissue and is the source of energy for the
brain.
▶ Some carbohydrates are high in fibre, which helps prevent constipation
▶ Structural components
▶ Carbohydrates are also important for the correct working of our brain, heart and nervous,
digestive and immune systems.
▶ Polysaccharides: storage of energy (e.g., starch and glycogen),
▶ structural components (e.g., cellulose in plants and chitin in arthropods).
▶ ribose in coenzymes (e.g., ATP, FAD, and NAD) and the backbone of RNA.
▶ Deoxyribose: component of DNA.
▶ Heparin is used to treat and prevent blood clots from forming, especially in the lungs and legs.
CLASSIFICATION
▶ Three major classes of carbohydrates:
▶ 1. Monosaccharaides,
▶ 2. Oligosaccharides, and
▶ 3. Polysaccharides
1. Monosaccharides

▶ (The word “saccharide” is derived from the Greek sakcharon, meaning

“sugar”).
▶ Monosaccharides, or simple sugars, consist of a single polyhydroxy aldehyde or
ketone unit.
▶ Depending upon the functional, Aldoses (CHO) or Ketoses (C=O)
▶ The most abundant monosaccharide D-glucose, sometimes referred to as
dextrose. Monosaccharides of more than four carbons tend to have cyclic
structures.
▶ Empirical formula (CH2O)n where n=3 or some large number.
The monosaccrides are white crystalline solids, very soluble in water, most have sweet taste .
Oligosaccharides

▶ Oligosaccharides consist of short chains condensation products of two and ten of

monosaccharide units, or residues, joined by covalent linkages called glycosidic bonds.
▶ E.g. most common sucrose, maltose and lactose.
▶ The most abundant are the disaccharides, with two monosaccharide units.e.g maltose
▶ Typical is sucrose (cane sugar), which consists of the six-carbon sugars D-glucose and D-
fructose.
▶ All common monosaccharides and disaccharides have names ending with the suffix “-ose.”
▶ In cells, most oligosaccharides consisting of three or more units do not occur as free entities
but are joined to non-sugar molecules (lipids or proteins) in glycoconjugates.
Polysaccharides
▶ The polysaccharides are sugar polymers containing more than 20 or so
monosaccharide units, and some have hundreds or thousands of units.
▶ Some polysaccharides, such as cellulose, are linear chains. Others are
glycogen and starch.
Classifications of polysaccharides
▶ Homopolysaccharides:
▶ On hydrolysis they yield only one type of monomer which may be a pure
monosaccharide or complex monosaccharide e.g. B (1-4) linked N-Acetyl
glucosamine.
▶ Heteropolysaccharides:
▶ This is a very large group containing two or more types of monosaccharaides
derivatives.
▶ They are further subdivided into:
▶ A. Glycos-amino-glycans (GAGs) These are also called mucopolysaccharides
and include: Hyaluronic acid, Heparin, Blood group polysaccharides & serum
mucoids. They also contain acid groups .
▶ B. Glycoconjugates: Class of carbohydrates covalently linked with other
chemical species such as proteins and lipids. They include proteoglycans,
glycoproteins, and glycolipids.
C: Mucilage:
They form viscous solution (gel) which is occasionally sticky. They include: Agar
(Microbial culture), Vegetable gums (Fruit pulp Citrus fruits), & Pectin (plants).
D. Derived Carbohydrates: These are derived from carbohydrates by various
chemical reactions.
These include oxidation products (sugar acids) such as: Gluconic Acid, Glucuronic
Acid & Glucaric Acid etc.
Reduction Products i.e. Poly Hydroxy Alcohol e.g. Glyceral and deoxy sugar (2-
deoxyribose), amino sugar: glucosamine.
▶ Oxidation is the gain of oxygen.
▶ Reduction is the loss of oxygen.
Exceptions

General formula: Cm (H2O)n

▶ Carbohydrates with different formula

▶ Uronic acids: C6H9O7
▶ Fucose: C6H12O5

▶ Noncarbohydrates with formula of carbohydrates

▶ Formaldehyde: CH2O
▶ Inositol: C6(H2O)6
Biomedical Importance
▶ Most abundant dietary source of energy.
▶ Brain cells and RBCs are almost wholly dependent on carbohydrates as the
energy source. Also serve as storage form of energy –Glycogen.
▶ Carbohydrates are precursors for many organic compounds (fats, amino
acids).
▶ Participate in the structure of cell membrane & cellular functions (cell
growth, adhesion and fertilization).
▶ Certain carbohydrate derivatives are used as drugs, like cardiac glycosides /
antibiotics. (aminoglycosides, macrolides)
▶ DM (diabetes mellitus)
Carbohydrate
Part #2
By Dr. Muhammad Nabi
Pharm-D, M.Phil Biochemistry
M.Phil Pharmacology
Ph.D Pharmacology
ISOMERISM IN MONOSACCHARIDES

▶ Compounds that possesses the same molecular formula & different structural
formula are called isomers and the phenomena is known as isomerism. Glucose
, Fructose, Mannose , & Galactose all have same chemical formula but different
structural formula and therefore these are isomers of each other .
▶ Isomerism in Monosaccharides are of several types
Stereoisomerism:
(stereo= having three dimensions)
Two or more monosaccharides having the same structure i.e. same linkage
between atoms but different from each other in configuration i.e. Arrangement
of atoms in space .
Enantiomers:
▶ These are pairs of stereoisomers that are mirror images of each other in regard to
asymmetric c-atoms. An asymmetric C- atom or Chiral Carbon is a C-atom that is
attached to four different types of atoms or group of atoms.
▶ D and L depends on the on last asymmetric carbon atom.
▶ D Glucose = “D” refers right hand side of the hydroxyl (OH) side chain.
▶ L Glucose = “L” refers left hand side of the hydroxyl (OH) side chain.
▶ Most of the sugar is exist in D form.
Anomers:

▶ These are two isomers that differ in configuration around the anomeric
carbon atom i.e the carbon atom of the carbonyl group which is carbon No 1
and carbon No 2 in ketoses. The two types of anomers are called alpha and
beta anomers. They are not mirror images of each other.
▶ Type is based on the position of the C-1 OH
▶ Alpha glycosidic bond
▶ OH is below
▶ - linkage between a C-1 OH and a C-4 OH
▶ Beta glycosidic bond
▶ OH is above
▶ - linkage between a C-1 OH and a C-4 OH
Epimers:
▶ These are two isomers which differ in configuration around one specific carbon
atom other than carbon atom of carbonyl group. Glucose & Galactose differ from
each other only in the position of (OH) at C-4. They are called carbon-4 epimers.
▶ Isomers in which orientation of –H and –OH is different at a particular carbon.
Optical Isomerism:
▶ The enantiomeric carbon monosaccharides by virtue of their content asymmetric
carbon atoms can rotate the plane - polarized light either to right or to the left.
▶ Those monosaccharides that rotate this light to right are called dextrorotatory and
are designated (+) type clockwise. Those rotating this light to left are called
levorotatory and are designated (-) type anticlockwise.
Pyranose & Furanose Isomerism:
The ring structures of monosaccharides may be similar to either Pyran
OR Furan and accordingly monosaccharide is said to occur in pyranose or
furanose forms.
 Fischer projection

 The Fischer projection is a two-dimensional representation of a

three-dimensional organic molecule by projection.
Haworth projectionsHaworth projections

 A Haworth projection is a common way of representing the cyclic

structure of monosaccharides with a simple three-dimensional
perspective.
CHEMICAL REACTIONS OF
MONOSACCHARIDES
▶ Chemical properties depends upon the presence of various groups in monosaccharides
i.e. aldehyde ,ketone & hydroxyl groups.
▶ 1: Reaction with Hydrazines to form Osazones:
▶ • Osazones which are actually phynylosazones which are yellowish crystalline
compounds and are produced as a result of heating sugar solutions with
phenylhydrazines.
▶ • Glucose react with three molecules of phenylhydrazine to form glucasazone.
▶ 2: Reduction to form sugar alcohols:
▶ • Both aldoses & ketoses may be reduced at their aldehyde and ketone groups to form
the corresponding poly hydroxy alcohols.
▶ • Glucose → Sorbital, Mannose →Mannitol
▶ • Galactose→ Galactitol (Dulcitol)
▶ • Fructose → Sorbital & Mannitol
▶ • Ribose→ Ribitol , Glyceraldehyde→ Glycerol
▶ • Dihydroxyacetone → Glycerol
CHEMICAL REACTIONS OF
MONOSACCHARIDES
▶ 3. Oxidation to produce sugar acids:
▶ • When oxidize under proper conditions the aldoses gives rise to the following
three types of sugar acids.
▶ • Gluconic Acid (at C-1)
▶ • Glucuronic Acid (at C-6)
▶ • Glucaric Acid (at C-1 & C-6)
▶ 4: Reducing Action Of Sugar In Alkaline Solution:
▶ • Sugars in alkaline solutions are very powerful reducing agents and the sugars are
oxidized to complex mixture of acids . e.g. Cu+, Ag+ etc.
▶ • The reducing action of sugars i.e. benedict's solution and Barfoed’s solution have
been employed for both qualitative and semi qualitative determination of
reducing sugars especially glucose in urine.
▶ 5: Action Of Acids:
▶ • Monosaccharides are resistant to action of hot dilute mineral acids. Strong acids
remove water from sugar converting them to furfurals which condense with phenol
to give characteristics colored products.
▶ • C5 H10 O5 → C5 H4 O2 + 3H2O
▶ • Ribose → Furaldehyde → water removed
▶ • This reaction is the basis of Molisch’s test for carbohydrates.
▶ 6: Action Of Basis:
▶• Dilute basis solution at low temperature can bring about rearrangement of groups
around anomeric C-Atom and its adjacent C-atoms . e.g. Glucose can be changed to
fructose and mannose.
▶ 7: Formation Of Glycosides:
▶ Glycosides are compounds in which a carbohydrate residue such as glucose is attached
by Acetyl linkage at anomeric carbon atom to an alcoholic residue called aglycone
which is non carbohydrate .
▶ 8: Formation Of esters:
▶ • The OH group of sugar may be esterified to form esters such as phosphate acetates,
propionates etc.
▶ • Sugar phosphate backbone form structural framework of nucleic acid (DNA & RNA ).
▶ • Hexose + Phosphate = Hexose phosphate
▶ • Ribose+ Phosphate = Ribose phosphate
▶ 9: Formation Of Amino Sugars :
▶ • A hydroxyl group of monosaccharides can be replaced by an amino group forming an
amino sugar .e.g.
▶ • D – glycose amine = Hyaluronic Acid
▶ • D – galactose amine = Chondroitin
▶ • D – mannose amine = Mucoprotein
▶ • Being derived from hexoses they are called hexose amine. Amino sugars are also
present in antibiotics . e.g. Erythromycin.
▶ 10: Fermentation:
▶ • Breakdown of sugars by bacteria and yeast using a method of anaerobic respiration.
▶ • Glucose→ Yeast or Bacteria→ 2 Ethanol+2 carbon dioxide
▶ • C6 H12O6 → 2 (C2H5OH) + CO2
PHARMACEUTICAL IMPORTANCE OF
CARBOHYDRATES
▶ 1. Glucose:
▶ Glucose is used to treat very low blood sugar level i.e. hypoglycaemia most often in people in
diabetes mellitus .Glucose is also used to provide carbohydrate calories to a person who cannot
eat because of illness trauma etc. ( primary source of energy ).
▶ 2. Component Of Cell Membrane: Carbohydrates are covalently linked to proteins
(glycoproteins) lipids (glycolipids) are parts of cell membrane and function as adhesion.
▶ 3. Pectin: is the heteropolysaccaride Pectin is used to reduced blood cholesterol level and
gastrointestinal disorders.
▶ 4. Agar: Microbial culture → nutrient agar is a nutrient medium most effectively used for the
cultivation of microorganism supporting growth of a wide range of non fastidious organism and
blood ager is most appropriate for human related organism in clinic practice.
▶ 5. Chondroitin Sulphate & Glucosamine Sulphate: For joints disorder treatments such as
osteoarthritis.
▶ 6. Dextran: It is used to treat hypovolemia or hypovolemic shock (decrease volume of circulating
blood plasma) that can result from surgery, trauma.
▶ 7. Inulin: (Polymer of fructose) Inulin is used to measure kidney function by
determining glomerular filtration rate ( GFR) which is volume of fluid filtered from
glomerular capillaries into bowman capsule per unit time .
▶ 8. Heparin: Heparin act as an anticoagulant, prevent formation of clots .
▶ 9. Mannitol: It is osmotic diuretic used to reduce swelling and pressure inside the eye
all around the brain.
▶ 10. Lactose: Used as excipient in tablets.
▶ 11. Ribose & Deoxyribose: Form structure of hereditary material such as DNA &RNA.
▶ 12. Aminoglycosides: They are broad spectrum bactericidal antibiotics commonly
prescribe for children.
▶ 13. Hyaluronic Acid : Used in in topical serum, eye drops & injections. Also form
structural bases of joints, skin & aqueous humor of eye.
▶ 14. Gums: Used as foods as well as suspension preparations.
▶ 15. Glycogen & Starch: Energy storage → Glycogen (animals) Starch (Plants).
Lipids
 Course Contents
• Functions of lipids
• structure of lipids
• Properties of Lipids
• Biological significance of Lipids
• Classifications of Lipids
– 1. Simple lipids
– 2. Compound Lipids
– 3. Derived Lipids
• Fatty Acids
• Fats & oil
• Saturated and unsaturated fatty acids
• Uses of fats in the body
• Physical and chemical properties of fats
• Role of phospholipids in cell membranes.
• Role of steroids (cholesterol )
• Distinguish between soap and detergents.
 Lipids
• Hydrophobic
• amphiphilic
• small molecules

• the amphiphilic nature of some lipids allows them to form

structures such as
•
• Vesicles
• Liposomes
• membranes in an aqueous environment
 Examples
• Fats
• Waxes
• Sterols
• fat-soluble vitamins
– (such as vitamins A, D, E, and K)
• Glycerides
– Monoglycerides
– Diglycerides
– Triglycerides
• phospholipids.
 • Functions

• Source of heat and energy

• structural components of cell membranes
• signaling molecules
• Insulation for the organs and nerves
• Regulator of fat soluble vitamins
• Source of essential fatty acids
• Lipids regulate membrane permeability.
• They act electrical insulators to the nerve fibres, where the myelin sheath contains lipids.
• Lipids are components of some enzyme systems.
• Some lipids like prostaglandins and steroid hormones act as cellular metabolic regulators.
• Cholesterol is found in cell membranes, blood, and bile of many organisms.
• Layers of fat in the subcutaneous layer, provides insulation and protection from cold. Body temperature maintenance is done by brown fat.
• Polyunsaturated phospholipids are important constituents of phospholipids, they provide fluidity and flexibility to the cell membranes.
• Lipoproteins that are complexes of lipids and proteins, occur in blood as plasma lipoprotein, they enable transport of lipids in aqueous environment,
and their transport throughout the body.
• Cholesterol maintains fluidity of membranes by interacting with lipid complexes.
• Cholesterol is the precursor of bile acids, Vitamin D and steroids.
• Essential fatty acids like linoleic and linolenic acids are precursors of many different types of ecosanoids including prostaglandins, thromboxanes.
These play a important role in pain, fever, inflammation and blood clotting.
 Biological functions
• Membranes

• The glycerophospholipids are the main structural component

of biological membranes, such as the cellular plasma
membrane and the intracellular membranes of organelles
 • Energy storage

• Triglycerides, stored in adipose tissue, are a major form of

energy storage both in animals and plants.
• The complete oxidation of fatty acids provides high caloric
content, about 9 kcal/g, compared with 4 kcal/g for the
breakdown of carbohydrates and proteins.
 • Signaling

• In recent years, evidence has emerged showing that lipid

signaling is a vital part of the cell signaling
 • Other functions

• The "fat-soluble" vitamins (A, D, E and K) – are essential

nutrients stored in the liver and fatty tissues, with a diverse
range of functions.
 Fats vs lipids
• fats are a subgroup of lipids called triglycerides.

• Lipids also encompass molecules such as

– fatty acids and their derivatives
– sterol-containing metabolites such as cholesterol
 Fats vs oil
Fats Oil

solid at room temperature Fats that are liquid at room

temperature

saturated unsaturated
 Fats vs Oil
• The triesters of fatty acids with glycerol (1,2,3-
trihydroxypropane) compose the class of lipids known as fats
and oils. These triglycerides (or triacylglycerols) are found in
both plants and animals, and compose one of the major food
groups of our diet. Triglycerides that are solid or semisolid at
room temperature are classified as fats, and occur
predominantly in animals.
 Fats
• Esters of fatty acids with glycerol solid at room temperature.
 Oil
• Oils are fats in the liquid state at room temperature. Because
they contain unsaturated fatty acids.
Classification
 Simple lipids
• A simple lipid is a fatty acid ester of different alcohols and
carries no other substance. These lipids belong to a
heterogeneous class of predominantly nonpolar compounds,
mostly insoluble in water, but soluble in nonpolar organic
solvents such as chloroform and benzene.
 Complex lipids
• Lipids combined with carbohydrates, proteins, aminoacids,
phosphates or other non lipid compounds.
• Glycolipids
• Phospholipids
• Lipoproteins etc.
 Derived lipids
• These are substances derived from simple lipids and compound
lipids by hydrolysis. They also, include substances related to lipids.
• Derived lipids include:
• 1- Fatty acids
• 2- Glycerol
• 3- Steroids
• 4- Isoprenoids
• 5- prostglandins and leukotriens derived from arachidonic acid.
 Advanced classification

• lipids may be divided into eight categories:

• fatty acids
• Glycerolipids
• Glycerophospholipids
• Sphingolipids
• Saccharolipids
• polyketides
• sterol lipids
• prenol lipids
Structure of lipids
Fatty acids
there is the possibility of either a cis or a trans geometric
isomerism,

• Cis-double bonds cause the fatty acid chain to bend, an effect

that is more pronounced the more double bonds there are in a
chain. This in turn plays an important role in the structure and
function of cell membranes
• Most naturally occurring fatty acids are of the cis configuration
 properties
• decompose into glycerol and fatty acids.
• float on water
• insoluble in water
• greasy to the touch
• lubricating
• not readily volatile
• burn without leaving any residue, i.e., ash.
• Low density, low mp, bp.
 Hydrogenation

• This process has a vital role in the fats and oils industry
because it achieves two main goals.
• Firstly, liquid oils into semisolid fats
• secondly, improved stability.
 auto-oxidation and rancidity

• Unsaturated fatty acids undergo a chemical change known as

auto-oxidation.
• The process requires oxygen (air) and is accelerated by the
presence of trace metals.
• Vegetable oils resists this process because they contain
• antioxidants, such as tocopherol
• Trans fats and oils have higher melting points than cis ones
because the packing isn't affected quite as much. Naturally
occurring unsaturated fats and oils tend to be the cis form.
 Fatty acids

• hydrocarbon with a carboxylic acid group;

• polar, hydrophilic end, and a nonpolar, hydrophobic end
• chain, typically between 4 and 24 carbons
• may be saturated or unsaturated,
• and may be attached to functional groups
 Triglycerides
• A triglyceride (TG, triacylglycerol, TAG, or triacylglyceride) is an
ester derived from glycerol and three fatty acids.
 Waxes
• Esters of fatty acids with high molecular weight monohydroxy
alcohols. Example: Beeswax, Carnauba wax.
 Phospholipids
• Phospholipids or Phosphatids are compound containing fatty acids and
glycerol in addition to a phosphoric acid, nitrogen bases and other
substituents. Phospholipids can be phosphoglycerides,
phosphoinositides and phosphosphingosides.
 Steroids
• Steroids comprise a group of cyclical organic compounds
whose basis is a characteristic arrangement of seventeen
carbon atoms in a four-ring structure linked together from
three 6-carbon rings followed by a 5-carbon ring and an eight-
carbon side chain on carbon 17
 Sterol (a steroid sub group)
• Sterols, also known as steroid alcohols, are a subgroup of the
steroids and an important class of organic molecules.
 Cholesterols (A sterol)
• a compound of the sterol type found in most body tissues,
including the blood and the nerves.
 Uses of fats in the body
• A healthy body needs some fat, which contains essential
nutrients. Your body uses dietary fat to make tissue and
manufacture biochemicals, such as hormones. Fats in your diet
are sources of energy that add flavor to food — the sizzle on
the steak, you can say. However, fats may also be hazardous to
your health.
• Provides a source of stored energy

• Gives shape to your body

• Cushions your skin (imagine sitting in your chair for a while as you enjoy your visit to
Dummies.com without your buttocks to pillow your bones)

• Acts as an insulation blanket that reduces heat loss

• Part of every cell membrane (the outer skin that holds each cell together)
• A component of myelin, the fatty material that sheathes nerve cells and makes it possible
for them to fire the electrical messages that enable you to think, see, speak, move, and
perform the multitude of tasks natural to a living body; brain tissue also is rich in fat
• A shock absorber that protects your organs (as much as possible) if you fall or are injured
• A constituent of hormones and other biochemicals, such as vitamin D and bile
 Physical and chemical properties of fats
• Pure fats and oils are colorless, odorless, and tasteless.
• The characteristic colors, odors, and flavors that we associate with some of
them are imparted by foreign substances that are lipid soluble and have
been absorbed by these lipids.
• Fats and oils are lighter than water, having densities of about 0.8 g/cm3.
• They are poor conductors of heat and electricity and therefore serve as
excellent insulators for the body, slowing the loss of heat through the skin.
• Fats and oils can participate in a variety of chemical reactions—for
example, because triglycerides are esters, they can be hydrolyzed in the
presence of an acid, a base, or specific enzymes known as lipases. The
hydrolysis of fats and oils in the presence of a base is used to make soap
and is called saponification.
 Role of phospholipids in cell membranes.
• Phospholipids form the basic structure of a cell membrane,
called the lipid bilayer.

http://www.rsc.org/Education/Teachers/Resources/cfb/images/09A.jpg
November 11, 2015
 Role of steroids (cholesterol )
• The body makes cholesterol in the liver and uses it for a variety of
important functions, ranging from maintaining healthy cell membranes to
building crucial hormones and vitamins.
• Cholesterol is an essential lipid constituent of cell membranes
• Cholesterol is a precursor of steroid hormones and of bile acids
• Intermediates of cholesterol biosynthesis are required to make vitamin D
and for posttranslational modification of membrane proteins
• High plasma cholesterol promotes atherosclerosis
• Scattered in the lipid bilayer are cholesterol molecules, which help to keep
the membrane fluid consistent.
 Distinguish between soap and detergents.
• Carboxylic acids and salts having alkyl chains longer than eight carbons exhibit
unusual behavior in water due to the presence of both hydrophilic (CO2) and
hydrophobic (alkyl) regions in the same molecule. Such molecules are termed
amphiphilic (Gk. amphi = both) or amphipathic.
• Fatty acids made up of ten or more carbon atoms are nearly insoluble in water,
and because of their lower density, float on the surface when mixed with water.
• fatty acids spread evenly over an extended water surface, eventually forming a
monomolecular layer in which the polar carboxyl groups are hydrogen bonded at
the water interface, and the hydrocarbon chains are aligned together away from
the water.
• Substances that accumulate at water surfaces and change the surface properties
are called surfactants.
• Alkali metal salts of fatty acids are more soluble in water than
the acids themselves, and the amphiphilic character of these
substances also make them strong surfactants.
• The most common examples of such compounds are
– soaps and detergents.
– The use of such compounds as cleaning agents is facilitated by their
surfactant character, which lowers the surface tension of water,
allowing it to penetrate and wet a variety of materials.
• Very small amounts of these surfactants dissolve in water to give a
random dispersion of solute molecules. However, when the
concentration is increased an interesting change occurs. The
surfactant molecules reversibly assemble into polymolecular
aggregates called micelles. By gathering the hydrophobic chains
together in the center of the micelle, disruption of the hydrogen
bonded structure of liquid water is minimized, and the polar head
groups extend into the surrounding water where they participate in
hydrogen bonding. These micelles are often spherical in shape, but
may also assume cylindrical and branched forms, as illustrated on
the right. Here the polar head group is designated by a blue circle,
and the nonpolar tail is a zig-zag black line.
• Micelles are able to encapsulate nonpolar substances such as
grease within their hydrophobic center, and thus solubilize it so
it is removed with the wash water. Since the micelles of anionic
amphiphiles have a negatively charged surface, they repel one
another and the nonpolar dirt is effectively emulsified. To
summarize, the presence of a soap or a detergent in water
facilitates the wetting of all parts of the object to be cleaned,
and removes water-insoluble dirt by incorporation in micelles.
• The oldest amphiphilic cleaning agent known to humans is soap. Soap is manufactured by the base-catalyzed
hydrolysis (saponification) of animal fat.
• Before sodium hydroxide was commercially available, a boiling solution of potassium carbonate leached from
wood ashes was used.
• Soft potassium soaps were then converted to the harder sodium soaps by washing with salt solution.
• The importance of soap to human civilization is documented by history, but some problems associated with its
use have been recognized. One of these is caused by the weak acidity (pKa ca. 4.9) of the fatty acids. Solutions
of alkali metal soaps are slightly alkaline (pH 8 to 9) due to hydrolysis. If the pH of a soap solution is lowered by
acidic contaminants, insoluble fatty acids precipitate and form a scum. A second problem is caused by the
presence of calcium and magnesium salts in the water supply (hard water). These divalent cations cause
aggregation of the micelles, which then deposit as a dirty scum.
• These problems have been alleviated by the development of synthetic amphiphiles called detergents (or
syndets). By using a much stronger acid for the polar head group, water solutions of the amphiphile are less
sensitive to pH changes. Also the sulfonate functions used for virtually all anionic detergents confer greater
solubility on micelles incorporating the alkaline earth cations found in hard water. Variations on the amphiphile
theme have led to the development of other classes, such as the cationic and nonionic detergents. Cationic
detergents often exhibit germicidal properties, and their ability to change surface pH has made them useful as
fabric softeners and hair conditioners. These versatile chemical "tools" have dramatically transformed the
household and personal care cleaning product markets over the past fifty years.
https://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/lipids.htm
November 11, 2015
Thank You
 By
Dr. Muhammad Nabi
PharmD, RPh, M.Phil. (Biochemistry),
M.Phil. (Pharmacology), PhD
(Pharmacology)
1
Genetic Code

2
Genetic Code, DNA

3
Genetic Code, RNA

4
Anti-Codon

5
Anticodon, tRNA

6
Anticodon, tRNA

7
Protein Translation

8
Protein Translation

9
Practical 2

10
 HM135519: DNA: + or sense strand
ATGTCACAAGCTGCCCCATATATCGAGCAAGCTCAGGTAATAGCCCACCAGTTCAAGGAAAA
AGTCCTTGGATTGCTGCAGCGAGCCACCCAACAACAAGCTGTCATTGAGCCCATAGTAGTTA
CCAACTGGCAAAAACTTGAGACCTTCTGGCACAAGCACATGTGGAACTTTGTGAGTGGGAT
CCAGTACCTAGCAGGTCTTTCTACTTTGCCCGGCAACCCCGCTGTGGCGTCTCTTATGGCGTT
CACCGCTTCAGTCACCAGTCCCCTGACGGCCAACCAAACTATGTTCTTCAACATACTTGGGG
GATGGGTTGCCACCCATTTGGCAGGACCCCAAAGCTCTTCTGCATTCGTGGTGAGCGGCTTG
GCTGGCGCTGCCATAGGGGGCATCGGCCTGGGCAGGGTCTTACATGACATCCTGGCAGGAT
ACGGGGCTGGAGTCTCAGGCGCCTTGGTGGCTTTTAAGATCATGGGAGGGGAACTCCCCAC
TGCCGAGGACATGGTCAACCTATTGCCCGCCATACTATCTCCAGGCGCTCTCGTCGTCGGCGT
AATATGCGCTGCCATACTGCGTCGGCACGTGGGACCTGGGGAGGGGGCGGTGCAGTGGAT
GAACAGGCTCATCGCATTCGCATCCCGGGGCAATCACGTCTCACCGACGCATTATGTTCCCGA
GAGCGATGCTGCGGCGAGGGTCACTTTGCTGCTGAACTCTCTAACTATCACAACTCTGCTCC
GACGGTTGCACAAGTGGATCAATGAAGACTACCCAAGCCCTTGT

11
HM135519: DNA: - or antisense strand
ACAAGGGCTTGGGTAGTCTTCATTGATCCACTTGTGCAACCGTCGGAGCAGAGTTGTGATAG
TTAGAGAGTTCAGCAGCAAAGTGACCCTCGCCGCAGCATCGCTCTCGGGAACATAATGCGTC
GGTGAGACGTGATTGCCCCGGGATGCGAATGCGATGAGCCTGTTCATCCACTGCACCGCCCC
CTCCCCAGGTCCCACGTGCCGACGCAGTATGGCAGCGCATATTACGCCGACGACGAGAGCG
CCTGGAGATAGTATGGCGGGCAATAGGTTGACCATGTCCTCGGCAGTGGGGAGTTCCCCTCC
CATGATCTTAAAAGCCACCAAGGCGCCTGAGACTCCAGCCCCGTATCCTGCCAGGATGTCAT
GTAAGACCCTGCCCAGGCCGATGCCCCCTATGGCAGCGCCAGCCAAGCCGCTCACCACGAA
TGCAGAAGAGCTTTGGGGTCCTGCCAAATGGGTGGCAACCCATCCCCCAAGTATGTTGAAG
AACATAGTTTGGTTGGCCGTCAGGGGACTGGTGACTGAAGCGGTGAACGCCATAAGAGAC
GCCACAGCGGGGTTGCCGGGCAAAGTAGAAAGACCTGCTAGGTACTGGATCCCACTCACAA
AGTTCCACATGTGCTTGTGCCAGAAGGTCTCAAGTTTTTGCCAGTTGGTAACTACTATGGGCT
CAATGACAGCTTGTTGTTGGGTGGCTCGCTGCAGCAATCCAAGGACTTTTTCCTTGAACTGG
TGGGCTATTACCTGAGCTTGCTCGATATATGGGGCAGCTTGTGACAT

12
 HM135519: DNA: + or sense strand
ATGTCACAAGCTGCCCCATATATCGAGCAAGCTCAGGTAATAGCCCACCAGTTCAAGGAAAA
AGTCCTTGGATTGCTGCAGCGAGCCACCCAACAACAAGCTGTCATTGAGCCCATAGTAGTTA
CCAACTGGCAAAAACTTGAGACCTTCTGGCACAAGCACATGTGGAACTTTGTGAGTGGGAT
CCAGTACCTAGCAGGTCTTTCTACTTTGCCCGGCAACCCCGCTGTGGCGTCTCTTATGGCGTT
CACCGCTTCAGTCACCAGTCCCCTGACGGCCAACCAAACTATGTTCTTCAACATACTTGGGG
GATGGGTTGCCACCCATTTGGCAGGACCCCAAAGCTCTTCTGCATTCGTGGTGAGCGGCTTG
GCTGGCGCTGCCATAGGGGGCATCGGCCTGGGCAGGGTCTTACATGACATCCTGGCAGGAT
ACGGGGCTGGAGTCTCAGGCGCCTTGGTGGCTTTTAAGATCATGGGAGGGGAACTCCCCAC
TGCCGAGGACATGGTCAACCTATTGCCCGCCATACTATCTCCAGGCGCTCTCGTCGTCGGCGT
AATATGCGCTGCCATACTGCGTCGGCACGTGGGACCTGGGGAGGGGGCGGTGCAGTGGAT
GAACAGGCTCATCGCATTCGCATCCCGGGGCAATCACGTCTCACCGACGCATTATGTTCCCGA
GAGCGATGCTGCGGCGAGGGTCACTTTGCTGCTGAACTCTCTAACTATCACAACTCTGCTCC
GACGGTTGCACAAGTGGATCAATGAAGACTACCCAAGCCCTTGT

13
 HM135519
AUGUCACAAGCUGCCCCAUAUAUCGAGCAAGCUCAGGUAAUAGCCCACCAGUUCAAGGAAAAAGUCCUUGGAU
UGCUGCAGCGAGCCACCCAACAACAAGCUGUCAUUGAGCCCAUAGUAGUUACCAACUGGCAAAAACUUGA
GACCUUCUGGCACAAGCACAUGUGGAACUUUGUGAGUGGGAUCCAGUACCUAGCAGGUCUUUCUACUUUG
CCCGGCAACCCCGCUGUGGCGUCUCUUAUGGCGUUCACCGCUUCAGUCACCAGUCCCCUGACGGCCAACC
AAACUAUGUUCUUCAACAUACUUGGGGGAUGGGUUGCCACCCAUUUGGCAGGACCCCAAAGCUCUUCUGC
AUUCGUGGUGAGCGGCUUGGCUGGCGCUGCCAUAGGGGGCAUCGGCCUGGGCAGGGUCUUACAUGACAUC
CUGGCAGGAUACGGGGCUGGAGUCUCAGGCGCCUUGGUGGCUUUUAAGAUCAUGGGAGGGGAACUCCCCA
CUGCCGAGGACAUGGUCAACCUAUUGCCCGCCAUACUAUCUCCAGGCGCUCUCGUCGUCGGCGUAAUAUG
CGCUGCCAUACUGCGUCGGCACGUGGGACCUGGGGAGGGGGCGGUGCAGUGGAUGAACAGGCUCAUCGCA
UUCGCAUCCCGGGGCAAUCACGUCUCACCGACGCAUUAUGUUCCCGAGAGCGAUGCUGCGGCGAGGGUCA
CUUUGCUGCUGAACUCUCUAACUAUCACAACUCUGCUCCGACGGUUGCACAAGUGGAUCAAUGAAGACUA
CCCAAGCCCUUGU
14
Genetic Code, RNA

15
Anticodon, tRNA

16
 Protein

MSQAAPYIEQAQVIAHQFKEKVLGLLQRATQQQAVIEPIVVTNWQKLETFWHKHMWNF
VSGIQYLAGLSTLPGNPAVASLMAFTASVTSPLTANQTMFFNILGGWVATHLAGPQSSSAF
VVSGLAGAAIGGIGLGRVLHDILAGYGAGVSGALVAFKIMGGELPTAEDMVNLLPAILSPG
ALVVGVICAAILRRHVGPGEGAVQWMNRLIAFASRGNHVSPTHYVPESDAAARVTLLLNS
LTITTLLRRLHKWINEDYPSPC

17
18
19
20
21
Structure
Amino acid (Building blocks of
proteins)

From: https://katysstudynotes.files.wordpress.com/2010/10/protein-1.png
Date: October 25, 2015
Naming the carbon atoms in amino acids
 Amino Acids: Atom Naming
• Organic nomenclature: start from one end
• Biochemical designation: start from
-carbon and go down the R-group
Alpha, Beta and Gamma amino acids

Depending on
amino group

From: http://patentimages.storage.googleapis.com/US7179789B2/US07179789-20070220-C00001.png
Date: October 25, 2015
 B2 vs B3 amino acids

From: http://3.bp.blogspot.com/-9LW6E3a 8s/UMeYjGqplnI/AAAAAAAAckE/zyTj5FKWmgk/s1600/amino+acids.png

Date: October 25, 2015

Depending
on R group
Structures of different Amino Acids
 Glycine
Gly
G
R: H
 Alanine
Ala
A
R: CH3
A: means one CH3 only
Serine
Ser
S
Cysteine
Cys
C
Meth thio nine Methionine
Methyl Thio Isnain:2(CH2) Met
M
 Phenylalanine
Phe
F
Phenyl

Alanine
 Tyrosine
Tyr
Tyr osine
Y
Aey tair-e-lahoti
Tryptophan
Trp
W
Histidine
His
H
Valine
Val
V
Threonine
Thr
T
 Leucine
Leu
L
Yo: means one CH2
 Isoleucine
Ile
I
Isomer of leucine: One methyl group drops one step down

From: http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/L/Leu_ile.gif
Date: October 25, 2015
 Aspartic acid
Asp
Asp: Starts with A D
A: One: One Carbon
 Glutamic acid
Glu
E
Glu: Two: Two carbons
 Asparagine
Asn
N
Asp: From Aspartic acid
Ine: For amine: NH2 instead of OH in
COOH
 Glutamine
Gln
Q
Glut: From Glutamic acid
Ine: For amine: NH2 instead of OH in
COOH
 Lysine
Lys
K
4 carbons with one amino group
Arginine
Arg
R
Proline
Pro
P
Amino acids differ in the R group
 Amino Acids
• Amino acids: structural units of proteins.

• When joined together: peptides or Proteins.

From: http://www.ucl.ac.uk/~sjjgsca/peptide1.gif
Date: October 25, 2015

• Linear and unbranched

From: http://science.halleyhosting.com/sci/ibbio/chem/notes/chpt3/primary.gif
Date: October 25, 2015
Essential and non essential amino acids
 Lysine: K

Essential Tryptophan: W

Amino acids Threonine: T

Valine: V

KW TV FILM
Phenylalanine: F

Isoleucine: I

Leucine: L

Methionine: M
 Nonessential
Alanine
Asparagine
Aspartic acid
Cysteine
Glutamic acid
Glutamine
Glycine
Proline
Selenocysteine
Serine
Tyrosine
Arginine
Histidine
Ornithine
Taurine
 All above mentioned amino acids show
chirality except glycine
• What is chirality?
Chirality
From: http://www.chemtech.org/cn/cn2323/images/4-chiral.gif
Date: October 25, 2015
 Most -Amino Acids are Chiral
• The -carbon has always
four substituents and is
tetrahedral
• All (except proline) have an
acidic carboxyl group, a basic
amino group, and an alpha
hydrogen connected to the -
carbon
• Each amino acid has an
unique fourth substituent R
• In glycine, the fourth From: https://encrypted-tbn3.gstatic.com/images?q=tbn:ANd9GcTyTDeiU0RySqPUeBueNvymtq1ZwKVVn8l3GVYhJ936wBEYI8WI
Date: 2014

substituent is also hydrogen

Classification
 Amino Acids: Classification
Common amino acids can be placed in five
basic groups depending on their R substituents:

• Nonpolar, aliphatic (7)

• Aromatic (3)
• Polar, uncharged (5)
• Positively charged (3)
• Negatively charged (2)
Aliphatic Amino Acids
Aromatic Amino Acids
Charged Amino Acids
Polar Amino Acids
Special Amino Acids
Peptides and peptide bond formation
 Peptides and Peptide bonds
“Peptides” are small condensation
products of amino acids

They are “small” compared to proteins

(di, tri, tetra… oligo-)
Importance and functions
• As a source of energy: CO2+Urea
• Gluconeogenesis: glucose formation
• Synthesize other molecules e.g. neurotransmitters, alkaloids,
nucleotides and porphyrine etc.
• Defense against herbivores in plants
• Flavor enhancer: glutamic acid
• Artificial sweetener: Aspartame

• 5-hydroxytryptopan: Depression treatment

• 1. building blocks of proteins
• Structure of living things.
• muscles, ligaments, tendons, organs, glands, nails, hair, and many vital body
fluids, and are essential for the growth of bones.
• Catalysts: enzymes
• Messengers: hormones
• regulate the body's water balance
• maintain the proper internal pH.
• structural basis of chromosomes, through which genetic information is passed
from parents to offspring.
• 2. neurotransmitters or as precursors of neurotransmitters, the
chemicals that carry information from one nerve cell to another.
• Certain amino acids are thus necessary for the brain to receive and send
messages.
• neurotransmitters are able to pass through the blood-brain barrier.
• 3. Alanine: aids in the metabolism of glucose
• beta-alanine, is a constituent of pantothenic acid (vitamin 65) and coenzyme
A, a vital catalyst in the body.
• 4. Arginine retards the growth of tumours and cancer by enhancing
immune function.
• It increases the size and activity of the thymus gland, which manufactures T
lymphocytes (T cells), crucial components of the immune system.
• useful in treating sterility in men.
• helpful for healing and repair of damaged tissue.
• important for muscle metabolism.
• This amino acid aids in weight loss
• It aids in stimulating the pancreas to release insulin
• 5. Asparagine: maintain balance in the central nervous system; it
prevents you from being either overly nervous or overly calm
• 6: aspartic acid: increases stamina,
• it is good for fatigue and plays a vital role in metabolism.
• It is beneficial for neural and brain disorders.
• 7: Cysteine: helps to detoxify harmful toxins and protect the body
from radiation damage.
• 8: Glutamic acid: neurotransmitter
• 9: Glutamine: most abundant free amino acid found in the muscles of
the body.
• Because it can readily pass the blood-brain barrier, it is known as brain fuel.
Glutathione is a powerful antioxidant that is produced in the liver.
• 10: Glycine: retards muscle degeneration by supplying additional creatine,
a compound that is present in muscle tissue and is utilized in the
construction of DNA and RNA.
• Glycine is essential for the synthesis of nucleic acids, bile acids, and other
nonessential amino acids in the body.
• 11: Histidine: significant in the growth and repair of tissues.
• 12: Isoleucine: needed for haemoglobin formation
• stabilizes and regulates blood sugar levels.
• 13: Lysine: needed for proper growth and bone development in children; it
helps calcium absorption and maintains a proper nitrogen balance in
adults.
• 14: Methionine: assists in the breakdown of fats, thus helping to prevent a
build-up of fat in the liver and arteries that might obstruct blood flow to
the brain, heart, and kidneys.
• 15: Phenylalanine: it can be converted into another amino acid, tyrosine,
which in turn is used to synthesize two key neurotransmitters that promote
alertness: dopamine and nor-epinephrine.
• can elevate mood, decrease pain, aid in memory and learning, and suppress the
appetite.
• 16: Proline: improves skin texture by aiding in the production of collagen and
reducing the loss of collagen through the aging process.
• It also helps in the healing of cartilage and the strengthening of joints, tendons, and heart
muscle.
• 17: Serine: needed for the proper metabolism of fats and fatty acids, the growth
of muscle, and the maintenance of a healthy immune system.
• It aids in the production of immunoglobulin and antibodies. 18: Threonine: helps to maintain
the proper protein balance in the body.
• 19: Tryptophan: necessary for the production of vitamin 63 (niacin).
• 20: Tyrosine: a precursor of the neurotransmitters norep-inephrine and
dopamine, which regulate mood, among other things.
• Tyrosine acts as a mood elevator; a lack of adequate amounts of tyrosine leads to a
deficiency of norepinephrine in the brain, which in turn can result in depression.
• Tyrosine attaches to iodine atoms to form active thyroid hormones. Not surprisingly,
therefore, low plasma levels of tyrosine have been associated with hypothyroidism.
• Symptoms of tyrosine deficiency can also include low blood pressure, low body temperature
(such as cold hands and feet), and restless leg syndrome.
• 21: Valine: needed for muscle metabolism, tissue repair, and the maintenance of
a proper nitrogen balance in the body.
• Valine is found in high concentrations in muscle tissue.
 Proteins

http://www.redrooster.com.au/media/360/WholesomeRoast.75.12824.png
November 1, 2015
 Proteins
• 1: Biochemical compounds: Polymers of amino acids
• 2: Composition: one or more polypeptides (amino acids)
• 3: Structure: folded into a globular or fibrous form
• 4: Function: It carries out several biological functions.
Importance and Functions of Proteins
 Importance or Functions of proteins
• 1. cell structure: cytoskeleton (mircrofilamints, microtubules)
• 2. contractile machinery of muscle: Actin Myosin
• 3. Oxygen transport: Hemoglobin
• 4. Search for foreign invaders: Antibodies
• 5. Reaction catalysis: Enzymes
• 6. Sensing and responding: Receptors
• 7. Many other functions previously explained in amino acids section
 http://people.eku.edu/ritchisong/RITCHISO/receptorprotein.gif
http://academic.brooklyn.cuny.edu/biology/bio4fv/page/ind_fit.gif
Date: 2014
November 1, 2015

https://upload.wikimedia.org/wikipedia/commons/4/48/Actin_Myosin.gif
Date: 2014

http://www.ps-19.org/Crea07Eukary/index_files/cytoskeleton-1.gif
November 1, 2015

http://2.bp.blogspot.com/-l8oNf7cLsM4/Upc9cQcrP4I/AAAAAAAABWI/LTy5cDpxO_4/s1600/first-animatin.gif
November 1, 2015

https://upload.wikimedia.org/wikipedia/commons/b/ba/Hemoglobin_t-r_state_ani.gif
November 1, 2015
Types or Classes of Proteins
 Type: 1

http://moleculesoflife2010.wikispaces.com/file/view/typ
es_of_proteins_table_Nelson.jpg/174923423/734x534/ty
pes_of_proteins_table_Nelson.jpg
November 1, 2015
 Types:2
• Simple proteins (Only polypeptide chains)
e.g. Albumin, glubulin, glutinin, prolamin
• Conjugated proteins (Polypeptide chain + other molecules)
e.g. nucleoproteins, glycoprotein
• Derived proteins (obtained from simple proteins by the action of enzymes
and chemical agents)
e.g. Peptides i.e. proteoses (by water) and peptones (by enzymes)
 Types:3

http://image.slidesharecdn.com/structureoforganiccompounds-120929105636-phpapp01/95/structure-of-organic-compounds-25-728.jpg?cb=1348917245
November 1, 2015

http://images.slideplayer.com/1/273296/slides/slide_43.jpg
November 1, 2015
Levels of Protein Structures
Levels of protein structure
 Protein Primary Structure

MSQAAPYIEQAQVIAHQFKEKVLGLLQRATQQQAVIEPIVVTNWQKLETFWHKHMWNF
VSGIQYLAGLSTLPGNPAVASLMAFTASVTSPLTANQTMFFNILGGWVATHLAGPQSSSAF
VVSGLAGAAIGGIGLGRVLHDILAGYGAGVSGALVAFKIMGGELPTAEDMVNLLPAILSPG
ALVVGVICAAILRRHVGPGEGAVQWMNRLIAFASRGNHVSPTHYVPESDAAARVTLLLNS
LTITTLLRRLHKWINEDYPSPC

85
 Primary Structure
• Sequence of the amino acids
Levels of protein structure
Beta sheet and its types
 Secondary structure
• Folding of short polypeptide units into geometrically ordered units
• The secondary protein structure is the specific local geometric shape
caused by intramolecular and intermolecular hydrogen bonding of
amide groups.
Antiparallel
Parallel
 Types of secondary structures
• Alpha Helix: In the alpha helix, the polypeptide chain is coiled tightly
in the fashion of a spring.
• Beta Sheets: Beta sheets consist of beta strands connected laterally
by at least two or three backbone hydrogen bonds, forming a
generally twisted, pleated sheet. A beta strand (also β strand) is a
stretch of polypeptide chain typically 3 to 10 amino acids long with
backbone in an almost fully extended conformation.
Structural Motifs or super secondary
structures
 Structural Motifs
• a supersecondary structure, which also appears in a variety of other
molecules.
• compact three-dimensional structure of several adjacent elements of
secondary structure
• smaller than a protein domain or a subunit.
• Motifs do not allow us to predict the biological functions:
• they are found in proteins and enzymes with dissimilar functions.
• structural motif does not have to be associated with a sequence
motif.
• Examples include β-hairpins, α-helix hairpins, and β-α-β motifs
Examples
• Beta hairpin:
• Extremely common. Two antiparallel beta strands connected by a tight turn of a few amino acids
between them.
• Greek key:
• 4 beta strands folded over into a sandwich shape.
• Omega loop:
• a loop in which the residues that make up the beginning and end of the loop are very close
together.
• Helix-loop-helix:
• Consists of alpha helices bound by a looping stretch of amino acids. This motif is seen in
transcription factors.
• Zinc finger:
• Two beta strands with an alpha helix end folded over to bind a zinc ion. Important in DNA binding
proteins.
Tertiary Structure
 Tertiary structure
• The three dimensional assembly of secondary structure into a
functional unit.
 Quaternary structure
More than one polypeptide chains
Domains
 Protein Domains
• Several motifs pack together to form compact, local, units called domains.
• conserved part of a given protein sequence and structure
• evolve, function, and exist independently of the rest of the protein
• Each domain forms a compact three-dimensional structure
• often can be independently stable and folded.
• Many proteins consist of several structural domains.
• One domain may appear in a variety of different proteins.
• may be recombined in different arrangements to create proteins with
different functions.
• vary in length from between about 25 amino acids up to 500 amino acids in
length.
 Multidomain Proteins
• Two or more than two domains
• each domain may fulfill its own function independently, or in a
concerted manner with its neighbours.
Summary
Fibrous and Globular Proteins
 Fibrous proteins
• Scleroproteins: fibrous proteins,

• Examples: Keratin, collagen, elastin, and fibroin are all scleroproteins.

• The roles of such proteins include protection and support, forming

connective tissue, tendons, bone matrices, and muscle fiber.
 Keratin

Collagen

Elastin
• Shape: long protein filaments: rods or wires.
• Function: structural and storage
• Solubility: inert and water-insoluble.
• Occurrence: occurs as an aggregate due to hydrophobic side chains
that protrude from the molecule.

• has limited residues with repeats

• The structures often feature cross-links between chains (e.g., cys-cys

disulfide bonds between keratin chains).

• Does not denature as easily as globular proteins.

Examples
 Collagen
• in the flesh and connective tissues of vertebrates.

• most abundant protein in mammals, making up about 25% to 35% of the

whole-body protein content.

• found in fibrous tissues such as tendon, ligament and skin,

• also abundant in cornea, cartilage, bone, blood vessels, the gut, and
intervertebral disc.

• Gelatin, which is used in food and industry, is collagen that has been
irreversibly hydrolyzed.
 •Structure
• a triple helix,

• two identical chains (α1) and an (α2).

• high hydroxyproline content.

• The most common motifs in the amino acid sequence of

collagen are

• glycine-proline-X

• glycine-X-hydroxyproline, w

• X is any amino acid other than glycine, proline or hydroxyproline.

 Elastin
• in connective tissue
• Elastic: allows many tissues to resume their shape after stretching or
contracting.
• Elastin helps skin to return to its original position when it is poked or
pinched.
• Elastin is also an important load-bearing tissue in the bodies of
vertebrates and used in places where mechanical energy is required
to be stored.
• rich in hydrophobic amino acids such as glycine and proline,
• which form mobile hydrophobic regions bounded by crosslinks
between lysine residues.
Globular Proteins
 Globular proteins
• Globular proteins: spheroproteins
• Globular proteins are spherical ("globe-like")
• somewhat water-soluble
• they actually form colloids in water
• The term globin can refer more specifically to proteins including the
globin fold
 Continued
• The molecule's apolar (hydrophobic) amino acids are bounded
towards the molecule's interior
• whereas polar (hydrophilic) amino acids are bound outwards,
allowing dipole-dipole interactions with the solvent, which explains
the molecule's solubility.
• folding in a different way can effect function of globular proteins

• Less stable as compared to fibrous proteins

Functions
 Functions
• Unlike fibrous proteins which only play a structural function, globular
proteins can act as:

• Enzymes,
• Messengers: hormones, i.e. insulin etc.
• Transporters of other molecules through membranes
• Stocks of amino acids.
• Regulatory roles are also performed by globular proteins
• Structural proteins, e.g., actin and tubulin, which are globular and soluble
as monomers, but polymerize to form long, stiff fibers
Examples
• hemoglobin, a member of the globin protein family.

immunoglobulins (IgA, IgD, IgE, IgG and IgM),

• Nearly all enzymes with major metabolic functions are globular in
shape
• many signal transduction proteins.
• Albumins are also globular proteins, although, unlike all of the other
globular proteins, they are completely soluble in water.
The End
Amino acids differ in the R group
 Amino Acids
• Amino acids: structural units of proteins.

• When joined together: peptides or Proteins.

From: http://www.ucl.ac.uk/~sjjgsca/peptide1.gif
Date: October 25, 2015

• Linear and unbranched

From: http://science.halleyhosting.com/sci/ibbio/chem/notes/chpt3/primary.gif
Date: October 25, 2015
Essential and non essential amino acids
 Lysine: K

Essential Tryptophan: W

Amino acids Threonine: T

Valine: V

KW TV FILM
Phenylalanine: F

Isoleucine: I

Leucine: L

Methionine: M
 Nonessential
Alanine
Asparagine
Aspartic acid
Cysteine
Glutamic acid
Glutamine
Glycine
Proline
Selenocysteine
Serine
Tyrosine
Arginine
Histidine
Ornithine
Taurine
 All above mentioned amino acids show
chirality except glycine
• What is chirality?
Chirality
From: http://www.chemtech.org/cn/cn2323/images/4-chiral.gif
Date: October 25, 2015
 Most -Amino Acids are Chiral
• The -carbon has always
four substituents and is
tetrahedral
• All (except proline) have an
acidic carboxyl group, a basic
amino group, and an alpha
hydrogen connected to the -
carbon
• Each amino acid has an
unique fourth substituent R
• In glycine, the fourth From: https://encrypted-tbn3.gstatic.com/images?q=tbn:ANd9GcTyTDeiU0RySqPUeBueNvymtq1ZwKVVn8l3GVYhJ936wBEYI8WI
Date: 2014

substituent is also hydrogen

Classification
 Amino Acids: Classification
Common amino acids can be placed in five
basic groups depending on their R substituents:

• Nonpolar, aliphatic
• Aromatic
• Polar, uncharged
• Positively charged
• Negatively charged
Aliphatic Amino Acids
Aromatic Amino Acids
Charged Amino Acids
Polar Amino Acids
Special Amino Acids
Peptides and peptide bond formation
 Peptides and Peptide bonds
“Peptides” are small condensation
products of amino acids

They are “small” compared to proteins

(di, tri, tetra… oligo-)
Importance and functions
• As a source of energy: CO2+Urea
• Gluconeogenesis: glucose formation
• Synthesize other molecules e.g. neurotransmitters, alkaloids,
nucleotides and porphyrine etc.
• Defense against herbivores in plants
• Flavor enhancer: glutamic acid
• Artificial sweetener: Aspartame

• 5-hydroxytryptopan: Depression treatment

• 1. building blocks of proteins
• Structure of living things.
• muscles, ligaments, tendons, organs, glands, nails, hair, and many vital body
fluids, and are essential for the growth of bones.
• Catalysts: enzymes
• Messengers: hormones
• regulate the body's water balance
• maintain the proper internal pH.
• structural basis of chromosomes, through which genetic information is passed
from parents to offspring.
• 2. neurotransmitters or as precursors of neurotransmitters, the
chemicals that carry information from one nerve cell to another.
• Certain amino acids are thus necessary for the brain to receive and send
messages.
• neurotransmitters are able to pass through the blood-brain barrier.
• 3. Alanine: aids in the metabolism of glucose
• beta-alanine, is a constituent of pantothenic acid (vitamin B5) and coenzyme
A, a vital catalyst in the body.
• 4. Arginine retards the growth of tumours and cancer by enhancing
immune function.
• It increases the size and activity of the thymus gland, which manufactures T
lymphocytes (T cells), crucial components of the immune system.
• useful in treating sterility in men.
• helpful for healing and repair of damaged tissue.
• important for muscle metabolism.
• This amino acid aids in weight loss
• It aids in stimulating the pancreas to release insulin
• 5. Asparagine: maintain balance in the central nervous system; it
prevents you from being either overly nervous or overly calm
• 6: aspartic acid: increases stamina,
• it is good for fatigue and plays a vital role in metabolism.
• It is beneficial for neural and brain disorders.
• 7: Cysteine: helps to detoxify harmful toxins and protect the body
from radiation damage.
• 8: Glutamic acid: neurotransmitter
• 9: Glutamine: most abundant free amino acid found in the muscles of
the body.
• Because it can readily pass the blood-brain barrier, it is known as brain fuel.
Glutathione is a powerful antioxidant that is produced in the liver.
• 10: Glycine: retards muscle degeneration by supplying additional creatine,
a compound that is present in muscle tissue and is utilized in the
construction of DNA and RNA.
• Glycine is essential for the synthesis of nucleic acids, bile acids, and other
nonessential amino acids in the body.
• 11: Histidine: significant in the growth and repair of tissues.
• 12: Isoleucine: needed for haemoglobin formation
• stabilizes and regulates blood sugar levels.
• 13: Lysine: needed for proper growth and bone development in children; it
helps calcium absorption and maintains a proper nitrogen balance in
adults.
• 14: Methionine: assists in the breakdown of fats, thus helping to prevent a
build-up of fat in the liver and arteries that might obstruct blood flow to
the brain, heart, and kidneys.
• 15: Phenylalanine: it can be converted into another amino acid, tyrosine,
which in turn is used to synthesize two key neurotransmitters that promote
alertness: dopamine and nor-epinephrine.
• can elevate mood, decrease pain, aid in memory and learning, and suppress the
appetite.
• 16: Proline: improves skin texture by aiding in the production of collagen and
reducing the loss of collagen through the aging process.
• It also helps in the healing of cartilage and the strengthening of joints, tendons, and heart
muscle.
• 17: Serine: needed for the proper metabolism of fats and fatty acids, the growth
of muscle, and the maintenance of a healthy immune system.
• It aids in the production of immunoglobulin and antibodies. 18: Threonine: helps to maintain
the proper protein balance in the body.
• 19: Tryptophan: necessary for the production of vitamin B3 (niacin).
• 20: Tyrosine: a precursor of the neurotransmitters norep-inephrine and
dopamine, which regulate mood, among other things.
• Tyrosine acts as a mood elevator; a lack of adequate amounts of tyrosine leads to a
deficiency of norepinephrine in the brain, which in turn can result in depression.
• Tyrosine attaches to iodine atoms to form active thyroid hormones. Not surprisingly,
therefore, low plasma levels of tyrosine have been associated with hypothyroidism.
• Symptoms of tyrosine deficiency can also include low blood pressure, low body temperature
(such as cold hands and feet), and restless leg syndrome.
• 21: Valine: needed for muscle metabolism, tissue repair, and the maintenance of
a proper nitrogen balance in the body.
• Valine is found in high concentrations in muscle tissue.
 Proteins

http://www.redrooster.com.au/media/360/WholesomeRoast.75.12824.png
November 1, 2015
 Proteins
• 1: Biochemical compounds: Polymers of amino acids
• 2: Composition: one or more polypeptides (amino acids)
• 3: Structure: folded into a globular or fibrous form
• 4: Function: It carries out several biological functions.
Importance and Functions of Proteins
 Importance or Functions of proteins
• 1. cell structure: cytoskeleton (mircrofilamints, microtubules)
• 2. contractile machinery of muscle: Actin Myosin
• 3. Oxygen transport: Hemoglobin
• 4. Search for foreign invaders: Antibodies
• 5. Reaction catalysis: Enzymes
• 6. Sensing and responding: Receptors
• 7. Many other functions previously explained in amino acids section
 http://people.eku.edu/ritchisong/RITCHISO/receptorprotein.gif
http://academic.brooklyn.cuny.edu/biology/bio4fv/page/ind_fit.gif
Date: 2014
November 1, 2015

https://upload.wikimedia.org/wikipedia/commons/4/48/Actin_Myosin.gif
Date: 2014

http://www.ps-19.org/Crea07Eukary/index_files/cytoskeleton-1.gif
November 1, 2015

http://2.bp.blogspot.com/-l8oNf7cLsM4/Upc9cQcrP4I/AAAAAAAABWI/LTy5cDpxO_4/s1600/first-animatin.gif
November 1, 2015

https://upload.wikimedia.org/wikipedia/commons/b/ba/Hemoglobin_t-r_state_ani.gif
November 1, 2015
Types or Classes of Proteins
 Type: 1

http://moleculesoflife2010.wikispaces.com/file/view/typ
es_of_proteins_table_Nelson.jpg/174923423/734x534/ty
pes_of_proteins_table_Nelson.jpg
November 1, 2015
 Types:2
• Simple proteins (Only polypeptide chains)
e.g. Albumin, glubulin, glutinin, prolamin
• Conjugated proteins (Polypeptide chain + other molecules)
e.g. nucleoproteins, glycoprotein
• Derived proteins (obtained from simple proteins by the action of enzymes
and chemical agents)
e.g. Peptides i.e. proteoses (by water) and peptones (by enzymes)
 Types:3

http://image.slidesharecdn.com/structureoforganiccompounds-120929105636-phpapp01/95/structure-of-organic-compounds-25-728.jpg?cb=1348917245
November 1, 2015

http://images.slideplayer.com/1/273296/slides/slide_43.jpg
November 1, 2015
Nucleic Acid Structure and
Organization

Dr. Muhammad Nabi (Ph.D.)

Khyber Medical University

(KMU)
Enzymes

Dr. Muhammad Nabi

Doctor of Pharmacy,
M. Phil Biochemistry
M. Phil Pharmacology,
Ph. D Pharmacology
 Enzymes
• Enzymes are biological molecules that catalyze
(i.e., increase the rates of) chemical reactions.
• In enzymatic reactions, substrates is
converted into products.
• Enzymes are selective for their substrates and
speed up only a few reactions from among
many possibilities.
 Characteristics
• lowering the activation energy. As a result, products
are formed faster and reactions reach their equilibrium
state more rapidly.
• Most enzyme reaction rates are millions of times faster
than those of comparable un-catalyzed reactions.
• As with all catalysts, enzymes are not consumed by the
reactions they catalyze, nor do they alter the
equilibrium of these reactions.
• highly specific for their substrates.
• A few RNA molecules called ribozymes also catalyze
reactions
• Inhibitors: decrease enzyme activity;
• activators are molecules that increase activity.
• Many drugs and poisons are enzyme
inhibitors.
• Activity is also affected by temperature,
pressure, chemical environment (e.g., pH),
and the concentration of substrate.
• Enzymes are in general globular proteins and
range from just 62 amino acid residues in size,
to over 2,500 residues
• A small number of RNA-based biological
catalysts exist, with the most common being
the ribosome; these are referred to as either
RNA-enzymes or ribozymes.
• only a small portion of the enzyme (around 2–
4 amino acids) is directly involved in catalysis.
• The region that contains these catalytic
residues, binds the substrate, and then carries
out the reaction is known as the active site.
• Enzymes can also contain sites that bind
cofactors, which are needed for catalysis.
• Enzymes are long, linear chains of amino acids
that fold to produce a three-dimensional product.
• Individual protein chains may sometimes group
together to form a protein complex.
• Most enzymes can be denatured—that is,
unfolded and inactivated—by heating or chemical
denaturants, which disrupt the three-dimensional
structure of the protein.
• Depending on the enzyme, denaturation may be
reversible or irreversible.
 Lock and key model
• Enzymes are very specific,

• Nobel laureate organic chemist Emil Fischer in 1894

suggested

• both the enzyme and the substrate possess specific

complementary geometric shapes that fit exactly into
one another.

• However, while this model explains enzyme specificity,

it fails to explain the stabilization of the transition state
that enzymes achieve.
 Induced fit model
• In 1958, Daniel Koshland suggested a modification to the lock and
key model:

• Since enzymes are rather flexible structures, the active site is

continuously reshaped by interactions with the substrate as the
substrate interacts with the enzyme.

• As a result, the substrate does not simply bind to a rigid active site;
the amino acid side-chains that make up the active site are molded
into the precise positions that enable the enzyme to perform its
catalytic function.

• In some cases, such as glycosidases, the substrate molecule also

changes shape slightly as it enters the active site
 Allosteric sites
• Allosteric sites are sites other than active sites on the
enzyme that bind to molecules in the cellular environment.

• The sites form weak, noncovalent bonds with these

molecules, causing a change in the conformation of the
enzyme.

• This change in conformation translates to the active site,

which then affects the reaction rate of the enzyme.

• Allosteric interactions can both inhibit and activate

enzymes and are a common way that enzymes are
controlled in the body.
 Cofactors

• Cofactors: Some enzymes require non-protein

molecules called cofactors to be bound for
activity
– inorganic (e.g., metal ions and iron-sulfur clusters)
– organic compounds (e.g., flavin and heme).

– prosthetic groups, which are tightly bound to an

enzyme
– coenzymes, which are released from the enzyme's
active site during the reaction. E.g. NADH, NADPH
and adenosine triphosphate
• Aponzymes: Enzymes that require a cofactor
but do not have one bound are called
apoenzymes or apoproteins.
• Holoenzymes: An apoenzyme together with its
cofactor(s) is called a holoenzyme (this is the
active form).
 Biological function

• They are indispensable for signal transduction and cell regulation, often
via kinases and phosphatases.
• They also generate movement, with myosin hydrolyzing ATP to generate
muscle contraction
• moving cargo around the cell as part of the cytoskeleton.
• Other ATPases in the cell membrane are ion pumps involved in active
transport.
• Enzymes are also involved in more exotic functions, such as luciferase
generating light in fireflies.
• Viruses can also contain enzymes for infecting cells, such as the HIV
integrase and reverse transcriptase, or for viral release from cells, like the
influenza virus neuraminidase.
• amylases and proteases break down large molecules (starch or proteins,
respectively) into smaller ones, so they can be absorbed by the intestines.
• Several enzymes can work together in a specific order,
creating metabolic pathways.
• In a metabolic pathway, one enzyme takes the product
of another enzyme as a substrate.
• After the catalytic reaction, the product is then passed
on to another enzyme.

• Without enzymes, metabolism would neither progress

through the same steps nor be fast enough to serve the
needs of the cell.
• Indeed, a metabolic pathway such as glycolysis could
not exist independently of enzymes.
 Factors affecting enzyme activity
• Concentration:
• Changing the concentration of a substance only affects the rate of
reaction if it is the limiting factor: that is, it the factor that
is stopping a reaction from preceding at a higher rate.
• If it is the limiting factor, increasing concentration will increase the
rate of reaction up to a point, after which any increase will not
affectthe rate of reaction. This is because it will no longer be
the limiting factor and another factor will
be limiting the maximum rate of reaction.
• As a reaction proceeds, the rate of reaction will decrease, since the
Substrate will get used up. The highest rate of reaction, known as
the Initial Reaction Rate is the maximum reaction rate for
an enzyme in an experimental situation.

http://alevelnotes.com/Factors-affecting-Enzyme-Activity/146?tree=
November 18, 2015
 Substrate Concentration
• Increasing Substrate Concentration increases the rate of
reaction. This is because more substrate molecules will be
colliding with enzyme molecules, so more product will be
formed.
• However, after a certain concentration, any increase will have
no effect on the rate of reaction, since Substrate
Concentration will no longer be the limiting factor. The
enzymes will effectively become saturated, and will be
working at their maximum possible rate.

http://alevelnotes.com/Factors-affecting-Enzyme-Activity/146?tree=
November 18, 2015

http://alevelnotes.com/content_images/i73_Image3.gif
 Enzyme Concentration
• Increasing Enzyme Concentration will increase
the rate of reaction, as more enzymes will be
colliding with substrate molecules.
• However, this too will only have an effect up
to a certain concentration, where the Enzyme
Concentration is no longer the limiting factor.

http://alevelnotes.com/Factors-affecting-Enzyme-Activity/146?tree=
November 18, 2015

http://alevelnotes.com/content_images/i74_Image4.gif
 Temperature
• as temperature increases, initially the rate of
reaction will increase, because of increased
Kinetic Energy.
• However, the effect of bond breaking will
become greater and greater, and the rate of
reaction will begin to decrease.

http://alevelnotes.com/Factors-affecting-Enzyme-Activity/146?tree=
http://alevelnotes.com/content_images/i71_gcsechem_18part2.gif
November 18, 2015
 pH
• Different enzymes have different Optimum pH values. This is the pH
value at which the bonds within them are influenced by H+ and OH-
Ions in such a way that the shape of their Active Site is the most
Complementary to the shape of their Substrate. At the Optimum
pH, the rate of reaction is at an optimum.
• Any change in pH above or below the Optimum will quickly cause a
decrease in the rate of reaction, since more of the enzyme
molecules will have Active Sites whose shapes are not (or at least
are less) Complementary to the shape of their Substrate.
• Small changes in pH above or below the Optimum do not cause a
permanent change to the enzyme, since the bonds can
be reformed. However, extreme changes in pH can cause enzymes
to Denature and permanently lose their function.
• Enzymes in different locations have different Optimum pH values
since their environmental conditions may be different.
http://alevelnotes.com/Factors-affecting-Enzyme-Activity/146?tree=

http://alevelnotes.com/content_images/i72_enzyme_ph_graph.gif
Types of Enzyme inhibitors

http://www.wiley.com/legacy/college/boyer/0470003790/animations/enzyme_inhibition/enzyme_inhibition.htm
November 18, 2015
http://www.wiley.com/legacy/college/boyer/0470003790/animations/enzyme_inhibition/enzyme_inhibi
tion.htm
November 18, 2015
Medical applications of enzymes

http://www1.lsbu.ac.uk/water/enztech/medical.html
November 18, 2015
Thank You
Bioenergetics and
Metabolism
Roshan Ali
Assistant Professor
IBMS, KMU
Course contents
• Definition of Bioenergetics
• Free Energy
• Biogenetic Metabolism
• Biological Oxidation
• Oxidation
• Electron transport chain
• Electron Carriers
• Biological Redox Reaction
• Role of ATP in linking Catabolism and Anabolism
 Bioenergetics
• Bioenergetics is the part of biochemistry concerned with the energy
involved in making and breaking of chemical bonds in the molecules
found in biological organisms. It can also be defined as the study of
energy relationships and energy transformations in living organisms.

• https://en.wikipedia.org/wiki/Bioenergetics

• December 9, 2015
 Free Energy
• the energy in a physical system that can be converted to do work, in
particular:
 Metabolism
• Metabolism is a term that is used to describe all chemical reactions
involved in maintaining the living state of the cells and the organism.
Metabolism can be conveniently divided into two categories:

• Catabolism - the breakdown of molecules to obtain energy

• Anabolism - the synthesis of all compounds needed by the cells

• By Dr Ananya Mandal, MD

• http://www.news-medical.net/health/What-is-Metabolism.aspx

• December 9, 2015
 Biological Oxidation
• All reactions which involve electron flow are considered oxidation-
reduction reactions. The basic definition can be defined as: One
reactant is oxidized (loses electrons), while another is reduced (gains
electrons).
• The flow of electrons is a vital process that provides the necessary
energy for the survival of all organisms. The primary source of energy
that drives the electron flow in nearly all of these organisms is the
radiant energy of the sun, in the form of electromagnetic radiation or
Light. Through a series of nuclear reactions, the sun is able to
generate thermal energy (which we can feel as warmth)
from electromagnetic radiation (which we perceive as light).
 Electron transport chain
• An electron transport chain (ETC) is a series of compounds that transfer
electrons from electron donors to electron acceptors via redox reactions,
and couples this electron transfer with the transfer of protons (H+ ions)
across a membrane.

• https://en.wikipedia.org/wiki/Electron_transport_chain

• December 9, 2015

https://upload.wikimedia.org/wikipedia/commons/8/89/Mitochondrial_electron_transport_chain%E2%80%94Etc4.svg
https://i.ytimg.com/vi/VER6xW_r1vc/maxresdefault.jpg
December 9, 2015
 Electron Carriers
• I (NADH-ubiquinone oxidioreductase): An integral protein that receives electrons in the form of hydride ions
from NADH and passes them on to ubiquinone
• II (Succinate-ubiquinone oxidioreductase aka succinate dehydrogenase from the TCA cycle): A peripheral
protein that receives electrons from succinate (an intermediate metabolite of the TCA cycle) to yield
fumarate and [FADH2]. From succinate the electrons are received by [FAD] (a prosthetic group of the
protein) which then become [FADH2]. The electrons are then passed off to ubiquinone.
• Q (Ubiquinone/ ubiquinol): Ubiquinone (the oxidized form of the molecule) receives electrons from several
different carriers; from I, II, Glycerol-3-phosphate dehydrogenase, and ETF. It is now the reduced form
(ubiquinol) which passes its electron off to III.
• III (Ubiquinol-cytochrome c oxidioreductase): An integral protein that receives electrons from ubiquinol
which are then passed on to Cytochrome c
• IV (Cytochrome c oxidase):An integral protein that that receives electrons from Cytochrome c and transfers
them to oxygen to produce water within the mitochondria matrix.
• ATP Synthas: An integral protein consisting of several different subunits. This protein is directly responsible
for the production of ATP via chemiosmotic phosphorolation. It uses the proton gradient created by several
of the other carriers in the ETC to drive a mechanical rotor. The energy from that rotor is then used to
phosphorolate ADT to ATP.
 Role of ATP in linking Catabolism and
Anabolism
• Catabolic pathways = Metabolic pathways that release energy ( ATP) by breaking down
complex molecules to simpler compounds (e.g., cellular respiration which degrades
glucose to carbon dioxide and water; provides energy (ATP) for cellular work).

• Anabolic pathways = Metabolic pathways that consume energy ( ATP) to build

complicated molecules from simpler ones (e.g., photosynthesis which synthesizes
glucose from CO2 and H2O; any synthesis of a macromolecule from its monomers).

• Metabolic reactions may be coupled, so that energy released from a catabolic reaction
can be used to drive an anabolic one. ( HERE also there is the role of ATP observed).

• https://answers.yahoo.com/question/index?qid=20080716151534AANfps8

• December 9, 2015
Thank You
Metabolism of
Carbohydrates
Roshan Ali
Assistant Professor
IBMS, KMU
• 1. Discuss the importance of glucose in blood
• 2. Role of Glycogenesis and glycogenolysis
• 3. role of oxidative glucose catabolism in the citric acid cycle.
• 4. Describe the role of gluconeogenesis
• 5. Discuss the overall scheme of carbohydrate metabolism
 Importance
• Energy is required for the normal functioning of the organs in the
body. Many tissues can also use fat or protein as an energy source but
others, such as the brain and red blood cells, can only use glucose.
 Glycogenesis

http://lh3.ggpht.com/-
NzhvB_wnJvE/UJHehTZse5I/AAAAAAAAAyE/n78rFO-
8too/Glycogenesis2_thumb3.gif?imgmax=800
December 16, 2015
Glycogenolysis
http://lh5.ggpht.com/-
xDhgIAuEd1M/UJPvZY0YENI/AAAAAAAAAzY/NUONHUs0oQ8/Gl
ycogenolysis_thumb%25255B2%25255D.gif?imgmax=800
December 16, 2016
Kreb’s cycle

https://upload.wikimedia.org/wiki
pedia/en/4/45/Citric_acid_cycle_
noi.JPG
December 16, 2015
 Gluconeogenesis

http://www.biochemd
en.com/wp-
content/uploads/2015/
03/Gluconeogenesis.jp
g
December 16, 2015
Thank you
Metabolism of Proteins
Roshan Ali
Assistant Professor
IBMS, KMU
Course Contents
• Metabolism of Protein
• Review the digestion and absorption of Proteins
• Nitrogen balance
• General pathway of Protein metabolism
• De-amination
 Digestion
and
Absorption
of
Proteins

Biochemistry for Medics 3

Digestion of dietary proteins

Biochemistry for Medics 4

◾ Proteolytic enzymes responsible for degrading proteins are
produced by three different organs;

◾ stomach,
◾ pancreas
◾ small intestine.

Biochemistry for Medics 5

Characteristics of proteolytic enzymes

Biochemistry for Medics 6

Digestion in the oral cavity

Biochemistry for Medics 7

Digestion by gastric juice

Biochemistry for Medics 8

◾ Too dilute to hydrolyze but can cause denaturation of dietary
proteins
-
◾ Required for activation of inactive proteolytic enzymes
secreted by the gastric mucosa.
-
◾ Has a strong bacteriostatic action.

Biochemistry for Medics 9

Functions of Proteolytic enzymes
Pepsin

10
Biochemistry for Medics
Functions of proteolytic enzymes
Rennin

Biochemistry for Medics 11

Functions of proteolytic enzymes
Gastriscin and Gelatinase

Biochemistry for Medics 12

Digestion by Pancreatic Juice

13
Biochemistry for Medics
Role of Trypsin

-Secreted in the zymogen form (Trypsinogen)and

activation is brought about by Enterokinase (secreted
by the intestinal mucosa ) and by Trypsin itself. Trypsin
is specific for cleaving peptide bonds contributed by
basic amino acids.
 Required for activation of Chymotrypsin
 Required for conversion of pro-elastase to elastase
 It is required for conversion of fibrinogen to fibrin
 It has weak action on casein
Biochemistry for Medics 14
Role of Chymotrypsin

Biochemistry for Medics 15

Role of Carboxy-peptidases

Biochemistry for Medics 16

Role of Elastase and Collagenase

Biochemistry for Medics 17

Biochemistry for Medics 18
Digestion by intestinal Juice

Biochemistry for Medics 19

Functions of the Intestinal enzymes

Biochemistry for Medics 20

Functions of Intestinal enzyme(Contd.)

Biochemistry for Medics 21

Biochemistry for Medics 22
Absorption of amino acids

Biochemistry for Medics 23

Absorption of amino acids

Biochemistry for Medics 24

Absorption of Oligopeptides

Biochemistry for Medics 25

Role of glutathione

Biochemistry for Medics 26

Transamination & Deamination of Amino Acids and urea
cycle
 CONTENT
• TRANSDEAMINATION
• TRANSAMINATION
• DEAMINATION
 TRANSDEAMINATION
The amino group of amino acids is released
by a coupled reaction called
TRANSDEAMINATION

Transamination followed by (Cytoplasm of all

body cells)

oxidative deamination (Mitochondria of liver

cells)
 Transamination
• Transamination is a chemical reaction between two molecules.

• One is an amino acid, which contains an amine (NH2) group.

• The other is a keto acid, which contains a keto (=O) group.

• In transamination, the NH2 group on one molecule is exchanged with the =O

group on the other molecule. The amino acid becomes a keto acid, and the keto
acid becomes an amino acid.

• Transamination in biochemistry is accomplished by enzymes

called transaminases or aminotransferases.
Reaction
General scheme of transamination
R CH COOH + HOOC C CH2CH2COOH
NH2 O
aminokyselina
amino acid 2-oxoglutarate
2-oxoglutarát

aminotransferase
aminotransferasa
pyridoxalfosfát
pyridoxal phosphate

R C COOH + HOOC CH CH2CH2COOH

O NH2

2-oxokyselina
2-oxo acid glutamát
glutamate
32
 DEAMINATION
• Deamination is the removal of an amine group from a molecule.

• Enzymes which catalyze this reaction are called deaminases.

• In the human body, deamination takes place primarily in the liver,

however glutamate is also deaminated in the kidneys.

• Deamination is the process by which amino acids are broken down if

there is an excess of protein intake. The amino group is removed from
the amino acid and converted to ammonia.
 Deamination of amino acids
•Deamination - elimination of amino group from amino acid
with ammonia formation.

• Four types of deamination:

• - oxidative (the most important for higher animals),

• - reduction,
• - hydrolytic, and
• - intramolecular
 Reduction deamination:

R-CH(NH2)-COOH + 2H+  R-CH2-COOH + NH3

amino acid fatty acid

Hydrolytic deamination:

R-CH(NH2)-COOH + H2O  R-CH(OH)-COOH + NH3

amino acid hydroxyacid

Intramolecular deamination:

R-CH(NH2)-COOH  R-CH-CH-COOH + NH3

amino acid unsaturated fatty acid
 Oxidative deamination
 During oxidative deamination, an amino acid is converted into the
corresponding keto acid by the removal of the amine functional
group as ammonia.
 The amine functional group is replaced by the ketone group. The
ammonia eventually goes into the urea cycle.
 Oxidative deamination occurs primarily on glutamic acid because
glutamic acid was the end product of many transamination
reactions.
 The glutamate dehydrogenase is controlled by ATP and ADP. ATP
acts as an inhibitor whereas ADP is an activator.
Intake, catabolism, and excretion of nitrogen
proteolysis
Proteins amino acids

transamination

glutamate
detoxication dehydrogenation + deamination
in other tissues
glutamine NH3
deamidation
in kidney detoxication in liver

glutamate + NH4+ urea

deamination (excretion by urine)
(excretion by urine)
in kidney

2-oxoglutarate + NH4+
(excretion by urine)

37
Introduction of Urea
• Discovered in 1727
• By Dutch scientist Herman Boerhaave
• In 1828, the German chemist Friedrich Wohler obtained urea artificial
• By treating silver cyanate with ammonium chloride.
AgNCO + NH4Cl → (NH2)2CO + AgCl
Introduction of Urea (cont.…)
• This was the first time an organic compound was artificially synthesized from
inorganic starting materials, without the involvement of living organisms.
• Wohler said
"I must tell you that I can make urea without the use of kidneys, either man or
dog. Ammonium cyanate is urea."
Introduction of Urea (cont.…)
• For this discovery, Wohler is considered by many the father of organic chemistry.
Urea Cycle
 Urea Cycle
• Also known as “ornithine cycle”

• cycle of biochemical reactions occurring in many animals

• Produces urea ((NH2)2CO) from ammonia (NH3).

• In mammals, the urea cycle takes place primarily in the liver, and to a lesser extent in
the kidney.
 Urea Cycle (cont.…)
• Urea is synthesized in the liver

• Than secreted into blood stream

• And taken up by the kidneys for excretion in the urine.

• Partly takes place in mitochondria and partly in cytoplasm.

• End product of protein metabolism.

 Urea Cycle (cont.…)
• Ammonia is toxic to body

• Detoxified and converted into urea in urea cycle.

• The overall reaction of the urea cycle is as follow:

NH4+ + HCO3- + H2O + 3ATP + Aspartate Urea + 2ADP + AMP +

2Pi + PPi + Fumarate
Thank You
Metabolism of Fats
Roshan Ali
Assistant Professor
IBMS, KMU
• 1. Describe the mechanism of fatty acid oxidation
• 2. Discuss the amount of energy produced during the oxidation of a
fat.
• 3. Explain the significance of the role of ketone bodies.
 Fatty acid oxidation

http://ph
armaxch
ange.info
/press/w
p-
content/ 
uploads/
2013/10/
Beta-
oxidation
-of-
fats_1.gif
Decembe
r 16,
2015
 Ketone bodies

http://eatingacademy.com/wp-
content/uploads/2012/11/Ketone-figures-1-645x230.jpg
December 16, 2015
 Importance of ketone bodies
• Ketone bodies are three water-soluble molecules
• Produced by the liver from fatty acids during periods of low food intake (fasting) or carbohydrate
restriction for cells of the body to use as energy instead of glucose.
• Two of the three are used as a source of energy in the heart and brain while the third (acetone) is
a degradation breakdown product of acetoacetic acid.
• Radioactive tracing of acetone determines that between 2% and 30% is excreted from the body.
• Ketone bodies are picked up by cells and converted back into acetyl-CoA which then enters the
citric acid cycle and is oxidized in the mitochondria for energy.
• In the brain, ketone bodies are also used to make acetyl-CoA into long chain fatty acids, which
cannot pass through the blood-brain barrier.

• https://en.wikipedia.org/wiki/Ketone_bodies
• December 16, 2015
Thank you
Hormones
Roshan Ali
Assistant Professor
IBMS, KMU
Course Contents
• Introduction of hormone
• Classes of Hormones
• o Steroid Hormone
• o Amino Hormone
• o Peptide Hormone
• Mode of Action of steroid & peptide hormones
• cardiac, pineal and gastrointestinal hormones.
 Introduction to hormone
• Hormones are chemical messengers that are secreted directly into the
blood, which carries them to organs and tissues of the body to exert
their functions.
 Classes of hormones
• amines, these are simple molecules. E.g. epinephrine and
norephinephrine

• proteins and peptides which are made from chains of amino acids.
E.g. Insulin and glucagon

• steroids which are derived from cholesterol. E.g. Androgens and

Estrogens
 Mode of Action of steroid & peptide
hormones
• Hormones are released into the bloodstream from which they will diffuse into the interstitial fluid surrounding the target cells and into the blood
stream to travel to target sites.
• The target cell has receptors specific to a given hormone and will be activated by either a lipid-soluble (permeable to plasma membrane) or water-
soluble hormone (binds cell-surface receptor).
• Lipid-soluble hormones (steroid hormones and hormones of the thyroid gland) diffuse through the plasma membrane to enter the target cell and
bind to a receptor protein that will in turn activate expression of specific genes that influence specific physiological cell activities.
• Water-soluble hormones (such as polypeptides, proteins and most amino acid hormones) bind to a receptor protein on the plasma membrane of the
cell.
• The ligand-bound receptor protein will activate other membrane-bound proteins to give rise to cyclic AMP (cAMP) which then triggers an enzyme that
generates specific cellular changes.
• The ligand-bound receptor protein will activate other membrane-bound proteins to give rise to cyclic AMP (cAMP) which then triggers an enzyme that
generates specific cellular changes.
• Water-soluble hormones (such as polypeptides, proteins and most amino acid hormones) bind to a receptor protein on the plasma membrane of the
cell.
• The ligand-bound receptor protein will activate other membrane-bound proteins to give rise to cyclic AMP (cAMP) which then triggers an enzyme that
generates specific cellular changes.

• Source: Boundless. “Mechanisms of Hormone Action.” Boundless Anatomy and Physiology. Boundless, 21 Jul. 2015. Retrieved 09 Dec. 2015 from
https://www.boundless.com/physiology/textbooks/boundless-anatomy-and-physiology-textbook/the-endocrine-system-16/hormones-
150/mechanisms-of-hormone-action-774-807/
 Cardiac, pineal and gastrointestinal
hormones
• In response to a rise in blood pressure, the heart releases two peptides: Atrial Natriuretic Peptide (ANP) This
hormone of 28 amino acids is released from stretched atria. Brain Natriuretic Peptide (BNP) This hormone
(32 amino acids) is released from the ventricles.

• The pineal gland, also known as the pineal body, conarium or epiphysis cerebri, is a small endocrine gland in
the vertebrate brain.
• It produces melatonin, a serotonin derived hormone, which affects the modulation of sleep patterns in both seasonal and
circadian rhythms.

• Cholecystokinin: Stimulates gallbladder contraction and intestinal motility; stimulates secretion of pancreatic
enzymes, insulin, glucagon, and pancreatic polypeptides
• Gastrin: Gastrins stimulate the secretion of gastric acid, pepsinogen, intrinsic factor, and secretin; stimulate
intestinal mucosal growth; increase gastric and intestinal motility

• Secretin: Stimulates pancreatic secretion of HCO3, enzymes and insulin; reduces gastric and duodenal
motility, inhibits gastrin release and gastric acid secretion
Thank You