e-

Dr Islam Khan P+
Po+
n
o+
nP
n+ oP+
Professor P
Po+
P+n
o

n
Biochemistry Department
Faculty of Medicine
Islam@hsc.edu.kw e-

IK-10 1
 Topics
1. Elements and life

2. Electronic configuration: Subatomic

structure, Pauli’s and Hund’s rules

3. Classification of elements in the

Periodic Table: elements and isotopes
and their significance

IK-10 2
 Reference

1. Fundamentals of General, Organic

and Biological Chemistry 6th edition
by McMurry et al

2. Handouts

IK-10 3
 Examination format
Multiple Choice Questions (MCQ)
from the lectures, workshops and laboratory
classes

1. In-course  40%

2. Final  60%

IK-10 4
 Example of MCQ
Which subatomic particle defines an
isotope?

A.Antiproton
B.Electron
C.Neutrino
D.Neutron
E.Positron

IK-10 5
 Elements and life
Life is manifestation of self-sustained chemical reactions

IK-10 6
 Objectives
1. Elemental composition of human body
2. Classification of elements with reference to
human body (living cells): Structural and
functional
3. Most abundant elements as building blocks
of human body
4. Functional aspects of some elements in
humans
5. Definition of life in terms of elements

IK-10 7
 Elements and life

Systems Organs Tissues Cells

IK-10 8
 Ca

Elements and life P

Fe
Na
C K
Carbohydrates
H Cl
Lipids
O
Cells Organelles Biomolecules
Proteins + Se
N Zn
Nucleic acids
Humans P Mn
S Cu
Structural elements Mg
Co
Functional elements

IK-10 9
 % Element mass in human body
Elements Human body Elements Earth crust

O 61% O 46 %
C 23% Si 28 %
H 10% Fe 5.6 %
N 2.6% Ca 4.1 %
P 1.1% Na 2.4 %
S 0.2% Mg 2.3 %
An average 70 kg adult human body is composed of
60 elements

IK-10 10
 % Atomic abundance of element
Elements % Abundance Atoms
O 24 1.61 x 1027
C 12 8.03 x 1026
H 63 4.22 x 1027
N 0.58 3.9 x 1025
Ca 0.24 1.6 x 1025
P 0.14 9.6 x 1024
S 0.038 2.6 x 1024
Fe 0.00067 4.5 x 1022
An average 70 kg adult human body contains about
6.7x1027 atoms and is composed of 60 elements

IK-10 11
 Trace elements
Trace Elements together less than 0.1%
 Copper (Cu)
 Selenium (Se)
 Manganese (Mn)
 Zinc(Zn)
 Cobalt (Co)
 Fluorine (F) Act as a cofactor in
 Iodine (I)
 Iron (Fe) various enzyme reactions
 Boron (B)
 Chromium (Cr)
 Molybdenum (Mo)
 Silicon (Si)
 Tin(Sn)
 Vanadium(V)

IK-10 12
 Classification
1. Structural
2. Functional

IK-10 13
 Structural elements
1. Backbone of native biomolecules
2. C, H, O, N, P, S
3. C, H, O = Present in all biomolecules
4. P = Always present in the nucleic acids (DNA/RNA)
5. S = Present in proteins only
6. N = Protein and nucleic acids

IK-10 14
 Functional elements
1. Mainly regulate biological functions
2. Excitation-contraction - Ca, Na, K
3. Strength – Ca, P as part of bone and teeth
4. Antioxidants – Cu, Mn, Zn, Se
5. As cofactors – Co in vitamin B12, Mg in
certain enzymes
6. Oxygen carrier- Fe in hemoglobin

IK-10 15
 Elements and life
• Ca – found mainly in bones and teeth – important for nerve impulses,
muscle contractions, and blood clotting.
• P – found in the nucleic acids, high-energy compounds, and phosphate
buffer system; a major component of bone; necessary for growth.
• Cl – the major anion in body fluids, important for water absorption
• Na – major cation in body fluids, Muscle contraction
• K - important for proper membrane function, nerve impulses, and muscle
contractions; major cation in cytoplasm
• Co – a vital part of vitamin B12; helps production of red blood cells.
• I – a major component of thyroid hormones (thyroxine and T3)
• Fe – component of Hb, myoglobin, and cytochromes, essential in cell
respiration for O2 transport
• Mg – required for activation of several enzymes DNA synthesizing enzymes
• Cu – involved in the synthesis of hemoglobin, melanin, and collagen,
• Mn – cofactor for some enzymes, antioxidant
• Se – a powerful antioxidant; vital to the immune system
• Zn –a cofactor for enzyme function, and antioxidant

IK-10 16
 Life is a unique arrangement of
elements, and disruption of which
leads to death

IK-10 17
 Summary
1. Human body is made up of (60) elements
2. The most abundant elements are those that make up
the structure of biomolecules (structural elements)
and are non metals
3. Functional elements are mostly metals, and
transitional elements
4. Functional elements act as cofactor and work in
coordination with specific proteins or enzymes
5. Deficiency of elements leads to diseases
6. Life is manifestation of specific arrangement of
elements
7. Disruption of these arrangements is death

IK-10 18
 Electronic configuration

IK-10 19
 Objectives
1. Atom
2. Atomic structure (Rutherford experiment)
3. Atomic mass
4. Atomic number
5. Quantum numbers
6. Shells
7. Sub shell, (spdf notation)
8. Orbital
9. Aufbau’s principle
10. Pauli’s exclusion principle
11. Hund’s rule

IK-10 20
 Atom
1. The smallest particle of an element
2. Represents properties of the element
3. Atoms combine to form compounds

IK-10 21
 Rutherford experiment
1. A vast majority of a-particles
passed straight through the foil
2. Only a small fraction ~1 in
Gold foil 8000 particles were deflected
Source of a
particles
Conclusions
1. The mass of the atom is
Detecting screen Slit contained in a positively
charged nucleus
2. The rest of the atom is mostly
an empty space in which –ve
charged electrons orbit

IK-10 22
 e-

Po+
n
P+ o+
nP
n+ oP+
Sub atomic structure P
Po+
n
P+no

IK-10 23
 Atomic number
Does loss of e-
1. Number of protons
change the atomic
2. Atom is electrically neutral number?
3. Number of p+ = e-
Elements Protons Electrons
Neutrons
1H 1 1
2He 2 2
3Li 3 3
4Be 4 4 Protons
5B 5 5
6C 6 6

IK-10 24
 Atomic mass = Atomic weight = Mass number

1. Number of protons and neutrons

2. Unit is amu (atomic mass unit)
3. 1 amu = 1/12 of C atom
= 10-24 gm

IK-10 25
 Atomic mass
Atomic Atomic Protons Electrons Neutrons
number mass
(A) (B) (A-B)

C 6 12 6 6 6

Cl 17 37 17 17 20

IK-10 26
 Atomic number/mass

n=2

How many neutrons?

IK-10 27
 Atomic number/mass

IK-10 28
 Electrons
• Negatively charged
• Revolve in the shells around the nucleus

+ e-

How to define the location of electrons?

IK-10 29
 Significance of electrons
1. Participate in bio/chemical reactions
2. Define valency of an atom
3. Define state of an element; active or
inactive
4. Their arrangement in atom defines
the properties of elements

IK-10 30
 Electrons
1. Not perfectly free to move in an atom
2. Have restricted movement only in certain
regions
3. These regions differ in terms of energy
4. Energy is quantized, restricted to certain
value  quantum numbers

How to identify electrons?

IK-10 31
 Location of electrons
Complete description of electron in an atom
is given by four quantum numbers:

1. Principal quantum number (n)  Size

2. Azimuthal quantum number (l)  Shape
3. Magnetic quantum number (m)  Orbital
4. Spin quantum number (s)  Spin

IK-10 32
 1. Principal quantum number (n)

Principal
1. Main energy levels 5
or shells (n= 1. 2. 4
3 ... shell) 2
3
2. No. of electrons in 1
a shell = 2n2 +++
+++
3. Energy of e-
increases with its
distance from the
nucleus

IK-10 33
 Shell capacity
Shell Maximum
(n) electrons
(2n2)
1 2 N
2 8
3 18
4 32

IK-10 34
 2. Azimuthal quantum number (l)
1. Defines electron’s location in a shell
2. Known as sub shell (s, p, d, f …)
3. Describes the shape of a subshell
4. No. of subshells (l) = 0 to n-1, where n = shell number

n l Types of subshell
1 0 s
2 0,1 s, p
3 0,1, 2 s, p, d
4 0,1, 2, 3 s, p, d, f

Number of shell = number of sub shells

IK-10 35
 Number subshells
How does l define a subshell

l Subshell
0 s
1 p
2 d
3 f

IK-10 36
 Capacity of sub shell
No. of electrons in a subshell = 4 l +2
Sub shell l 4 l +2 Electrons
s 0 4x0+2 2
p 1 4x1+2 6
d 2 4x2+2 10
f 3 4x3+2 14

IK-10 37
 3. Magnetic quantum number
1. Magnetic behavior of electrons makes them orient in a
sub shell at certain specific positions, called orbitals

2. No. of orbitals in a subshell = (- l) to 0 to (+ l)

l = 0 (s)  m = 0  1 orbital  2e-

l = 1 (p)  m = +1, 0, -1  3 orbitals  6e-
l = 2 (d)  m = +2,+1, 0, -1, -2  5 orbitals  10e-
l = 3 (f)  m = +3, 2,+1, 0, -1, -2, -3  7 orbitals  14e-

No. of orbitals in a sub shell = lx2+1

l = azimuthal quantum number
IK-10 38
 4. Spin quantum number
Electron spins clockwise or anti clockwise

IK-10 39
 Summary
Shell (n)

Subshells (l) Orbitals (m)

s 1

p 3

d 5
f 7

IK-10 40
40
 Summary

(in subshells)

(in shells)

IK-10 41
 Summary
1. Main energy level  shell (n)
2. Shell is divided into sub-shells, l (s, p, d, f)
3. Sub-shell is divided into orbitals
4. Orbital is a space where an e- is most likely
to be present
5. There are 1, 3, 5 and 7 orbitals in s, p, d,
and f sub shells respectively
6. An orbital can occupy maximum 2e-

IK-10 42
 Electronic configuration
Filling electrons into the shell(s) and sub
shells/orbitals of an atom is known as electronic
configuration

IK-10 43
 Electronic configuration: Why?
1. Chemical state; reactive or inactive
2. Electropositive/electronegative
3. Valency
4. Type of bonds
5. Position in periodic table

IK-10 44
 Guidelines
1. Number of e- in a shell (n) = 2n2
2. Aufbau’s principle
3. Pauli’s exclusion principle
4. Hund’s rule

IK-10 45
 Aufbau principle
1. Electrons tend to occupy
the lowest energy level
2. The orbitals within a
subshell are always of
equal energy 
degenerate. For example

p orbitals
d orbitals

IK-10 46
 Pauli’s exclusion
1. No two e- can have the same values of all quantum numbers
2. Two e- in the same orbital must have opposite spin: counter
clockwise
3. An orbital can hold maximum 2e- in opposite spin

Ҳ Ҳ

No two students in the same class be identical

Or
No two apartments in the same building have the
IK-10
same address 47
 Hund’s rule
1. Hund’s rule states that the electrons should spread
within a subshell as much as possible
2. Electrons are filled singly in parallel spin
3. Extra e- are placed in opposite spin

Shell 1 Shell 2
Atomic number = 8  2 6

1s2 2s2 2px2 2py1 2pz1

Atoms tend to have Half-filled or

fully filled orbitals
IK-10 48
 Electronic configuration
1s Lower energy level
2s
2p
3s
3p
4
s,p,d,f
4s 3
3d s,p,d
4p 2
5s s,p
4d 1
5p s
6s
4f
5d
6p
7s
5f
6d
Higher energy level

IK-10 49
 General scheme of writing e-
configuration
1s
2s
2p
3s
3p
4s 3d
4p
5s 4d
5p 4f
6s 5d
6p 5f
7s 6d
IK-10 50
 Electronic configuration
7 Nitrogen (atomic number = 7)
Shells (n) = 1 2
Electrons = 2 5

Sub shells (l) = 1s 2s 2p

Orbitals =
Number of single electrons = Valency
1s2, 2s2, 2p3

wrong
IK-10 51
 Practice
Atomic number = 10, 16, 28

10 = 2, 8
1s2, 2s2, 2p6
16 = 2, 8, 6
1s2, 2s2, 2p6, 3s2, 3p4
28 = 2, 8, 16 2
1s2, 2s2, 2p6, 3s2, 3p6, 4s2 , 3d8

IK-10 52
 4s 2

Shell Electrons
Sub shell

3p6

IK-10 53
 Periodic table

IK-10 54
 Periodic Table
1. Grouping of elements according to their
properties (atomic mass and atomic
number)
2. Several attempts were made but most
successful were those of:
1. Mendeleev
2. Moseley (Modern periodic table)

IK-10 55
 Mendeleev’s Periodic Table
1. Elements when arranged according to their
atomic mass they exhibit an apparent
periodicity of properties
2. Physical and chemical properties of
elements are periodic function of atomic
mass
2. Grouped elements in a tabular form:

1. 9 vertical columns  8+0 Groups

2. Horizontal columns  7 Periods

IK-10 56
 Mendeleev’s Periodic Table

IK-10 57
 Mendeleev’s Table: Problems
1. Position of H not clear
2. Elements with marked similarities were placed
in separate groups and vice versa
3. Elements with higher atomic mass appeared
before those with lower atomic mass
4. Isotopes had different places in the table
5. Lanthanides and actinides were placed
outside the table

Elements unknown at his time were

predicted with their properties
IK-10 58
58
 Moseley’s Periodic Table

1. Developed after the

discovery of atomic
theory
2. Physical and
chemical properties
of elements are
periodic functions of
their atomic number

1. 7 periods
2. 8+0 Groups

IK-10 59
Modern periodic table
1. Based on atomic
number
2. 18 groups & 7
periods
3. Groups 1,2, 13-17
elements have their
outer most shell
incomplete
4. Groups 3-12
elements have two
outer most shells
incomplete 
transition elements
except for Zn
5. Group 18 (8A) 
inert / nobel gases
6. Period 7 elements
are radioactive 7 17

IK-10 60
Group 1A - 7A elements

Outer most shell

incomplete
+

Group 1B - 8B elements

Two outer most shells

Incomplete. Exception
group 12 elements
+

IK-10 61
 s p

f
3 outer most shells incomplete

f
IK-10 62
 Elements in human body
Non metal are the major structural elements:

Metal are the major regulator elements:

IK-10 63
 e- configuration

30 Zn = 2, 8, 18, 2
1s2 2s2, 2p6 3s2, 3p6, 4s2, 3d10

29 Cu = 2, 8, 18, 1
1s2 2s2, 2p6 3s2, 3p6, 4s1, 3d10

IK-10 64
 Alkali metals
1. Group 1 elements except H,
very reactive metals, do not
occur freely in nature
2. Can explode when exposed to
water
3. Softer, malleable, ductile, and
good conductors of heat and
electricity
4. Have only one electron in their
outer shell electropositive

5. Monovalent

• Hydrogen
• Lithium
e-
• Sodium +ve
• Potassium
• Rubidium
• Cesium e-
• Francium
IK-10 65
 Alkaline earth metals

1. Group 2 elements
2. Have 2e- in their
outermost shell
3. Bivalent, electropositive
4. Very reactive, not found
free in nature

Beryllium
Magnesium S2
Calcium
Strontium e-
Barium
Radium +ve

e-
e-
IK-10 66
66
 Non-metals
1. 17 elements
2. Do not conduct
electricity or heat very
well No metallic luster
& are very brittle

Carbon
Nitrogen Most abundant
Oxygen elements in
human body
Phosphorus
Sulphur

Selenium Antioxidant
IK-10 67
 Metalloids
1. Total 7 elements are
metalloid
2. Have properties of
both metals and
non-metals
2. Silicon and
Germanium used as
semi-conductors in
computers and
calculators

Boron
Silcon
Germinium
Arsenic
Antimony
Tellurium
IK-10 68
 Transition metals
1. The elements in groups
3 -12 (1B-8B). All are metals
2. Have an incomplete d subshell
(except Zn, group 12)
3. Two outer most shells are
incomplete
4. Ductile and malleable
5. Conduct electricity and heat
6. Fe, Cu, Zn, Mn  important trace elements

Hemoglobin Neutralize free

antioxidants radicals

Transport O2
Protect cells
IK-10 69
Halogens
1. Halogen  Salt-former
2. Compounds containing
halogens are called "salts”
3. Group 17 elements
4. All halogens have 7e- in their
outer shell
5. Can accept one electron 
electronegative
6. Monovalent

Fluorine
Chlorine Bleaching action, sterilize drinking water
Bromine
Iodine
Astatine 7e- 8e-

e-
IK-10 70
 Noble gases
1. Group 18 elements
2. Inert & stable
3. Valency is zero

Helium
Neon
Argon
Krypton
Xenon
Radon Cancer treatment

8e-

IK-10 71
 Electronegativity
Increase
H ** H

1. Tendency of an atom in a
molecule to attract the shared
electrons is electronegativity
(EN)
2. EN increases from left to right in
a period
3. EN decreases from top to
bottom in a group
4. Fluorine has the highest EN.
5. Although Fr is the least EN, but
because it is extremely rare and Decrease
radioactive, Cesium is
considered is the least EN
IK-10
72
 Electronegativity difference ( EN) of the
participating atoms in a molecule determines
the type of bond between them

H2
O2 Non polar covalent
Cl2
H2O Polar covalent
NaCl Ionic bond
IK-10 73
 Atoms with similar EN form non polar covalent bond

H * H
*

O ** O EN = 0 - 0.4
**

Cl * Cl
*

IK-10 74
 Atoms with dissimilar EN form polar covalent bond

d-
O
* *
d+ EN = 0.4 - 1.7
H * * H d+

IK-10 75
 Atoms with hugely dissimilar EN form ionic bond

+ -
Na * Cl EN = 1.7 - 4.0
*

Complete dislocation of electron pair

EN = >2.0

76
IK-10
 Summary
0 0.4 1.7 4.0 EN

Non Polar Ionic

polar Covalent bonds
Covalent bonds
bonds

Difference in electronegativity determines

the type of bonds between participating
atoms
IK-10 77
 Isotopes
Atomic number

Atomic mass

IK-10 78
 Isotopes
1. Elements having same atomic number
but different atomic mass
2. Have same number of electrons and
protons  Similar chemical properties
3. Have different number of neutrons 
different physical properties
4. Occupy same position in periodic table

IK-10 79
 Atomic mass of chlorine
35Cl 76% (Abundance)

37Cl 24% (Abundance)

Average atomic mass = 35 x 0.76 + 37 x 0.24

= 35.45 amu

IK-10 80
 Isotopes types
1. Stable
2. Radioactive

IK-10 81
 Radioactive isotopes
1. Emit energy/radiations to get
stable state
2. Emit a, b and g radiations
3. Some radioactive isotopes
occur naturally, most are
artificially created
b and g isotopes are routinely used in
medicine as therapeutic and diagnostic
tools in disease management

IK-10 82
 Types of radioisotopes
1. a emitters  a particles
2. b- emitters  b particles
3. b+ emitters  positrons
4. g emitters  g radiations

IK-10 83
 b- particles
High energy electron
Produced from neutron:
0n  1H + e-1
0
1 1

6C
14
 147N + b 15 P  16S +b
32 32

27Co
60
 28Ni
60
+b

IK-10 84
 Positron b+
1. A positively charged b+ particle
(positron)
2. An example, 18F (fluorine)
3. Used in Positron emission
tomography (PET), imaging
technique; Extremely important in
disease diagnosis

IK-10 85
 g - particles
Radiations with high energy
Ionization radiations
No mass or charge

43Tc  43Tc + g
99m 99

Short half-life, Atomic mass and number remain

Used in disease unchanged same
diagnosis
IK-10 86
 Biological effects
1. Damage all Biomolecules
2. Cause mutations  Cancer
3. Cause birth defects

Proper shielding is important

IK-10 87