 Textbook;
Lehninger Principles of
Biochemistry by David L Nelson and Michael
M cox. Third edition.
 Recommended References;
 Biochemistry , Donald Voet , Judith G. Voet.
Second edition.
 Biochemistry by Jeremy M Berg , John L
Tymoczco and Lubert Stryer.
 Mark
distribution;
First continuous 20 marks.
Second continuous 20 marks.
Quizzes 10 marks.
Final 50 marks.
Exam dates;
First continuous 21/3 .
Second continuous 2/5 .
 Definition
and Introduction;
 Definition of Biochemistry.
 Living matter vs. non-living matter.
 Introduction to Elements , Atoms .
 The
hierarchy in the molecular
organization of cells.
 Bimolecular structures and functions
briefly.
Definition of Biochemistry;
It is the chemistry of life . It is that field of science
that describes in molecular terms the structures ,
mechanisms, and chemical processes that occur in
the living cell.


Living matter vs. non-living matter.
Distinctive properties of living organisms;
1-Their degree of chemical complexity and
organization.

2-living Organisms extract , transform and use energy
from their environment
 3-
Their capacity for precise self –replication
and self-assembly.
 4-each component of a living organism has a
specific function.
 Both
living matter and non-living matter are
made up of Elements.
 There are 110 different type of elements
only 30 elements predominate in living
organisms.
 Elements
are made up of atoms.
 Atoms; They are the smallest unit of an
element , which shows all the characteristics
of that element.
 It consists of a dense positively charged
nucleus which is surrounded by negatively
charged electrons circling around the
nucleus.
 The nucleus contains positively charged
protons, and neutrons that are not electrical
charged.
 The number of protons in an atom
determine the identity of the element.
 Orbits;
Electrons with negative charges and a
very small mass are organized in a series of
orbits around the nucleus called shells .
Chemical reactions involve the electrons
especially those in the outer shell.
 The atomic number of the element denotes
the number of protons.
 The number of electrons is = to the number
of protons.
 The
most abundant elements in living
organisms are H , O , N, C , P and S , all of
which readily form covalent bonds and make
up 92% of the dry wt of living things.
 What is unique about them?
 The four most abundant are H , O , N, and C
,they are the lightest elements capable of
forming 1, 2, 3 and four bonds respectively
(the lightest elements form the strongest
bonds).
 Living
matter is made up mainly of organic
compounds which consist mainly of C , O and
H.
 Carbon atom holds the center stage in
organic compounds and living organisms.
 What is it that makes carbon so special?
 Its tremendous bonding versatility is what
makes it so special compared to all the other
elements in the periodic table.
Versatility of carbon bonding. Carbon can
form covalent
single, double, and triple bonds (in red), particularly with other
carbon atoms. Triple bonds are rare in biomolecules.
The carbon atom has 4 unpaired electrons in its outer shell
thus it is capable of forming 4 highly stable covalent
bonds.
-thus allowing it to form infinite number of compounds with
other atoms such as H, O ,N …..etc.
- Most significantly is the ability of carbon atoms to share
electrons pairs with each other to form very stable single,
double , and triple covalent bonds.(linear chains, branched
chains, and cyclic structures) , thus allowing it to form
infinite skeletons or structures to which other atoms can
also bind .


It can also form covalent bonds with other atoms such as
O, H, N and S ,thus allowing the introduction of many
different kinds of functional .

Its unique
configuration in space
which allows the
presence of a
limitless no. of
carbon molecules that
have different shapes
and dimensions giving
rise to a large no. of
different three
dimensional
structures
(biomolecules).
Geometry of carbon bonding.
(a) Carbon atoms have a characteristic tetrahedral arrangement of their four
single bonds.
(b) Carbon–carbon single bonds have freedom of rotation, as shown for the
compound ethane (CH3OCH3).
(c) Double bonds are shorter and do not allow free rotation. The two doubly
bonded carbons and the atoms designated A, B, X, and Y all lie in the same
rigid plane.
a)The carbon atom is present in space in a tetrahedral
arrangement where the 4 single covalent bonds of the C
atom are around 0.154nm long and 109.5 degrees angle
apart The angle between the carbon covalent bonds can
vary slightly from one carbon atom to another in different
organic molecules thus giving rise to different 3
dimensional structures.
b)The second important feature is that there is a complete
freedom of rotation around each single C-C covalent bond
thus allowing the formation of different shapes in space.
 As a result no other chemical element can form molecules
of such widely different , structures , sizes and shapes.
The hierarchy in the molecular
organization of cells
Functional groups
Chemical bonds
All biomolecules are hydrocarbon derivative
compounds (mainly composed of H , and C
atoms) with a backbone that consists of carbon
atoms joined by covalent bonds.
 One or more H atoms of the hydrocarbon can be
replaced by different functional groups yielding
different families of organic compounds.
 Common functional groups in biochemical
molecules include, alcoholic groups (which
contain one or more hydroxyl groups),amino
groups , ketone groups …..etc.



Functional groups are
specific groups of atoms
within molecules that are
responsible for the
characteristic behavior
and chemical reactions of
those molecules , they
also determine the class
of compounds it belongs
to .
The chemical“personality”
of a compound is
determined by the
chemistry of its functional
groups and their
disposition in threedimensional space.
Characteristics of functional groups;
(OH- ) Hydroxyl group (alcoholic group) is a
water soluble group , it also has a high
tendency to form hydrogen bonds.
( C=O ) Carbonyl group , has the ability to
form H bonds , it is present in all sugars ,
If the remaining two covalent bonds of the
carbon atom bind to carbon atoms it is called
a ketone group.
If one of the covalent bonds binds H it is called
aldehyde group which has reducing
properties.

Carboxyl group ; It has a high tendency to
form H bonds ,
 Has
acidic properties , it oftenly ionizes
 Amino
group ; -NH2
,
 Can form H bonds .
 Shows basic properties (can accept proton)
-NH3+
,
 (-PO4--
) Phosphates,
Very soluble , oftenly
ionized , readily forms
H bonds.
Sulfhydryl group ( -SH)
Can form weak H bonds.
Two –SH groups can unite to form –S-Sdisulfide bond.
All are very important functional groups in
biomolecules.
It is these functional groups that give the
biomolecules their distinctive characteristics and
help predict their chemical and physical
behavior.
Most of the biomolecules are polyfunctional thus
possessing more than one functional group which
allow it to assume a number of characteristics
dictated by those functional groups.
For example amino acids have at least two
functional groups an amino and a carboxylic
group.
Glucose has two functional groups an alcoholic and
an aldehde group.
 • The highest occupied electron shell is called the valence shell,
and the electrons occupying this shell are called valence electrons.
• The number of valence shell electrons an atom must gain or lose
to achieve a valence octet is called valence.
In covalent compounds the number of bonds which are
characteristically formed by a given atom is equal to that atom's
valence .
The following general valence assignments have been documented
for the elements:
Electronegativity is a measure of the tendency of
an atom to attract a bonding pair of electrons.
 If the electronegativity of an atom is high, then
it attracts and holds on to electrons.
 If the electronegativity of an atom is low, then
it tends to give electrons away.
 Electronegativity differences thus determine
bond type and explains what is meant by polar
bonds and polar molecules.

• If the difference in electronegativities is
between:
 – 1.7 to 4.0: Ionic
 – 0.3 to 1.7: Polar Covalent
 – 0.0 to 0.3: Non-Polar Covalent
 Example: NaCl
 Na = 0.8, Cl = 3.0
 Difference is 2.2
 So this is an ionic bond .


What is a bond?
A bond is a link or force that binds two or a group of
atoms together to form a compound.
The type of bonds found in biomolecules can be divided
into two types ;
1-Covalent bonds. They are strong bonds and can be
intermolecular (such as the disulfide bridge –S-S- ) and
intramolecular, mainly intramolecular.
2-Non-covalent bonds. They are weaker bonds and can be
intermolecular and intramolecular (but are mainly
intermolecular). Including , H bonds, ionic bonds,
hydrophobic bonds, Van derWaals forces .



Bond energy;The amount of energy required to break a
bond is called bond dissociation energy .
Bond energy is a measure of the strength of a chemical
bond. The larger the bond energy, the stronger the bond.
C----C , bond energy is 348 Kj/mole.
C=C ,bond energy is 614 Kj/mole.
, bond energy is 839 kj/mole.
Covalent bonds; a covalent bonds forms when two atoms share
a pair of electrons together ( thus each atom will be donating
an electron to form the bond) .If each atom donates 2electrons
a double bond is formed which is stronger and more rigid, and
a triple bond is formed when 3electrons is donated by each
atom.
-It is the strongest chemical bond.
-It can be a non- ploar covalent bond , which arises when the
two atoms involved are of the same element thus having the
same electronegativity thus share the pair of electrons equally.
Non-polar covalent bond.

Or a polar covalent bond
when it is formed between
two different atoms of
different electronegativity
,thus one atom has a stronger
pull on the pair of electrons
resulting in a shift of
electron density toward the
more electronegative atom.

Such a covalent bond is
polar, and will have a dipole
(one end is positive and the
other end negative). The
degree of polarity and the
magnitude of the bond dipole
will be proportional to the
difference in
electronegativity of the
bonded atoms.

In an ionic bond one atom has
such a strong attraction for the
electrons (electronegativity)
that it pulls an electron away
from another atom. This results
in the two atoms now having
charge

The atom which gained the
electron now has a charge of -1
(anion). The atom which lost the
electron has a charge of +1
(cation). These oppositely
charged atoms (now called ions)
attract one another, this
attraction force is the ionic
bond.

Generally chemists consider this
to be the strongest of all bonds,
as long as no water is present. In
biological systems, ionic bonds
are weak due to this fact .It is
the strongest non-covalent
bond..

Weak bonds are bonds that form between different molecules or
within different parts of a large molecule. While these bonds are
not strong enough to hold a molecule together they are
extremely important because of their large number. There are
three basic types of weak bonds (Hydrogen bonds, Hydrophobic
Interactions and Van der Waals Forces).
Hydrogen bonds;
The hydrogen bond is a special dipole-dipole interaction between
the hydrogen atom in a polar N-H,O-H, or F-H bond and an
electronegative O, N, or F atom.
The molecules involved in a hydrogen bond have partial charges
on different parts of the molecule ( are polar molecules) .
Although these bonds are very weak (3-5 kcal/mole), in
biological systems they are very important.
Water is a good example of a molcule that readily forms hydrogen
bonds. Each molecule contains polar covalent bonds between the
hydrogen atoms and the oxygen atom. The result is that the
oxygen end of each molecule has a partial negative charge and
the hydrogen end of each molecule a partial positive charge.
These partial charges attract one another resulting in a weak
bond that holds molecules of water to each other.
. Hydrophobic Interactions;
When non-polar substances such as fats or oils are placed in water they
tend to clump together. The attraction of the hydrophobic (or nonpolar)
parts of molecules to each other in the presence of water (or another polar
fluid) resembles the hydrophobic attractions . Molecules containing
substantial non-polar regions will attract one another as a result of these
hydrophobic interactions.Such as between non-polar side chains of a.a in
proteins, and in the plasma membrane.

Van der Waals Forces;
van der Waals' forces are forces that exist between MOLECULES of
(they are intermolecular bonds or forces) the same substance .
They can be dipole-dipole attractions; Which can be resembled by
the attraction that occurs between polar molecules (between
their opposite partial charges) ,when they are in close proximity
to one another.
They can be dispersion attractions; which occurs between non-polar
molecules due to the small attractions resulting from the constant
movement of the electrons around the atoms of the molecules ( a
temporary dipole forms in one molecule leading to a temporary dipole to
form in the other molecule). These are very weak and short lived forces.