كيمياء كامل محلول

Introduction to the course
Biomedical Sciences-2
Semester 2; Level-2 (1441-1442)
By
Dr.Hiba Mahgoub Ali

Course Information
Course Title: Biomedical Sciences -2
Course Code: 102 MDS
Program: B.Sc. Medical Laboratory Sciences
Department: Basic medical sciences
College: Applied medical sciences
Institution: University of Bisha

Course Description
This course introduces the second level/first year student , This is a four credit hours course which
will be conducted during the second semester of year one to introduce the first year students of
health and medical specialties to the concepts of chemistry, biochemistry and biophysics
Main objective of the course
• Provide students with basic concepts and skills of chemistry, biochemistry and physics.
List of Topics
Theoretical part
A. Chemistry part
Introduction to chemistry, molecules and molecular formula(Role of chemistry in medicine,

the International system of units, matter, elements-compounds and mixtures, structure of
1
atoms-ions and isotopes, chemical formula and naming of chemical compounds).
Chemical bonding and chemical reactions(chemical bonds such as hydrogen, ionic, covalent,
2
Vander Waals bonds, atomic mass, chemical reaction, chemical kinetics)
Solubility and solutions (solute-solutions and solvents, factors affecting solubility, types of
3
solutions, concentration of solutions and osmotic and hydrostatic pressure).
Overview of periodic table and organic chemistry (features of periodic table, periodic
4
properties of elements, aliphatic and aromatic organic compounds).
A. Biochemistry part
Chemistry of water, acids, bases and buffers (structure, functions,

properties of water, acids and bases, pH and its applications in medical field,
1
biological buffers and their mechanism of action, acid base disturbances).
Molecules of life (structure-functions-classification of carbohydrates, lipids,

amino acids, peptides and proteins, nucleoproteins-nucleic acids structure and
2
functions, enzymes structure, properties and classifications).
A. Biophysics part
Sound and hearing (sound waves in media, pitch and loudness, the human ear).
1
Pressure (pressure, density, Pascal′s principles and pressure and human body).
2
Fluids dynamics (terminology, the equation of continuity, Bernoulli′s equation and

3
viscosity).
Temperature (thermal equilibrium, measuring temperature, breathing).
4
Electricity (coulomb′s law, the electrical field, electrical potentials, human heart and ECG).
5
Eye and vision (lenses, parts of human eye, emmetropia, myopia, hypermetropia)
6
Practical part
1 Lab safety and safety measurements
2 Find the chemical formula of Magnesium Oxide (MgO)
3 Chemistry Identification of unknown salt
4 Identification of unknown alcohol
5 Identification of unknown organic acids
6 General view for biochemistry lab and lab utensils
7 Physical and chemical examination of monosaccharide's
8 Biochemistry Physical and chemical examination of disaccharides
9 Physical and chemical examination of polysaccharides
10 General scheme for identification of unknown carbohydrates
11 Speed of sound (resonance tube)
12 Measurement of viscosity of transparent Newtonian liquids
13 Physics Finding the focal length and power of diverging lens
14 Ohm′s law
15 Tutorial
Assessment Tasks for Students
Percentage of Total Assessment

# Assessment task Week Due
Score
First midterm exam 6 10%

1
Second midterm exam 12 10%
2
blackboard assignments All through 10%
3
Final practical exam 16 20%

4
Final theoretical exam 17 50%
5
References:
1. Chemistry for preparatory year students.2015. Prof Abdullah, prof.
Shaeel Al-Thabaiti, Dr. Mohamed Mukhtar, Dar Khawarizm for academic
publishing and disterbutation, 2012. King Fahad National library
Cataloging in publication data. ISBN: 978-603 8122-92-1.
• Biochemistry for students.2014. VK Malhotra.12th edition. Jaypee

Brothers Medical Publishers.
Introduction to chemistry
• What is chemistry?
Chemistry is the branch of science that deals with the composition and
structure of matter and the changes that matter undergoes.
Astronomy
Physics
Geology
Chemistry Is a central science
Material
Biology sciences
14
What is Chemistry?
 Chemistry : is studying the composition, behavior, structure
and properties of matter besides changes it undergoes.
 Matter : is any thing that has mass and occupies space
Property : is a characteristic to recognize the type of matter
to distinguish it from others.
15
Atom: is the smallest building block of matter
Element: composed of unique type of atoms
Molecules: are made up of two or more atoms joined
together in specific shapes
16
What is matter?
• Matter is anything that has mass and occupies space.
17
18
States of matter
Solid Liquid Gases
19
6 Major Areas of Chemistry
Analytical Chemistry- concerned with the composition of substances.
Inorganic Chemistry- primarily deals with substances without carbon
Organic Chemistry- essentially deals with all substances containing carbon
Biochemistry- Chemistry of living cells
Physical Chemistry- describes the behavior of chemicals (ex. stretching);

involves lots of math!
Nuclear Chemistry - dealing with radioactivity, nuclear processes and nuclear

properties 20
‫بسم هللا الرحمن الرحيم‬
SI units and density calculation
Dr. Hiba Mahgoub
1
Objectives
2. . SI units
3. Calculate density
4. Define element, compound and molecules
5. Define Atoms and list the three main component of it
6. Define the atomic and mass number
7. Calculate the number of electrons, protons, and neutrons
2
3
The scientific method
• After defining a problem
– Experiments must be designed and conducted

M
E
T
– Measurements must be made
H
O– Information must be collected
D
– Guidelines are then formulated based on a pool of observations
• Hypotheses (predictions) are made, using this data, and then tested, repeatedly.
• Hypotheses eventually evolve to become laws and these are modified as new data
become available
• An objective point of view is crucial in this process. Personal biases must not
4
surface.
Measurements
• An important part of most experiments involves the determination (often, the
estimation) of quantity, volume, dimensions, capacity, or extent of something
– these determinations are measurements
5
SI units
6
7
SI units
SI base units SI derived units SI prefixes
8
SI base Units
9
Derived SI units
Units are made of some combination of SI base units
10
Derived SI units:
Property Unit Symbol Definition
Force Newton N Kg m/s2
Pressure Pascal Pa N /m2 or kg /m s2
Energy Joule J Kg m2 /s2 or N m
Electrical charge Coulomb c As
Electrical potential Volt V J/C
Frequency Hertz S-1 or Hz 1/s
11
SI prefixes
12
Prefix-Base Unit System
Prefixes convert the base units into units that
are appropriate for the item being measured.
Know these prefixes and conversions
13
• Example 1:
• Convert 6.83 pm to meters
• Replace p with x 10-12
= 6.83 x 10-12
• Example 2:
• Convert 5.847 x 102 kjoules to joules
• Replace k with x103
= 5.847 x102 x 103 =5.847 x 105 J
14
• See examples in page:17,18
15
Density calculations
• Density can be used to determine the identity of unknown substances
• Mass or volume of substance will vary from sample to sample
• Density will remain same at a given temperature

e.g. The density of water at room temperature (25oC) is ~1.00 g/mL; at 100oC = 0.96 g/mL
16
Density:
Density does not have an assigned SI unit – it’s a

combination of mass and length SI components.
Mass (g)
Density Volume
(g/ml) (ml)
17
• A student determine that a piece of an unknown material has a mass of 5.854g and a
volume of 7.57 cm3 what is the density ?
• Density = mass/volume
• Density = 5.57/ 7.57= 0.77331571994 g/cm3
• = 0.773 g/cm3
18
Atoms
19
The modern atomic theory
Done by English school teacher John Dalton in 1808
Atomic theory has four assumptions:
1. Atoms make up all matter
2. The atoms of one element differ from the atoms of another

element
3. Atoms combine in definite ratios to make compounds
4. Combination of atoms in compounds can change only when a

chemical reaction happens
20
Atoms are made of three particles:
• Protons (P+)
• Neutrons (N)
• Electrons (e-)
21
Protons Neutrons Electrons
Located in Located in have a

the nucleus the nucleus negative
charge
Have a orbit the
Have no
positive nucleus of
charge
charge the atom
Have a Have a mass

of one – are very small
mass of (have basically
similar to the
one proton
NO mass)
Number of electrons equal the number of protons

22
How to write elements symbols
23
Atomic Number (Z): is the number of protons in the nucleus of
the atom.
Z= n of p
• The number of protons (atomic number) determine the identity of

an element.
• Every element has its own unique atomic number
• Neutral atom : no of protons = no of electrons
24
Periodic table is arranged in sequence of increasing number of
electrons which is equal to atomic number
25
Mass Number (A):
•The sum of the protons and neutrons in the nucleus.
A = no of p + no of N
•Massive particles in the nucleus of atom (protons and neutrons )
26
Summary
Number of neutron = A - Z
27
Ex: how many neutrons, electrons
23
and protons are
in an atom of Sodium-23 11
Na
Answer:
• Atomic number = 11
• So : no of p = 11
• no of e = 11
• number of neutrons = A – Z = 23 – 11 = 12
28
Ex: how many neutrons, electrons and protons are in an
atom of sulfur S with mass number 33?
• The atomic number of sulfur is 16 so
• Number of neutrons = A – Z = 33 – 16 = 17
• Electrons = 16
• Protons = 16
29
Ex: An atom contains 24 neutrons and 25 protons what is the
mass number?
• Mass number = no of p + no of N
• = 25 + 24 = 49
Ex: an atom with a mass number of 39 contains

20 neutrons. What is the atomic number and
identity of the element
Atomic number = 39 – 20 = 19 the identity is potassium because
k is element 19
30
Isotopes
of an element have
different mass numbers
because
they have
different numbers of neutrons,
but they have
the same atomic number.
31
Example:
Isotopes of Carbon and Hydrogen
Isotopes of Hydrogen
protium deuterium tritium
H H H
Istopes of Carbon
32
33
 Atomic Mass: is the weighted average mass of all the naturally
occurring isotopes of that element.
 Atomic Mass Unit: is a unit used to compare the masses of atoms and
has the symbol u or amu.
1 amu or u: is approximately equal to the mass of a single proton or

neutron.
Chemists have defined the carbon-12 atom as having a mass of 12 atomic

mass units.
34
Average Atomic Mass
• The decimal number on periodic table
• Weighted average of all isotopes of an element
• Depends on percent (relative) abundance and mass of each isotope
• Measured in “atomic mass units” (amu)
35
Example
• Element lithium have two isotopes one of them have Mass=6
amu and Relative Abundance= 7.5% while the second
Mass=7 amu and Relative Abundance=92.5%
• What is the average mass of lithium?
• First convert relative abundance to decimals
Eg: 7.5 0.075
92.5 0.925
36
To solve example
Average atomic mass=
[(mass #1)x(abundance #1)] + [(mass #2)x(abundance
#2)]
(6 x .075) + (7 x .925)=
0.45 + 6.475=
6.925 amu
See examples of handout page 22

37
Now You Try
 Identify the element and tell how many protons it
has:
1) Atomic number 7 Nitrogen: 7 protons
2) Atomic Number 20 Calcium: 20 protons
• Identify the element and give its atomic number.

3) 15 protons Phosphorus: Atomic number 15
4) 4 protons Helium: Atomic Number 4
• Give the atomic number and number of protons.
5) potasium Atomic number 19; 19 protons
6) Sulfur Atomic number 16; 16 protons 38
The periodic table
Periods (rows)
Groups
(column)
39
• Different rows in the periodic table are called periods
• The number of electrons in a period increases as one traverse down
the periodic table
• Elements lie in the same column on periodic table are called a group
and behave in a similar fashion chemically
• All group 18 elements are inert gases (noble gases)
40
41
MOLECULES, ION, AND CHEMICAL FORMULA
By
Dr. Hiba Mahgoub

Chemical formula is used to illustrate the composition of molecules and compounds.
Molecular formula shows how many of each type of atom are in a molecule
eg: ethanol C2H6O
 Empirical formula (simplest formula) shows the simplest hole number ratio of
atom molecule eg: hydrogen peroxides chemical formula is H2O2 but empirical
formula is HO
 Example: the empirical formula for glucose C6H12O6 is CH2O
 MOLECULAR FORMULA = N X EMPIRICAL FORMULA
EG: C6H12O6 = N X CH2O
N= 6
MOLECULES AND IONS
 Molecules are compounds in which the element are in definite fixed ratio and those
atoms are held together by usually by a chemical bonds
Examples :
 Water
 Glucose
 alanine
MOLECULE
atom atom atom
Chemical bonds
 Ions are electrically charged particles produced by either removing electrons from
neutral atom to give positive ion (cation) or adding electrons to a neutral atom to give
a negative ion (anion)
 The name of cation is the same as original atom name but add ion after
 The suffix ide is added to anion

EXAMPLES OF IONS
 Li+ ………. Lithium ion
 Na+ ……….Sodium ion
 Mg2+ …….. Magnesium ion
 Ca2+ ………Calcium ion

Cations
 Al3+ ………. Aluminium ion
 K1+ ……….. Potassium ion
 Cl1- ……….. Chloride
 Br1- ……….. Bromide
 S2- …………. Sulfide
 O2- …………. Oxide

Anion
 N3- ………… Nitride
 P3- ………… phosphide
 C4- …………. Carbide
 Si4- …………. Silicide

 Note: the number of protons does not change
 The change in number of electrons

EXAMPLES
 Sodium have 11 protons and electrons
 By removing electron it will become positive charge
 Number of electrons become 10
 Na Na+
 Chloride -17 have 17 protons and 17 electrons
 By adding one electron it becomes (18 electrons) negative
charge
Protons + neutrons
65 2+
Zn 30e – 2 = 28 electron
30
protons
Number o protons = 30
Number of neutrons= 65 – 30 = 35 neutron

Protons + neutrons
35 1-
Cl 17e + 1 = 18 electron
17
protons
Number o protons = 17
Number of neutrons= 35 – 17 = 18 neutron

POLY ATOMIC IONS
Nam Formula Name Formula
Ammonium (NH41+)
Chlorate (ClO31-) Bicarbonate HCO31-
Cyanide CN1- Hydroxide OH1-
Nitrate NO31- nitrite NO21-
Permenganate MnO41- Thiocyanate SCN1-
Carbonate CO32- Chromate CrO42-
Dichromate CrO42- Sulfate SO42-
Sulfite SO32-
Phosphate PO43-
RULES FOR NAMING COMPOUNDS
 ionic compound ( compounds contain cation and anion)
The cation named first and anion named second
Be sure the net charge is zero
Write the oxidation state of transition metals

containing cations between two brackets
Examples
Compound Name Compound name

ALCl3 Aluminum chloride Na2S Sodium sulfide
K2O Potassium Oxide MgH2 Magnesium hydride
FeO Iron (II) oxide Fe2O3 Iron (III) oxide
CaCO3 Calcium carbonate AlPO4 Aluminum

phosphate
Zn (OH)2 Zinc hydroxide KMnO4 Potassium
permanganate
CuSO4 Copper (II) sulfate AgNO3 Silver nitrate

HOW TO WRITE THE FORMULA
Identify the symbol for both cation and anion
Write them and charge underneath them
Remove the charge (- or +) and leave the

number
Exchange the numbers
Make the number as simple as possible
Write the formula using the final numbers

from
 Example: write the chemical formula for calcium sulfate, aluminum
oxide, iron nitrate
Ca SO4
2+ 2-
Ca SO4
2 2
Ca SO4
2 2
Ca SO4
Divide both number by 2
1 1
The formula is Ca1(SO4)1 or CaSO4

 Example: write the chemical formula for calcium sulfate, aluminum
oxide, iron nitrate
Al O
3+ 2-
Al O
3 2
Al O
2 3
Al O
2 3
The formula is Al2O3

2- COVALENT COMPOUNDS
 These compound contain no charge
 Formed from nonmetals at the right side of the periodic

table
 The number of the atoms must be written before the name

of element
1. If the number is one ….. Mono
2. If the number is two ….. Di
3. If the number is tree ….. Tri
4. If the number is five ….. penta

 Examples
 Write the name of the following molecules: CO,
N2O4, NO, SO2, PCl5, HCl
Answer:
Compound Name Compound Name
CO Carbon monooxide N2O4 Dinitrogen
tetraoxide
NO Nitrogen monoxide SO2 Sulfur dioxide
PCl5 Phosphorus HCl Hydrogen
pentachloride monochloride
 Example 2: write the chemical formula for: carbon dioxide, sulfur trioxide,
dihydrogen monoxide, phosphorus trichloride, nitrogen dioxide
Name Formula Name Formula

Carbon dioxide CO2 Sulfur trioxide SO3
Dihydrogen monoxide H2O Dihydrogen monoxide H2O
Phosphorus trichloride PCl3 Nitrogen dioxide NO2

Thanks
Chapter 2
Stoichiometry
By
Dr. Hiba Mahgoub

Objectives
Atomic Mass or atomic weight
molecular mass
The Mole concept
Avogadro's number
Molar Mass
Percent Composition of Compounds

What is Stoichiometry?
The study of the quantitative aspects of chemical

reactions
Atomic mass
 also known as Atomic weight (periodic table)
Average atomic mass of an element calculated using the relative
abundance of isotopes in a naturally occurring element represented by
unit called Atomic mass unit (amu)
See p.35
Molecular Mass
The molecular mass of a compound is the sum of atomic masses
of the atoms in the molecules that form these compounds
Example: calculate the molecular mass of the sugar molecule
found in cane sugar C12H22O11:
(12x12.011)+ (22x1.0079) + (11x15.9994) = 342.299

The mole
 A unit of measurement in SI for amount of substance
Similar to dozen
 One mole is defined as the number of carbon atoms in exactly 12
grams of pure 12C

 From the sugar of cane example a mole of C12H22O11 would have
a mass of 342.299 g
 This quantity known as molar mass
 Molar mass a term that often used in place of the terms atomic mass
or molecular mass
Example: Find the molar mass of sodium carbonate,
Na2CO3 .
See examples page:36

Molar mass (g/mole) for some element only check
the periodic table
To determine the number of moles
Number of moles = mass (g)
molar mass (g/mole)
Example 2.3
How many moles are there in 23g of sodium?
number of moles = 23g = 1 mole
23(g/mole)
Example:
How many grams are there in 0.10 mole of CH4?
Calculate the molar mass of CH4
= 1 * 12 +4 * 1= 16 g/ mole
then use the formula
mass of CH4 =number of moles * molar mass of
CH4 = 0.10 mole * 16 g/mole = 1.6g

Avogadro's number and the mole
1 mole of anything contains the Avogadro's Number (NA) of

this thing.
1 mole of particles = 6.022×1023 particles for any substance.
Number of particles(atoms, molecules,…..) = number of moles

×Avogadro's
number
Example:
Calculate the number of atoms in 3 mole of hydrogen
Number of hydrogen atoms = 3x 6.022×1023
= 3 moles × 6.022 ×1023 H atom/mole
=1.80×1024 H atom
Example:
Calculate the number of atoms in 6.46 grams of helium (He)
number of moles = mass (g)
molar mass(g/mole)
= 6.46 g = 1.61 mole

4.0 g/mole
number of He atoms = number of moles ×Avogadro's number

=1.61 mole of He×6.02214×1023 He atom/mole= 9.66×1023He
atom
This could be done in one step
Mass percent
The mass percent of an element is defined as

Example:
Calculate the molar mass of C2H6O
MW of C2H6O = 2*C+6*H+1*O
= 2*12+6*1+1*16= 46 g/mole
Mass percent of C = 100 x mass of C = 100 x 2 x12 = 52.14%

Total molar mass 46
Calculate the mass percent of hydrogen and oxygen in C2H6O
Mass percent of H = 100 * 6 = 13.13%

46
Mass percent of O =100 * 16 = 34.72 %

46
The molar mass of C2H6O = 52.14+13.13+34.72 = 99.99%
See Example 2.13 -2.14 page 41,42,43

Thanks
Combustion Analysis,chemical reactions and molarity

By
Dr. Hiba Mahgoub Ali
Bisha University
Objectives:
Combustion analysis
to calculate the percent composition of each

element in a compound.
to calculate the molarity of a solution
To find empirical formula of a new compound
to solve the stoichiometry problems.

• Combustion analysis is a method used in organic chemistry to determine the
mass % for different element of (organic) compound.
• To analyze the mass percent of carbon and hydrogen chemist use a combustion
device.
• How combustion analysis is done?
By burning a sample of unknown elemental composition in the presence of excess

oxygen
• Products of combustion include:
• CO2
• H2O
Sample Oxygen
CO2
Burning ⁺ H2O
• CO2 and H2O are absorbed in two different stages according to their
masses.
• Masses determined by measuring the increase in weight of the

absorbers.
• If the sample contain oxygen can be determined by calculation

Calculate the mass of each element
Calculate the mass percent of each element
Mass of an element in a sample = mass of product X number of atoms X atomic mass of the element
its molar mass
Mass % of element (H or C or O2) = 100 X mass of element

total sample mass
• See Example 2.16:
Ethanol contains carbon, hydrogen and oxygen. Up on the combustion of 1.15 g

sample of ethanol gives 2,20 g of CO2 and 1.35 g of H2O.
Calculate the mass percent for carbon, oxygen, and hydrogen
C H O
1 Mass of element /g = mass of product x no of atoms x atomic mass of atom 2.20 x 1 C x 12 = 1.35 x 2 H x 1 = 1.15-0.15-0.60= 0.40
its atomic mass 44.0 0.60 18 0.15
2 Mass % = 100 x mass of element 100 x 0.60 =52.2% 100 x 0.15=13.0% 100 x 0.40=34.8%
total sample mass 1.15 1.15 1.15
• The empirical formula shows relative ratio of different atoms in a
compound
Example:
H2O composed of two atoms of hydrogen and one atom of oxygen

• Calculate the mass of each
To element
determine • Calculate number of moles
empirical • Divide number of mole of each
element / smallest number
formula: • Write empirical formula
Ste C H O
ps
1 Mass / g 0.60 0.15 0.40
2 No of moles = Mass/ molar 0.60/12 = 0.15/ 1 = 0.40/ 16 =
mass 0.05 0.15 0.025
3 No of moles / smallest 0.05/0.025 = 0.15/ 0.025 0.025/ 0.025
number (0.025) 2 =6 =1
4 Empirical formula 2C 6H 1O
Chemical reactions
• Definition of chemical reaction:
A process in which one or more different pure substance are converted into one or
different pure substance.
• Chemical reactions involve change in :
 Substance
 Energy
• Neither matter nor energy is created or destroyed in a chemical reaction only
changed
• The chemical equation shows:
1. Chemicals that react (reactant)
2. Chemicals that they produce (products)
• In the chemical equation:
1. Reactant on the left hand side and products on the right hand.
2. Chemicals can be represented by their names or by their chemical symbols.
3. Some times physical condition of reactants and products might be written
( (s) for solid, (l) for liquids, (g) for gases, and (aq) for aqueous solution, and (ppt)
for precipitate.)
Heat/ catalyst
Reactants Products
Example:
Methane gas + oxygen gas Liquid water + carbon dioxide gas
CH4 (g) + 3 O2 (g) 2H2O (l) + CO2 (g)

Chemical equation balancing:
• CH4 + O2 > CO2 + H2O
• Balanced? No
• Reactants: C=1, H=4, O=2
• Products: C=1, H=2, O=3
• H and O are not equal

• Use coefficients to balance equations
CH4 + 2O2 > CO2 + 2H2O
• C=1, H=4, O=4 > C=1, H= 4, O=4
• Now the equation is balanced

Amount of reactants and products
aA+ bB cC+ dD
• To calculate the number of moles for unknown (eg: C), by knowing

number of moles of knowing substance (for example A)
Number of moles of C = Number of moles of AX c

a
• Calculate the number of moles of H2O resulted from the reaction of
4.5 moles of C2H6 with excess oxygen according to equation:
2C2H6 + 7 O2 4CO2 + 6 H2O
• Number of moles of H2O = Number of moles of C2H6 X 6/2
Number of moles of H2O = 4.5 X 6/2 = 13.5 moles of H2O

Calculate the mass of unknown
• If the unknown (C)
• Knowing mass of knowing substance (A)
Mass of C = mass of A X molar mass of C X c

molar mass of A a
• Example: calculate the mass of hydrogen that reacts with 169.3 g of
chlorine to form hydrogen chloride according the following equation
H2 + Cl =2HCl
Mass of hydrogen = 169.3 x 2 x 1 = 4.77 g

71.0 1
Solutions and Concentration
• A solution is homogeneous mixture of 2 or more substances.it

contains:
• Solutes is the substance that dissolved in a solvent.
• Solvent a liquid in which a substance is dissolved.
• When the solvent is water, the solution is said to be aqueous.
Molarity (M)= moles of solute
Volume of solution(Liter)
See example 2.29,30,31

• Another way to express the concentration is the weight percent
Weight percent = mass of solute

mass of solution
Example:
What is the molarity of a solution containing 0.32 moles of NaCl in 3.4 litres?
Molarity = number of moles

volume/L
Molarity of NaCl = 0.32 moles of NaCl = 0.094moles of NaCl

3.4 litres
Dilution of concentrated solutions
• Solution is usually diluted by adding more solvent to it
Note:
• The amount of solute present does not change
• Total volume and the concentration of solution do change
• To calculate the molarity after dilution we can use the following formula:
No. of Moles x volume before dilution = no. of moles after dilution x volume after dilution
M1 X V1 = M2 X V2
Example:
- How many milliliters of 18.0 M H2SO4 are required to prepare 1.00 L of a 0.900
M solution of H2SO4?
V1 = ? , M1 = 18.0M , V2 = 1.00 L , M2 = 0.900M
V1 x M1 = V2 x M2
V1 = V2 x M2
M1
V1 = 1.0M x 0.900 L = 0.0500 L = 50ml
18.0 M
Periodic Table of Elements
by
Dr. Hiba Mahgoub Ali

Mendeleev
• In 1869, Dmitri Ivanovitch Mendeléev created the first

accepted version of the periodic table.
• He grouped elements according to their atomic mass, and

as he did, he found that the families had similar chemical
properties.
• Blank spaces were left open to add the new elements he

predicted would occur.
First classification
• Metals is the larger group heat and electricity conductor

• Nonmetals are closely associated with the living system
• Metalloid heat and electricity conductor better than nonmetals but not as well
as metals
Second classification
• Groups or families (vertical column)
• Periods (horizontal rows)
Groups Periods
• Columns of elements are called • Each horizontal row of elements is
groups or families. called a period.
• Elements in each family have similar • The elements in a period are not alike
but not identical properties.
in properties.
• For example, lithium (Li), sodium
• In fact, the properties change greatly
(Na), potassium (K), and other
across even given row.
members of family IA are all soft,
white, shiny metals. • The first element in a period is
• All elements in a family have the always an extremely active solid. The
same number of valence electrons. last element in a period, is always an
inactive gas.
- Element can be grouped based on their last orbitals
Periodic Table Groups
• A group in the periodic table
 includes elements with the same number of outer electrons.
Have similar chemical properties (loss or gain the same
number of electrons in the reactions.
• The similarities are strongest in

Alkali metals in group1A
Halogens in group 7A
The important groups in periodic table
1. Alkaline metals :
• In column 1
• Is a group of elements that have 1 electron in their outermost
shell.
2. Representative elements:
• In the groups from group 1A to group 7
3. Alkaline earth metals:
• All have 2 electrons in their completely filled outer shell.

• Group III, IV, V, VI, and VII all have the number of outer shell electron
as the group number.
• Group VII elements are known as halogens.
4. Group VIII (noble gases or inert gases):
• Inert because these elements do not combine with themselves or

any other element under normal conditions
• Characterized by having completely filled with 8 electrons in their

outermost shells.
5. Transition metals:
• Occur between the alkaline earths group II and group III
6. Lanthanides (rare earth elements):
• Element from 58 to 71 - Ce (cerium) to Lu (lutetium)
7. Actinides:
• Elements 90 to 103 - Th (thorium) to Lr (lawrencium)

Periodic properties of elements
1) Atomic radius:
• The atomic radius for an atom is measured from the length

of a bond between this atom and other one divided by 2
Trend in Ionization Energy
P104
• The energy required to remove the valence
electron from an atomic specie.
Example 5.1
Trend in Electron Affinity
change in energy that occurs when electron is added to an
atom
• Example 5.2 P105

Trend in Electronegativity
P106
The ability of an atom to attract electrons in a

molecule
Compounds and chemical bonding
• Elements combine to form chemical compounds through the
formation of chemical bonds.
• Chemical bonds are forces that hold atoms together in

compounds.
The octet rule:
• Atoms usually gain, lose or share electrons until they have 8

electrons in the outer shell to reach the same number of
electrons of noble gases.
The noble gases have full valence electron shells
Lewis dot representation:
represents the valence electrons of an atom (outer most shell electrons)
are represented by dots.
• There are two main types of chemical bonds:
1- Ionic (electrostatic bond):
Sodium (metal) + cholrine gas (non metal) Sodium chloride

2- Covalent bond:
Non metal atoms share electrons
One pair of e two pair of e Three pair of e
Thanks
Organic chemistry
By
Dr. Hiba Mahgoub
Organic chemistry
• Is a very important branch of chemistry
Definition:
• Organic chemistry is the study of compound which contain carbon and hydrogen
(hydrocarbons) in general and may contains other atoms such as oxygen (O), nitrogen (N),
sulfer (S) ….etc

Organic compound
Acyclic
(open chain compounds) Cyclic
(closed chain compounds)
Aliphatic
compounds
Aliphatic Aromatic
Alkane Alkene Alkyne

CnH2n+2 CnH2n CnH2n-2
Aliphatic hydrocarbons
• Organic compound contains C and H only
Example:
CH4 (methane)
Alkanes
• Saturated hydrocarbons
• All carbon atoms are bonded with 4 single covalent bond
• General formula is: CnH2n+2
• Sp3 hypridization
• The angle between bonds is 109.28

ₒ
• sp3 hybridization
Nomenclature:
• According to International Union of Pure and Applied Chemistry

(IUPAC) alkanes are named by
• Number of carbon atoms in the longest chain (prefix )
• Adding the suffix –ane.
See examples P163-164

Alkenes
• Unsaturated hydrocarbons
• Contains at least one C C double bond
• General formula CnH2n
• Sp2 hypridization
• The angle between bonds is 120◦

Nomenclature:
• Number of carbon atoms in the longest chain from the side where the
double bond takes the lowest number
• Add suffix ene
• See P165
Nomenclature
• Ethene
• Propene
• Butene
• 1- butene
• 2-butene
Cis-trans isomerism
• Cis: the large groups are at the same side of the double bond
• Trans: the large group opposite to each other across the double bond
• cis-2-butene
• trans-2-butene
Alkynes
• Unsaturated hydrocarbons
• Contain at least one C C triple bond
• General formula CnH2n-2
• Sp hybridization
• The angle between bonds is 180◦

Naming alkynes
• Number of carbon atoms in the longest chain
• Add the suffix yne at the end
• Examples :
• Ethyne (acetylene)
• Propyne
• butyne
Organic functional groups and their names
Aromatic hydrocarbons
• The most common aromatic hydrocarbon is benzene
• Benzene ring is named as phenyl group
• Benzene ring is named as a phenyl group when it substituent e.g;

phenylethylene
Benzene ring substitution positions
• In ortho-substitution, two substituents occupy positions next to each
other, which may be numbered 1 and 2.
• In meta-substitution the substituents occupy positions 1 and 3
• In para-substitution, the substituents occupy the opposite ends
(positions 1 and 4, corresponding to R and para in the diagram).

Examples
Toluene o-xylene styrene
Biphenyl: involve two benzene ring bonds together
Polycyclic aromatic hydrocarbons contain fused benzene rings:
Number of bonds
• For each single bond count one sigma bond
• For each double bond count one sigma one pi bond
• For each triple bond count one sigma and 2 pi bonds

Theme
5
Water, acids,
bases and buffers
07-10-2018 AASER ABDELAZIM BMS-2-221 1

Lecture 1
1. Structure of water
2. Water bonding
3. Properties of water
4. Acids alkalis and bases

Water is very important due to:
1. Water constitutes 45%-73% of total human body
weight.
2. It is distributed in intracellular (55%) and extracellular
(45%) compartments.
3. It provides a continuous solvent phase between body
compartments so it has a role in (metabolsim-
absorption-digestion-transportation and excretion).
4. Regulates body temerature.

WATER
Regulate body Carry oxygen and
temperature nutrients to all cells
83% of blood Moisten oxygen for

breathing
Remove wastes
Production of energy
75% of muscles Protect and cushion

for organs and joints.
22% of bones Absorption of all staff

nutrients.
(A) STRUCTURE OF WATER
One molecule of water is made up of 2 hydrogen atoms bonded with 1 oxygen atom (H2O)
H H

(B) WATER BONDING
One molecule of water
NOTE:
The bond that forms one water molecule is a covalent bond while water
molecules join each other by hydrogen bond . (one molecule of water can
share 4 hydrogen bonds)
(C) ELECTRONEGATIVITY OF WATER MOLECULES
Electronegativity describes the degree to which an atom attracts electrons in a chemical bond.
The difference in the electronegativity of two atoms determines their bond type.
Electronegativity difference Chemical bond

>1.7 An ionic bond
0.4-1.7 Polar covalent bond
< 0.4 Non-polar covalent bond
In water molecules, Oxygen atom has electronegativity =3.5 while hydrogen is 2 so the difference
is 1.5 this indicate that water is polar covalent molecule.
In water, an electron from each of the hydrogen atoms is drawn towards the oxygen atom. In this
case, the oxygen atom has a partial negative charge, whereas the hydrogen atoms have partial
positive charges.

(D) WATER CHEMISTRY/water properties
A. water is the most abundant chemical in the body.

B. Water has many characteristics that make it vital to our bodies.
.
Size
Heat
capacity
Water properties Polarity

Buffer
Cohesion
and
Adhesion
Crystals

WATER PROPERTIES
(1) Size
1. Water is a very small molecule (10-1 nm).
2. It moves fast and can squeeze into tiny gaps between other molecules.
3. Its size enable it to be the fastest absorbed molecule in the body.
NOTE: nm=10-9 meter

(2) Polarity
+ DURACELL
_
Hydrogen has a slightly positive charge while oxygen has a Polar molecules that carry a charge
slightly negative charge. This makes it easy for water

DURACELL
to attarct other charged molecules, dissolving them.

Non-Polar molecules that do not carry a charge
Water is Called as [Universal Solvent].

+ +
Hydrogen (1 proton) bind to oxygen by NOTES
covalent bond – carry +ve charge The positive hydrogen ends of 1
molecule are attracted to the negative
end of the oxygen of another molecule.
Cohesion, adhesion, specific heat,
universal solvent, capillary action, surface
tension ALL HAPPEN BECAUSE WATER IS A
Oxygen (8 protons/8 neutrons) bind to POLAR SUBSTANCE!
hydrogen by covalent bond- carry –ve
charge
-
Bohr model of water
(3) Crystal structure
Due to polarity, water forms a crystal structure with metals that is less dense than liquid
water. Examples Calcium chloride (CaCl2·2H2O)- Zinc chloride (ZnCl2(H2O)4)- cupper sulphate
([Cu(H2O)4]SO4·H2O)
(4) Heat capacity
water absorbs and releases heat energy slowly, and can hold a great deal of heat energy. This helps
organisms maintain their body temperature in the safe range.
(5) Cohesion and
adhesion
 Polarity allows water to stick to itself (cohesion) and to any charged material (adhesion).
 Water can glue materials together.
(6) Buffer
Water can act as either an acid or a base, maintaining a stable pH in our bodies (will be
discussed later).
ACIDS, ALKALIS AND BASES
ACID
Any substance gives H+ ions in a solution
CH3COOH CH3COO- + H+
Acid Conjugate base Hydrogen ion
ACID Acidity
is the concentration of H ions in a
solution
Types:
Strong Intermediate Weak 1. Free (true/ actual): amount of H
present free in solution it is high in
strong acids
2. Combined: amount of H present
 HCl H3PO4 H2CO3 combined with conjugate base
 H2SO4 3. Total (titratable) = total amount
of free H + combined H

ALKALI
Is a substance that gives (OH-) in a solution
NaOH Na +
+ OH -
ALKALI
Strong Weak
NaOH NH4OH
BASE
Is the substance that can accept (H+) ion in a solution

Examples for bases
Ammonia
Nucleic acid bases
All alkalis are bases but not all bases are alkalis why ?
That is because all alkalis can produce (OH-) and by role (OH-) can accept (H+) to
form H2O while bases like NH3 (ammonia) only can accept (H+) to form NH4
(ammonium).
Example (1): Sodium hydroxide is an alkali and base
H+
NaOH Na+ + OH- H 2O

Example (2): Ammonia is only a base
H+
NH3 NH4 It can accepts H+ but not give OH-

QUIZ on water chemistry
1. The bond which join two molecules of water together is ----------------

a) Hydrogen bond
b) Electrostatic bond
c) Covalent bond
d) Hydrophobic bond
2. The cohesion of water is the attachment of water molecules to -----------------------------

a) Non-polar surfaces
b) Polar surfaces
c) Each others.
d) Hard surfaces
3. The polarity of water is due to ----------------

a) Presence of polar bonds.
b) Partial negative charge of oxygen
c) Partial positive charge of hydrogen.
d) Positive charge of hydrogen and negative charge of oxygen.
4. Adhesion of water molecules is known as ----------------

a) Sticking to charged surfaces.
b) Joining to each others.
c) Holding non-polar surfaces.
d) Dissolving polar molecules.
5. One molecule of water is made up of -----------------

a) Two molecules of hydrogen
b) Two molecules of oxygen
c) One molecule of hydrogen and two molecules of oxygen
07-10-2018 AASER ABDELAZIM
d) One molecule of oxygen and two molecules BMS-2-221
of hydrogen. 15
6. The bond H-O-H angle in water equals-----------
a) 104º
b) 104.5º
c) 105º
d) 105.4º
7. Which one is true regarding electronegativity in water molecules?
a) Oxygen is more electronegative than hydrogen
b) Hydrogen is more electronegative than oxygen
c) Hydrogen and oxygen have the same electronegativity
d) Both have no electronegativity
8. Theoretically, one molecule of water can form how many hydrogen bonds?
a) Two
b) Three
c) Four
d) Five
9. The hydrogen bond in water is -------------------

a) 10% covalent and 90% electrostatic
b) 25% covalent and 75% electrostatic
c) 20% covalent and 80% electrostatic
d) 15% covalent and 85% electrostatic
10. The life span of hydrogen bond between two molecules of water in solution is ------------
a) 1-20 seconds
b) 1-20 microseconds
c) 1-20 nanoseconds One picosecond= 10-12 second
d) 1-20 picoseconds
QUIZ on acid, alkalis and bases
1. Acid is known as any substance gives --------------------in solution.

a) Hydrogen
b) Hydroxyl
c) Water
d) Oxygen
2. Which one is a strong acid?

a) Hydrochloric acid
b) Phosphoric acid
c) Acetic acid
d) Carbonic acid
3. Which of the following structures represents the conjugate acid of HPO42- ?

a) H2PO4-
b) H3PO4
c) H4PO4+
d) PO43-
4. Which of the following relationships is true for an acidic solution at 25ºC?
a) [H+] > [OH-]
b) pH > 7.00
c) Kw > 1 10-14
d) The solution is negatively-charged
5. Which one of the following relationships is true in water at 25ºC?
a) [H+] = [H2O]
b) [OH-] = [H2O-]
c) Kw > 1 10-14
07-10-2018
d) [H+] = [OH-] AASER ABDELAZIM BMS-2-221 17
QUIZ on acid, alkalis and bases
6. Which of the following is NOT an example of a weak acid?

a) Lactic acid
b) Carbonic acid
c) Sulfuric acid
d) Pyruvic acid
7. In Universal indicators, red color shows----------
a) Strong acids
b) Strong alkalis
c) Weak acids
d) Weak bases
8. When an acid (H+) is added to alkali (OH-), product is----------
a) Hydroxides
b) Water
c) Salts
d) Hydrogen gas
9. More corrosive acid is-------------------------
a) Carbonic acid
b) Nitric acid
c) Gluconic acid
d) Sulforic
10. Which one is a phosphoric acid?
a) H2PO3
b) H2PO4
c) H3PO4
07-10-2018
d) H3PO3 AASER ABDELAZIM BMS-2-221 18
Lecture 2
1. Dissociation of water
2. pH scale
3. Henderson-Hasselbalch Equation

(1) DISSOCIATION OF WATER Now we can consider
water as an acid
(1) H2O H+ + OH-

And we can consider it
as a alkali!
(2) H2O + H+ H 3 O+
And we can consider it
also as a base!
water is acting as both acid and base

DISSOCIATION OF WATER
H2O H+ + OH-
Water dissociates to give equal amounts of (OH-) and(H+)
The equilibrium constant of water (K)
[H+] [OH-]
K =
[H2O]
NOTES
[H+] = molecular concentration of H+ ions
[OH-]= molar concentration of OH- ions
[H2O]= molar concentration of water molecules(un dissociated)
DISSOCIATION OF WATER
One liter of water = 1000g
One mole of water = 18 gm/L
Molar concentration of water = 55.5 M
[H+] [OH-]= 55.5M X 1.8x10-16

Ion product of water/dissociation constant of water =K w
Kw= [H+] [OH-]= 1 x10-14 M2

Water dissociates to give equal amounts of (OH-) and(H+)
[H+] =[OH-]= 1 x10-7 M

This means
Each molecule of water contains 10-7 mole of (OH-) and (H+)
Or each liter of water contains 10-7 gram of (H+) and 10-7 gram of (OH-)
pH(hydrogen ion concentration)
Definition: Is a term used to describe hydrogen ion concentration in a solution with the
measurement of acidity.
How term pH was obtained and used ?
Each litter of water contains 10-7 gm of free H and 10-7 gm of free OH.
According to the low of mass action the dissociation constant of water (Kw)
[H+] x [OH-] 10-7 x 10-7
Kw = = 1
= 10-14
[H2O]
Kw = ion product of water/ (dissociation constant of water)= 10-14
Notes:
1. If H increased to be 10-6, -5, -4, …….This means that OH should be lowered to
achieve the Kw of water.
2. And if the H decreased to be 10-8,-9,-10,….. This means also that OH should be
increased also to achieve the Kw of water.
pH (hydrogen ion concentration)
pH is used to express the concentration of both H and OH ions
[H+]= 100 101 102 103 104 105 106 107…………………………. 1014
pH = -log10 [H+] = log 1/[H+]

So pH will be a number from 1 to 14
Note: The pH value of 7 for pure water at Similarly: pOH = -log10 [OH-]= log 1/[OH-]
25ºC is considered to be neutral, values For water: log10 [H+]+ log10[OH-]= 10-14
below 7 are considered acidic, and values pH + pOH=14
above 7 are considered basic.
Determination of pH
1. Electronic method by PH meter

2. Colorimetric method by indicators
3. pH paper
Indicators: usually are weak acids or alkalis
Indicator Colorless yellow Yellow to red Red

Phenol red --- < 6.8 6.8-8.4 > 8.4
Phenolphthalein <8.3 --- 8.3 – 10.0 More 10.0
Topfer reagent --- > 4.0 2.9-4.0 Less 2.9
Blood pH:
Normal= 7.4±0.03
1) Increase the pH indicate alkalosis while decrease pH indicates acidosis (will be discussed later)
2) Only slight change in pH can lead to disturbances and stop of enzymatic activities
induce life threatening and lead to death
pH values in the body:

Henderson – Hasselbalch equation
(A)Definition
Describes the derivation of pH as a measure of acidity (using pKa in biological and chemical
systems.
(B) Uses of Henderson- Hasselblach
1. Estimating pH of buffer systems.

2. Finding equilibrium pH in acid base reactions.
3. Calculation of isoelecteric points of proteins.
(C) Derivation of the equation
An acid (HA) will be dissociate as follow:
HA A- + H+
According to the low of mass action:
[H+] x [A-]
K =
[HA]
07-10-2018 27
[HA] X K [H+] x BMS-2-221
=AASER ABDELAZIM [A-]
By dividing both sides by conjugate base [A-]: we did not need the conjugate base
[HA] X K [H+] x [A-] [HA]

[H+] K X
[A-]
=
[A-]
ֶ =
[A-]
By taking the log of both sides:
{K }
[HA] [HA]
Log [H+] = Log K + Log
Log [H+] = Log
[A-]
ֶ [A-]
By multiplying both sides by -1:

[HA]
- Log K - Log
ֶ - Log [H+] =
[A-]
ֶ - Log [H+] = pH
- Log K = pK
[HA] [A-]
ֶ pH
07-10-2018
= pK - Log
[AABDELAZIM
AASER
-]
OR pH =
BMS-2-221
pK + Log
[HA] 28
D. Limitations of the equation:
1. The equation assumed that the conc. of acid and its conjugate bas will remain the same
forever. And this occurs only at equilibrium state.
2. It neglected the following: dissociation of acid and hydrolysis of base and dissociation of
water in non equilibrated conditions.
3. The equation assumptions will fail when deals with:
 Strong acids or bases (need pK near from7).
 Dilute or very concentrated solutions (< 1 mM or > 1 M).
 Skewed acid/base ratios (> 100/1).
4. The equation does not take into effect the dilution factor of the acid and conjugate base in
water. If the proportion of acid to base is 1, then the pH of the solution will be different if the
amount of water changes from 1mL to 1L.

E. Use Henderson- hasselblach in estimating blood pH
A modified version of the Henderson–Hasselbalch equation can be used to relate the pH of blood
to constituents of the bicarbonate buffering system:
This is useful in arterial blood gas, but these usually state pCO2, that is, the partial pressure of carbon
dioxide, rather than H2CO3. However, these are related by the equation:
kH CO2 is approximately= 0.03 mmol/mmHg

Taken together, the following equation can be used to relate the pH of blood to the concentration of
bicarbonate and the partial pressure of carbon dioxide:

Example #1:
pKa for phenophthalein is 9.3 at room temp.
a) Calculate ratio of its anionic form to acid form at pH 8.2 and at pH
10.
b) Using these values, explain the colour change within this pH range.
Answer to part (a):

1) At pH = 8.2:
8.2 = 9.3 + log (base form / acid form) log (base form / acid form) = -1.1
ratio of base form to acid form = 0.0794 to 1 (call it 8 to 100)
2) At pH = 10.:
10 = 9.3 + log (base form / acid form) log (base form / acid form) = 0.7
ratio of base form to acid form = 5.01 to 1 (call it 500 to 100)
Answer to part (b):

1) Key fact:
it's the anionic (or base) form that is colored pink. The acid form is colorless. 2) At pH =
8.3:
the pink form is in the minority at this pH. For every 100 acid (colorless) forms, there are
only 8 base (pink) forms. 3) At pH = 10.:
the colorless form is in the minority. For every 100 acid (colorless) forms present, there are
now 500 base (pink) forms present. 4) This means:
From pH = 8.3 to pH = 10., there has been a 6250% increase in pink forms (from 8:100 to
500:100). While there might be a slight pink color (viewed against a white background) at
pH 8.3, the population of pink forms has greatly increased by pH = 10., to the point where
the pink color is now easily seen, even without the aid of a white background.
Example #2:
Aspirin has a pKa of 3.4. What is the ratio of A¯ to HA in:
(a) the blood (pH = 7.4)
(b) the stomach (pH = 1.4)
General comment about the solutions: You have to find the ratio between A¯ and HA so
the concentrations are not needed
Answer to part (a):

pH = pKa + log [A¯] / [HA]
7.4 = 3.4 + log [A¯]/ [HA]
7.4 - 3.4 = 4 = log [A¯]/ [HA]
104 = 10000 = [A¯]/ [HA]
Answer to part (b):

1.4 = 3.4 + log [A¯]/ [HA]
1.4 - 3.4 = - 2.0 = log [A¯]/ [HA]
10-2 = 0.01 = [A¯]/ [HA]

Example #3:
Calculate the pH of the solution that results from the addition of
0.040 moles of HNO3 to a buffer made by combining 0.500 L of 0.380 M
HC3H5O2 ( Ka = 1.30 x 10¯5) and 0.500 L of 0.380 M NaC3H5O2
Assume addition of the nitric acid has no effect on volume.

Answer:
1a) The nitric acid will reduce the amount of NaC3H5O2 (base):
(0.380 mol/L) (0.500 L) = 0.190 mol of NaC3H5O2
0.190 mol - 0.040 mol = 0.150 mol NaC3H5O2 remaining
1b) The reaction in 1a will increase the amount of HC3H5O2 (acid):
the increase will be by the same amount of the decrease
0.190 mol + 0.040 mol = 0.230 mol of HC3H5O2
2) Calculate the new pH:
pH = pKa + log [base] / [acid]
pH = 4.886 + log (0.150 / 0.230)
pH = 4.700
Note: the ratio of the moles is the same as the ratio of the molarities. You can
demonstrate that to yourself by calculating the new molarities in 0.500 L, them
adding the two solutions together, thereby cutting the molarities in half. Then, insert
them into the Henderson-Hasselbalch Equation. You will get 4.700 for your answer.

Example #4:
You need to produce a buffer solution that has a pH of 5.27. You
already have a solution that contains 10.0 mmol (millimoles) of acetic
acid. How many millimoles of sodium acetate will you need to add to
this solution? The pKa of acetic acid is 4.75.
Answer:
1) Substitute into the Henderson-Hasselbalch Equation and solve:
5.27 = 4.75 + log (x/10)
log (x/10) = 0.52
x/10 = 3.3113
x = 33.1 millimoles of sodium acetate

Example #5:
What is the pH when 25 mL of 0.2 M of CH3COOH has been titrated
with 35 mL of 0.1 M NaOH?
Answer:
1) Determine moles of acetic acid and NaOH before mixing:
CH3COOH: (0.2mol/L) (0.025 L) = 0.005 mol
NaOH: (0.1 mol/L) (0.035 L) = 0.0035 mol
2) Determine moles of acetic acid and sodium acetate after mixing:
CH3COOH: 0.005mol - 0.0035mol = 0.00150 mol
CH3COONa: 0.0035 mol<.blockquote> The above comes from consideration of this reaction:
CH3COOH + NaOH <===> CH3COONa + H2O
3) Use the Henderson-Hasselbalch Equation:
pH = 4.752 + log [(0.0035 mol/0.06L) / (0.0015 mol/0.06L)]
pH = 4.752 + log 2.333
pH = 4.752 + 0.368 = 5.120

Example #6:
If NaOH is added to 500mL of 2M acetic acid (pKa of acetic acid 4.8)
what volume of 2M NaOH should be added to the solution to make pH
equals 4.8?
Answer
We have 500 mL of 2M CH3COOH and as (M = mol/L) so actual moles of acetic equals 2M x 0.5L= 1M of acetic acid
We need how much? Of 2M NaOH to make pH=pKa
the equation of the reaction is CH3COOH+ NaOH ---------- CH3COO- + Na + H2O
We can neglect Na and water so the equation become
CH3COOH+ NaOH ---------- CH3COO- this means when you add one mole of NaOH you will lose one mole of CH3COOH
and gain CH3COO- (ratio become 1:1).
Use Henderson-Hasselbalch equation -- pH=pKa +log base/acid (CH3COO- / CH3COOH)
According to the eqaution If we have 1 mole of acetic added to 0.5 mole of NaoH we will lose 0.5 mole of acetic and gain 0.5
mole from acetate
We have 2M/L of NaoH and we need 0.5 mole only so we need how much?
2M----- L
0.5M---?
0.5/2 = 0.25 L = 250 mL so we need 250 mL of 2M NaOH
For more examples on Henderson – Hasselblach please visit
(https://www.varsitytutors.com/mcat_physical-help/henderson-hasselbalch-equation)
QUIZ on pH and Hendersen-hasselbalch equation
1. Which one of the following is equal to the pKa of a weak acid?

a) Its relative molecular mass
b) The pKb of its conjugate base
c) The pH of a solution containing equal amounts of the acid and its conjugate base
d) The equilibrium concentration of its conjugate base
2. Which one is a strong acid?
a) Hydrochloric acid
b) Phosphoric acid
c) Acetic acid
d) Hard surfaces
3. Which of the following structures represents the conjugate acid of HPO42- ?

a) H2PO4-
b) H3PO4
c) H4PO4+
d) PO43-
4. A solution of HCl with a concentration of 4 x10-4 mol L-1 has a pH of which of the following?
a) 2.67
b) 3.21
[H] = 0.0004 M , pH = -log 0.0004 = 3.39
c) 3.40
d) 4.31
5. An aqueous solution containing a concentration of 2.5 10-8 OH- ions will have a pH of which of the
following?
a) 6.40 [OH] = 0.000000025 M , pOH = -log 0.000000025= 7.6
b) 6.42 pH =7.6-14=6.4
c) 7.40
d) 7.60
6. Acid become colorless when added with----------------
a) Screened methyl orange indicators
b) Phenolphthalein indicator
c) Litmus indicator
d) Universal indicator
7. Which one is less corrosive acid?
a) H2CO3
b) H2SO4
c) HNO3
d) HCl
8. What are products of given reaction? CO2 + H2O →
a) CO
b) H3O
c) H2CO3
d) CO2 + OH-
9. In presence of phenolphthalein, alkali shows------------ color
a) Pink
b) Green
c) Yellow
d) Blue
10. Blood has an approximate pH of--------------------
a) 7-8
b) 9-10
c) 2-3
d) 13-14

11. What is the pH value of sodium chloride?
a) 7
b) Less than 7
c) More than 7
d) Zero
12. More accurate and quick measure of pH value is done by---------
a) Indicator
b) pH scale
c) pH meter
d) Universal indicator
13. PH is an abbreviation of--------------------------
a) Power of hydrogen
b) Power of hydroxide
c) Power of hydronium
d) Power of hydrates
14. The molecular weight of water equals--------------------
a) 10 g/mol
b) 18 g/mol
c) 55 g/mol
d) 60 g/mol
15. What is the concentration of (OH) in a solution with (H) ions concentration equals 1.3x10-4 M
a) 7.7x 10-11
b) 7.7x 10-10
c) 1.4x 10-11
d) 1.4x 10-10

16. According to Henderson-Hasselbalch equation a solution become a buffer when its pH equals its Pka, this
condition will be achieved when ------------------------
a) The concentration of proton donor equals the concentration of proton acceptor.
b) The concentration of proton donor becomes zero.
c) The concentration of proton acceptor becomes zero.
d) The concentration of proton donor equals –log 1/10 the concentration of proton acceptor.
17. The solution becomes a buffer if its pH
a) At the same level of its Ka value
b) Equals its Pka value
c) Equals 7
d) Equals 14
18. Which one is correct regarding the Henderson-Hasselbalch equation?
a) pH =pKa +log [A]/[HA]
b) pH = pKa –log [A]/[HA]
c) pH= pKa + log [HA]/[A]
d) pH = pKa = log [A]/[HA]
19. A solution X with pH= 2.75 and pKa =4.75 what is the ratio of A to HA for this solution?
a) 1 HA to 100 A
b) 100 HA to 1 A
c) 0.01 HA to 1 A
d) 100 HA to 0.01 A
20. If NaOH is added to 500mL of 2M acetic acid (pKa of acetic acid 4.8) what volume of 2M NaOH should be
added to the solution to make pH equals 4.8?
a) 250 mL
b) 500 mL
c) 1 L
d) 2 L
21. The normal pH of the blood is approximately is-------------------------
a) 7.2
b) 7.4
c) 7.6
d) 7.8
22. The pH-------------------

a) Increases with acidity
b) Measured on a scale from 0-10
c) Is the measure of hydrogen ion concnetration
d) Refelcts the O2 contents of the body
23. What your expectation for venous blood pH?

a) More acidic than arterial blood
b) More alkaline than arterial blood
c) The same like arterial blood
d) Neutral

Lecture 3
1. Buffers composition
2. Mechanism of buffer action
3. Buffering capacity
4. Important biological buffers
5. Acid base disturbances

Definition
BUFFER
Buffers are the solutions, which resist changes in pH, when small amount of acid
or alkali is added to them.
The best buffer is the one which gives the smallest change in pH.
Buffers act like shock absorber against the sudden changes of pH.
Composition
Weak alkali and Weak acid and its
its salt with a salt with a
strong acid strong base

Buffers
Ideal buffer is a solution at
which pH equals its pKa

How buffer works?!/mechanism of buffer action
(a) H2CO3/ NaHCO3

Carbonic acid/bicarbonate buffer
Weak acid
Salt with strong base
When acid added:
HCL + NaHCO3 NaCl + H2CO3
Weak acid
When alkali added:
NaOH + H2CO3 NaHCO3+ H2O

07-10-2018 AASER ABDELAZIM BMS-2-221 Water 45
(b) Acetic acid /sodium acetate buffer system
1)CH3COONa (aq) CH3COO- (aq) + Na+ (aq)

2) CH3COOH (acetic acid)
This buffer has two arms
CH3COOH CH3COONa
When an alkali like NaOH added When an acid like HCl added
NaOH Na+ OH- HCl H+ Cl-
CH3COOH ------- CH3COO- + H+ CH3COONa ------- CH3COO- + Na+
CH3COONa H2 O CH3COOH NaCl

BUFFERING CAPACITY
It is the ability of the buffer system to maintain pH constant when an acid or alkali is added
Capacity of acetic acid buffer when (a) NaOH or (b) HCl are added
Buffer can resist changes in pH for a limit after that pH will fall or rise according
to acid or alkaline added.

IMPORTANT BIOLOGICAL BUFFERS
Buffer system of body fluids
H2CO3
HHb
HHbO2
Proteins
Organic acids
Sources of acids production in the body Lactic acid
Pyruvic acid
Citric acid
Salicylic acid
Sulforic acid
Phosphoric acid

Bicarbonate/carbonic acid buffer system
Protein buffer system

Hemoglobin buffer system
Phosphate buffer system

Site of buffer systems
Buffer systems
ICF ECF
Phosphate Protein buffer Bicarbonate Protein buffer

buffer system system buffer system system
Hemoglobin Amino acids Plasma proteins

buffer system buffer system buffer system

(1) Protein buffer system

• In proteins, ionizable R groups (COOH groups of aspartate and glutamate, NH2 groups of lysine,
arginine and histidine) and N-terminale -NH2 groups of some amino acids are responsible for
buffering.
• Proteins, especially albumin, account for the %95 of the non-bicarbonate buffer value of the
plasma. Buffering effect of proteins is low in plasma
• Proteins are much more effective buffers in intracellular medium.
• The most important buffer groups of proteins in the physiological pH range are the imidazole
groups of histidine which has a pKa value of 6.5
• Each albumin molecule contains 16 histidines.

(2) Hemoglobin buffer system
• Hemoglobin (Hb) is a protein which carries O2 to tissues and CO2 from tissues to lungs and is
an effective buffer.
• The most important buffer groups of Hb are histidines. Each globin chain contains 9 histidine.
• %95 of CO2which is released from tissues to plasma is diffused into erythrocytes.
• In erythrocytes, carbonic anhydrase constitutes H2CO3 from CO2 and H2O and then HCO3-
and H+ are released by the ionization of H2CO3.
Carbonic anhydrase
CO2 + H2O ----------------------- H2CO3 + HCO3- + H+
• Released protons take part in the formation of salt bridges between globin chains of Hb, and
lead the change in the conformation of Hb molecule in tissue capillaries.
• The binding of proton and CO2 is conversely related to binding of oxygen.
• In tissue capillaries proton and CO2 binding decreases the oxygen binding capacity of Hb so
that oxygen is released by Hb.
• This effect of pH and CO2 concentration on the binding and release of oxygen by Hb is called
the Bohr Effect.
• Because of the accumulation of HCO3- formed by ionization of H2CO3 within erythrocytes, there
is a concentration gradient for HCO3- between plasma and erythrocytes.

• In that case, HCO3- ions rapidly move from erythrocytes to plasma, and Cl- ions move from
plasma to erythrocytes to provide electrochemical balance.
• This shift of Cl- is referred to as the chloride shift.
• All those phenomenons occur in capillaries of peripheral erythrocytes conversely change in
capillaries of lungs.
• When Hb reaches the lungs, the high oxygen concentration promotes binding of oxygen and
release of protons from broken salt bridges. Protons associate with HCO3- and H2CO3 forms.
H2O and CO2 form by the reaction catalyzed by carbonic anhydrase
Carbonic anhydrase
H2CO3 --------------------------CO2 + H2O
• This phenomenon is referred as Haldane Effect. H2O and CO2 are excreted to atmosphere
by respiration.

(2) Hemoglobin buffer system
Tissue
Lungs
HCO3- HCO3- HCO3-

Venous circulation
HHb HHb HHb
O2
O2 H+
H2CO3
H+ H2CO3
H2 O
HbO2 HbO2 HbO2
CO2 Arterial circulation H2 O
CO2
CO2 To expiration CO2

07-10-2018 AASER ABDELAZIM BMS-2-221 From metabolism54
(3) Phosphate buffer system
• Phosphate buffer system is most effective in intracellular medium, especially in kidneys.
• Phosphoric acid has 3 ionization steps:
• H3PO4 H2PO4- + H+ pK1= 1.9
• H2PO4- HPO42- + H + pK2= 6.8
• HPO42- PO43- + H+ pK3= 12.4

• Among the 3 ionization steps, H2PO4-/ HPO42- is a good buffer because of its pKa value (6,8)
which is close to physiological pH (7,4).
• HPO42- / H2PO4- = 4 at the pH (7,4).
• Phosphate buffer system is not effective in plasma, because phosphate ion concentrations are
low. However it is important in the excretion of acids in the urine.
• H+ secreted into the tubular lumen by the Na+–K+ exchanger react with HPO42- to form H2PO4-.
• Some organic phosphates (2,3 biphosphoglycerate (2,3 BPG) in erythrocytes) has also
buffering capacity.

HCO3- 20 H+/HCO3 Kidneys
=
H2CO3 1
Blood pH CO2
Lungs
7.4

disturbances in acid base balance
Acid base balance

disorders
Acidosis Alkalosis
Respiratory Metabolic Respiratory Metabolic

Acidosis
Respiratory acidosis Metabolic acidosis
Increase in acid production or decrease in

defects in lungs to eliminate CO2 resulting
acid excretion
in formation of more H2CO3
Increase acid production Decrease the excretion of

Pneumonia Severe muscular exercise acids in renal failure
produce more lactate Increase the loss of bases as
Emphysema Increase ketone bodies in severe diarrhea
Asphyxia Increase protein diets
:contains acids as phosphoric,
Bronchial asthma sulfuric and uric acids
morphine poisoning
Kidneys compensate: absorbs more

HCO3 to achieve ratio of HCO3/H2CO3 = Lungs compensate: do hyperventilation
20/1
07-10-2018 AASER ABDELAZIM
and eliminates more CO2
BMS-2-221 58
Alkalosis
Respiratory alkalosis Metabolic alkalosis
increase of blood HCO3 and loss of acids

Defect in lungs cause high elimination of
CO2 and so increase in HCO3/H2CO3 ratio
 Prolonged vomiting as in pyloric stenosis

Hyperventilation resulted from  Prolonged suction in high surgical operations
Fever  High dose of alkalis during treatment of acidosis
 Salicylates poisoning  Hypokalemia
Encephalitis  Excess mineralocorticoids
 Climbing of high altitudes
 Hysterical
Kidneys compensate: retains H+ ions
NOTE
Kidneys compensate: Prevent the If HCO3- caused the acidosis or the alkalosis, it is METABOLIC
reabsorption of HCO3 / retains H+ ions If CO2 caused the acidosis or alkalosis, it is RESPIRATORY
07-10-2018 AASER ABDELAZIM HCO3- caused the imbalanced, it is COMBINED 59
BMS-2-221
If CO2 and
pCO2 (mm Hg) as a marker for acid base balance disorders
Condition pH pCO2 (mm Hg) HCO3- (mEq/L)
Metabolic acidosis <7.35 <35 <22
Respiratory acidosis <7.35 >45 <22
Metabolic alkalosis >7.45 >45 >26
Respiratory alkalosis >7.45 <35 >26
Note: plasma bicarbonate concentration of less than 12 mmol/L is unusual in pure respiratory alkalosis alone and should
prompt the consideration of a metabolic acidosis.
Note: you should know that pCO2 is indicated AASER

07-10-2018 for respiratory
ABDELAZIMconditions while [HCO3] is indicated for metabolic conditions. 61
BMS-2-221
QUIZ on buffers and acid base balance
1. A buffer solution comprises which of the following?.

a) A weak acid in solution
b) A strong acid in solution
c) A weak base in solution
d) A weak acid and its conjugate base in solution
2. A buffer solution contains ethanoic acid and its conjugate base; the pKa of ethanoic acid is 4.74. At what pH
does the solution buffer?
a) 3.0
b) 4.0
c) 5.0
d) 6.0
3. The buffering capacity of protein is due to presence of ---------------------
a) Histamine
b) Histidine
c) Ethanolamine
d) Lysine
4. Bicarbonate/carbonic acid buffer system is the main buffer system in-----------------------
a) Renal tubules
b) Blood cells
c) Extracellular fluids
d) Urine
5. A student is nervous for a big exam and is breathing rapidly, what do you expect out of the followings
a) Metabolic Acidosis
b) Metabolic Alkalosis
c) Respiratory Acidosis
07-10-2018
d) Respiratory Alkalosis AASER ABDELAZIM BMS-2-221 62
6. A 45-year-old female with renal failure, missed her dialysis and was feeling sick, what could be the reason ?
d) Respiratory Alkalosis
7. An 80-year-old man had a bad cold. After two weeks he said, “It went in to my chest, I am feeling tightness in my
chest, I am coughing, suffocated and unable to breathe!” What could be the possible reason?
8. The pH of the body fluids is stabilized by buffer systems. Which of the following compounds is the most effective
buffer system at physiological pH ?
a) Bicarbonate buffer
b) Phosphate buffer
c) Hemoglobin buffer
d) Amino acid buffer
9. A young woman is found comatose, having taken an unknown number of sleeping pills an unknown time before.
An arterial blood sample yields the following values: pH=6.90, HCO3- =13meq/liter, PaCO2 =68 mmHg. This patient’s
acid-base status is most accurately described as
a) Uncompensated metabolic acidosis
b) Uncompensated respiratory acidosis
c) Simultaneous respiratory and metabolic acidosis
d) Respiratory acidosis with partial renal compensation
10. Which of the following laboratory results below indicates compensated metabolic alkalosis?
a) Low pCO2, normal bicarbonate and, high pH
b) Low pCO2, low bicarbonate, low pH
c) High pCO2, normal bicarbonate and, low pH
07-10-2018
d) High pCO2,high bicarbonate and High AASER
pH ABDELAZIM BMS-2-221 63
11. The greatest buffering capacity at physiological pH would be provided by a protein rich in which of the following
amino acids?
a) Lysine
b) Histidine
c) Aspartic acid
d) Leucine
12. Which of the following is most appropriate for a female suffering from Insulin dependent diabetes mellitus with a
pH of 7.2, HCO3=17 mmol/L and pCO2=20 mm HG
13. Which of these 3 primary systems in H+ regulation happens immediately?
a) Buffering system response
b) Renal response
c) Respiratory response
d) Hormonal response
14. What buffer can do?
a) Minimizes the pH
b) Prevents pH changes
c) Resists the changes of pH
d) Increases pH
15. Chemicals that function to minimize changes in the pH of body fluids are called:
a) Buffers
b) Inhibitors
c) Accelerators
d) Activators
16. Which of the following is Not a buffer system of the body?
a) Bicarbonate buffer system
b) Chloride buffer system
c) Phosphate buffer system
d) Protein buffer system
17. Which of the following can play a role in buffering the pH of urine?
a) Phosphate buffer system
b) Ammnoia
c) Bicrbonate buffer system
d) All of these
18. As a result of hyperventilation-----------------------------

a) pH decreases
b) pCO2 decreases
c) Hydrogen excretion from kidneys increases
d) More HCO3 is added to plasma
19. Once alkalosis has occurred, which of the following would you expect to happen?
a) Respiratory rate will be increased.
b) Plasma pH fall down
c) Hydrogen ions will be retained by kidneys.
d) Kidneys reabsorb more bicarbonates.
20. When normal buffer mechanisms are overwhelmed by excessive numbers of hydrogen ions, which of the following
will result?
a) Acidosis
b) Alkalosis
c) Acidosis and alkalosis
d) Nothing happens
21. A falling blood pH and a rising concentration of carbon dioxide due to emphysema, indicate--------------
22. Respiratory alkalosis can occur as a result of--------------------

a) Asphyxia
b) Pneumonia
c) Emphysema
d) Hyperventillation
23. Prolonged vomiting of stomach contents will result in--------------

24. During exercise, ventilation initially increases due to----------------

a) Increase pCO2
b) Decrease pO2
c) Decrease pH
d) Increase HCO3
25. An increase of blood pCO2 is followed by----------------
a) Low pH and high [H+]
b) Low pH and low [H+]
c) High pH and low [H+]
d) High pH and high [H+]

Theme
6
Molecules of life

Lecture 1
1. Structure and functions of carbohydrates
2. Classification of carbohydrates
3. Structure and functions of lipids
4. Classification of lipids

C Carbon
Atomic Number: 6
H Hydrogen
Atomic Number: 1
Atomic mass: 12.01 Atomic mass: 1.00797
MOLECULES OF LIFE
O Oxygen
Atomic Number: 8
N Nitrogen
Atomic Number: 7
Atomic mass: 16 Atomic mass: 14.01

Molecules of life
Monomers
Polymers
Macromolecules
Notes: Most organic molecules are arranged like chains

Each link is a monomer
A chain is a polymer
A large molecule made of a long
07-10-2018
chain or chains
AASER ABDELAZIM
is a macro molecule
BMS-2-221 4
Carbohydrates
Structure and function

(A) General view on CARBOHYDRATES
CARBOHYDRATES H2 O
C
Cn(H2O)n
Ketones Aldehydes
Ketone Brain
Aldehyde
Sweet
RBCs
Soluble
main source of
energy in the body
Glucose
sucrose

(B) FUNCTIONS OF CARBOHYDRATES
(1) Source of energy
Each gm gives 4 Kcal of energy
CARBOHYDRATES (2) Structure bases of major chemicals
DNA and RNA

Nucleosides and nucleotides
Carbon skeleton of amino acids
(3) Principle part of cell membrane structure
(4) Intracellular messenger

(C) CLASSIFICATION OF CARBOHYDRATES
Carbohydrates
Monosaccharide Disaccharides Oligosaccharides Polysaccharides
Carbohydrates Starch
Aldoses (glucose) Sucrose
contains 2-10 units Glycogen
Ketoses (fructose) Maltose
of monosaccharides. Cellulose
Lactose
Can be Dextrin
disaccharides or
trisacchrides etc…,

(a) MONOSACCHARIDES
Monosaccharides consists of single polyhydroxy aldehyde or ketone unit which cannot be

broken down to simpler substances on acid hydrolysis.
They are also called simple sugars.
Monosaccharides are further divided into:
i. Aldoses, i.e. Aldo sugars (all are from glyceraldehyde)
ii. Ketoses, i.e. Keto sugars (all are from dihydroxyacetone)
Glyceraldehyde Dihydroxyacetone
(1) Aldoses
Monosaccharide containing aldehyde group as the functional group are called Aldoses.
They are classified according to the number of carbon atoms present.
 Monosaccharide containing three to seven carbon atoms are called trioses, tetroses,
pentoses, hexoses and heptoses respectively.
(2) Ketoses
Monosaccharide containing ketone group as the functional group are called ketoses.
Examples: Xylulose, Ribulose, Fructose, etc.
ALDO AND KETO SUGARS
Carbon# Sugar Aldoses Ketoses

3C Trioses glyceraldehyde Dihydroxy acetone
(aldotriose) (ketotriose)
4C Tetroses Erythrose (aldotetrose) Erythrulose

5C Pentoses Ribose (aldopentose) Xylulose (ketopentose)
Deoxyribose
(aldopentose)
Xylose (aldopentose)
xylulose (aldopentose)
6C Hexoses Glucose Fructose (ketohexose)
Galactose,
Mannose (aldohexose)
7C Heptoses pseudoheptose Pseudoheptulose

Aldoses Ketoses
(A) TETROSES
Erythrose Erythrulose
(B) PENTOSES
Ribose
Ribulose
Aldoses Ketoses
(C) HEXOSES
Erythrose
Glucose Fructose
(D) HEPTOSES
Heptose Heptulose
How we can sketch a monosaccharide?
1 6
1
2 5
2
3
3 4 1
4
4
5 3 2
5
6
6 Haworth projection formula
Open chain formula (a) Pyran formula
Fischer's formula 6
5C
6
4 6 5 4C 1
1 1 C
5
3 2 4 3 2 C 2C
3
Boat formula Chair formula

Haworth projection formula
07-10-2018 AASER ABDELAZIM BMS-2-221 (b) Furan formula 13
(b) DISACCHARIDES
They are two monosaccharides joined

together by glycosidic linkage
Disaccharides Reducing disaccharides (lactose and

maltose), Non-reducing (sucrose).
Their properties are the same like

monosaccharides
Glycosidic linkage

MALTOSE
Maltose

LACTOSE
Lactose

SUCROSE
Sucrose

(c) POLYSACCHARIDES
Long chains of monosaccharides linked by

glycosidic linkage.
Usually they are non-reducing sugars due to

long chain of non-reducing free groups. only
contain one free carbonyl group.
Polysaccharides They named by add (an) to end of sugar e.g.

Glycans polymers of glucose as (starch,
glycogen), mannan (polymer s of mannose).
Their functions are – storage of energy and a

structure components e.g. cellulose
They classified into

Homopolysacchrides: consist of one type of
sugar
Heteropolysacchrides: consist of two or
more types of sugars.
(1)Homopolysaccharides
STARCH
(a) Amylose part
(b) Amylopectin part

GLYCOGEN
Straight linear chain
Branching point
What are the differences between starch and glycogen (activity)?

CELLULOSE
It is a polymer of B-glucose linked by (1,4) glycosidic linkage
DEXTRIN
Partial hydrolytic products of starch formed from amylose part or

amylopectin part.
So they may be linear (amylose) or branched (amylopectin).
They also carry free carbonyl group so can reduce alklaine cupper
sulphate.

(2)Heteropolysaccharides
Hyaluronic acid Heparin
07-10-2018 Chondroitin sulphate

AASER ABDELAZIM BMS-2-221 22
Lipids
Structure and function

(A) Genral view on LIPIDS
Wide varieties of naturally occurring compounds consisting fatty acids
Not soluble in water- soluble in fat solvents (benzene-chloroform).
LIPIDS Many compounds are associated with lipids (vitamins A,D,E andK)
and carotenes, ketone bodies, and cholesterol
Lipids in diet may be visible (butter-oils-ghee) or invisible (egg-fish-

meat-nuts).
Lipids functions:
A main source of energy (each gram gives 9 Kcal).

Easily stored inside the body so it is a fast source for energy.
Enter in the structure of cell membrane.
Transport form of energetic compounds.
Fixative for internal organs (kidneys-intestines-heart).
Protective role and as insulator.
Play an important role in the absorption of fat soluble vitamins.

(B) LIPIDS MEMBERS
Member Function
Fatty acids The building blocks for other lipids
Energy source
Triglycerides The main store for fatty acids
Phospholipids Cell membrane structure
Main source for arachidonic acid .
Sphingolipids Membrane structure
Glycolipids structure
Ketone bodies As a source of energy mainly in brain

(C) LIPIDS CLASSIFICATION
Lipids
Simple lipids Compound lipids Derived lipids
Esters of fatty acids with alcohol.

If the alcohol is glycerol (triglycerides/neutral fats)
If they are liquid at RT it called (oils).
Fatty acids
If the alcohol is more higher molecular weight than glycerol it will be (waxes)
Steroids
Fat soluble vitamins
Carotenes
Phospholipids Ketone bodies
Glycolipids Terpenes
Lipoproteins
Sulpholipids
Note: The three fatty acid (R) may be different (mixed

triglyceride)or the same(simple triglycerides)
FATTY ACIDS
Long chain monocarboxylic aliphatic compounds.
May be odd /even fatty acids (according to # of carbons).
They may be saturated (no double bond) or unsaturated (one (monounsaturated) or
more (polyunsaturated) double bonds).
Short chain fatty acids are water soluble-long chain one fat soluble.
Last methyl group (ώ)(omega carbon)

Carboxyl group
Fatty acid

Essential fatty acids (polyunsaturated)
Important fatty acids in mammalian tissues

QUIZ on Carbohydrates and lipids chemistry
1. Which of the following is a non-reducing disaccharide?
a) Maltose
b) Sucrose
c) Galactose
d) Trehalose
2. Which about glucose is true?
a) It is a disaccride.
b) It is a monosacchride
c) It is a polysacchride
d) It is an oligosachride
3. Sucrose is composed of-----------------
a) Glucose and Fructose
b) Glucose and Maltose
c) Mannose and Trehalose
d) Galactose and Mannose
4. Which one is NOT a homoplysacchride?
a) Starch
b) Glycogen
c) Cellulose
d) Heparin
5. Which one is fructosan in nature?
a) Strach
b) Inulin
c) Cellulose
d) Glycogen
6. Choose the sugar which abundant present in honey?
a) Fructose
b) Mannose
c) Galactose
d) Lactose
7. Which one is an aldo-pentose?
a) Mannose
b) Ribose
c) Ribulose
d) Erythrose
8. Choose the keto-tetrose?
a) Ribulose
b) Fructose
c) Erythrose
d) Erythrulose
9. Which one is NOT a homoplysacchride?
a) Starch
b) Glycogen
c) Cellulose
d) Heparin
10. Which one is a keto hexaose?
a) Fructose
b) Glucose
c) Mannose
d) Galactose
11. Choose the polysaccride formed by α1-4 glycosidic linkage?
a) Amylose
b) Amylopectin
c) Inulin
d) Cellulose
12. Choose the correct formula of glucose?
a) C6H12O12
b) C6H12O6
c) C6H6O12
d) C12H12O6
13. Which one id the storage form of glucose in plant?
a) Cellulose
b) Glycogen
c) starch
d) Agar
14. Which one is have not a nutritional value?
a) Starch
b) Glycogen
c) Cellulose
d) Dextrin
15. All the following about polysaccharides is true except?
a) They are formed from a repeated units of sugars.
b) They can be used as atorage for energy.
c) Consisted of a collections of amino acids.
d) Can be classified into homopolysacchrides and heteropolysacchrides.
16. Choose the storage form of lipids?
a) Triglycerides
b) Phospholipids
c) Cholesterol
d) Sulfolipids
17. Which one is monounsaturated fatty acid?
a) Oleic
b) Linoleic
c) Linolinic
d) Stearic
18. Choose the correct statement about fatty acid?
a) All fatty acids can be synthesized inside the body.
b) Fatty acid stored in the form of cholesterol inside cells.
c) The monounsaturated fatty acids are nonessential.
d) body can oxidizes only the saturated fatty acids.
19. Which one of the following forms of lipids mainly composed in the structure of cell membrane?
a) Triglycerides
b) Phospholipids
c) Ketone bodies
d) Cholesterol
20. Compound lipid is formed from-------
a) Triglycerides +glycerol
b) Triglycerides + carboydrates
c) Sphingolipids + glycerol
d) All are incorrect
21. Cholesterol is consisted in all the following except?
a) Sex hormones
b) Bile acids
c) Vitamin D
d) Cardiolipin
22. Glycerol is important in the structure of the following except?
a) Triglycerides
b) Phospholipids
c) Waxes
d) Glycolipids
23. Arachidonic acid is polyunsaturated fatty acid contains --------------double bonds?
a) 4
b) 3
c) 2
d) 1
24. Glycerol is consisted in the structure of ------------------
a) Lecithins
b) Cardiolipin
c) Cerbrosides
d) Gangliosides
25. Which one of the following macromolecules is structurally diverse in the living world?
a) Lipids
b) Crabohydrates
c) Proteins
d) Ncleic acids
26. Generally the unsaturated fats are --------in room temperature.
a) Liquid
b) Solid
c) Semi liquid
d) Semisolid
27. Fats can be transported in the blood in which form?
a) Lipoproteins
b) Glycolipids
c) Triglycerides
d) Shingolipids
28. If the fatty acid is esterified with an alcohol of high molecular weight instead of glycerol, the resulting
compound is---------------------
a) Lipositol
b) Waxes
c) Triglycerides
d) Cephalin
29. A lipid is formed by the condensation of -----------------
a) Fatty acid and alcohol
b) Fatty acid and amino acids
c) Fatty acid and carbohydrates
d) Fatty acids and amines
30. Which one is a derived lipid?
a) Fats
b) Oils
c) Steroids
d) Waxes
31. Compounds formed from lipids along with carbohydrates is-----------
a) Neutral lipids
b) Waxes
c) Glycolipids
d) Phospholipids
32. Liquids form triglycerides at room temperature are called --------------
a) Fats
b) Oils
c) Waxes
d) Glycrides
33. Natural lipids are soluble in -------------------------
a) Water
b) Alcohols
c) Ether
d) Oils
34. Which one produces the highest number of ATPs?

a) Lipids
b) Carbohydrates
c) Proteins
d) Nucleic acids
35. Which one is a compound lipid?
a) Triglycerides
b) Lipoproteins
c) Cerbrosides
d) Cardiolipin
Lecture 2
1. Chemistry of amino acids
2. Proteins chemistry
3. Nucleoproteins and nucleic acids

Proteins and
nucleoproteins
Chemistry

(A) Amino acids chemistry
What do amino acid mean?
Are chemical compounds contains amino groups and carboxyl

group on alpha carbon- with hydrocarbon chain (R).
 they are all optically active except (glycine).
Naturally occurring amino acids are L-α- amino acids.
Amino acids are classified chemically (chemical contents)-
Nutritionally (essential and non essential) or Metabolically
(glucogenic and ketogenic).

What are the amino acid classes?
Amino acids
Aliphatic Aromatic Heterocyclic
Phenylalanine Histidine
Tyrosine Proline
Hydroxy proline
Tryptophan
Neutral Acidic Basic

Glutamic acid Arginine
Aspartic acid Lysine
Hydrocarbon containing Sulfur containing Hydroxy containing
Alanine Cysteine Serine

Valine, leucine, isoleucine Cystine Threonine
Glycine
07-10-2018 Methionine
AASER ABDELAZIM BMS-2-221 39
Neutral hydrocarbon containing

Neutral sulfur containing amino acids
Neutral hydroxy containing amino acids

Aliphatic – acidic amino acids
Aliphatic – basic amino acids

Aromatic amino acids
Heterocyclic amino acids
Tryptophan

Non-protein amino acids

List the different functions of amino acids?
They are the building blocks of peptides and proteins.

They act as precursors for hormones (Thyroxine, adrenaline), vitamins (niacin,
Pantothenic acid), purines and pyrimidines and prophyrias.
They act as neurotransmitters in CNS.
They are the main carriers for nitrogen in the body (e.g. glutamine and alanine)
Detoxifying materials (benzoic acid, phenyl acetate, ammonia).
List the essential and nonessential amino acids?
Essential amino acids (Isoleucine, Leucine, Histidine, Tryptophan, Methionine, Valine,

Threonine, Phenylalanine, Arginine, and Lysine).
(I Left Home To Make Visit Through Philippine, Argentine and London)

Non-essential amino acids (the remain)
Semi-essential (histidine and Arginine).
(B) Peptides
What do peptides mean?
Two or more amino acids connected to each other by peptide bond
What do polypeptides means?
A peptide at which a number of amino acids (n) connected by a (n-1)

number of peptide bonds
Give examples of biologically active peptides?
Glutathione
Oxytocin
Vasopressin
Angiotensin

Locate the peptide bond in the following peptide?
•This is glutathione
•Contains (3) amino acids (tripeptide)
•Number of peptide bonds = (n-1) = 2 peptide bonds
The peptide bond

(C) Proteins
What do proteins mean?
More than 50 amino acids connected together by peptide bonds so they

have a high molecular weight if compared by peptides.
Classify proteins?
proteins
Simple proteins Conjugated proteins Derived proteins
Nucleoproteins
Fibrous Globular Primary derived Secondary derived
Lipoproteins
Glycoproteins Fibrin
Collagens Albumin Proteoglycans Proteoses
Elastins Globulins Metaproteins
Metaloproteins Coagulated Peptones
Keratins Glutelins  chromoproteins Peptides
proteins
Gliadins
Protamines
07-10-2018 Histones AASER ABDELAZIM BMS-2-221 48
Conjugated proteins

Proteins Vs peptides
Protein
If the number in chain > 50 amino acids
Peptide
If the number in chain < 50 amino acids

Differentiate between peptide and proteins?
Items Peptides Proteins
# of amino acids Less 50 More 50
# of chains One One or more
Molecular weight Low High
Primary structure Present Present
Secondary structure - Present
Tertiary structure - Present
Quaternary structure - Present
Synthesis Through metabolic pathways Through translation
Breakdown By enzymatic digestion Denaturation
Examples Bradikinins, glutathione, Insulin, enzymes, albumin

Oxytocin

(D) Nucleoproteins
What do nucleoproteins mean?
Nucleoprotein belongs to the category of conjugated proteins, the nucleic

acid part is the prosthetic group and the protein part consists of protamines
and histones, which are basic in nature.

Nucleic acid
DNA and RNAs
Nucleotide
Base + sugar (ribose/deoxyribose)+ (1-3) phosphate groups
Nucleoside
Base + sugar (ribose/deoxyribose).
Base
Purines: adenine (A) and guanine (G)

Pyrimidines (thymine (T) cytosine (C) uracil (U)

(E) Nucleic acids
Comparison between DNA and RNA

Items DNA RNA
•Sugar Deoxyribose Ribose
•Bases A, G, C & T A, G, C& U
(1) Structure •Unusual bases Not present Present

Double strands Single strand
•Strands (except in some viruses with (except in some viruses with
single strand DNA ssDNA ) double strands RNA dsRNA )
(2) Site of synthesis Nucleus Nucleus
(3) Site of action Nucleus and mitochondria Cytoplasm
Three main types (tRNA,
(4) Types only one type
mRNA& rRNA )
1. Gene expression
(5) Functions 2. Storage of genetic Synthesis of proteins
information.

QUIZZES on Proteins and nucleoproteins chemistry
1. The repeating units of proteins are ---------------

a) Amino acids
b) Peptides
c) Peptones
d) Amines
2. In a protein, the amino acid is joined to each others by ---------------------

a) Ionic bond
b) Glycosidic bond
c) Hydrogen bond
d) Peptide bond
3. A tripeptide is consisted of ---------------

a) Two amino acids and one peptide bond.
b) One amino acid and two peptide bonds.
c) Three amino acids and two peptide bonds
d) Three amino acids and one peptide bonds
4. Which one involved in the disulfide bridge in proteins?

a) Cysteine
b) Cystine
c) Methionine
d) Threonine
5. Which one is fibrous protein?

a) Hemoglobin
b) Myoglobin
c) Albumin
07-10-2018
d) Keratin . AASER ABDELAZIM BMS-2-221 55
6. Protamines and histones are ------------------
a) Acidic proteins
b) Basic proteins
c) Neutral proteins
d) Metalloproteins
7. Which is correct about amino acids?

a) They are neutral uncharged molecules.
b) They are classified according to their structure.
c) Total number of proteogenic amino acids is twenty four.
d) They are the main components of cell membrane?
8. Which one is the smallest amino acid?

a) Alanine
b) Glycine
c) Serine
d) Valine
9. Which one is neutral amino acid?

a) Glutamate
b) Aspartate
c) Arginine
d) Serine
10. Which one is a precursor for a vitamin (Niacin)?

a) Glutamate
b) Tryptophan
c) Phenylalanine
07-10-2018
d) Alanine AASER ABDELAZIM BMS-2-221 56
11. Choose the peptide from the following?
a) Alanine
b) Albumin
c) Glutathione
d) Glutamate
12. The highest contents of cystine is found in-------------------

a) Collagen
b) Keratin
c) Fibrin
d) Albumin
13. Choose the heterocyclic amino acid?

a) Phenylalanine
b) Tryptophan
c) Tyrosine
d) Serine
14. Peptones are--------------------

a) Nucleoproteins
b) Derived proteins
c) Metalloproteins
d) Chromoproteins
15. The peptide bond is formed between the amino group and ------------------- group of the second amino acid.
a) Carboxyl
b) Hydroxyl
c) Sulfide
07-10-2018
d) Methyl AASER ABDELAZIM BMS-2-221 57
16. What is the lowest number of amino acids in a protein?
a) 51
b) 50
c) 49
d) 48
17. Choose the essential amino acid?

a) Valine
b) Serine
c) Glycine
d) Alanine
18. Catalase is belonging to -----------------

a) Derived proteins
b) Metalloproteins
c) Nucleoproteins
d) Simple proteins
19. Which one is a nucleic acid?

a) DNA
b) Histidine
c) Guanine
d) NAD
20. Which one is a nucleoside base?

a) Arginine
b) Histidine
c) Guanine
07-10-2018
d) Alanine AASER ABDELAZIM BMS-2-221 58
Lecture 3
1. What is enzyme?
2. Enzymes and coenzymes.
3. Enzymes classes

ENZYMES
: En- zyme = in yeast
What do enzymes mean?
Enzymes are biological catalysts which catalyze the chemical reactions in

all living cells.
Most of them are proteins in nature.
Can do their activity when they extracted from their original source!
What are the differences between enzymes and inorganic catalyst?
Enzymes Inorganic catalysts

Thermo labile Thermos table
Organic inorganic
Protein Non-protein
Specific Non specific
High catalytic efficiency Low catalytic efficiency
Act at body temperature and pressure Need high temperature and pressure
Dr/ Aaser Abdelazim Lecturer of

10/7/2018 60
Biochemistry
What are the general properties of enzymes?
All enzymes are proteins (except ribosomes).

Enzymes accelerate and increase the rate of the chemical reaction through
Keep reaction equilibrium.
Needed by very small amount (nmol).
Not consumed through their chemical reaction.
 They are highly specific for their substrates. Through their specific active site.
They lower the activation energy consumed during the reactions.
Enzymes that possesses key reactions (committed steps) are regulatory in their
work.
They act at particular pH and temperature.
Substrate
Active site
Key-lock theory
Coenzyme

ENZYME (Protein)
Conjugated
Simple (Holoenzyme)
Only proteins
Protein part Non Protein part
e.g. Maltase, sucrase (Apoenzyme) (cofactor)
Active site
Coenzyme Coenzyme Prosthetic group

Enzyme
Prosthetic group
Allosteric site
Enzyme
Enzyme

10/7/2018 62
Biochemistry
Cofactor
Organic Inorganic
It called Coenzyme Mainly are minerals
like Cu, Fe, Mg, Mn
Tight bound to the enzyme loose bound to the enzyme

Like, NAD, NADP, Pyridoxal
It called prosthetic group Can be separated from

Like, FAD, Biotin enzyme after performing
the chemical reaction
Can not be separated
from enzyme after
performing the chemical
reaction it added to it
during its synthesis.
10/7/2018
Biochemistry
63
Coenzyme Prosthetic groups
Organic Inorganic
Loosely attached to protein part Firmly attached to protein part
Dialyzable(can leave enzyme) Non dialyzable(don’t leave

enzyme)
Derived from a vitamin as FAD Usually a metal as copper

10/7/2018 64
Biochemistry
Hydrogen carriers Non hydrogen carriers
NAD CoA: acid carrier

NADP TTP: CO2 and Ketol carrier
FAD Biotin: CO2 carrier
FMN Pyridoxal -P : Co2 carrier
Lipoic acid Folic acid: one carbon group carrier
CoQ Cobalamine: Methyl group carrier.
Enzyme-substrate complex
Substrate
Enzyme substrate complex Enzyme

Product
+
Enzyme
10/7/2018 65
Biochemistry
Class Members Action
(1) Oxidoreductases Oxidases-Dehydrogenases Add and remove hydrogen
-Hydroperoxidases
(2) Transferases Transaminases –Kinases – Transfer functional groups
Translocases
(3) Hydrolases Esterases- Peptidases- Hydrolysis of substrate by
Phosphatases- Deamidases- adding water
Lipases- Amidases
(4) Lyases Decarboxylases-Carboxylase- Splitting of substance with out
Carbonic anhydrase- Aldolase- hydrolysis (addition or removal
Enolase, etc. of groups)
(5) Isomerases Racemases- Epimerases- Catalysis the conversion
Isomerases- Mutases. between a compound isomers.
(6) Ligases glutamine synthetase and Legate two chemical groups or
succinic thiokinases compounds.

QUIZZES on enzymes
1. Enzymes are ---------------------

a) Amino acids
b) Proteins
c) Carbohydrates
d) Lipids
2. The term Apoenzyme is referring to ---------------------

a) Protein part of conjugate enzymes
b) Cofactor
c) Coenzyme
d) Prosthetic group
3. A which one regarding enzymes is true?

a) They lower the activation energy.
b) They require no activation energy.
c) They increase the activation energy.
d) They do not change the activation energy.
4. What do Zymogen means?

a) Enzyme cofactor
b) Enzyme activator
c) Enzyme modulator
d) Enzyme precursor
5. Enzymes usually act in----------------------

a) The same pH
b) Different pH
c) Different temperatures.
07-10-2018
d) The same cells AASER ABDELAZIM BMS-2-221 67
6. Which one considered an enzyme prosthetic group?
a) NAD
b) Biotin
c) NADP
d) Pyridoxal
7. Choose the inorganic cofactor for enzyme?
a) Cupper
b) Sodium
c) Iodine
d) Gold
8. All coenzymes are ---------------------
a) Metals
b) Cofactors
c) Prosthetic groups
d) Inhibitors
9. Some enzymes covalently bind a non-protein organic molecule to the active site. The organic molecule
concerned is required if the enzyme is to catalyse a reaction on a substrate. What is the term used for
such a molecule?
a) Cofactor
b) Coenzyme
c) Prosthetic group
d) Modulator
10. Fitting of a substrate in an enzyme active site is called-------------------
a) Condensation
b) Polymerization
c) Key and lock theory
d) Hydrolysis

11. Choose the correct regarding enzyme properties?
a) The enzyme is changed during chemical reaction.
b) The enzyme binds both substrate and products.
c) The enzyme is a biological catalyst.
d) The enzyme is degraded after performing the reaction.
12. Enzyme activity can be blocked or retarded on minute disturbance in------------

a) pH
b) Density
c) Concentration
d) Temperature
13. Oxidoreductases perform which one of the following actions?

a) Breakdown of chemical bonds by adding water
b) Join two molecules.
c) Transfer a chemical groups during the reaction.
d) Add and remove hydrogen during chemical reaction.
14. Which one of the following enzymes induces a breakdown of substance with out adding water?
a) Lyase
b) Hydrolase
c) Ligase
d) Isomerase
15. Kinases is belonging to which one of enzyme classes?

a) Oxidoreductases
b) Lyases
c) Transferases
d) Ligases


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Introduction to the course

Semester 2; Level-2 (1441-1442)

Dr.Hiba Mahgoub Ali

Course Title: Biomedical Sciences -2

Course Code: 102 MDS

Program: B.Sc. Medical Laboratory Sciences

Department: Basic medical sciences

College: Applied medical sciences

Institution: University of Bisha

Main objective of the course

Introduction to chemistry, molecules and molecular formula(Role of chemistry in medicine,

Chemistry of water, acids, bases and buffers (structure, functions,

Molecules of life (structure-functions-classification of carbohydrates, lipids,

Fluids dynamics (terminology, the equation of continuity, Bernoulli′s equation and

Percentage of Total Assessment

First midterm exam 6 10%

Final practical exam 16 20%

• Biochemistry for students.2014. VK Malhotra.12th edition. Jaypee

Chemistry Is a central science

 Chemistry : is studying the composition, behavior, structure

and properties of matter besides changes it undergoes.

 Matter : is any thing that has mass and occupies space

Property : is a characteristic to recognize the type of matter

to distinguish it from others.

Element: composed of unique type of atoms

Molecules: are made up of two or more atoms joined

together in specific shapes

• Matter is anything that has mass and occupies space.

Solid Liquid Gases

Analytical Chemistry- concerned with the composition of substances.

Inorganic Chemistry- primarily deals with substances without carbon

Organic Chemistry- essentially deals with all substances containing carbon

Biochemistry- Chemistry of living cells

Physical Chemistry- describes the behavior of chemicals (ex. stretching);

Nuclear Chemistry - dealing with radioactivity, nuclear processes and nuclear

SI units and density calculation

Dr. Hiba Mahgoub

4. Define element, compound and molecules

5. Define Atoms and list the three main component of it

6. Define the atomic and mass number

7. Calculate the number of electrons, protons, and neutrons

– Experiments must be designed and conducted

• An important part of most experiments involves the determination (often, the

estimation) of quantity, volume, dimensions, capacity, or extent of something

– these determinations are measurements

SI base units SI derived units SI prefixes

Units are made of some combination of SI base units

Property Unit Symbol Definition

Force Newton N Kg m/s2

Pressure Pascal Pa N /m2 or kg /m s2

Energy Joule J Kg m2 /s2 or N m

Electrical charge Coulomb c As

Electrical potential Volt V J/C

Frequency Hertz S-1 or Hz 1/s

• Convert 6.83 pm to meters

• Replace p with x 10-12

• Convert 5.847 x 102 kjoules to joules

• Replace k with x103

= 5.847 x102 x 103 =5.847 x 105 J

• Density can be used to determine the identity of unknown substances

• Mass or volume of substance will vary from sample to sample

• Density will remain same at a given temperature

Density does not have an assigned SI unit – it’s a

volume of 7.57 cm3 what is the density ?