Download Glycolysis Lecture

DEPARTMENT OF
CLINICAL BIOCHEMISTRY
SECOND YEAR
MEDICAL STUDENTS
BIOCHEMICAL BASIS OF MEDICINE
Study Guide
KING ABDULAZIZ UNIVERSITY
FACULTY OF MEDICINE
1431- 1432
2010-2011
–
TABLE OF CONTENTS
Topic
3
INTRODUCTION
COURSE DESCRIPTION AND ORGANIZATION
4
5
MAJOR COURSE OBJECTIVES
STUDY STRATEGIES AND CLASS PARTICIPATION
EXPECTATIONS
6
7
INSTRUCTIONAL METHODS
8
ASSESSMENT & EVALUATION
10
TIME ALLOCATION
CLINICAL BIOCHEMISTRY DEPARTMENT STAFF
LISTING
11
14
DEPARTMENT WEB SITE
15
ICONS
17
TOPIC OUTLINES
18
LECTURES
PRACTICALS
231
2
Introduction
Welcome to the Department of Clinical Biochemistry. The aim of this course guide is to
provide you with clear description of the course objectives, contents of each topic together with
its lectures, tutorials and practicals, which are presented in a sequential manner. Also it states
clearly what is expected from you to achieve together with the evaluation procedures. There is
no reason to suppose that Biochemistry is intrinsically uninteresting, difficult to understand or
an obstacle to be overcome during your progress to a professional qualifications. In the
contrary you can enjoy its study if you remember the simple biological principals that the body
is formed from organs and tissues and these are formed from aggregates of cells. The cell is
build up from sub-cellular structures which by itself is an aggregate of molecules. Every
human actively, like walking, breathing and even thinking are the result of the interactions of
these molecules. Defective molecular processes result in disease state. Moreover Biochemistry
has become a background subject for a great family of medical sciences. Understanding
Biochemistry will build for you a good foundation for understanding disease states, their
prevention, diagnosis and treatment. We advice you to read the objectives of each topic before
the start of its lectures and focus your attention on the important points. Take another look
after the end of the lecture to make sure that these points have been understood.
Dr. Mohamed Aly Ajb Noor
Chairman, Department of Clinical Biochemistry
3
COURSE DESCRIPTION AND ORGANIZATION
The aim of Clinical Biochemistry course for second year student is to
introduce you to the basic concepts of structure and metabolism in relation to
the mechanisms by which primary foodstuffs, proteins, carbohydrates and
lipids, are manipulated by the body in order to provide energy and to allow for
biosynthesis of cellular material. Also you will have a good view of storage,
transmission and expression of genetic information. Clinically relevant
examples will be discussed.
Biochemical basis of medicine course includes and covers the following
topics: allosteric proteins, enzymes, membrane and transport, bioenergetics
and oxidative metabolism, anaerobic metabolism, tricarboxylic acid cycle,
carbohydrate storage and synthesis in liver and muscle, oxidative metabolism
of lipid in liver and muscle, biosynthesis and storage of fatty acids, lipid and
lipoproteins, and cholesterol metabolism, Protein metabolism, Nucleotide and
Nucleic Acid metabolism.
The course consists of lectures, practical classes and tutorials.
Core Course
Biochemistry For
Second Year
Code/No
Course Units
Credit Hours
Lectures
Practical
Tutorial
46
15
15
4
5
MAJOR COURSE OBJECTIVES
On completion of the course in Clinical Biochemistry I student will:
1. Evaluate the biochemical logic of the human cell.
2. Explain the maintenance of cellular life in the term of energy
production and biosynthetic ability.
3. Apply biochemical knowledge to solve problems of human health and
disease.
4. Practice basic skills in applying laboratory techniques encountered in
hospital's clinical biochemistry laboratories.
5. Appreciate the functional role of membrane proteins as pumps, gates
and channels
5
STUDY STRATEGIES AND CLASS PARTICIPATION EXPECTATIONS
The course offered to 2nd year medical students in clinical biochemistry consists of
scheduled lectures, tutorials and practicals which ensure smooth flow of the scientific material,
in a controlled manner, through several pathways to achieve our objectives. There is some
suggestion for optimal utilization of these classes by the students.
A. Lectures: The aim of the lecture is not to give information but to frame up the subject,
pointing out its relation to other parts of the course, its relevance to clinical situations and
to explain difficult points. To prepare your self for the lecture:
1.
Give a thorough look to the course objectives and the topic outline delivered by the
department and try to read the topic from the recommended textbook.
2.
Note taking in lectures keeps the student in track during studying the subject.
3.
If is recommended to study the topic of the lecture, if possible, in the same day, to
prevent fading of knowledge. You can utilize different ways of self-testing in order
to assess your grasping of the subject.
B. Practicals: For optimal utilization of the practical class time it is advisable to:
C.
1.
Read your practical worksheet so as to have view of what is expected from you to
perform, observe and draw conclusions on your practical work.
2.
A record of the practicals should be used according to instructions.
3.
The practical time can also be used for discussing difficult theoretical or practical
points with the instructor.
Tutorials: For optimal benefit of the tutorial, the tutorial will be reserved for open
discussion about the subjects listed in the tutorial schedule. The students will be
assigned these topics and will be asked to present them and be ready to change the most
recent knowledge about these topics and how to defend their thoughts on scientific
bases
6
Instructional Methods
The main instructional material includes lectures, practicals to steamline the applied and
clinical aspects of the lectures and tutorials session to stimulate the students to participate
in the teaching/learning activities.
Instructional Materials And Resources
1. Required Texts And Resources
a. Lippincott Illustrated Reviews, 3rd edition, Champe & Harvey
b. Baynes, Medical Biochemistry, Mosby, London.
2. Supplementary Texts And Resources
a.
Thomas M. Devlin, Textbook of Biochemistry with Clinical Correlations, Jon
Willey & sons, New York.
b.
Lubert Stryer, Biochemistry, W.H. Freeman and Company, San Francisco.
c.
Pamela C. Champe, Biochemistry, Lippincott Raven.
7
ASSESSMENT
1. Formative:
This form of assessment is designed to give you feedback to help you to identify areas for
improvement. It includes a mixture of MCQs, short answer-questions (SAQs), extended
matching questions (EMQs), problems-solving exercises and independent learning
activities in all subjects. These will be given during tutorial sessions and practicals. The
Answers are presented and discussed immediately with you after the assessment. The
results will be made available to you.
2. Summative
This type of assessment is used for judgment or decisions to be made about your performance.
It serves as:
a. Verification of achievement for the student satisfying requirement
b. Motivation of the student to maintain or improve performance
c. Certification of performance
d. Grades
In this Course your performance will be assessed according to the following:
1. Continuous Assessment
20 Marks
2. Mid- term exam
20 Marks
3. OSPE
20 Marks
4. Final End of Semester Exam (Three Hours)
40 Marks
Total = 100 Marks
8
85 - 100
A
Excellent
75 - 84
B
Very good
65 - 74
C
Good
60 - 64
D
Pass
Less than 60
F
Fail
All grades
will be assigned as follows:
Exams: Exams will include short answer and multiple choice questions (MCQs). They will
cover material presented in lecture, readings, and discussion. All exams must be taken on the
date scheduled. In case of an emergency, the coordinator must be notified. No make-up exams
will be provided if you fail to notify and discuss your situation with the coordinator.
Note: We will be making the journey from "womb to tomb" in 15 weeks. Therefore, this
course requires an intensive coursework load. Class attendance and participation are extremely
important to your learning and as such are considered in the evaluation of your course grade.
This course is recommended for students that can make the required time and energy
commitment. If there is anything that the coordinator can do to assist you during the course,
please feel free to contact him.
9
Time Allocations
BIOCHEMICAL BASIS OF MEDICINE
N
Topic
L
1.
Introduction: The role of clinical biochemistry in
medicine & Water biochemistry
1
2.
Proteins structure functions relationship
5
3.
Catalytic proteins – Enzymes
6
4.
Membrane and transport
1
5.
Carbohydrate chemistry
1
6.
Introduction to Metabolism, Bioenergetics, and the
Role of ATP
2
7.
Glycolysis
1
8.
The tricarboxylic acid cycle
1
9.
Gluconeogenesis
1
10.
Pentose phosphate pathway
1
11.
Metabolism of Monosaccharides and Disaccharides
1
12.
Lipid chemistry
2
13.
Fatty acid oxidation
2
14.
Fatty acid synthesis
1
15.
Ketone bodies metabolism
1
16.
Phospholipids metabolism
1
17.
Disposal of amino acid nitrogen
1
18.
Urea cycle and detoxification of ammonia
1
19.
Individual amino acid catabolism
metabolism)
Individual amino acid catabolism
(Phenylalanine and tyrosine)
20.
10
(glycine
1
1
T
P
22.
Individual amino acid catabolism (Tryptophan,
aspartic acid , glutamic acid, alanine and serine)
and (sulfur containing amino acids)
Individual amino acid catabolism (sulfur containing
amino acids)
23.
Nucloetides Structure and Functions
1
24.
Purine Nucleotide Metabolism
1
25.
Pyrimidine Nucleotide Metabolism
1
26.
Structure of Nucleic Acids
1
27.
Organization of eukaryotic chromatin
1
28.
DNA sequence and function
1
29.
Replication of DNA (DNA Synthesis)
1
30.
DNA Repair
1
31.
Structure of Ribonucleic Acid (RNA)
1
32.
Transcription of DNA (RNA Synthesis)
Posttranscriptional
processing
Regulation of Gene Expression
33.
Translation of RNA (Protein Synthesis)
1
34.
Recombinant DNA Techniques
1
21.
and
and
1
1
1
46
Total
11
CLINICAL BIOCHEMISTRY DEPARTMENT STAFF LISTING
The following is a list of the faculty members and staff of the Department of Clinical
Biochemistry. Students are welcome to contact any of the members of the department to
answer any of their inquiries.
Male Section: Men Medical Complex
Room
Phone No
No
Prof. Mohammed Ali
22-100, 222/942
Ajabnoor
174
B.Pharm.,M.S., Ph.D.
Name/Status
E-Mail Address
[email protected]
Office Hours
Sat, Mon, Wed
1.00-2.00
Professor
Chairman
Prof. Adil Abdel
Rafee
M.B., B.ch.,
D.M.Sc.,Ph.D.
Professor
Prof. Mohammed
Saleh Ardawi
B.Med. Sc., M.A.,
Ph.D.
Professor
Prof. Zohair M. H.
Marzouki
B.Pharm., M.Sc.,
Ph.D.
Professor
22-112, 22194
22-102, 222/924
173
2/946
[email protected]
12.00-1.00
2/925
22-103, 22177
[email protected]
G/640
51-701
zmarzouki@ Kau .edu .sa
2/853
22-099, 22170
Daily
12.00-1.00
Dean Off., Faculty of
Pharmacy
Prof. Abdulwahab A.
22-097, 222/911
Noorwali
172
B. Phar., Ph.D.
Professor
Prof. Mohammed
22-098, 222/852
Zelai A. Abdu
169
B.Sc., M.Sc., Ph.D.
Professor
Prof. Mamdouh
2/940
Youssef Souaida
M.B.ch., M.Sc.,Ph.D.
Professor
Dr. Zainy M. A.
Daily
22-128
[email protected]
[email protected]
Sat, Sun, Mon
1.00-2.00
[email protected]
Sat, Sun, Mon
1.00-2.00
2/945 51-048, 22-
[email protected]
12
Banjar
116
[email protected]
Dr Osama Abdul
Aziz Gaber
Daily
[email protected]
2/766
22-096
WWW.kaau.edu.sa/ogaber
www.osamagaber.com
M.B., B.ch., M.D.
Associate Professor
Dr Mohammed A
Hassanien
M.B., B.ch., M.D.
Assistant Professor
Dr. Mohammed
Shoaib Jarullah
B.Sc., M.Sc., Ph.D.
Technician
Mr. Ahmad AlShamrani
B.Sc.
11-12
2/941
22-118
[email protected]
WWW.kaau.edu.sa/mhassanien
2/912
22-130
Lab
22-120, 22121
2/922
22-117
Lab
22-120, 22121
[email protected]
[email protected]
Technician
13
Female Section: Women Medical Complex
Name/Status
Prof Suhad Matoug
Bahijri
B.Sc.,M.Sc., Ph.D.
Professor
Prof Enayat Mohd.
Hashem
M.B., B.ch., h.D.
Professor
Dr Amina Mohd. AlGhareeb
M.B., B.ch., h.D.
Associate Professor
Dr Huda Gad
M.B., B.ch., h.D.
Assistant Professor
Dr. Eman Mokbel
Alissa(BSc MSc PhD)
Assistant Professor
Dr. Fayza F Al Fayez
(BSc MSc PhD )
Assistant Professor
Ms. Areej Al-Turki
B.Sc.
Technician.
Zain Mohd.AL-Shareef
B.Sc.
Technician.
Hana Abdullah Basaffar
B.Sc.
Technician.
Rehab Aboobakar AlAydoos
B.Sc.
Technician.
Nada Saleh Al-Saykhan
B.Sc.
Technician.
Reem Foad Ghazali
B.Sc.
Technician.
Room
No
Phone No
E-Mail Address
2/622
23-601
[email protected]
2/618
23-437
[email protected]
2/617
23-431
[email protected]
2/613
23-433
[email protected]
[email protected]
2/621
23-432
Webpage:
www.kau.edu.sa/ealissa
23-486
2/670
[email protected]
2/659
23-468
23-470
2/653
23-489
2/620
23-436
2/690
23-467
[email protected]
2/652
23-611
[email protected]
2/623
23-438
[email protected]
[email protected]
14
Office Hours
Icons
The following icons have been used to help you identify the various experiences
you will be exposed to.
Learning objectives
Content of the lecture
Independent learning from textbooks
Independent learning from the CD-ROM.
Independent learning from the Internet
Home Work
Problem-Based Learning
15
Self- Assessment (the answer to self-assessment exercises will be
discussed in tutorial sessions)
The main concepts
16
Topic Outlines
17
18
LECTURE# (1): Introduction: The role of clinical biochemistry in
medicine & water biochemistry
DEPARTMENT: Clinical Biochemistry
Tutor: Dr.
TEACHING LOCATION: Auditorium
Dr.
By the end of this lecture, you will be able to:
1. Identify the importance of studying clinical biochemistry in college of
medicine
2. Compare between water and other solvents.
3. Recognize water properties which make the universal solvent.
4.Appreciate the role of buffer in human body homeostasis





Molecular structure of water
Non-covalent forces
Properties of water
Ionization of water
Buffers
 Water is essential for life. It covers 2/3 of the earth's surface and
every living thing is dependent upon it. The human body is
comprised of over 70% water, and it is a major component of many
bodily fluids including blood, urine, and saliva.
1. Required Texts And Resources: Lippincott Illustrated Reviews, 3rd
edition, Champe & Harvey
2. Reading Handouts will be distributed
3- Lectures and power point presentation will be published on
department website: www.kaau.edu.sa/faculties/medicine/dcbcweb

19


You have the opportunity to watch the CD-ROM about Water & Chemical
Bonds. You can access the CD-ROM during your spare time.
1- Biochemistry of water:
http://library.thinkquest.org/28751/review/biochem/2.html
2- Water http://www.chm.bris.ac.uk/motm/water/water.htm
3- Water animation
http://www.rkm.com.au/ANIMATIONS/animation-water-molecule.html
4- Hydrogen bonding animation
www.elmhurst.edu/~chm/vchembook/163boilingpt.html
5- All about chemical bonding
http://www.promotega.org/UGA06004/covalent_bonds.html
1- List different types of chemical bonds. In a table form compare
different types of bonds and their biological importance.
Clinical Question
The human body is greater than 80% water, but a relatively small loss of
water content, such as that created by vigorous exercise or diarrhea, can have
profound physiologic consequences. From a biochemical point of view, and
from what you have learned in this course so far, why would small changes in
water content alter biochemical processes?
I- MCQ:
Which of the following is NOT a "weak" interaction?
A. hydrogen bonds
B. van der Waals forces
C. disulfide bonds
D. ionic interactions
2- What is the maximum number of hydrogen bonds that one water
molecule can have with neighboring water molecules?
A. 1
B. 2
20
C. 3
D. 4
3- The pH of a 10-4 M solution of HCl is
A. 3
B. 10
C. 4
D. 4.5
III- True / False
a. Electrostatic interactions occur between atoms have the same
charge
b. In water molecule, Oxygen is highly electrophilic.
c. Water molecules are bound together through Ionic bonds.
d. Buffers are made up of a mixture of a weak acid with its
conjugate base or a weak base with its conjugate acid.
e. pH + pOH = 10 For any substance dissolved in water
21
Lectures # (2-6) : Protein structure function relationship
DEPARTMENT: Clinical Biochemistry
Tutor: Dr.
TEACHING LOCATION: Auditorium
By the end of this lecture, you will be able to:
1. Relate the structural properties of
particular
proteins
such
as
hemoglobin and myoglobin to their
functions in human health and
disease.
2. Discuss the genetic bases of protein
structure and how molecular defects
lead to diseases such as sickle cell
anemia.
3. Be able to recognize the structure of
the commonly found amino acids in
specific proteins and explain the
their importance.
 Hemoglobin:
 Quaternary structure of hemoglobin,
cooperative binding of oxygen, effect
of hydrogen ion and carbon dioxide
(Bohr effect)
 Functional significance of DPG, fetal
hemoglobin, abnormal hemoglobin,
(sickle cell anemia).
 Myoglobin:
 Globular proteins, myoglobin
configuration and conformation.
 Oxygen binding site.
 Microenvironment and reversible
oxygen binding.
22
Student Notes:
.
Myoglobin and hemoglobin are two
oxygen – binding proteins with a very
similar primary structure. However,
myoglobin is a globular protein
composed of a single polypeptide chain
that has one O2 binding site. Hemoglobin
is a tetramer composed of two different
types of subunits. Each subunit has a
strong sequence homology to myoglobin
and contains an O2 binding site. A
comparison between myoglobin and
hemoglobin illustrates some of the
advantages of a multisubuniut
quaternary structure.
1. Required Texts And Resources: Lippincott
Illustrated Reviews, 3rd edition, Champe &
Harvey P : 25 - 42
2. Reading Handouts will be distributed
3- Lectures and power point presentation
will be published on department website:
www.kaau.edu.sa/faculties/medicine/dcbcweb



You have the opportunity to watch the CDROM about Hemoglobin. You can access the
CD-ROM during your spare time.
23
1- Haemoglobin
http://www.ebi.ac.uk/interpro/potm/2005_10/Page1.htm
2- Haemoglobin
http://www.iscid.org/encyclopedia/Haemoglobin
3- Haemoglobin animations
http://www.umass.edu/microbio/chime/hemoglob/2frmcon
t.ht]
4- Oxygen dissociation curve
http://www.bio.davidson.edu/Courses/anphys/1999/Dicken
s/Oxygendissociation.htm
5- Oxygen dissociation curve 2
http://www.ventworld.com/resources/oxydisso/dissoc.html
6- Haemoglobin dissociation curve 3
http://www.manbit.com/Hbdiss.htm
7- Carbon dioxide and Oxygen transport
http://cal.man.ac.uk/student_projects/2001/MNQC7NDS/h
omepage.htm
2- In a table form compare between
Hemoglobin
and
Myoglobin
including the difference in the :
Structure, Function, Oxygen binding
and Oxygen dissociation curve.
Clinical Question
A 67 – year old man presented to the
emergency department with one week history of
angina and shortness of breath. He complained
that his face and extremities had a "blue color" .
His medical history included chronic stable
angina trated with isosorbide dinitrate and
nitroglycerin. Blood obtained for analysis was
chocolate – colored. What is the possible
diagnosis
I- Short Questions:
24
a- What of the effects of the following on
oxygen dissociation curve of Hemoglobin
1- 2,3 – BPG
2- CO2
3- pH
b- What is the molecular defect which leads
to the following?
1- Sickle cell disease
2- Methemoglobinemia
3- Thalassemias
II- MCQ:
1- Hemoglobin is
A. A tetramer of 4 myoglobin proteins.
B. A tetramer of four globin chains and one
heme prosthetic group.
C. A dimer of subunits each with two distinct
protein chains (alpha and beta).
D. A dimer of subunits each with two
myoglobin proteins.
2- Hydrophobic amino acid sequences in
myoglobin are responsible for
A. Covalent bonding to the heme prosthetic
group
B. The folding of the polypeptide chain
C. The reversible binding of oxygen
D. b and c above
3- Cooperative binding of oxygen by
hemoglobin
A. Is induced by hemoglobin
B. Is a result of different affinities for oxygen
by each subunit protein
C. Is induced by oxygenation
D. Is a result of interaction with myoglobin
III- True / False
f. Proteins often consist of multiple
subunits so that they may have
different functions under different
conditions.
g. The porphyrin prosthetic group is
held into the interior of globin
molecules by covalent bonds to
specific amino acid residues
h. Myoglobin has a greater affinity
for oxygen than hemoglobin.
i. Cooperative
binding
and
25
allosterism of hemoglobin allow
oxygen to be unloaded at low
partial pressures of oxygen in the
tissues.
j. The Bohr effect is a description of
the effect of pH on hemoglobin,
oxygen bound more tightly at
low pH (in tissues) and less tightly
at higher pH values.
26
LECTURE # (7) : Introduction to the enzymes
DEPARTMENT: Clinical Biochemistry
TUTOR:
TEACHING LOCATION: Auditorium
By the end of this lecture you will be
able to:
1. Summarize the importance of
enzymes in many aspects in health
and disease
2. Describe general properties of
enzyme molecule and the process
of enzyme catalysis
3. Define terms used in enzymology
4. Compare and contrast between
enzymes and inorganic catalysts
5. Identify the nomenclature of
enzymes
6. Outline the classification of
enzymes
7. Distinguish the different types of
enzyme specificity
 Enzymes are important for medical
students
for
diagnosis
and
treatment
 Enzymes are typically large globular
proteins that accelerate reactions
by million folds
 Substrate, product, apoenzyme,
holoenzyme, cofactor, coenzyme,
27
Student Notes:
.
active site and catalytic site, all are
terms used in study of enzymes
 There are many differences between
enzymes and inorganic catalysts as
reversibility and specificity of
enzyme action
 Naming of enzymes is either
convenient for everyday use, or
more complete systematic name
divided into six major classes
 Enzyme specificity are absolute,
relative, stereochemical and group
Remember that all reactions in the body are
mediated by enzymes, which are protein catalysts
that increase the rate of reactions without being
changed in the overall process. Enzymology is
important as inborn errors of metabolism are due
to deficiency of some enzymes. Also assay of
particular enzymes can help in diagnosis of many
diseases. The most striking characteristics of
enzymes are their catalytic power and specificity
which is of many types.
1. Required Texts And Resources: Lippincott
Illustrated Reviews, 3rd edition, Champe &
Harvey , chapter 27 ( pp:365-367)
2. Supplementary Texts And Resources:
Medical
Biochemistry,
Baynes
and
Dominiczek, 1st edition, Mosby. Chapter
18 (pp:217-218)
28



You have the opportunity to watch the CDROM about enzymes. You can access the
CD-ROM during your spare time.
1- http://web.indstate.edu/thcme/mwkin
g/enzyme-kinetics.html
2- http://www.stolaf.edu/people/qiannin
i/fashanimat/enzymes
3- http://
www.reachoutmichigan.org/funexpe
riments/quick/eric/enzymes
4- http://www.pubmedcentral.nih.gov/a
rticlerender.fcgi?artid
5- http://www.ncbi.nlm.nih.ov/entrez/qu
ery/fcgi?cmd
6- http://www.wiley.com/legacy/college/
boyer/0470003790
7- http:/www.siu.edu/departments/bioc
hem/som_pbl/ms_ppt_anim.html
8- http://www.lewport.wnyric.org/wana
maker/animations/Enzymes%20activ
ity.
** Enzymes are biological catalysts that
accelerate the rate of reaction, by using
the library and the internet try to explain
how this occurs.
Clinical Case: A 52-year-old-man
29
presented at ER of a hospital
with severe chest pain which had
present for the past hour. He had
a 2-year history of angina of
efforts.
How
can
you
use
enzymes in?:
a. Diagnosis of this case
b. Treatment of it
I- Short Questions:
1- Enumerate enzyme specificity
2- Differentiate between enzymes
and inorganic catalysts
II- MCQ:
1.Enzymes are:
a) Proteins
b) Chloroplasts
c) Genes
d) Mitochondria
2. Enzymes are catalysts. They increase the
rate of chemical reactions by:
a) Raising the activation energy
b) Temporarily increasing the temperature
c) Covalently binding the substrate
d) Lowering the activation energy
3. Enzymes are classified by the:
a) Size of the enzyme
b) Size of the substrate
c) Type of reaction
d) Rate of reaction
4. Shown below is a graph describing energy
versus reaction coordinate for a catalyzed
and uncatalyzed reaction. Fill in the blanks
with the letter that corresponds to each stage
of the graph.
30
_____ ES
_____ S (substrate)
_____ P (product)
_____ Uncatalyzed reaction
III- Complete the following:
Some enzymes require another chemical to
function. These helper compounds are called
__________. If a cofactor is covalently bound to the
enzyme, it is called a __________ group. An
enzyme with its cofactor attached is called a
__________, while an enzyme minus its extra
component is called an __________.
31
LECTURE # (8) : Mechanism of enzymatic catalysis
Student Notes:
DEPARTMENT: Clinical Biochemistry
.
TUTOR:
TEACHING LOCATION: Auditorium
By the end of this lecture you will be
able to:
1. Describe the two models of binding
the enzyme to its substrate
2. Identify what is meant by transition
state
3. Understand the difference between
∆G and ∆G‡
4. Explain the mechanism of enzymatic
catalysis by acid-base catalysis,
covalent catalysis, substrate strain
and entropy effect
 Two models have been proposed to
explain how an enzyme binds its
substrate; lock-and-key model and
induced-fit model
 Lock-and-key model assumes that
an enzyme active site will accept a
specific substrate
 Induced-fit model recognizes that
there is much flexibility in an
enzyme’s substrate . Accordingly,
an enzyme is able to conform to a
substrate
 Transition
state
is
state
of
maximum energy through which the
enzymatic reaction proceeds. It is
not an intermediate compound.
32
 The differences in free energy (∆G)
between the transition state and
substrate is the free energy of
activation (∆G‡)
 Enzyme can enhance the rate of
reaction
by
four
processes:
general/acid
base
catalysis,
covalent catalysis, substrate strain
and entropy effect
When correctly positioned and bound on the
enzyme surface, the substrate may be “strained”
toward the transition state. At this point the
substrate has been “set up” for acid-base and/or
covalent catalysis. Proper and the nearness of the
substrate with respect to the catalytic groups
(proximity effect) contribute to decrease in
entropy and so enhance the rate of enzymatic
reaction.
1. Required Texts And Resources: Lippincott
Illustrated Reviews, 3rd edition, Champe &
Harvey , chapter 27 ( pp:365-367)
2.Supplementary Texts And Resources:
Medical
Biochemistry,
Baynes
and
st
Dominiczek, 1 edition, Mosby. Chapter
18 (pp:217-218)



You have the opportunity to watch the CDROM about enzymes. You can access the
CD-ROM during your spare time.
33
1http://web.indstate.edu/thcme/mwking/e
nzyme-kinetics.html
2http://www.stolaf.edu/people/qiannini/fash
animat/enzymes
3- http://
www.reachoutmichigan.org/funexperiment
s/quick/eric/enzymes
4http://www.pubmedcentral.nih.gov/articler
ender.fcgi?artid
5http://www.ncbi.nlm.nih.ov/entrez/query/
fcgi?cmd
6http://www.wiley.com/legacy/college/boy
er/0470003790
7http:/www.siu.edu/departments/biochem/s
om_pbl/ms_ppt_anim.html
8http://www.lewport.wnyric.org/wanamaker/
animations/Enzymes%20activity
9http://www.bio.winona.edu/berg/308/oldex
am/308exam1.txt
** How does the enzyme bind its
substrate?
By using the library and the internet
try to answer this question.
I- Short Questions:
1. What is meant by transition
state
2. Enzymes can enhance the rate
34
of reaction. Enumerate the
processes by which this occurs.
II- MCQ:
1. The minimum amount of energy necessary
for a molecule(s) to react is the:
a) Activation energy
b) Free energy
c) Thermal energy
d) Potential energy
2. The state produced when two or more
molecules collide with just the right energy
and just the right orientation so that a
chemical reaction might occur is:
a) Catalytic state
b) Transition state
c) Activation state
d) Transient state
3. One of the following statement describing
the mechanism of enzyme action is
INCORRECT:
a) Many enzymes have flexible structures
that allow them to enfold their substrate
b) The substrate is often distorted when it
enters an enzyme-substrate complex
c) Amino acid side chains involved in the
formation of the active site center are
usually close together in the amino acid
sequence of the enzyme protein
d) Amino acid side chain near the active
site center often have a role in the catalytic
process
4.Which of the following statement about
enzyme catalyzed reaction is NOT TRUE:
a) Enzymes form complexes with their
substrate
b) Enzymes increase the activation energy
for chemical reaction
c) Many enzymes change shape slightly
when substrate binds
d) Reactions occur at the “active site” of
enzymes, where a precise quaternary
orientation of amino acids is an
important feature of catalysis
III- Complete the following:
35
Enzymes carry out different chemical reactions in
catalysis. Fill in the blanks with the name of the
mechanism that matches with the example described
in each line. Mechanism names to choose from are:
covalent catalysis, acid-base catalysis, and metal ion
catalysis.
__________ catalysis may involve Glu, Asp, His, Lys,
or Arg residues.
__________ catalysis may involve Na+, K+ or Mg2+,
Ca2+.
__________ catalysis may involve serine proteases.
36
LECTURE # (9) : Enzyme kinetics
DEPARTMENT: Clinical Biochemistry
TUTOR:
TEACHING LOCATION: Auditorium
By the end of this lecture you will be able
to:
1. Distinguish the several terms used in
enzyme kinetics as rate or velocity,
rate constant, order of a reaction,
turnover number ..etc
2. Identify Michaelis-Menten equation
and Linweaver-Burk equation
3. Recognize the factors affecting
enzyme
activity
as
substrate
concentration, pH and temperature
 The enzyme (E) combines with its
substrate (S) to form an enzymesubstrate complex (ES).
 The ES complex can dissociate
again to form E + S, or can proceed
chemically to form E and the
product P.
 The rate constants k1, k2 and k3
describe the rates associated with
each step of the catalytic process.
 The initial velocity (Vo) at low
substrate concentration is directly
proportional to [S], while at high
substrate concentration the velocity
tends towards a maximum value
(Vmax) which is independent of [S].
 Michaelis-Menten
equation
37
Student Notes:
.
describes a “hyperbolic curve” of
the relationship between [S] and
velocity of the reaction
 Lineweaver-Burk
plot
(double
reciprocal plot) gives a straight line
if Vo is measured at different
substrate concentration
 Not only substrate concentration ,
but also pH and temperature can
affect enzymatic activity
Kinetics is a study of the rate of changes of
substrates to products. Kinetics properties for many
enzymes reveals that, the rate of catalysis V varies
with [S] in a hyperbolic manner which is expressed in
Michaelis-Menten equation. Lineweaver-Burk plot
gives a straight line of relationship between [S] and
the rate of reaction..
1. Required Texts And Resources: Lippincott
Illustrated Reviews, 3rd edition, Champe &
Harvey , chapter 27 ( pp:365-367)
2. Supplementary Texts And Resources:
Medical
Biochemistry,
Baynes
and
Dominiczek, 1st edition, Mosby. Chapter
18 (pp:217-218)



You have the opportunity to watch the CDROM about enzymes. You can access the
CD-ROM during your spare time.
1.http://web.indstate.edu/thcme/mwking
/enzyme-kinetics
2.htmlhttp://www.stolaf.edu/people/qian
nini/fashanimat/enzymes
38
3.http://
www.reachoutmichigan.org/funexperim
ents/quick/eric/enzymes
4.http://www.pubmedcentral.nih.gov/art
iclerender.fcgi?artid
5.http://www.ncbi.nlm.nih.ov/entrez/que
ry/fcgi?cmd
6.http://www.wiley.com/legacy/college/
boyer/0470003790
7.http:/www.siu.edu/departments/bioch
em/som_pbl/ms_ppt_anim.html
8.
http://www.lewport.wnyric.org/wanama
ker/animations/Enzymes%20activity.
By using the library and the internet
try to illustrate the relationship between
substrate concentration and reaction
velocity.
I- Short Questions:
a) Would you think that all enzyme
assays need the same pH? Why?
b) What is the meaning of optimum
temperature?
II- MCQ:
1. Which of the following does not influence
enzyme activity?
a) pH
b) Temperature
c) Product degradation
d) Substrate concentration
2. The Michaelis constant Km is:
a) Numerically equal to ½ Vmax
b) Dependent on the enzyme concentration
39
c) Independent on pH
d) Numerically equal to the substrate
concentration that gives half-maximal
velocity
3. What effect does temperature have on
enzymes?
a) Boiling will denature them, as will being
too cold
b) Boiling will not harm them, but being
too cold will denature them
c) Boiling and cooling will both reduce the
speed of their rate
d) Boiling will denature them, but cooling
will only slow down their work
4. The Michaelis-Menten equation is Vo=Vmax
[S]/(Km+[S]).
Fill in the blanks with the letters shown to
correctly label each part of the graph
_____ Vmax
_____ [S]
_____ Vo
_____ Point used to determine the Km
III- Complete the following:
Often the kinetic values of an enzyme are
plotted using the Lineweaver-Burk
equation:
1/vo=Km/Vmax·1/[S]
+1/Vmax
40
Enter "yes" or "no" to indicate if the
equation and graphical terms match in each
statement.
_____
Y-intercept
and
-1/Km
_____
X-intercept
and
1/Vmax
_____ Slope and Km/Vmax
41
LECTURE # (10) : Enzyme inhibitors
DEPARTMENT: Clinical Biochemistry
TUTOR:
TEACHING LOCATION: Auditorium
By the end of this lecture you will be
able to:
1. Outline the importance of enzyme
inhibition studies
2. Discriminate the two broad classes of
enzyme inhibitors that based on the
extent of inhibition
3. Compare the mechanisms of enzyme
inhibition
4. Interpret the use of enzyme inhibition
as drugs in the treatment of diseases
 There are two broad classes of
enzyme inhibitors: reversible and
irreversible
 Reversible inhibitors interact with an
enzyme via noncovalent association
 Irreversible inhibitors interact with
an enzyme via covalent association
 Competitive inhibitors binds only to
enzyme (E) and not to enzymesubstrate complex (ES)
 Noncompetitive inhibitors binds
either to (E) and/or to (ES)
 Uncompetitive inhibitors binds only
to (ES) and not to (E)
 Enzyme inhibition may affect Vmax
or Km or both
 Many natural occurring and man42
Student Notes:
.
made compounds are irreversible
enzyme inhibitors
 There are therapeutic application for
enzyme inhibition
A competitive inhibitor prevents the substrate from
binding to its enzyme, while noncompetitive or
uncompetitive do not. Competitive inhibitor increases
Km without change Vmax. Noncompetitive inhibitor
decreases Vmax without change in Km. But
uncompetitive inhibitor decreases both Vmax and Km
.
1. Required Texts And Resources: Lippincott
Illustrated Reviews, 3rd edition, Champe &
Harvey , chapter 27 ( pp:365-367)
2. Supplementary Texts And Resources:
Medical
Biochemistry,
Baynes
and
Dominiczek, 1st edition, Mosby. Chapter
18 (pp:217-218)



You have the opportunity to watch the CDROM about enzymes. You can access the
CD-ROM during your spare time.
1http://web.indstate.edu/thcme/mwking/e
nzyme-kinetics.html
2http://www.stolaf.edu/people/qiannini/fa
shanimat/enzymes
43
3- http://
www.reachoutmichigan.org/funexperime
nts/quick/eric/enzymes
4http://www.pubmedcentral.nih.gov/articl
erender.fcgi?artid
5http://www.ncbi.nlm.nih.ov/entrez/query/
fcgi?cmd
6http://www.wiley.com/legacy/college/boy
er/0470003790
7http:/www.siu.edu/departments/biochem
/som_pbl/ms_ppt_anim.html
8http://www.lewport.wnyric.org/wanamak
er/animations/Enzymes%20activity.
**How can the irreversible inhibitors
bind the active site of the enzyme?
By using the library and the internet
try to explain how this occurs.
Clinical Case: A young girl was
brought to the pediatric clinic with
infected wound on her knee. The
mother was instructed to give the
child penicillin. The child had
improved after a week.
a) What the possible mechanism
of action of this antibiotic?
b) What is the target enzyme of
penicillin?
I-
Short Questions:
44
1. Classify enzyme inhibitors
2. Tabulate the effect of competitive,
noncompetitive and
uncompetitive on Vmax and Km
II- MCQ:
1. Which type of reversible enzyme inhibitor
binds to the free enzyme and the enzymesubstrate complex?
a) Noncompetititive
b) Competitive
c) Uncompetitive
d) None of the above
2. In competitive inhibition, one of the following
statement is CORRECT:
a) Vmax is increased
b) The concentration of active enzyme
molecule is unchanged
c) The apparent Km is increased
d) The apparent Km is decreased
3. Enzyme action can be influenced by the
presence of inhibitors. Which of the following
statements correctly matches the type of
inhibitor with its effect on an enzyme.
a) Irreversible and Renders the enzyme
permanently inactive
b) Competitive and Inhibitor binds only to
ES complex, only important when[S]
high, Vmax lower, Km lower
c) Noncompetitive and Can be overcome
with high [S], Vmax unchanged, Km higher
d) Uncompetitive and Cannot be overcome
with high[S], Vmax lower, but Km unchanged
4. In Lineweaver-Burk plot below:
a) Mention the type of inhibition of
enzymatic reaction
b) Which one of the lines of the plot
represents the enzymatic reaction
without inhibition?
45
III- Complete the following:
Any molecule that acts directly on an
enzyme to lower its catalytic rate is
called ---------. Enzyme inhibition may
be
of
--------types.
Reversible
inhibition can be overcome by-----but
this is not possible for ----------inhibition.
46
LECTURE # (11) : Enzyme regulation
DEPARTMENT: Clinical Biochemistry
TUTOR:
TEACHING LOCATION: Auditorium
By the end of this lecture you will be
able to
1. Integrate enzymes into metabolic
pathways
2. Identify the terms of the rate-limiting
enzyme and the committed step in a
metabolic pathway
3. Know the different ways of enzyme
regulation under physiological and
pathological conditions
4. Recognize the allosteric regulation
5. Explain
a
feedback
control
mechanism
 There are key enzymes in a metabolic
pathway which can be regulated and
hence control the pathway
 The activity of these enzymes can be
regulated by:
 Changing the amount of enzyme by
enzyme induction, enzyme repression,
and enzyme degradation
 Changing the activity of enzyme by
allosteric regulation, feedback control,
covalent modification, and activation
by cleavage
 Compartmentation of pathways is also
a way of enzyme regulation
47
Student Notes:
.
Control of a pathway occurs through modulation
of the activity of one or more key enzymes in the
pathway . The rate-limiting enzyme and the
committed step enzyme can be regulated by
changing the amount (enzyme induction, repression,
or degradation), or changing the activity (allosteric
regulation,
feedback
inhibition,
covalent
modification,
or
enzyme
cleavage)
or
compartmentation of the pathways.
1. Required Texts And Resources: Lippincott
Illustrated Reviews, 3rd edition, Champe &
Harvey , chapter 27 ( pp:365-367)
2. Supplementary Texts And Resources:
Medical
Biochemistry,
Baynes
and
st
Dominiczek, 1 edition, Mosby. Chapter
18 (pp:217-218)



You have the opportunity to watch the CDROM about enzymes. You can access the
CD-ROM during your spare time.
1http://web.indstate.edu/thcme/mwking/e
nzyme-kinetics.html
2http://www.stolaf.edu/people/qiannini/fa
shanimat/enzymes
3- http://
www.reachoutmichigan.org/funexperime
nts/quick/eric/enzymes
4http://www.pubmedcentral.nih.gov/articl
erender.fcgi?artid
48
5http://www.ncbi.nlm.nih.ov/entrez/query/
fcgi?cmd
6http://www.wiley.com/legacy/college/boy
er/0470003790
7http:/www.siu.edu/departments/biochem
/som_pbl/ms_ppt_anim.html
8http://www.lewport.wnyric.org/wanamak
er/animations/Enzymes%20activity.
9- en.wikipedia.org/wik/Enzymes
10.www.elmhurst.edu/~chm/vchembook/
573 regulate
** By using the library and the internet
try to illustrate covalent modification of
an enzyme (e.g. glycogen phosphorylase)
II-
Short Questions:
1. List some of the molecular
mechanisms by which the
catalytic activity of enzymes is
controlled.
2. Using a graph, illustrate the
kinetic behavior of an allosteric
enzyme
II- MCQ:
1. Allosteric enzymes are large, oligomeric
proteins that have catalytic sites for binding
substrates and regulatory sites that bind
effectors. The separate oligomers influence
one another; they work cooperatively. This is
evidenced by the characteristic rate curves
for allosteric enzymes which have:
a) Michaelis-Menten kinetics
b) Hyperbolic kinetics
c) Sigmoidal kinetics
d) Regulatory kinetics
49
2. Some enzymes are first synthesized in an
inactive form. These zymogens must undergo
proteolytic cleavage to produce the active
enzyme. Which of the following statements
are true of proteolytic cleavage?
a) It is reversible
b) It is irreversible
c) It is random
d) It occurs in the region of zymogen
synthesis
3. Increased synthesis of an enzyme is known
as:
a) Ac
a) Activation
b) Inhibition
c) Induction
d) Repression
4. In the graph below
a) Which one of the plot explains the
behavior of an allosteric enzyme?
b) What is the meaning of cooperativity?
III- Complete the following:
The rate- limiting enzyme in a pathway is the
enzyme with the-------Vmax, while the enzyme
catalyzing the committed step is -----------.
50
LECTURE # (12) : Enzymes in clinical practice
DEPARTMENT: Clinical Biochemistry
TUTOR:
TEACHING LOCATION: Auditorium
By the end of this lecture you will be
able to:
1. Evaluate the use of enzymes and
isoenzymes in the diagnosis of
diseases
2. Know the use of enzymes in
treatment of some diseases
3. Recognize the ribozymes and
catalytic antibodies
4. Identify the site-directed mutagenesis
 Enzymes are used clinically in
three principal ways:
- in diagnosis and prognosis
of various disease
- as analytical reagents in the
measurement of activity of
other enzyme or non-enzyme
substances
- as therapeutic agents
 RNA enzymes (hammerhead
ribozymes)
and
catalytic
antibodies
are
recently
discovered
 Site-directed mutagenesis is
used for design a new drug
therapy
51
Student Notes:
.
Isoenzymes are forms of an enzyme which are
structurally different but have similar catalytic
properties. Measurements of the isoenzymes of lactate
dehydrogenase (LDH), alkaline phosphatase (ALP),
and creatine kinase (CK) are of clinical value. Studies
have shown that catalysis for biochemical reactions
are not limited to naturally occurring proteins. Sitedirected mutagenesis (modification of amino acid
sequence of known enzymes) is used for design new
drug therapy.
1. Required Texts And Resources: Lippincott
Illustrated Reviews, 3rd edition, Champe &
Harvey , chapter 27 ( pp:365-367)
2. Supplementary Texts And Resources:
Medical
Biochemistry,
Baynes
and
Dominiczek, 1st edition, Mosby. Chapter
18 (pp:217-218)



You have the opportunity to watch the CDROM about enzymes. You can access the
CD-ROM during your spare time.
1http://web.indstate.edu/thcme/mwking/
enzyme-kinetics.html
2http://www.stolaf.edu/people/qiannini/f
52
ashanimat/enzymes
3- http://
www.reachoutmichigan.org/funexperi
ments/quick/eric/enzymes
4http://www.pubmedcentral.nih.gov/arti
clerender.fcgi?artid
5http://www.ncbi.nlm.nih.ov/entrez/quer
y/fcgi?cmd
6http://www.wiley.com/legacy/college/b
oyer/0470003790
7http:/www.siu.edu/departments/bioche
m/som_pbl/ms_ppt_anim.html
8http://www.lewport.wnyric.org/wanama
ker/animations/Enzymes%20activity.
9www.dcnutrition.com/Miscellaneous/D
etail
**It was believed that all enzymes were
proteins till a recent discovery , by using
the library and the internet try to explain
this statement.
Clinical Case: A 52-year-old-man
presented at ER of a hospital with
severe chest pain which had
present for the past hour. He had a
2-year history of angina of efforts.
a) What specific tests would you
request from the biochemistry
laboratory?
b) How can use of an enzyme
share in the treatment of this
condition?
53
I- Short Questions:
1. Enumerate five enzymes used in
clinical diagnosis and mention
the major diagnostic use for
each
2. What are the causes of presence
of non-plasma specific
enzymes?
II- MCQ:
1. In normal blood, the alkaline phosphatase activity is derived
mainly from:
a) Bone and small intestine
b) Bone and liver
c) Small intestine and placenta
d) Bone and placenta
2. How many different isoenzymes of normal
LDH can be identified by electrophoresis at pH 8.6
a) Two
b) Three
c) Four
d) Five
3. LDH assays are useful in diagnosing diseases
of the:
a) Heart
b) Pancreas
c) Liver
d) a and c
54
Lectures # ( 13- a ) : Membrane Structure and transport
DEPARTMENT: Clinical Biochemistry
Tutor: Dr.
TEACHING LOCATION: Auditorium
By the end of this topic the you will be
able to:
1. Comprehend the fluid mosaic
model of biologic membrane.
2. Understand how change in
membrane composition changes
its function.
Chemical compositions of
membranes:
 Separation of cells and
intracellular organells into
different chemical
compartments by membranes.
 Lipids of membranes.
 Distribution of membrane
lipids.
 Membrane proteins.
 Carbohydrates of membranes.
Molecular structure of
membranes:
 The fluid mosaic model of
biologic membranes.
 Asymmetry of membrane.
 Membrane fluidity
55
Membranes are highly viscous, plastic
structures. Plasma membranes form
closed compartments around cellular
protoplasm to separate one cell from
another and thus permit cellular
individuality. The plasma membrane has
selective permeabilities and acts as a
barrier, thereby maintaining differences
in composition between the inside and
outside of the cell.
1. Required Texts And Resources: Lippincott
Illustrated Reviews, 3rd edition, Champe &
Harvey P :
2. Reading Handouts will be distributed
3- Lectures and power point presentation
will be published on department website:
www.kaau.edu.sa/faculties/medicine/dcbcweb



You have the opportunity to watch the CDROM about Membrane structure. You can
access the CD-ROM during your spare time.
1- Membrane structure
http://cellbio.utmb.edu/cellbio/membrane.htm
2- Biological membrane structure
http://www.pnas.org/cgi/content/abstract/66/3/615
3- Biological membrane structure
http://www.pnas.org/cgi/content/abstract/66/3/615
4- Membrane Composition
http://www.pnas.org/cgi/content/abstract/66/3/615
56
1- Draw a figure for cell membrane,
mention the basic composition for the
membrane and explain how membrane
structure serves its function?
I- Short Questions:
a- Which component (s) of membranes give
it its fluid characteristics?
b- Which part of a membrane helps it keep
its shape (prevents deformation)?
c- How are proteins arranged in a
membrane? What is the difference between
a transmembrane protein and a peripheral
membrane protein?
d- What feature in a membrane helps to
prevent freezing? Be specific.
II- MCQ:
1- Triacylglycerols cannot form lipid bilayers
because they
A.
B.
C.
D.
Have hydrophobic tails
Do not have polar heads
Cannot associate with cholesterol
Have polar heads
2- In a typical eukaryotic plasma membrane
A. Proteins can move in and out of the
bilayer
B. Lipids can move and diffuse through the
bilayer
C. Some lipids can rotate within the bilayer
D. All of the above
3- The arrangement of lipid bilayers and other
components is the basis for the currently
widely accepted description which is called the
A. Lipid bilayer model
B. Mosaic model
C. Diffusion model
57
D. Fluid mosaic model
III- True / False
A. According to the current model of cell
membrane structure, the two layers of
lipids in the bilayer are nearly identical
B. Cholesterol accounts for 20% to 25% of
the mass of lipids in a typical
mammalian plasma membrane
C. The
distribution
of
peripheral
membrane proteins is generally identical
on both sides of a given membrane.
58
Lectures #(13 - b) : Membrane Transport
DEPARTMENT: Clinical Biochemistry
Tutor: Dr.
TEACHING LOCATION: Auditorium
By the end of this topic you will be able
to:
1. Explain how molecules move through
membranes and the forms of energy
needed to derive this process and to
differentiate between active and
passive transport.
2. Appreciate the functional role of
membrane proteins as pumps, gates,
channels and receptors.
Movement of molecules across
membranes:
 Diffusion
across
cellular
membranes.
 Mediated
transport
passive
mediated transport system, active
mediated transport system: Na+
K+.
 ATpase, Ca2+ translocation and
Na+ dependent transport system.
 Endocytosis and phagocytosis
Molecules can passively traverse the
lipid bilayer of the membranes down
electrochemical gradients by simple
diffusion or by facilitated diffusion. This
59
Student Notes:
.
spontaneous
movement
toward
equilibrium contrasts with active
transport, which requires energy because
it constitutes movement against an
electrochemical gradient.
1. Required Texts And Resources: Lippincott
Illustrated Reviews, 3rd edition, Champe &
Harvey P :
2. Reading Handouts will be distributed
3- Lectures and power point presentation
will be published on department website:
www.kaau.edu.sa/faculties/medicine/dcbcweb



You have the opportunity to watch the CDROM about Membrane transport. You can
access the CD-ROM during your spare time.
1-Membrane transport 1
http://www.emc.maricopa.edu/faculty/farabee/biobk/B
ioBooktransp.html
2-Transport across cell membrane
http://users.rcn.com/jkimball.ma.ultranet/BiologyPage
s/D/Diffusion.html
3-Membrane transport mechanisms
http://physioweb.med.uvm.edu/bodyfluids/membrane.
htm
4- Cell membrane and transport mechanisms
http://staff.jccc.net/PDECELL/cells/transport.html
60
1- In a table form, describe Major
mechanisms used to transfer material,
mention the characteristics of each of
them including the factor affecting and
the need for energy.
I- Short Questions:
1- Give the definition for the following:
a- Simple diffusion
b- Facilitated diffusion
c- Uniport, antiport, symport
d- Active transport
e- Endocytosis
II- MCQ:
1- Very large molecules (macromolecules)
can be transported across membranes by :
A. pores or channels with very large
openings through the center
B. active transport proteins
C. diffusion down a concentration gradient
D. endocytosis or exocytosis
2- Another name for facilitated diffusion is
A. Active transport
B. Transverse diffusion
C. Lateral diffusion
D. Passive transport
3- Facilitated diffusion (passive transport)
through a biological membrane is:
A. generally irreversible
B. driven by the ATP to ADP conversion
C. driven by a concentration gradient
D. endergonic
III- True / False
a- Proteins that transport water across cell
membranes are called aquaporins.
b- Symport and antiport proteins must be
active transport proteins.
61
c- Active transport involves the conversion of
ADP to ATP.
d- Endocytosis is the process by which cells
take up large molecules
e- In adipocytes and muscle, glucose enters by
facilitated diffusion
62
LECTURE # (14): carbohydrate Chemistry
DEPARTMENT: Clin. Biochemistry UTOR: Dr.
63
Dr.
TEACHING LOCATION: Auditorium
By the end of this lecture, you will be able to:
1. Identify the wide range of functions of carbohydrates.
2. Classify carbohydrates.
3. Differentiate isomers, epimers and enantiomers.
4. Identify cyclization of manosaccharides to know anomers,
mutarotation and glycosides.
5. Discuss some important chemical reactions of manosaccharides.
 Introduction
 Functions of carbohydrates
 Classification:
- Monosaccharides
- Disaccharides
- Polysaccharides
 Homopolysaccharides
 Heterapolysaccharides
Carbohydrates are aldhyde or ketone derivatives of
polyhydric alcohol, they contain the elements carbon,
hydrogen and oxygen. Hydrogen and oxygen are
64
present in the same ratio as water 2:1.
Carbohydrates are important biomolecules performing
several Biological functions
1. Required Texts And Resources: Lippincott Illustrated
Reviews, 3rd edition, Champe & Harvey
2. Reading Handouts will be distributed
3- Lectures and power point presentation will be published on
department website: www.kaau.edu.sa/faculties/medicine/dcbcweb



You have the opportunity to watch the CD-ROM about
Carbohydrate Chemistry. You can access the CD-ROM during your
spare time.
1- Properties of Biomolecules
http://www.phschool.com/science/biology_place/biocoach/bioprop
/intro.html
2- Animated Biomolecules
http://www.umass.edu/microbio/rasmol/scripts.htm
3- Basic Biochemistry of Biomolecules:
http://web.indstate.edu/thcme/mwking/biomolecules.html
1. Describe and compare the structures of cellulose and
amylopectin. What is the general function of each of these
polymers? How are their polymeric structures suited to their
cellular functions? How does glycogen structure differ from
amylopectin? How is this important to the role of glycogen.
1- Both glycogen and cellulose are polymers of glucose,
65
however glycogen forms an open, water-filled structure,
while cellulose is linear and rigid. Compare the sructures of
these molecules and explain how they suit their respective
functions.
2- Cellulose and starch are both polymers of glucose, yet
most mammals can use starch, but not cellulose, as a source
of fuel. Explain.
I- Short Questions:
A- Describe the following, explain the difference between each
pair:
1. D versus L sugars (give an example of each)
2. Aldose versus ketose (give an example of each)
3. α and β anomers of D-glucose (give an example of each)
4. Glucose versus glucosamine.
B- Give one example for each of the following:
1- Ketohexose
2- Aldopentose
3- Aldotriose
4- Heteropolysaccharide
5- Homopolysaccharide
II- MCQ:
1- The sugar residues of amylose are:
(A)Glucose units liked in β-1,4 linkages
(B)Glucose units liked in α l,4-linkages
(C ) Both galactose and fructose units liked in α l,4linkages
(D) fructose units liked in α l,4-linkages
2. Which of the following contains ketone group?
(A) Glucose
(B)Mannose
(C) Ribulose
(D)Galactose
3. Hydrolysis of sucrose yields:
66
(A)Two moles of glucose
(B)Glucose and fructose
(C )Galactose and fructose
(D)Glucose and mannose
III- True / False
1. The chemical formula of a monosaccharide is C6H12O6
2. Monosaccharides are classified according to the
functional group into trioses, tetroses, pentoses,
hexoses, ….etc.
3. 3. Carbohydrates are hydrates of carbon in which
hydrogen and oxygen are present with the same ratio
in water (2:1)
4. Oligosaccharides contains more than 10 sugar units.
5. Asymmetric carbon atom is the carbon atom attached
to four different atoms or groups.
67
LECTURE # (15 - 16 ): Introduction to Metabolism, Bioenergetics, and the
Role of ATP
DEPARTMENT: Clin. Biochemistry
TUTOR:
TEACHING LOCATION: Auditorium
By the end of this lecture, you will be
able to:
1. Compare and contrast catabolism
and anabolism
2. Outline the general mechanisms
for regulating metabolic pathways
through enzymes.
3. Understand the role of ADP/ATP
in connecting catabolic and
anabolic reactions. How does the
structure of these molecules
allow them to mediate energy
requiring reactions?
4. Compare the two physiological
mechanisms for the net synthesis
of ATP
5. Be able to determine the direction
in which electrons would pass in
an oxidation-reduction couple,
given either ΔG’ or ΔE’.
6. Be familiar with the relative
oxidation reduction potentials of
NAD, FAD (FMN), ubiquinone,
cytochromes c and a, and
oxygen.
7. Understand the importance of
various
mitochondrial
compartments in cellular energy
production.
8. Explain the relationship between
electron flow and ATP production
in
the
mitochondria
(chemiosmotic theory of Peter
68
Student Notes:
.
Mitchell).
9. Describe the components of the
electron transport chain, including
the points where common
inhibitors act.
10. Discuss the mechanism of
ATP
production
in
the
mitochondria.
11. Understand the concepts of
respiratory control and coupling.
 Metabolic Pathways
1- Definition, classification
(Anabolism &
Catabolism)
2- Catabolic phase
3- Low and high energy
bonds – ATP – ADP
cycle
4- Mechanism of
collection of energy
 Regulation of Metabolism
1- Signals from within the
cells
2- Communication
between cells
3- Intracellular messenger
systems
 Electron transport chain (ETC)
1- Components of ETC
2- Electron transport
3- Chemiosmotic
hypothesis
4- ATP synthesis
5- Inhibition of ETC
6- Uncouplers
69
In order to survive, humans must
meet two basic metabolic requirements:
we must be able to synthesize everything
our cells need that is not supplied by our
diet, and we must be able to protect our
internal environment. In order to meet
these requirements, we metabolize our
dietary components through four basic
types of pathways: Fuel oxidative
pathways, fuel storage and mobalization
pathways, biosynthetic pathways, and
detoxification or waste disposal pathways.
1- Required Texts And Resources:
Lippincott Illustrated Reviews, 3rd
edition, Champe & Harvey P: 69 – 82 &
P: 89 - 94
2. Reading Handouts will be
distributed
3- Lectures and power point
presentation will be published on
department website:
www.kaau.edu.sa/faculties/medicine/
dcbcweb



You have the opportunity to watch the CDROM about Bioenergetics and introduction
to metabolism . You can access the CDROM during your spare time.
1- Overview of metabolism
http://www.elmhurst.edu/~chm/vchembook/5900verviewmet
.html
2- Introduction to metabolism (PowerPoint)
http://www.rit.edu/~pac8612/Biochemistry/503(703)/ppt/Intr
oduction_to_Metabolism.ppt
70
3- Electro Transport chain(ECT)
http://www.dentistry.leeds.ac.uk/biochem/lecture/etran/etra
n.htm
4- Electro Transport chain(ECT)
http://vcell.ndsu.nodak.edu/animations/etc/movie.htm
5- ECT Animation
http://www.sp.uconn.edu/~terry/images/anim/ETS_slo
w.html
6- ATP Synthesis Animation
http://www.sp.uconn.edu/~terry/images/anim/ATPmit
o.html
7- ECT Movie
http://vcell.ndsu.nodak.edu/animations/etc/movie.htm
1- Regulation of metabolism is
based on need, from your studying
outline the factors regulating
metabolism and how they work
according to body needs?
2- Summarize the composition of
each of the respiratory chain
complexes I, III, and IV. Diagram the
pathway of electron transfer in the
mitochondrial inner membrane from
matrix NADH to oxygen, including
the smaller electron carriers,
coenzyme Q and cytochrome?
1- If sodium ions rather than
protons were pumped across
the mitochondrial membrane,
would there be any energy
available to couple to ATP
synthesis?
2- Clinical Question
The desire for a quick weightloss drug has led to a number
of disasters. In the 1930s,
dinitrophenol was explored as
a possible weight-loss aid, but
71
it had a variety of severe side
effects, including
hyperthermia and death. Why
was dinitrophenol a bad idea?
Explain how dinitrophenol
induces hyperthermia
I- Short Questions:
1- Give the definition for the
following:
a- Anabolic reaction
b- Catabolic reaction
c- Free Energy Change
d- Electron Transport Chain
2. Enumerate components of Electron
Transport Chain, How many ATP
molecules will be produced from
oxidation of One NADH+H+,
FADH2 respectively, in the chain?
3-
How cAMP activates some
metabolic reactions and inhibits
others?
II- MCQ:
1. In the mitochondria NADH and QH2 are
oxidized by ____________.
(a) carbon dioxide
(b) hydrogen peroxide
(c) ozone
(d) oxygen
2. The synthesis of one molecule of ATP
from ADP requires _________ to be
translocated across the inner mitochondrial
membrane.
(a) one proton
72
(b) about two protons
(c) hundreds of protons
(d) 1 mole of protons
3. The degradation of which class of
biochemicals
does
not
significantly
contribute to the release of
energy to cells?
(a) nucleic acids
(b) Proteins
(c) Lipids
(d) carbohydrates
III- True / False
a. The biochemical reactions
that degrade molecules,
such as nutrients, are
called anabolic reactions
b. Metabolic
pathways
generally
have
easily
distinguished starting and
stopping points
c. All metabolic reactions
occur in the cytosol of
cells
d. In mammals the enzyme
complexes of oxidative
phosphorylation are in
the inner mitochondrial
e. Most of the free energy
needed
to
drive
ATP
formation
in
the
mitochondria is the result
of an
electrical
contribution
from a charge gradient
across
the
inner
mitochondrial membrane
matrix.
73
LECTURE # (17) : Glycolysis
DEPARTMENT: Clinical Biochemistry
TUTOR:
TEACHING LOCATION: Auditorium
By the end of this lecture you will
be able to:
1- Define glycolysis, form a working
definition knowing the substrates
and products involved and any
other key intermediates produced.
2- Trace
tissue
location
of
glycolysis, particularly tissues or
cells in the body where the
pathway is most important.
3- Locate the cell site of glycolysis,
where in the cell it occurs
(cytosol).
4- Describe the sequence of events,
the overall reaction sequence and
the number of stages and
reactions:
a. Material Flow:: Trace the
fate of labeled carbon or
other elements through the
pathway
b. Energy flow: Trace
the
production and consumption
of ATP
c. Electron flow: trace the
production and consumption
of reducing power
74
Student Notes:
.
5- Identify the Key steps, either
those which form major control
sites or those which are main "
branch points"
6- Describe connections to other
pathways especially citric acid
cycle .





Overview of Glycolysis
Coupled Reactions in Glycolysis
First Phase of Glycolysis
Second Phase of Glycolysis
Metabolic Fates of NADH and
Pyruvate
 Anaerobic Pathways for Pyruvate
 Energetic Elegance of Glycolysis
 Other Substrates in Glycolysis
The glycolytic pathway is employed by all
tissues for the breakdown of glucose to
provide energy ( in the form of ATP) and
intermediates
for
other
metabolic
pathways.
1.
Required Texts And Resources:
Lippincott Illustrated Reviews, 3rd
edition, Champe & Harvey
2. Supplementary Texts And Resources:
Medical Biochemistry, Baynes and
Dominiczek, 1st edition, Mosby


75

You have the opportunity to watch the CDROM about glycolysis. You can access
the CD-ROM during your spare time.
1. Introduction to Glycolysis:
http://www.terravivida.com/vivida/glyintro/
2. Glycolysis Lecture:
http://web.indstate.edu/thcme/mwking/glyc
olysis.html
3. Glycolysis Animation:
http://www.johnkyrk.com/glycolysis.html
4. Glycolysis Home:
http://biotech.icmb.utexas.edu/glyco
lysis/glycohome.html
3- List the enzymes that convert glucose
to glyceraldehyde 3-PO4. Add to your
list the substrates, products, and
cofactors for each of these enzymes. It
might be handy to make up a table
for this.
4- List the enzymes that convert
glyceraldehyde 3-PO4 to pyruvate.
Add to your list the substrates,
products, and cofactors for each of
these enzymes. It might be handy to
make up another table for this.
2- Clinical Question
Predict the effect of a GLUT4
knockout (in mice) on the levels
76
of blood glucose before and after
a meal. Search the Internet and
report whether your predictions
were confirmed by experiment.
Of what use is a GLUT4 knockout
mouse?
3- Clinical Case
Ahmed entered the stadium
for the final lap of his
marathon race. He was well
ahead of his competitors. In
the last few minutes, he
became confused. In the
stadium, he started running
around the track in the wrong
direction and then collapsed.
What went wrong?
I- Short Questions:
1- Give the cellular location of the
glycolytic pathway.
2- Where is NADH produced ?
3. Which step produces ATP? Which
one of these is considered to be
'substrate level phosphorylation?
4- Name the enzyme that makes
anaerobic glycolysis possible by
using up the NADH that
accumulates.
5 -Consider
the ten steps of glycolysis,
starting with glucose. What would
be the effect on pyruvate
concentration (increase, decrease
or none) of increasing the
concentration of the following?
Give a brief (one sentence)
explanation for your answer.
77
a) ATP
b) AMP
c) citrate
d) fructose-1,6-bisphosphate
e) fructose-2,6-bisphosphate
II- MCQ:
1- Which of the following
metabolites does not regulate
glycolysis in liver cells?
A. glucose-6-phosphate
B. fructose-6-phosphate
C. fructose-1-phosphate
D. fructose-2,6-bisphosphate
2-During kinase reactions, the role
of magnesium ions is to
A. be catalytic metals at the active sites
of the enzymes.
B. interact with the hydroxyl groups of
the various sugar molecules.
C. interact with the negative charges on
phosphate groups.
D. provide a bridging atom between
substrate and product, stabilizing
the transition state.
3- Which of the following is not a
substrate for hexokinase?
A. glucose
B. fructose
C. galactose
D. mannose
3- How many ATP molecules are
produced from glucose during
78
anaerobic glycolysis?
A. 0
B. 1
C. 2
D. 3
III- True / False
a. Four molecules of ATP are
consumed per glucose
during the hexose stage
of glycolysis
b. The reaction catalyzed by
PFK-1
is
metabolically
reversible
c. Mammals
can
convert
pyruvate to either ethanol
or lactate depending on
the availability of oxygen
d. Glucose
is
normally
transported into cells by
an
active
transport
protein
since
the
concentration of glucose
inside cells is normally
higher than that in the
blood.
e. Two molecules of ATP are
consumed per glucose
molecule during the
hexose stage of glycolysis
79
LECTURE # (18) : Tricarboxylic Acid Cycle (TCA)
Student Notes:
DEPARTMENT: Clinical Biochemistry
.
TUTOR:
TEACHING LOCATION: Auditorium
By the end of this lecture you will
be able to:
1. Define TCA, form a working
definition
knowing
the
substrates
and
products
involved and any other key
intermediates produced.
2. Trace tissue location of TCA,
particularly tissues or cells in
the body where the pathway is
most important.
3. Locate the cell site of TCA,
where in the cell it occurs
(Mitochondria).
4. Describe the sequence of
events, the overall reaction
sequence and the number of
stages and reactions:
a- Material Flow:: Trace the
fate of labeled carbon or
other elements through
the pathway
b- Energy flow: Trace the
production
and
consumption of ATP
c- Electron flow: trace the
production
and
consumption of reducing
80
power
5. Identify the Key steps, either
those which form major control
sites or those which are main "
branch points"
6. Describe connections to other
pathways
related
to
carbohydrate, lipid and amino
acids metabolism
7. Describe
the
amphibolic
aspects of TCA and the role of
its intermediate in various
metabolic process.
8. Diagram the shuttles for the
transport of cytoplasmic reducing
equivalents into the mitochondria
 Overview of TCA
 Reaction of the TCA cycle
a- Oxidative decarboxylation
of pyruvate
b- The eight sequential
reactions of TCA
 Energy produced by the cycle
 Regulation of the TCA cycle
The tricarboxylic acid cycle (TCA) is
also called citric acid cycle or Kreb's cycle.
It is the major final common pathway of
oxidation of carbohydrates, lipids and
proteins since their oxidations yield Acetyl
Co A. It also plays a major role in
lipogenesis,gluconeogenesis,
transamination and deamination.
81
1.
Required Texts And Resources:
Lippincott Illustrated Reviews, 3rd
edition, Champe & Harvey P: 107 - 114
2. Supplementary Texts And Resources:
Medical Biochemistry, Baynes and
Dominiczek, 1st edition, Mosby



You have the opportunity to watch the CDROM about TCA. You can access the CDROM during your spare time.
1- TCA animation
http://www.science.smith.edu/departments/Biology/
Bio231/krebs.html
2-TCA animation
http://www.wiley.com/legacy/college/boyer/04700037
90/animations/tca/tca.htm
3- TCA
http://www.sigmaaldrich.com/Area_of_Interest/Life_
Science/Metabolomics/Key_Resources/Metabolic
_Pathways/TCA_Cycle.html
4- Step by step Kreb’s cycle
http://www.terravivida.com/vivida/tcasteps/
5- Biochemistry animations
http://www.wiley.com/college/fob/anim/
a. Diagram the Krebs Citric Acid Cycle,
82
beginning with pyruvate, giving the
names of all enzyme substrates and
products and names of enzymes (no
abbreviations). Indicate where NAD+,
NADH, FAD, FADH2, GDP, Pi, GTP,
coenzyme A, H2O, or CO2 are
substrates or products of reactions.
b. What is the fate of reducing equivalents
of FADH2 generated in Krebs Cycle?
1- Clinical Question
A patient diagnosed with
thiamine deficiency exhibited
fatigue and muscle cramps.
The muscle cramps have been
related to an accumulation of
metabolic acid. What is the
metabolic product leads to this
condition? Explain your
answer.
I- Short Questions:
1- What is the intercellular location of
TCA?
2- What is the sources of Acetyl
CoA?
3- What are the products of TCA?
4- Describe the functions of 2
intermediates of TCA?
5- Summarize the functions of TCA.
II- MCQ:
1- The citric acid cycle oxidizes
pyruvate and some of the pathway
intermediates are starting
materials for many biosynthetic
83
pathways. This means the citric
acid cycle is a/an
______________.
A.
B.
C.
D.
amplifying pathway
strictly catabolic pathway
anaerobic pathway
amphibolic pathway
2- In eukaryotes the enzymes of
the citric acid cycle are found in the
_________.
A. cytosol
B. mitochondria
C. nucleus
D. endoplasmic reticulum
3- The enzyme pyruvate
translocase is located
______________.
A. in the cytosol
B.in the inner mitochondrial
membrane
C. in the mitochondrial matrix
D. in the endoplasmic reticulum
III- True / False
1- The overall goal of the citric
acid cycle is to oxidize
pyruvate, form reduced
coenzymes and produce ATP
2- The citric acid cycle is an
anaerobic pathway that occurs
in the mitochondria of
eukaryotes.
3- ATP is consumed by the
pyruvate dehydrogenase
complex during the synthesis
of acetyl CoA
4- The citric acid cycle can be
viewed as a multi-step catalyst
simply because it returns to its
original state after each round
of reactions.
5- Isocitrate is more easily
84
oxidized than citrate because
it has a secondary alcohol
group, whereas citrate's
alcohol group is tertiary
85
LECTURE # (19) : Gluconeogenesis
DEPARTMENT: Clinical Biochemistry
TUTOR:
TEACHING LOCATION: Auditorium
By the end of this lecture you will be
able to:
1- Define
Gluconeogenesis,
form a working definition
knowing the substrates and
products involved and any
other key intermediates
produced.
2- Trace tissue location of
gluconeogenesis,
particularly tissues or cells
in the body where the
pathway is most important.
3- Locate the cell site of
gluconeogenesis, where in
the cell it occurs (cytosol)
Except for the carboxylation
of pyruvate, which occurs in
mitochondria.
4- Describe the sequence of
events, the overall reaction
sequence and the number of
stages and reactions:
a. Material Flow:: Trace
the fate of labeled
carbon
or
other
elements through the
pathway
b. Energy flow: Trace
86
Student Notes:
.
the production and
consumption of ATP
c. Electron flow: trace the
production
and
consumption
of
reducing power
5- Describe the sequence of
events, the overall reaction
sequence and the number of
stages and reactions
6- Identify the Key steps, either
those which form major
control sites or those which
are main " branch points"
7- Describe connections to
other pathways, especially
glycolysis and the reciprocal
regulation of both pathway
8- Identify
the
non
carbohydrate sources of
gluconeogenesis.
 Overview of gluconeogenesis
 Substrates for gluconeogenesis
 Reactions unique to
gluconeogenesis
 Regulation of gluconeogenesis
87
Gluconeogenesis is ' production of
glucose from non – carbohydrate sources'
For a period of starvation of longer than
about 12 hours. This pathway is very
important for tissues which require a
continuous supply of glucose as a
metabolic fuel such as the brain, red
blood cells, kidney medulla, lens and
cornea of the eye, testes and exercising
muscle.
1.
Required Texts And Resources:
Lippincott Illustrated Reviews, 3rd
edition, Champe & Harvey p: 115 - 122
2. Supplementary Texts And Resources:
Medical Biochemistry, Baynes and
Dominiczek, 1st edition, Mosby



You have the opportunity to watch the CDROM about gluconeogenessis. You can
access the CD-ROM during your spare
time.
1- Gluconeogenesis
http://web.indstate.edu/thcme/mwking/gluconeogenesi
s.html
2- Gluconeogenesis
http://www.answers.com/topic/gluconeogenesis
3- Gluconeogenesis animation
http://www.wiley.com/college/fob/quiz/quiz15/1522.html
4- Gluconeogenesis powerpoint presentation
http://www.sb.fsu.edu/~chapman/Classes/Bch4054/Co
ntent/Gluconeogenesis.pdf
88
1. a. Write out the two sequential
reactions
catalyzed
by
Pyruvate
Carboxylase,
giving
names
and
structures of reactants and products,
including the active site prosthetic
group. What is the nature and
significance of the linkage of the
prosthetic group to the Pyruvate
Carboxylase enzyme?
b. Describe and explain the significance
of the effect of acetyl coenzyme A on the
Pyruvate Carboxylase enzyme.
1- Why
would
it
be
disadvantageous
to
the
organism to have Glycolysis
and
Gluconeogenesis
operating
simultaneously
within
a
cell?
Briefly
describe one example of
reciprocal
regulation
of
Glycolysis
and
Gluconeogenesis, involving
an allosteric regulator. For
the example chosen, write
out the reaction catalyzed
by the enzyme in each
pathway, and indicate the
nature of the effect of the
regulator (e.g., inhibition or
activation).
89
I- Short Questions:
1- Give the cellular location of the
gluconeogenesis pathway.
2- Enumerate the sources for
gluconeogenesis ?
3. Define futile cycle, relate it to
gluconeogenesis?
4- What are the irreversible reactions
unique to gluconeogenesis?
5- How many ATP are consumed for
synthesis of one molecule glucose
from 2 pyruvates
II- MCQ:
1- Gluconeogenesis is
A. The formation of glycogen
B.The formation of starches
C.The formation of glucose from
noncarbohydrates
D.The formation of glucose from other
carbohydrates
2- Gluconeogenesis uses the same
enzymatic reaction of glycolysis
except for
A. Pyruvate kinase
B.4 irreversible reactions in glycolysis
C.3 irreversible reactions in glycolysis
D.2 irreversible reactions in glycolysis
3- Any compound that can be
converted
to
_____can
be
a
precursor for gluconeogenesis.
A. Citrate
B.Pyruvate
C.Oxaloacetate
D.b and c
III- True / False
1- Glucagon increases the
transcription of the gene
90
2-
3-
45-
for PEP carboxykinase in
gluconeogenesis,
while
insulin decreases it.
Fructose
2,6bisphosphate
is
a
modulator
that
can
stimulate
either
glycolysis
or
gluconeogenesis,
depending
on
cellular
glucose concentrations.
At
high
glucagon
concentrations
gluconeogenesis will be
favored over glycolysis.
The brain normally uses
both glucose and fatty
acids as energy sources.
Glycerol is one of the
precursor
for
gluconeogenesis.
91
LECTURE # (20) : Pentose phosphate pathway
Student Notes:
DEPARTMENT: Clinical Biochemistry
.
TUTOR:
TEACHING LOCATION: Auditorium
By the end of this lecture you will be
able to:
1. Define the pentose phosphate
pathwaw , form a working
definition knowing the substrates
and products involved and any
other key intermediates produced.
1- Trace tissue location of pentose
phosphate pathwaw, particularly
tissues or cells in the body where
the pathway is most important.
2- Locate the cell site of glycolysis,
where in the cell it occurs
(cytosol).
3- Describe the sequence of events,
the overall reaction sequence and
the number of stages and
reactions:
a. Material Flow:: Trace
the fate of labeled
carbon
or
other
elements through the
pathway
b. Energy flow: Trace
the production and
consumption of ATP
92
c. Electron flow: trace the
production
and
consumption
of
reducing power
4- Identify the Key steps, either
those which form major control
sites or those which are main "
branch points"
5- Describe connections to other
pathways, with the emphasis on
the role of NADPH in other
biochemical pathways
 Overview of pentose phosphate
pathwaw
 Irreversible oxidative reactions
 Reversible nonoxidative reactions
 Uses of NADPH
 Glucose 6 – phosphate
Dehydrogenase Deficiency
The pentose phosphate pathway occurs in
the cytosol of the cell. The pathway
provides a major portion of body's
NADPH, which functions as a biochemical
reductant. It also produces ribose 5phosphate required for the biosynthesis of
nucleotides.
93
1.
Required Texts And Resources:
Lippincott Illustrated Reviews, 3rd
edition, Champe & Harvey P: 143- 154
2. Supplementary Texts And Resources:
Medical Biochemistry, Baynes and
Dominiczek, 1st edition, Mosby



You have the opportunity to watch the CDROM about pentose phosphate pathway.
You can access the CD-ROM during your
spare time.
1- Pentose phosphate pathway
http://web.indstate.edu/thcme/mwking/pentosephosphate-pathway.html
2- Pentose phosphate pathway
http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/m
b2/part1/pentose.htm
3- Pentose phosphate pathway (PowerPoint)
presentation
www.cwu.edu/~geed/543/Pentose%20Phosphate%20Pat
hway.ppt
4- Pentose phosphate pathway (poweeroint )
www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb2/part1/15pentose.ppt
1- Diagram and describe the
mechanism of the reaction
catalyzed by the enzyme
Transaldolase, including structures
of major intermediates.
2. Write out the linear (oxidative)
portion of the Pentose Phosphate
Pathway, giving names and
structures of substrates and
reactants, and the name of each
enzyme. Summarize in words what
happens at each step. What two
94
products of the linear portion of the
Pentose Phosphate Pathway have
essential roles in anabolic
metabolism? What are these roles?
Clinical Question
1- In male patients who are
homozygous for glucose 6phosphate dehydrogenase (G6PD)
deficiency, pathophysiologic
consequence are more apparent in
erythrocytes (RBCs) than in other
cells, such as in the liver. EXPLAIN.
I- Short Questions:
1- Give the cellular location of the
pentose phosphate pathway
2- What are the main products of
pentose phosphate pathway ?
3. Enumerate sources of NADPH?
4- What are the uses of NADPH in our
body. Enumerate? .
5-
What are the effects of glucose 6phosphate dehydrogenase
deficiency
II- MCQ:
1- The major regulatory step of the
pentose phosphate pathway is
catalyzed by which enzyme?
A. transaldolase
B. phosphofructokinase-1
C. glucose 6-phosphate dehydrogenase
95
D. ribose 5-phosphate isomerase
2- The non-oxidative stage of the
pentose phosphate pathway
produces substances that are
intermediates of ___________.
A. glycolysis
B. the citric acid cycle
C. the Cori cycle
D. glycogenolysis
3- Which is not a function of the
main products of the pentose
phosphate pathway?
A. To maintain the reduced form of iron in
hemoglobin.
B.To provide reducing power for the
synthesis of fatty acids.
C. To serve as precursors in the
biosynthesis of RNA and DNA.
D.To raise the concentration of cAMP.
III- True / False
1- Glucose 1,6-bisphosphate is
the primary starting substrate
for the pentose phosphate
pathway.
2- Two molecules of NADPH are
generated for each molecule of
glucose 6-phosphate that
enters the pentose phosphate
pathway.
3- Rapidly dividing cells generally
have a high pentose phosphate
pathway activity.
4- The enzyme transketolase
transfers 2-carbon units from
ketose phosphates to aldose
phosphates
5- NADH and pentose are the
main products of pentose
phosphate pathway
96
LECTURE # (21): Metabolism of Monosaccharides and Disaccharides
DEPARTMENT: Clinical Biochemistry
TUTOR:
TEACHING LOCATION: Auditorium
By the end of this lecture you will
be able to:
1- Define pathways for fructose,
Galactose
and
Lactose
Metabolism , form a working
definition
knowing
the
substrates
and
products
involved and any other key
intermediates produced.
2- Trace tissue location of these
pathways, particularly tissues
or cells in the body where the
pathway is most important.
3- Locate the cell site of these
pathways, where in the cell it
occurs (cytosol).
4- Describe the sequence of
events, the overall reaction
sequence and the number of
stages and reactions:
a. Material Flow:: Trace
the fate of labeled
carbon
or
other
elements through the
pathway
b. Energy flow: Trace
97
Student Notes:
.
the production and
consumption of ATP
c. Electron flow: trace the
production
and
consumption
of
reducing powerIdentify
the Key steps, either
those which form
major control sites or
those which are main "
branch points"
5- Describe connections to other
pathways especially Glycolysis




Overview
Fructose metabolism
Galactose metabolism
Lactose synthesis
Although many monosaccharides have
been identified in nature, only a few
sugars appear as metabolic intermediates
or as structural components in mammals.
The major source of fructose is sucrose,
while the major dietary source of
galactose is lactose, entry of both to cells
is insulin - independent both can be
metabolized for energy generation through
glycolysis.
98
1.
Required Texts And Resources:
Lippincott Illustrated Reviews, 3rd
edition, Champe & Harvey P: 135 - 142
2. Supplementary Texts And Resources:
Medical Biochemistry, Baynes and
Dominiczek, 1st edition, Mosby



You have the opportunity to watch the CDROM about Monosaccharide metabolism.
You can access the CD-ROM during your
spare time.
1- Fructose Metabolism
http://www.gpnotebook.co.uk/cache/1798635578.ht
m
2-Fructosa Web site
http://www.drkaslow.com/html/fructose.html
3- Fructose and Galactose Metabolism
http://web.indstate.edu/thcme/mwking/non-glucosesugar-metabolism.html
4- Galactose Metabolism
http://www.gpnotebook.co.uk/cache/1899298874.htm
Describe, how different monosaccharides
can be interconverted, Explain the
benefits of this interconversion to body
metabolism.
99
1- Clinical Question
A newborn baby experienced
abdominal distension, severe
bowel cramps, and diarrhea
after being fed milk. A
hydrogen analysis of his
exhaled breath discovered an
eighty – fold increase in the
production of H2 ninety
minutes after milk feeding.
a- Explain the case
b- This condition is
preventable or not?
2- Clinical Case
A galactosemic female is able
to produce lactose, How?
I- Short Questions:
1- What is the main source of dietary
fructose?.
2- What is the main source of dietary
galactose?.
3. Although fructose is more sweaty
than Glucose it is not
recommended to be an exchange
to it in our diet
4- What is the effects Galactokinase
deficiency.
5- Define fructosuria, what is its
cause.
II- MCQ:
1- 1- Which is an intermediate
formed in the conversion of glucose
100
to fructose?
A. glucose-1-phosphate
B. sorbitol
C. ribose
D. aldose reductase
2- What types of reactions are
involved in the two-step conversion
of glucose to fructose?
A. reduction followed by oxidation
B. two sequential hydrolysis reactions
C. hydrolysis followed by isomerization
D. phosphorylation followed by
dephosphorylation
3- What is a cause of cataracts in
the eye lens of individuals with
diabetes?
A.Accumulation of sorbitol and protein
precipitation in the lens.
B. Precipitation of glucose not oxidized
by glycolysis in the lens.
C. The absence of membrane transport
proteins for pyruvate in the lens cells.
D. Lack of regulation of gluconeogenesis
in the lens and the accumulation of
fructose.
III- True / False
1- Lactose is the main source
of dietary fructose.
2- Absorption of fructose is insulin
dependent.
3- Aldose reductase reduces
glucose, producing sorbitol
4- Classic galactosemia results from
missing of Galactose kinase
5- Lactose is synthesized by lactase
synthase from UDP glucose and
Galactose.
101
102
LECTURE # (22-23): Structure of lipids
DEPARTMENT: Clin. Biochemistry
103
Student Notes:
.
TUTOR: Dr.
Dr.
TEACHING LOCATION: Auditorium
By the end of this lecture, you will be able
to:
1. Identify the functions of lipids
2. Classify lipids.
3. Discuss the different basis for
classification of fatty acids.
4. Identify the structure of different
substances of compound lipids.
5. Discuss the structure and functions of
different steroid compounds.
6. Identify caratenoids and their importance
to human body.
 Introduction
 Functions of lipids
 Fatty acids:
- Saturated
- Unsaturated
 Simple lipids
 Conjugated lipids:
- phospholipids
- glycolipids
- lipoproteins
 Derived lipids
- steroids
- caratenoids
Lipids are substances insoluble in water and
soluble in fat solvents. They are utilized in
the body. They are classified into simple,
conjugated and derived Lipids
104
1- Required Texts And Resources:
Lippincott Illustrated Reviews, 3rd
edition, Champe & Harvey
2. Reading Handouts will be distributed
3- Lectures and power point
presentation will be published on
department website:
www.kaau.edu.sa/faculties/medicine/dc
bcweb



You have the opportunity to watch the CDROM about Lipid Structure. You can access
the CD-ROM during your spare time.
1- Properties of Biomolecules
http://www.phschool.com/science/biology_pla
ce/biocoach/bioprop/intro.html
2- Animated Biomolecules
http://www.umass.edu/microbio/rasmol/script
s.htm
3- Basic Biochemistry of
Biomolecules:
http://web.indstate.edu/thcme/mwking/biomol
ecules.html
1- In table form, describe different
types of conjugated lipids, mention
their biological importance
1- Both Lipids and Carbohydrates are
organic compounds, formed mainly
from Hydrogen, Oxygen and Carbon,
Explain why energy content of lipids is
greater than carbohydrates.
105
I- Short Questions:
1- How can you tell whether a
particular fatty acid is, or is not,
essential?
2. How many fatty acids contain 18
carbon atoms, enumerate?
3- Enumerate different types of
glycerophospholipids.
4- What is main differences between
HDL and LDL?
5- Give 2 example for hormones
derived from cholesterol.
II- MCQ:
1. True statements about lipids include the
following except:
(a) They are an intracellular energy
source
(b) They are poorly soluble in water
(c) They are structural components of
membranes
(d) They are composed of only carbon,
hydrogen and oxygen
2. Fatty acids that are dietary essentials in
humans include which of the following:
(e) Palmitic acid
(f) Stearic acid
(g) Oleic acid
(h) Linoleic
3. A choline residue is present in which of
the following lipids?
(e) Phosphatidic acid
(f) Ganglioside
(g) Cholesterol
106
(h) Sphingomyelin
III- True / False
1- Sphingosine is the backbone of
lecithin
2- Palmitic acid is an essential
fatty acid
3- Stearic acid is non essential
fatty acid
4- Chylomicrons are synthesized
in the small intestine, formed
mainly of triglyceride.
5- Vitamin E is one of cholesterol
derivatives
107
LECTURE # (24-25) : Fatty acid oxidation
DEPARTMENT: Clinical Biochemistry
TUTOR:
TEACHING LOCATION: Auditorium
By the end of this lecture you will be able
to:
1- Sequence the reactions catalyzed by acylCoA synthetase, carnitine palmitoyl
transferaseI,carnitine-acylcarnitine
translocase, and carnitine palmitoyl
transferaseII.
2Indicate which of these enzymes is
regulated by malonyl-CoA.
3- Explain the importance of carnitine for the
oxidation of long-chain fatty acid but not
short- and medium-chain fatty acids.
4-
Discuss the steps of beta oxidation of
fatty acids.
5- Explain the importance of citric acid cycle
for the oxidation of fatty acids .
6-
Calculate the yield of ATP that is formed
through the complete oxidation of one
mole of palmitic acid.
7- Indicate the roles of long chain-, medium
chain- and short chain-acyl CoA
dehydrogenases in the oxidation of
long chain fatty acids. Explain why a
defect in the medium chain enzyme
results in excretion of dicarboxylic acids
and acyl carnitine esters in the urine.
 Tissues that are most active in
oxidation of fatty acids and its sub
108
Student Notes:
.








cellular location
Conditions which favor the process
of oxidation of fatty acids
Role of carnitine in the process of
beta oxidation
The difference in oxidation of long,
medium and short chain fatty acids
The steps of beta oxidation
Energy gained of beta oxidation
Regulation of beta oxidation
The other types of fatty acid
oxidation
Diseases associated with genetic
abnormality of fatty acid oxidation
Beta oxidation takes place in fed state in certain
tissues as a source of energy, in starvation it is
stimulated to provide energy for many tissues as
liver (which becomes completely dependent on it
as a source of energy.
1.
Required Texts And Resources:
Lippincott Illustrated Reviews, 3rd
edition, Champe & Harvey. (187-193)
2. Supplementary Texts And Resources:
Medical Biochemistry, Baynes and
Dominiczek, 1st edition, Mosby. (pp 169173)



You have the opportunity to watch the CDROM about fatty acid oxidation. You can
access the CD-ROM during your spare
time.
109
1http://www.dentistry.leeds.ac.uk/biochem/t
hcme/fatty-acid-oxidation.html
2-
http://www.biocarta.com/pathfiles/betaoxi
dationPathway.asp
3-
http://ull.chemistry.uakron.edu/Pathways/
b_oxidation/index.html
4-
http://www.biocarta.com/pathfiles/boxnpP
athway.asp
5http://www.biocarta.com/pathfiles/h_cptPathway.asp
6http://www.brookscole.com/chemistry_d/temp
lates/student_resources/shared_resources/an
imations/carnitine/carnitine1.html
7-
http://www.biocarta.com/pathfiles/oddnum
berchainPathway.asp
8http://www.biocarta.com/pathfiles/polyunsatfa
ttyacidPathway.asp
1- Try to explain the sequence of
events that takes place in the
mitochondria during beta oxidation
of fatty acid
2- Write down how beta oxidation is
regulated
1-
Clinical Question: In diabetic
patient type I, do you expect that
beta oxidation of fatty acid to be
increased, decreased or normal
and why?
110
2-
Clinical Case: A three month
old baby brought to you by his
mother, she was complaining that
the baby seemed to be lethargic
and does not grow well, and he
was on breast fed only. What
possible reason(s) may be the
cause of this condition?
I- Short Questions:
a) Name the different types of oxidation of
fatty acid
b) List the difference between fatty acid
synthesis and beta oxidation regarding
hydrogen carrier used and the site they
occur
II- MCQ:
1- Two high energy bonds are lost during
β oxidation of long chain fatty acids in:
a)
Transport of acyl carnitine
inside the mitochondria
b)
Formation of acyl CoA
inside the mitochondria
c)
Formation of acyl CoA in
the cytoplasm
d)
Release of acetyl CoA from
acyl CoA by the action of
thiolase enzyme
e) Non of the above
2- All the following are intermediate in βoxidation except:
a)
FADH
b)
NADPH
c)
NADH
d)
Acetyl CoA
e)
All of the above
111
III- True / False
a- The major type of fatty acid
oxidation in most of he tissues is
omega oxidation
b- Beta oxidation takes place in all
tissues
c- Compared to carbohydrate oxidation
of fatty acids generate smaller
quantity of ATP
112
LECTURE # (26) : Fatty acid synthesis
DEPARTMENT: Clinical Biochemistry
TUTOR:
TEACHING LOCATION: Auditorium
By the end of this lecture you will be
able to:
1-
Identify the substrate for the building of fatty
acid and where it is made. Explain how this
substrate is transferred to the cytoplasm.
2- Describe the importance of glycolysis in the
cytosol for fatty acid synthesis.
3- Discuss how the fatty acid synthase enzyme
complex works.
4- Explain how stearic acid and oleic acid are
synthesized from palmitic acid and in what
regions of the cell they are synthesized.
5- Describe the different mechanisms of shortterm control of the formation of fatty acids.
6- Indicate the roles of insulin and glucagon in the
regulation.
9- Describe long-term control (enzyme induction)
of the formation of fat. Indicate the enzymes that
are subject to long term control.
10-Explain what prevents the liver from oxidizing
fatty acids at the same time it is synthesizing fatty
acids.
 Tissue and subcellular location for
fatty acid synthesis
 Transport of the building block for
fatty acid synthesis from the
mitochondria to the cytoplasm
 The generation of the substrates for
fatty acid synthesis in the cytoplasm
 The arrangement and structure of
113
Student Notes:
.
fatty acid synthesase enzyme
 Energy requirement for fatty acid
synthesis
 Regulation of fatty acid synthesis
 Elongation and unsaturation of fatty
acid
Fatty acid synthesis is an anabolic process, so it
is favored during the fed state and inhibited
during starvation through hormonal regulation
which also activates fatty acid oxidation, so
during starvation fatty acid synthesis is shut down
and oxidation is turned on. Acetyl CoA is the
substrate for fatty acid synthesis which is
produced in the mitochondria and has to be
transported to the cytoplasm in the form of citrate.
In the cytoplasm the other requirement for fatty
acid synthesis are present (NADPH and fatty acid
synthesase complex)
1.
Required Texts And Resources:
Lippincott Illustrated Reviews, 3rd
edition, Champe & Harvey. (pp 179186)
2. Supplementary Texts And Resources:
Medical Biochemistry, Baynes and
Dominiczek, 1st edition, Mosby. (pp 179184)



You have the opportunity to watch the CDROM about fatty acid synthesis You can
access the CD-ROM during your spare
time.
1- http://ull.chemistry.uakron.edu/Path
114
ways/FA_synthesis/index.html#
2http://www.genome.ad.jp/kegg/pathway
/map/map00561.html
3http://ull.chemistry.uakron.edu/Pathways/FA_
synthesis/index.html
4http://ull.chemistry.uakron.edu/genobc/
Chapter_24/
5http://www.uic.edu/depts/mcam/mcbc/l
ect_2004/lecture_27.pdf
1- Outline and contrast the processes
of fatty acid synthesis and oxidation
2- Write down the source(s) of each of
the substrate for fatty acid synthesis
1Clinical Case
Obesity, which will be covered
in the tutorial.
I- Short Questions:
a) Name the key regulatory
enzyme in fatty acid
synthesis
b) Using a diagram drew how
this enzyme is controled
II- MCQ:
1- Acetyl groups for fatty acid synthesis is
derived mainly from:
a)
Only glucose
b)
Ketogenic amino acids
115
only
c)
Beta oxidation of fatty acid
d)
Glucose and amino acids
e) Non of the above
2- Acetyl CoA for fatty acid synthesis is
produced in the cytoplasm by the
action of:
a)
Acetyl CoA synthetase
b)
Citrate lyase
c)
Pyruvate dehydrogenase
d)
Thiolase
e)
Non of the above
II- True / False
a) The synthesis of fatty acids
occurs in the cytoplasm of
the cells
b) The key regulatory enzyme
in fatty acid synthesis is the
fatty acid synthesase
c) Insulin hormone inhibits
fatty acid synthesis
d) Citrate lyase enzyme has no
role in the process of fatty
acid synthesis
116
LECTURE # (27) : Ketone bodies metabolism
DEPARTMENT: Clinical Biochemistry
TUTOR:
TEACHING LOCATION: Auditorium
By the end of this lecture you will be able
to:
1- Define what is meant by ketogenesis
and ketolysis
2- Enumerate the different ketone bodies
3- Evaluate the process of synthesis of
ketone bodies
4- Explain the
ketogenesis
role
of
the
liver
in
5- Explain why ketone bodies synthesis is
activated during fasting and starvation
 Definition of ketogenesis and
ketolysis
 The central role of the liver in
ketogenesis and its inability to
utilize them
 The steps of ketogenesis in the liver
 The steps of ketolysis in extra
hepatic tissues
 Regulation of ketogenesis and
ketolysis
Remember that ketone bodies are used as a
major source of energy during starvation in
most of the tissues even the brain to decrease
the process of gluconeogenesis from muscle
protein and spare the glucose produced from
gluconeogenesis mainly to the brain and for
the tissues which do not have mitochondria
such as RBCs.
117
Student Notes:
.
1.
Required Texts And Resources:
Lippincott Illustrated Reviews, 3rd
edition, Champe & Harvey. (pp 193197)
2. Supplementary Texts And Resources:
Medical Biochemistry, Baynes and
Dominiczek, 1st edition, Mosby. (pp 173176)



You have the opportunity to watch the CDROM about fatty acid oxidation. You can
access the CD-ROM during your spare
time.
1- http://www.biocarta.com/pathfiles/ke
tonebodiesPathway.asp
2- http://ull.chemistry.uakron.edu/genobc/Chapter
_24/
3- http://ull.chemistry.uakron.edu/Pathway
s/ketone_bodies/index.html
1- Draw the steps of ketogenesis
indicating the steps during which
CoA-SH is regenerated
2- Drew a graph connecting both beta
oxidation and ketogenesis
1-
Clinical Question:
a) In type I diabetes, ketone
118
bodies tend to increase more than
type II, explain why?
2-
Clinical Case: A type I diabetic
patient delivered to you in a coma
in the ER , his blood glucose level
was 500 mg/dl (27.8 mmol/L), his
breath had the acetone
charachtristic odour.
a) What other investigation(s)
would you like to do?
b) What type of coma is it?
c) What is the biochemical bases
of this coma?
I- Short Questions:
1- Explain why ketogenesis is essential for
energy production in the liver during
starvation
2- Explain why the liver can not utilize ketone
bodies
II- MCQ:
1- Regarding ketogenesis and ketolysis:
a) Ketogenesis takes place in
the mitochondria of
extrahepatic tissues while
ketolysis in the cytoplasm
of extrahepatic tissues
b) Ketolysis takes place in
the cytoplasm of
extrahepatic tissues
c) Ketogenesis and ketolysis
takes place in liver
mitochondria
d) Ketogenesis takes place in
liver mitochondria only
e) All of the above
2- Regeneration of CoA-SH takes place
during ketogenesis in the step (s) of:
a)
formation of acetoacetyl
CoA
b)
formation of beta
hydroxybutyrate from
119
acetoacetate
c)
formation of
hydroxymethylglutaeyl
(HMG) CoA
d)
Both (a) and (c)
e)
All of the above
III- True / False
1- Ketogenesis takes place in all the
tissues
2- Ketone body oxidation is the major
source of energy for most of the
tissues in the absorptive state
3- Ketogenesis takes place in the
cytoplasm of the liver only
120
LECTURE # (28) : Phospholipids metabolism
DEPARTMENT: Clinical Biochemistry
TUTOR:
TEACHING LOCATION: Auditorium
By the end of this lecture you will be able
to:
1- Discussthe structures of phosphatidylcholine,
phosphatidylethanolamine,phosphatidylserine,
phosphatidylinositol, and cardiolipin.
2- Explain the different mechanisms for
complexlipid synhesis
3- Explain what is meant by a ceramide. Outline
how ceramide is synthesized beginning with
palmitoyl-CoA and serine. Show how a
ceramide
is converted into
sphingomyelin.
4- Describe the genetic abnormalities associated
with complex lipid metabolism
5- Evaluate the medical importance of
phospholipid and sphingolipids in the body
 Structure of the different
phospholipids
 Importance and function of
phospholipids
 Structure and different types of
sphyngolipids
 Nomenclature of sphingolipids
 The importance of complex lipids
Remember that phospholipids and
sphingolipids are very important compounds
in the body. They play many important roles
such as blood clotting, membrane structure
(almost half of membrane lipid is
phospholipids), signal transuduction, and
121
Student Notes:
.
nervous function.
1.
Required Texts And Resources:
Lippincott Illustrated Reviews, 3rd
edition, Champe & Harvey. (199-216)
2. Supplementary Texts And Resources:
Medical Biochemistry, Baynes and
Dominiczek, 1st edition, Mosby. (pp 321327)



You have the opportunity to watch the CDROM about lipolysis. You can access the
CD-ROM during your spare time.
1- http://www.med.unibs.it/~marchesi/lipsynt
h3.html
2- http://www.merck.com/mmhe/sec23/ch282
/ch282d.html
3- http://www.dentistry.leeds.ac.uk/biochem/t
hcme/lipid-synthesis.html#sphingolipids
4- http://www.lipidlibrary.co.uk
5- http://www.biocarta.com/pathfiles/sphingol
ipidPathway.asp
6- http://www.biocarta.com/pathfiles/h_ceram
idePathway.asp
7- http://www.biocarta.com/pathfiles/pcsynth
esispathway.asp
8- http://www.biocarta.com/pathfiles/h_ptdins
Pathway.asp
Search for the importance of
sphingolipids as signal
122
transduction
1-
Clinical Question:
Comment
on
respiratory
distress
syndrome (RDS).
2Clinical Case
Leukocyte samples isolated
from the blood of a newborn
infant are homogenized and
incubated with ganglioside
GM2. Approximately 47% of
the expected normal amount
of N-acetylgalactosamine is
liberated
during
the
incubation period. What is
most likely the diagnosis?
I Short Questions:
1II- MCQ:
1- All are true about phosphatidyl
inositol except:
a) These molecules contain almost
exclusively stearic acid at carbon
1 and arachidonic acid at carbon 2
b) Phosphatidylinositol
4,5bisphosphate, PIP2) is involved in
the transmission of signals for cell
growth and differentiation
c) The synthesis of phosphatidyl
inositol involves CDP-activated
1,2-diacylglycerol condensation
with myo-inositol
d) It is considered one of the
sphingolipids
2- About glycosphingolipids:
a) Are composed of a ceramide
123
backbone with a wide variety of
carbohydrate groups
b) They have exactly the same
structure of sphingomylines
c) They
never
contain
Nacetylneuraminic acid (NANA)
d) One of its subtype ; Cerebrosides
has more than one sugar group
III- True / False
1- Lecithin is important in blood
clotting mechanism
2- Ceramide is one of the classes of
glycerophospholipids
3- Phosphatidic acid is the precursor
of all sphingolipids
124
LECTURE # (29) : Disposal of amino acid nitrogen
DEPARTMENT: Clinical Biochemistry
TUTOR:
TEACHING LOCATION: Auditorium
By the end of this lecture you will be
able to:
1. Discuss
the
process
of
transamination
and
the
characters of the transaminase
enzymes.
2. Explain how the cooperation
by the enzymes alanine
aminotransferase and glutamate
dehydrogenase is accomplished
3. Evaluate the reaction of
glutamate dehydrogenase as an
example
of
oxidative
deamination, and the control of
glutamate dehydrogenase.
4. Correlate
the
reactions
catalyzed
by
glutamate
dehydrogenase,
glutamine
synthetase, glutaminase, and
aspartate aminotransferase,
5. Evaluate
the
clinical
importance of transaminase
enzymes
6. Evaluate the important role of
alanine and glutamine in
transport of amino groups
between different tissues and
the liver
125
Student Notes:
.
 Definition of tranamination and
deamination
 Site
of
transamination
and
deamination
 Importance of transamination as a
tool for synthesis of non essential
amino acids
 Co-enzyme of tranasaminases
 The
importance
of
glutamate
dehydrogenase
in
nitrogen
metabolism and its regulation
 The other types of deamination
 The central role of glutamate in
amino group transfer.
 The clinical application of
transaminases
Transamination and deamination are the process
through which the cell transfer and get rid of
nitrogen , some times for formation of non
essential amino acid as in transamination and
sometimes for urea formation as in deamination.
Transaminase
enzymes
have
absolute
requirement for PLP as coenzyme and are
present in most of the tissues. Liver
transaminases have great clinical application as a
parameter for liver function tests.
1.Required
Texts
And
Resources:
Lippincott Illustrated Reviews, 3rd
edition, Champe & Harvey. Chapter 19
(pp:247-250)
2. Supplementary Texts And Resources:
Medical Biochemistry, Baynes and
Dominiczek, 1st edition, Mosby. Chapter
18 (pp:218-222)
126



You have the opportunity to watch the CDROM about this topic in the library.
1- http://ull.chemistry.uakron.edu/Path
ways/nitrogen_pool/index.html
2- http://www.elmhurst.edu/~chm/vche
mbook/632oxdeam.html
3- http://www.elmhurst.edu/~chm/vche
mbook/631transam.html
4- http://drnelson.utmem.edu/aadeg.ht
ml
5- http://www.mesomorphosis.com/arti
cles/mcdonald/protein-04.htm
6- http://www.humboldt.edu/~rap1/C43
8.S07/C438Notes/C438nLec38.htm
7- http://www.albany.edu/faculty/cs812/
bio366/L08_AminoAcidMetab1.pdf
8- http://web.indstate.edu/thcme/mwkin
g/nitrogen-metabolism.html
9- http://seqcore.brcf.med.umich.edu/m
cb500/aasyl/aametab.html
1-
Clinical Question
2-
Clinical Case
III- Short Questions:
a) Enumerate the characters of
transaminases
b) The major deamination
127
pathways in the body is
through -------------- enzyme
IV-MCQ:
1) For amino acids to be used
in energy production, its
amino group should be
removed (deaminated).
Which of the following
statmnt is correct:
a)
The most active
enzyme in deamination is
AST which ispresent in
almost all tissues
b)
L- amino acid oxidase
is responsible for
deamination of most o the
amino cids
c)
D- amino acid oxidase
is very active in human
and is responsible for
domination of most of the
amino acids
d)
L-glutamate
dehydrogenase is the
major enzyme of
deamination
2) In chronic liver diseases,
ALT&AST are elevated,
these enzymes action
include all the following
except:
a)
Formation of non
essential amino acids
b)
Libration of free
ammonia
c)
Amino group of alanine
and asparatic acid by
their action end up in
lutamate
d)
Help in balancing
amino acid pool between
128
essential and non
essential amino acids
3) The coenzyme of Lglutamate dehydrogenase
is:
a)
NAD
b)
FAD
c)
CoASH
d)
Lipoic acid
4) Transaminase reaction:
a)
Is reversible
b)
Requires the presence
of PLP as coenzyme
c)
Is irreversible reaction
d)
Both a & b
V- True / False
a) One of the two pairs of
reactants in transaminase
reaction is almost glutamate
and α-ketoglutarate
b) ALT exists in the cytoplasm
and mitochondria of the
tissues
c) L-glutamate dehydrogenase
is stimulated by high
concentration of ADP & GDP
d) All amino acids can be
transaminated
e) Vitamin B6 acts as
coenzyme in some of the
transaminases reaction
129
LECTURE # (30) : Urea cycle and detoxification of ammonia
Student Notes:
DEPARTMENT: Clinical Biochemistry
.
TUTOR:
TEACHING LOCATION: Auditorium
By the end of this lecture you
will be able to:
1. Trace the source of the two
nitrogen in the urea molecule
2. Drew the steps of the urea
cycle and its site in the tissue
3. Explain the reaction catalyzed
by the enzyme carbamoyl
phosphate synthetase and its
regulation
4. Discuss how NH4+ and
aspartate share in the formation
of urea
5. Explain why the formation of
one molecule of urea requires
the hydrolysis of four-high
energy phosphate groups of
ATP.
6. Explain how the ammonium
ion produced in different
tissues is transported to the
liver for urea synthesis
7. Discuss the different inborn
errors in the urea cycle and
their consequences
8. Explain the cause of increasing
orotic acid in urine when there
is ornithin transcarbamoylase
deficiency.
9. Discuss the causes of acquired
130
hyperammonemia
10. Discuss the importance of
benzoic
acid
and
phenylbutyrate therapy in
patients with a defect in the
urea cycle.











Overview of the urea cycle
Importance of urea cycle
Location of the cycle
Steps of urea cycle
Energy utilization of the cycle
Regulation of the cycle
The sources of nitrogen in the urea
molecule
Connection between the urea cycle
and TCA cycle
Genetic abnormality and its
consequence
Acquired hyperammonemia
Clinical correlation
Ammonia is toxic compound produced in most of
the tissues during amino acid metabolism; it is
transported to the liver in the form of alanine and
glutamine in order to be converted into non toxic
form (urea). The liver is only tissue that converts
ammonia into urea through the urea cycle.
Remember that urea synthesis is energy
consuming process taking place in both he
mitochondria and the cytoplasm of liver cell. The
key regulatory enzyme is CPSI. Failure of
conversion of ammonia into urea results in
hyperammonemia which may congenital or
acquired with its toxicity especially on the
nervous system.
131
1.
Required Texts And Resources:
Lippincott Illustrated Reviews, 3rd
edition, Champe & Harvey pp (251-257)
2. Supplementary Texts And Resources:
Medical Biochemistry, Baynes and
Dominiczek, 1st edition, Mosby. Pp (222224)



You have the opportunity to watch the CDROM about urea cycle. You can access
the CD-ROM during your spare time.
1- http://www.albany.edu/faculty/cs812/bio36
6/L09_AminoAcidMetab2.pdf
2- http://www.wiley.com/college/fob/quiz/quiz20/
20-8.html
3- http://www.ureacycle.com/#
4- http://www.ureacycle.com/about_ureacycle.as
p
5- http://www.humboldt.edu/%7Erap1/C431.F01/
C431Notes/C431n14Dec.htm
6- http://web.indstate.edu/thcme/mwking/ureacy
cledisorders.html
7- http://www.elmhurst.edu/~chm/vchembook/63
3ureacycle.html
8- http://www.nucdf.org/
9- http://www.gwu.edu/~mpb/urea.htm
10- http://rarediseasesnetwork.epi.usf.edu/ucdc/i
ndex.htm
11- http://ull.chemistry.uakron.edu/Pathways/urea
_cycle/index.html
12- http://www.sickkids.ca/HowellLab/custom/rsc
hArginine.asp
13- http://www.idph.state.il.us/HealthWellness/fs/
urea.htm
132
Try to trace the sources of nitrogen
in urea molecule and connect the
urea cycle to the TCA cycle.
3-
4-
Clinical Question: what are the
causes of acquired
hyperammonemia?
Clinical Case: A 45 year old
male with long history of hepatitis C
was brought to the ER for acute
mental status changes. The family
reported that he has been very
disoriented and confused over the
last few days and has been
nauseated and vomited blood.
a)
What is most likely test you
would like to do, and what do you
except the result to be?
I- Short Questions:
a) What is the key regulatory
enzyme in the urea cycle
b) What are the types of
hyperammonemia
II- MCQ:
1- The major two amino acids
which transport ammonia
from peripheral tissues to
the liver are:
a)
Alanine and aspartic
acid
b)
Glutamine and alanine
c)
Glutamine and aspartic
acid
d)
Non of the above
2- The total energy loss in urea
133
synthesis is:
a)
Two molecules of ATP
b)
Four molecules of ATP
in the form of 5 high
energy bonds
c)
Three molecules of
ATP in the form of 4 high
energy bonds
d)
Non of the above
3- The molecule(s) that is (are)
regenerated during urea
synthesis is:
a)
Carbamoyl phosphate
b)
Arginine
c)
Ornithine
d)
All of the above
4- Orotic acid will mainly be
increased in:
a)
Argenenimia
b)
Argininosuccinate
aciduria
c)
Type I
hyperammonemia
d)
Type II
hyperammonemia
III- True / False
1. In CPSI reaction one molecule of
ATP is used
2. The all five reactions of urea
synthesis occur in the mitochondria
3. The highest concentration of
glutaminase enzyme is present in he
liver
4. During acidosis, the liver
synthesizes large amount of
glutamine which is transported to the
kidney
5. The carbons of fumarate in the
urea cycle can return back to the
cycle in the form of asprtate
134
LECTURES # (31): Individual amino acid catabolism (glycine metabolism)
Student Notes:
.
DEPARTMENT: Clinical Biochemistry
TUTOR:
TEACHING LOCATION: Auditorium
By the end of this lecture you will be able
to:
1. Describe how glycine is
converted
into
glucose
precursor
2. Discuss the importance of
glycine in collagen synthesis
3. Enumerate
the
different
compounds that are derived
from glycine
4. Explain how glycine is
converted into serine and the
reverse pathway
5. Discuss the inborn error of
glycine metabolism
 Overview of the fate for the different
amino acids
 Glycine amino acid and its role in
synthesis of many compounds such
as creatine, heme, collagen and bile
salts.
 The conversion of glycine into
serine and the role of THF
 The role of glycine in detoxification
 Glutathione formation and its
physiological role
 The role of γ-glutamyl cycle in amino
135
acid uptake by the tissues
 The genetic abnormality that is
associated with glycine metabolism
Remember that glycine is non essential
amino acid, glucogenic and enters in the
formation of many compounds in the body.
Glutathione which is formed from three
amino acids including glycine is very
important compound in the body as
antioxidant and detoxifying agent. Glycine
also enters in the formation of creatine in
the muscle and acts as source of energy
in the muscle (creatine phosphate).
1.
Required Texts And Resources:
Lippincott Illustrated Reviews, 3rd
edition, Champe & Harvey. Pp (259279)
2. Supplementary Texts And Resources:
Medical Biochemistry, Baynes and
Dominiczek, 1st edition, Mosby. Pp (225232)



You have the opportunity to watch the CDROM about individual amino acid
metabolism. You can access the CD-ROM
during your spare time.
4- http://web.indstate.edu/thcme/mwking/a
mino-acid-metabolism.html
5- http://web.indstate.edu/thcme/mwking/in
born.html#amino
136
6- http://www.genome.jp/kegg/pathway/ma
p/map01150.html
7- http://seqcore.brcf.med.umich.edu/mcb5
00/aasyl/aametab.html
8- http://www.dentistry.leeds.ac.uk/bioche
m/thcme/aminoacidmetabolism.pdf
9- http://www.med.unibs.it/%7Emarchesi/a
ametab.html
10- http://www.rpi.edu/dept/bcbp/molbioche
m/BiochSci/sbello/new_page_2.htm
11- http://www.sigmaaldrich.com/img/assets/
4202/MetabolicPathways_updated_02_0
7.pdf
12- http://www.sigmaaldrich.com/sigma/gen
eral%20information/inborn_errors_char
t.pdf
13- http://ghr.nlm.nih.gov/condition=primar
yhyperoxaluria
14- http://www.emedicine.com/med/topic302
7.htm
15- http://www.kidneyatlas.org/book2/adk2_
12.pdf
3- Glycine is an important amino acid,
its importance is due to it enters in
the formation of many molecules
and compounds in our body, try to
enumerate these compounds and
discuss the role of glutathione.
3-
Clinical Question:
I- Short Questions:
1- Enumerate the most common
compounds that are formed from
glycine
2- Using a graph drew the gamma
glutamyl cycle
137
I- MCQ:
4- Primary hyperoxaluria is due to:
a)
Deficiency of tryptophan
hydroxylae enzyme
b)
Argininosuccinate lyase
enzyme
c)
Deficiency in the conversion
of glyoxylic acid into formic
acid due to defect in the
oxidative decarboxylation of
this compound
d)
Deficiency in the renal
tubular reabsorption of glycine
5- Regarding creatine formation:
a)
It requires the cooperation
of two organs, the liver and the
kidney
b)
Three amino acids shares in
its formation (glycine, arginine
and methionine)
c)
Both (a) and (b)
d)
Non of the above
6- Glycine is considered glucogenic
amino acid as it can be converted
into:
a)
Succinyl CoA
b)
α-ketoglutarate
c)
propionyl CoA
d)
pyruvate
III True / False
1. Formation of creatine
from guanido acetate is
by tansmethylation
reaction and the methyl
donor is SAM
2. Three amino acids
(glycine, arginine and
methionine) enter in the
formation of creatine
3. Glycine combines with
propionyl CoA for heme
138
formation
4. Glutathione is tripeptides
(γ-glutamyl-cysteinylglycine)
139
LECTURES #(32):Individual amino acid catabolism (Phenylalanine and
tyrosine)
DEPARTMENT: Clinical Biochemistry
TUTOR:
TEACHING LOCATION: Auditorium
By the end of this lecture you will be able
to:
1. Recognize
the
important
compounds
derived
from
phenylalanine
2. Discuss how tyrosine is formed
from phenylalanine and the
importance of the enzyme of
this transformation
3. Explain the genetic defects in
these amino acid metabolism
and their consequences.
 Phenylalanine as essential amino
acid
 Tyrosine as non essential amino
acid
 The formation of melanin from
tyrosine
 Formation of thyroid hormone
 Formation of adrenaline and nor
adrenaline
 Genetic abnormalities associated
with phenylalanine and tyrosine
metabolism
140
Student Notes:
.
Remember that phenylalanine is essential
amino acid while tyrosine is not as it can
be synthesized from tyrosine. Tyrosine is a
precursor for many compounds in the
body e.g. thyroid hormone, melanin
pigments and adrenaline. Genetic defects
in phenylalanine metabolism represents
high percentage of the most common
defects in amino acid metabolism and
include phenylketonuria, alkaptonuria ,
tyrosinosis and albinism.
1.
Required Texts And Resources:
Lippincott Illustrated Reviews, 3rd
edition, Champe & Harvey. Pp (259279)
2. Supplementary Texts And Resources:
Medical Biochemistry, Baynes and
Dominiczek, 1st edition, Mosby. Pp (225232)



You have the opportunity to watch the CDROM about individual amino acid
metabolism. You can access the CD-ROM
during your spare time.
1- http://web.indstate.edu/thcme/mwkin
g/amino-acid-metabolism.html
2- http://web.indstate.edu/thcme/mwkin
g/inborn.html#amino
3- http://www.genome.jp/kegg/pathway/
map/map01150.html
4- http://seqcore.brcf.med.umich.edu/m
cb500/aasyl/aametab.html
141
5- http://dwb.unl.edu/Teacher/NSF/C11/
C11Links/www.bact.wisc.edu/microte
xtbook/metabolism/RespProteins.htm
l
6- http://en.wikipedia.org/wiki/List_of_a
mino_acid_metabolism_disorders
7- http://www.dentistry.leeds.ac.uk/bioc
hem/thcme/aminoacidmetabolism.pdf
8- http://www.med.unibs.it/%7Emarche
si/aametab.html
9- http://www.rpi.edu/dept/bcbp/molbio
chem/BiochSci/sbello/new_page_2.ht
m
10- http://www.sigmaaldrich.com/img/ass
ets/4202/MetabolicPathways_updated
_02_07.pdf
11- http://www.sigmaaldrich.com/sigma/
general%20information/inborn_erro
rs_chart.pdf
12- http://www.pnas.org/cgi/content/full/
96/6/3160
13- http://www.pubmedcentral.nih.gov/ar
ticlerender.fcgi?artid=1144976
14- http://www.lowvision.org/albinism.ht
m
15- http://ghr.nlm.nih.gov/condition%3D
tyrosinemia
16- http://www.ncbi.nlm.nih.gov/entrez/d
ispomim.cgi?id=203500
Using the net try to find out the
percentage of these genetic abnormalities in the
world and in KSA
4-
Clinical Question: what are the
different types of albinism?
5-
Clinical Case: During
screening for inborn error of
metabolism in KAU hospital, a
baby was discovered positive for
phenylpyruvate in urine. What is
142
your possible diagnosis? What
further investigation would you
like to do?
I- Short Questions:
1-
Enumerate the most common
inborn error in phenylalanine and
tyrosine metabolism
2How melanin is formed from
tyrosine
II- MCQ:
1- Alkaptonuria is due to deficiency
of:
a) Phenylalanine hydroxylase
enzyme
b) Tyrosine hydroxylase enzyme
c) Homogentisic acid oxidase
d) Tyrosine α-ketoglutarate
transaminase
2- All are true about
phenylketonuria except:
a) Tyrosine amino acid in this case
becomes essential amino acid
b) There is increased secretion of
phenyllactate in urine
c) Mental retardation is constant
feature in untreated cases
d) It is due to deficiency of tyrosine
hydroxylase enzyme
3- In tyrosinemia:
a) Phenylalanine hydroxylase is
deficient
b) Tyrosine α-ketoglutarate
transaminase and (or)
parahydroxyphenyl
pyruvate oxidase is (are)
deficient
c) Tyrosinase enzyme is absent
d) All of the above
III True / False
143
1. Glutathione is an
inhibitor for the
enzyme homogentisic
acid oxidase
2. Melanin is directly
formed from
phenylalanine
3. In phenylketonuria,
tyrosine becomes
essential amino acids
144
LECTURES # (33)
: Individual amino acid catabolism (Tryptophan, aspartic
acid , glutamic acid, alanine and serine)
DEPARTMENT: Clinical Biochemistry
TUTOR:
TEACHING LOCATION: Auditorium
By the end of this lecture you will be able
to:
1. Discuss the central role of
glutamic acid in amino acid
metabolism
2. Explain
the
connection
between glutamic acid and
aspartic acid
3. Show how these two amino
acid are both non essential and
glucogenic
4. Discuss how these two amino
acids act as neurotransmitter
5. Show how melatonin and
serotonin are made from
tryptophan
6. Trace how tryptophan in its
catabolism is both glucogenic
and ketogenic
7. Discuss the genetic defect in
Hartnup disease
8. Explain the role of alanine in
nitrogen transport
145
Student Notes:
.
 Central role of gutamic acid in amino
acid metabolism
 Important compound derived from
glutamic acid
 Aspartic and glutamic acids as
neurotransmitters
 Tryptophan amino acid as a
precursor of many important
compounds such as melatonin and
serotonin
 Inborn error in tryptophan
metabolism (Hartnup disease)
 Alanin as a major transporter of
nitrogen among tissues
Remember that tryptophan is essential
amino acid used for synthesis of many
biological compounds such as melatonin,
serotonin and niacin. It is both glucognic
and ketogenic. Glutamic acid and aspartic
acid are both non essential glucogenic
amino acids.
1.
Required Texts And Resources:
Lippincott Illustrated Reviews, 3rd
edition, Champe & Harvey. Pp (259279)
2. Supplementary Texts And Resources:
Medical Biochemistry, Baynes and
Dominiczek, 1st edition, Mosby. Pp (225232)



You have the opportunity to watch the CD146
ROM about individual amino acid
metabolism. You can access the CD-ROM
during your spare time.
1- http://web.indstate.edu/thcme/mwkin
g/amino-acid-metabolism.html
2- http://web.indstate.edu/thcme/mwkin
g/inborn.html#amino
3- http://www.genome.jp/kegg/pathway/
map/map01150.html
4- http://seqcore.brcf.med.umich.edu/m
cb500/aasyl/aametab.html
5- http://dwb.unl.edu/Teacher/NSF/C11/
C11Links/www.bact.wisc.edu/microte
xtbook/metabolism/RespProteins.htm
l
6- http://en.wikipedia.org/wiki/List_of_a
mino_acid_metabolism_disorders
7- http://www.dentistry.leeds.ac.uk/bioc
hem/thcme/aminoacidmetabolism.pdf
8- http://www.med.unibs.it/%7Emarche
si/aametab.html
9- http://www.rpi.edu/dept/bcbp/molbio
chem/BiochSci/sbello/new_page_2.ht
m
10- http://www.sigmaaldrich.com/img/ass
ets/4202/MetabolicPathways_updated
_02_07.pdf
11- http://www.sigmaaldrich.com/sigma/
general%20information/inborn_erro
rs_chart.pdf
12- http://www.emedicine.com/derm/topi
c713.htm
13- http://www.medstudents.com.br/nefr
o/nefro3.htm
14- http://www.biology.arizona.edu/bioch
emistry/problem_sets/aa/glutamate.ht
ml
15- http://www.springboard4health.com/
notebook/proteins_glutamic.html
16- http://www.chemie.fuberlin.de/chemistry/bio/aminoacid/as
147
p_en.html
17- http://www.anyvitamins.com/aspartic
-acid-info.htm
Using a diagram try to drew the
interconversion of glutamine, glutamic acid and
α-ketoglutarate showing tissue location, enzymes
and coenzymes.
1- Clinical Question: what do you
expect the level of glutamine
in CSF sample to be in a case
of comma due to liver cell
failure?
2- Clinical Case:
I- Short Questions:
1- How GABA is formed and
what is its role in the CNS
2- Why tryptophan is
considered both glucogenic
and ketogenic amino acid
II- MCQ:
1- Concerning 5hydroxytryptamine:
a)
It is produced from
tryptophan by
decraboxylation and then
hydroxylation and acts as
neurotransmitter
b)
It is produced from
tryptophan by
hydroxylation then
decraboxylation and acts
as neurotransmitter
c)
It is produced from
tyrosine by the action of
tyrosine hydroxylase
148
d)
Non of the above
2- All are true about melatonin
except:
a)
It is derived from
serotonin in the pineal
gland
b)
It is regulatory of
gonadal function
c)
Stimulates synthesis
of GABA
d)
It has sleeping
inducing effect
3- Concerning glutamic acid:
a)
It is essential amino
acid
b)
It is ketogenic amino
acid
c)
Shares in the formation
of glutathione
d)
It is inhibitory
neurotransmitter
1III True / False
1. Aspartic acid is non
essential ketogenic amino
acid
2. Tryptophan is the precursor
of melanin
3. GABA is derived from
glutamic acid and acts as
inhibitory neurotransmitter
4. Aspartic acid enters in the
formation of both purine
and pyrimidine
149
LECTURES # (34 - a)
:
Individual amino acid catabolism (Valine, leucine
and isoleucine)
DEPARTMENT: Clinical Biochemistry
TUTOR:
TEACHING LOCATION: Auditorium
By the end of this lecture you will be able
to:
1. Describe the common pathway
of catabolism for these three
amino acids
2. Trace the pathway to find out
which of them is glucogenic or
ketogenic or both
3. Discuss the importance of these
amino
acids
in
muscle
metabolism
4. Explain the genetic defect
associated with these amino
acids
 The common pathway for
catabolism of these amino acids
 The end product of those amino
acids (glucogenic, ketogenic or
both)
 Enzymes necessary for their
catabolic pathway
 Enzymes defect in their catabolic
pathway (Maple Syrup urine disease)
150
Student Notes:
.
Remember that these amino acids have a
common
catabolic
pathway.
Their
catabolic pathway after transamination has
similar features to that of beta oxidation of
fatty acids.
1.
Required Texts And Resources:
Lippincott Illustrated Reviews, 3rd
edition, Champe & Harvey. Pp (259279)
2. Supplementary Texts And Resources:
Medical Biochemistry, Baynes and
Dominiczek, 1st edition, Mosby. Pp (225232)



You have the opportunity to watch the CDROM about individual amino acid
metabolism. You can access the CD-ROM
during your spare time.
1- http://web.indstate.edu/thcme/mw
king/amino-acid-metabolism.html
2- http://web.indstate.edu/thcme/mw
king/inborn.html#amino
3- http://www.genome.jp/kegg/pathw
ay/map/map01150.html
4- http://seqcore.brcf.med.umich.edu
/mcb500/aasyl/aametab.html
5- http://dwb.unl.edu/Teacher/NSF/
C11/C11Links/www.bact.wisc.edu
/microtextbook/metabolism/RespP
roteins.html
151
6- http://en.wikipedia.org/wiki/List_
of_amino_acid_metabolism_disor
ders
7- http://www.dentistry.leeds.ac.uk/b
iochem/thcme/aminoacidmetabolis
m.pdf
8- http://www.med.unibs.it/%7Emar
chesi/aametab.html
9- http://www.rpi.edu/dept/bcbp/mol
biochem/BiochSci/sbello/new_pag
e_2.htm
10- http://www.sigmaaldrich.com/img
/assets/4202/MetabolicPathways_u
pdated_02_07.pdf
11- http://www.sigmaaldrich.com/sig
ma/general%20information/inbor
n_errors_chart.pdf
12- http://www.emedicine.com/derm/t
opic713.htm
13- http://www.medstudents.com.br/n
efro/nefro3.htm
14- http://www.biology.arizona.edu/bi
ochemistry/problem_sets/aa/gluta
mate.html
15- http://www.springboard4health.co
m/notebook/proteins_glutamic.ht
ml
16- http://www.chemie.fuberlin.de/chemistry/bio/aminoacid
/asp_en.html
17- http://www.anyvitamins.com/aspa
rtic-acid-info.htm
1-
Clinical Question: Four
types of MSD are present,
on what basis this
classification depends?
2Clinical Case:
I-Short Questions:
152
a) What are the end product of
catabolism of these branched
chain amino acids
b) What is the enzymatic defect in
MSU disease
II- MCQ:
1- All the following are branched
chain amino acids except:
a)
Methionine
b)
Valine
c)
Leucine
d)
Isoleucine
2- The defect in MSU disease is due
to deficiency of :
a)
Methionine synhesase
b)
Dihydro biopterine
reductase
c)
Branched chain α-amino
acid transferases
d)
Branched chain α- keto acid
dhydrogenase complex
III True / False
1. Leucine is purely
ketogenic amino acid
2. Branched chain amino
acids are mainly
metabolized by the liver
3. The oxidative
decraboxylation in the
pathway of catabolism of
branched chain amino
acids requires the same
coenzymes as those in
the pyruvate
dehydrogenase complex.
153
LECTURES # (34 - b)
:
Individual amino acid catabolism (sulfur containing
amino acids)
DEPARTMENT: Clinical Biochemistry
TUTOR:
TEACHING LOCATION: Auditorium
By the end of this lecture you will be able
to:
1. Discuss the function of both
cystein and cystin in protein
structure
2. Explain how the SH groups in
these amino acids are important in
metabolism
3. Show how SAM is formed and its
importance
4. Discuss the different inborn error
associated with these amino acids
 The catabolic pathway for cystein
and cystin
 Importance of cystein and cystin in
protein structure
 Inborn error of metabolism
associated with these two amino
acids
 Formation of SAM and its
importance as methyl donor
 Relation of SAM metabolic pathway
to cardiovascular disease
Remember that sulfur containing amino
acids are important in protein structure
154
Student Notes:
.
because of the SH groups, also this group
is important in their function in
detoxification. SAM is derived from
methionine amino acid and it acts as a
major methyl donor in the body in the
transmethylation reactions.
1.
Required Texts And Resources:
Lippincott Illustrated Reviews, 3rd
edition, Champe & Harvey. Pp (259279)
2. Supplementary Texts And Resources:
Medical Biochemistry, Baynes and
Dominiczek, 1st edition, Mosby. Pp (225232)



You have the opportunity to watch the CDROM about individual amino acid
metabolism. You can access the CD-ROM
during your spare time.
1- http://jn.nutrition.org/cgi/conte
nt/abstract/136/6/1750S
2- http://en.wikipedia.org/wiki/H
omocystinuria
3- http://web.indstate.edu/thcme/
mwking/amino-acidmetabolism.html
4- http://web.indstate.edu/thcme/
mwking/inborn.html#amino
5- http://www.genome.jp/kegg/pa
thway/map/map01150.html
6- http://seqcore.brcf.med.umich.
edu/mcb500/aasyl/aametab.ht
ml
7- http://jn.nutrition.org/cgi/conte
155
nt/abstract/137/2/339
Clinical Question: Try to explain
the role of homocystein in
cardiovascular diseases.
Clinical Case:
I-Short Questions:
II- MCQ:
1- Methionine adenosyl transferase
a)
Is the enzyme that
regenerates methionine from
homocysteine
b)
It is the enzyme that is
responsible for SAM formation
c)
Deficiency of this enzyme
will lead to homocysteinuria
d)
Non of the above
2- The major disposal pathway (s)
of homocystein is (are):
a)
Conversion to methionine
b)
Formation of cysteine
c)
Both (a) and (b)
d)
Non of the above
IIIIII True / False
E. During SAM synthesis ATP
molecule is converted into
AMP
F. Homocysteinuria is due to
deficiency in cystathionine
synthase enzyme
G. Cystein amino acids is
considered essential amino
acid as it can not be
synthesized in the body
156
LECTURE # 35 : Nucloetides Structure and Functions
Student Notes:
DEPARTMENT: Clinical Biochemistry
TUTOR:
TEACHING LOCATION: Auditorium
By the end of this lecture you will be
able to:
1. List the different functions of
nucleotides.
2. Describe the general structure
of nucleotides.
3. Identify
the
structural
components of nucleotides.
4. Name different types of
nucleotides.
5. List different types of free
nucleotides.
6. Discuss
digestion
and
absorption of nucleic acids.







Importance of nucleotides.
General structure of nucleotides.
Nitrogenous bases.
Structure of nucleosides.
Structure of nucleotides.
Free nucleosides and nucleotides.
Digestion and absorption of nucleic
acids.
Nucleotides are the basic building blocks of
nucleic acids (DNA & RNA). In addition,
157
.
nucleotides play a very important role as the
energy currency in cell metabolism. Most
coenzymes are free nucleotides that play a
major role in metabolism. Moreover, many
nucleotides are present in our soft drinks along
with tea, coffee and cocao.
1.
Required Texts And Resources:
Lippincott Illustrated Reviews, 3rd
edition, Champe & Harvey
2. Supplementary Texts And Resources:
Textbook of Biochemistry with Clinical
Correlations, Thomas M. Devlin, 5th
edition, Wiley-Liss



You have the opportunity to watch the CDROM about Structure of Nucleotides.
You can access the CD-ROM during your
spare time.
1.http://www.biochem.med.umich.edu/b
iochem/courses/bc452/downloads/nucl
eotides/nucleotide_metab_1.ppt
2.
www.rpi.edu/~bellos/Nucleotides_revised.ppt
3.
http://www.ucd.ie/indmicro/patrick2/BL
ec1(2004).ppt
4.http://www.pharmacy.umn.edu/img/as
sets/12622/lectures1and2.ppt
5.
http://academics.vmi.edu/biochem/28Biosynthesis%20&%20Degradation%20
of%20Nucleotides.ppt
158
4- Clinical Question
5- Clinical Case
I. Short Questions:
1. What are the important nucleotide
functions?
2. Identify the components of nucleosides
and nucleotides.
3. List Five of the important free
nucleotides:
II. MCQs:
1. A nucleoside is composed of:
a. Base and ribose sugar.
b. Base, ribose sugar and phosphates.
c. Base and phosphates.
d. Ribose and phosphates.
2. The following nucleotide acts as a second
messenger:
a. AMP.
b. cAMP.
c. SAM.
d. NADH.
3. The following nucleotide acts as a methyl
group donor:
a. AMP.
b. cAMP.
c. SAM.
d. NADH.
III. True / False
1. cAMP acts as a coenzyme for
159
dehydrogenase enzymes.
2. A nucleotide consists of a nitrogenous
base, a pentose sugar
and phosphate group.
3. ATP consists of adenine, deoxy ribose
and triphosphate
group.
4. NAD+ and NADP+ act as coenzymes for
dehydrogenase
enzymes.
5. Digestion of nucleic acids occurs
mainly in the stomach.
160
LECTURE # 36 - a: Purine Nucleotide Metabolism
DEPARTMENT: Clinical Biochemistry
TUTOR:
TEACHING LOCATION: Auditorium
By the end of this lecture you will be
able to:
1- List the different sources of atoms
of purine ring.
2- Define de novo pathway and
salvage pathway
3. List the main stages of de novo
synthesis of purine.
4- State the rate limiting step of de
novo synthesis of purine.
5. Describe synthesis of IMP.
6. Describe conversion of IMP to
AMP & GMP.
7.
Outline
regulation
of
Biosynthesis of Purine Nucleotides
8.
Outline
Interconversion
Nucleotides
regulation
of
of
Purine
9. List synthetic inhibitors of de
novo purine synthesis and their sites
of effect.
161
Student Notes:
.
10. Describe salvage pathway of
purine synthesis.

De novo synthesis of purine
nucleotides.
 Regulation of Purine Synthesis.
 Salvage pathway of purine synthesis.
In purne synthesis, the purine ring atoms are
added directly on the ribose phosphate giving
rise to the IMP nucleotide. IMP then acts as
the start point of synthesis of both AMP and
GMP nucleotides.
1.
Required Texts And Resources:
Lippincott Illustrated Reviews, 3rd
edition, Champe & Harvey
2. Textbook of Biochemistry with Clinical
Correlations, Thomas M. Devlin, 5th
edition, Wiley-Liss



You have the opportunity to watch the CDROM about Purine nucleotide
metabolism You can access the CDROM during your spare time.
1.http://www.biochem.med.umich.edu/b
iochem/courses/bc452/downloads/nucl
eotides/nucleotide_metab_1.ppt
2.
162
www.rpi.edu/~bellos/Nucleotides_revised.
ppt
3.
http://www.ucd.ie/indmicro/patrick2/BL
ec1(2004).ppt
4.http://www.pharmacy.umn.edu/img/as
sets/12622/lectures1and2.ppt
1. http://academics.vmi.edu/biochem/2
8Biosynthesis%20&%20Degradation
%20of%20Nucleotides.ppt
2.
6- Clinical Question
7- Clinical Case
I. Short Questions:
1. Contrast and compare the de novo
synthesis, salvage pathways
in nucleotide synthesis.
2. What is the significant nucleotide role of
inosine monophosphate
(IMP)?
3. How are ATP and GTP derived?
II. MCQs:
1. The amino acids involved in purine
synthesis include all the
following EXCEPT:
a. Aspartic acid.
b. Glutamine.
c. Glycine.
d. Glutamic acid.
163
2. The committed step in purine
biosynthesis is:
a. Synthesis of carbamayl phosphate.
b. Synthesis of orotic acid.
c. Synthesis of phosphoribosylamine.
d. Synthesis of IMP.
3. The first nucleotide formed in purine
biosynthesis is:
a. AMP.
b. GMP.
c. IMP.
d. ATP.
III. True / False:
1. De novo synthesis of nucleotides is
their synthesis from preformed bases
resulting from cell turn over or from
diet.
2. Salvage of nucleotides is their
synthesis from low molecular weight
precursors.
3. HMP provides ribose-5- phosphate
for synthesis of nucleotides.
4. The rate limiting step of purine
synthesis is catalyzed by PRPP
synthase.
5. Purine nucleotides are synthesized
by addition of different
atoms to the NH2 group of
phosphoribosylamine.
164
165
LECTURE # 36- b : Purine Nucleotide Metabolism
DEPARTMENT: Clinical Biochemistry
TUTOR:
TEACHING LOCATION: Auditorium
By the end of this lecture you will be able
to:
Discus catabolism of Purine
Nucleotides
and
identify
key
enzymes.
1.
2. List factors affecting plasma urate
3. List causes of increased plasma
urate
4. Define hyperuricemia.
5. State metabolic classification of
gout.
6. State clinical classification of gout.
7. Discus the biochemical basis of
treatment of gout.
8. Discus the biochemical basis of
treatment of Lesch-Nyhan syndrome.
9. Discus the biochemical basis of
treatment of SCIDS.
10. Define hypouricemia and its
causes.
166
Student Notes:
.
 Catabolism of Purine Nucleotides.
 Clinical Significances of Purine
Metabolism:
- Uric acid.
- Factors affecting plasma urate
- Causes of increased plasma urate
- Clinical considerations of Purine
Catabolism:
1. Gout.
2. Lesch-Nyhan syndrome.
3. Severe combined immunodeficiency
syndrome (SCIDS).
4. Hypouricemia.
The defect in purine metabolism is due to
accumulation of uric acid, the end product of
purine catbolism. This may result from a
defective enzyme in the purine metabolism or
as a consequence of other diseases. The
problem with uric acid accumulation is due to its
limited solubility and its precipitation as crystals
in the soft tissues. This promotes an immune
response with the consequent symptoms. The
proper treatment involves blocking the enzyme
xanthine oxidase with allopurinol a competitive
inhibitor.
1.
Required Texts And Resources:
Lippincott Illustrated Reviews, 3rd
edition, Champe & Harvey
2. Textbook of Biochemistry with Clinical
167
Correlations, Thomas M. Devlin, 5th
edition, Wiley-Liss


You have the opportunity to watch the CDROM about Purine nucleotide
metabolism. You can access the CD-ROM
during your spare time.
1- http://www.biochem.med.umich.edu/bioc
hem/courses/bc452/downloads/nucleotid
es/nucleotide_metab_1.ppt
2- www.rpi.edu/~bellos/Nucleotides_revise
d.ppt
3- http://www.ucd.ie/indmicro/patrick2/B
Lec1(2004).ppt
4- http://www.pharmacy.umn.edu/img/as
sets/12622/lectures1and2.ppt
5- http://www.ninds.nih.gov/disorders/le
sch_nyhan/lesch_nyhan.htm
6- http://ghr.nlm.nih.gov/condition=lesch
nyhansyndrome
7- http://www.nlm.nih.gov/medlineplus/e
ncy/article/001655.htm
8- http://www.healthatoz.com/healthatoz/
Atoz/common/standard/transform.jsp
?requestURI=/healthatoz/Atoz/ency/le
sch-nyhan_syndrome.jsp
9- http://www.niams.nih.gov/hi/topics/go
ut/gout.htm
10.
www.medicinenet.com/gout/article.htm
11.
http://www.footphysicians.com/footankle
info/gout.htm
12.www.uclasfvp.org/rheum/10%20min%
20Rheum%20talks/Crystal%20arthritis/G
out.ppt
13.
168
http://academics.vmi.edu/biochem/28Biosynthesis%20&%20Degradation%2
0of%20Nucleotides.ppt
Clinical Question:
Clinical Case:
I. Short Questions:
1. Outline the rate-limiting step for purine
synthesis and its regulation.
2. Outline the conversion of IMP to purine
nucleotide monophosphates and its
regulation.
3. Outline regulation of biosynthesis of purine
nucleotides.
4. Outline regulation of interconversion of
purine nucleotides.
5. What is the role of uric acid in nucleotide
metabolism?
6. List the causes of increased plasma urate
7. Contrast and compare gout and LeschNyhan syndrome with regards to their
biochemical abnormalities.
II. MCQs:
1. Allopurinol is the drug of choice for
treatment of:
a. Gout.
b. Orotic aciduria.
c. Chronic renal failure.
d. Non of the above.
2. Primary gout:
a. Is characterized by accumulation and
urinary excretion
169
of orotic acid.
b. May develop in the course of other
disease.
c. Resulted from defect of the enzyme
orotate phosphoribosyl
transferase.
d. Allopurinol is used in the treatment of this
disease.
3. Which one of the following is NOT a cause
of gout:
a. Leukemia and related malignancies.
b. Genetic diseases that limit the amount of
phosphate available
for purine salvage reactions.
c. Decreased sensitivity of the regulated step
in purine
biosynthesis to
its inhibitors.
d. Genetic defects that cause overproduction
of pyrimidines.
4. The end product of purine metabolism in a
person taking
allopurinol for gout is:
a. Orotic acid.
b. Hypoxanthine and Xanthine.
c. Urate.
d. dTMP.
5. The Lesch-Nyhan Syndrome is an
inherited disorder associated with
a complete deficiency of an enzyme
of purine metabolism, which is:
a. HGPRTase.
b. Aspartate carbamayl transferase.
c. Purine nucleotide phosphorylase.
d. Xanthine oxidase.
6. In humans, the end product of
catabolism of purines is:
a. -alanine.
b. Allantoin.
170
c. Urea.
d. Uric acid.
III. True / False
1. The end product of purine metabolism
in humans is
Allantoin.
2. Gout is a disease that results from
decrease of uric acid in blood.
3. Urate crystals deposited in soft
tissues as a result of the high
solubility of uric acid.
4. Allopurinol is a non-competitive
inhibitor of Xanthine
oxidase.
5. Allopurinol is a competitive inhibitor
of PRPP synthase.
171
LECTURE # 37 : Pyrimidine Nucleotide Metabolism
DEPARTMENT: Clinical Biochemistry
TUTOR:
TEACHING LOCATION: Auditorium
By the end of this lecture you will be able
to:
1- List the different sources of atoms
of pyrimidine ring.
2- List the main steps of de novo
synthesis of pyrimidine.
4- State the rate limiting step of de
novo synthesis of pyrimidine.
5. Outline synthesis of thymine
nucleotides.
6. Outline regulation of pyrimidine
nucleotides biosynthesis.
8. List synthetic inhibitors of
pyrimidine synthesis and their sites
of effect.
9. Describe salvage pathway of
pyrimidine synthesis.
10. Discuss catabolism of pyrimidine
nucleotides.
11. List end products of pyrimidine
catabolism.
172
Student Notes:
.
12. Discuss the biochemical basis of
orotic aciduria: causes, classification
and treatment.
13. Discuss the formation of dNTP.
 De novo synthesis of Pyrimidine
Nucleotides.
 Synthesis of Thymine Nucleotides.
 Clinical Relevance of
tetrahydrofolate.
 Regulation of pyrimidine synthesis.
 Clinical considerations of Pyrimidine
Catabolism:
- Orotic aciduria.
- Chemotherapeutic agents.
 Salvage of pyrimidine nucleotides.
 Catabolism of pyrimidine nucleotides.
 Formation of Nucleoside Di- and
Triphosphates
 Formation of Deoxyribonucleotides
 Regulation of dNTP formation.
 Interconversion of the Nucleotides.
In pyrimidine synthesis, the rate limiting step
is catalyzed by cytosolic carbamoyl phosphate
synthase II in contrast to the mitochondrial
carbamoyl phosphate synthase I that
catalyzes the committed step in urea cycle. In
contrast to purine synthesis the pyrimidine
base is formed first then added to ribose
phosphate to give the nucleotide.
In addition, the defect in pyrimidine
metabolism is due to deficiency of enzymes
that present in the synthetic pathway. As a
result the proper treatment involves the oral
administration of the required intermediate
after the enzymatic block. Accumulation of
orotic acid is not harmful as it is water soluble
173
and properly excreted by the kidneys.
1.
Required Texts And Resources:
Lippincott Illustrated Reviews, 3rd
edition, Champe & Harvey
2. Textbook of Biochemistry with Clinical
Correlations, Thomas M. Devlin, 5th
edition, Wiley-Liss



You have the opportunity to watch the CDROM about Pyrimidine nucleotides
metabolism. You can access the CDROM during your spare time.
16- http://www.biochem.med.umich.edu/bioc
hem/courses/bc452/downloads/nucleotide
s/nucleotide_metab_1.ppt
17- www.rpi.edu/~bellos/Nucleotides_revised.
ppt
18- http://www.ucd.ie/indmicro/patrick2/BL
ec1(2004).ppt
19- http://www.pharmacy.umn.edu/img/asse
ts/12622/lectures1and2.ppt
20- http://www.bdid.com/oa.htm
6-
Clinical Question:
d) Clinical Case:
174
I. Short Questions:
1. Outline the rate-limiting step for
pyrimidine synthesis and its regulation.
2. Define the role of uridine monophosphate
(UMP) in nucleotide metabolism.
3. Define orotic aciduria, its symptoms,
causes and treatment.
4. What is the significance of ribonucleotide
reductase and how is it regulated?
II- MCQs:
1. The first step of pyrimidines biosynthesis
is the synthesis of
carbamoyl phosphate catalyzed by:
a. Carbamoyl phosphate synthase I.
b. Carbamoyl phosphate synthase II.
c. PRPP synthase.
d. Phosphoribosyl transferase.
2. A diet rich in Uridine is the treatment
for:
a. Gout.
b. Orotic aciduria.
c. Chronic renal failure.
d. Steatorrhea.
3. Orotic aciduria:
a. Is characterized by accumulation and
urinary excretion of
uric acid.
b. May develop in the course of other
disease.
c. Resulted from defect of the enzyme
orotate phosphoribosyl
transferase.
a. Allopurinol is used in the treatment of
this disease.
III. True / False
1. The rate limiting step of pyrimidine
synthesis is catalyzed by carbamoyl
phosphate synthase I.
175
2. In pyrimidine nucleotides synthesis, the
pyrimidine ring is completed before a
ribose-5-P is added.
3. Carbamoyl-P and aspartate are the
precursors of the six atoms of the
pyrimidine
ring.
4. Orotic aciduria is a disorder of
pyrimidine catabolism.
5. Oral uridine is the treatment of orotic
aciduria.
176
LECTURE # 38 : Structure of Nucleic Acids
DEPARTMENT: Clinical Biochemistry
TUTOR:
TEACHING LOCATION: Auditorium
By the end of this lecture you will be
able to:
1. Explain the central dogma of
molecular biology.
2. Define the main functions of
nucleic acids.
3. Identify
the
structural
components
of
deoxyribonucleic acid (DNA).
4. Define primary structure of
DNA..
5. Define secondary structure of
DNA..
6. List
the
structural
characteristics of Watson and
Crick
model
of
DNA
secondary structure.
7. Differentiate between different
forms of DNA..
8. Define
nucleases
and
differentiate between exo- and
endonucleases.
9. List factors causing DNA
denaturation.
177
Student Notes:
.
 Central Dogma of Molecular Biology.
 Structure and function of nucleic
acids.
 Structural components of DNA:
Bases, Nucleosides and
Nucleotides.
 Primary structure of DNA.
 Watson and Crick model of DNA
secondary structure.
 Different forms of DNA structure.
 Nucleases and their specificity.
 Denaturation of DNA and melting
temperature.
All life on earth uses nucleic acids for storage of
genetic information. With the exception of some
viruses, the biomolecule utilized for information
storage is deoxyribonucleic acid (DNA).
This
molecule is remarkably well suited for its task because
of its chemical stability and its ability to encode vast
amounts of information using a simple four-letter
code.
The flow of genetic information in all cells is always
exclusively one way: DNA RNA  Protein (central
Dogma of molecular biology).
1.
Required Texts And Resources:
Lippincott Illustrated Reviews, 3rd
edition, Champe & Harvey
2. Supplementary Texts And Resources:
Textbook of Biochemistry with Clinical
Correlations, Thomas M. Devlin, 5th
edition, Wiley-Liss



You have the opportunity to watch the CDROM about Structure of DNA. You can
access the CD-ROM during your spare
178
time.
1. http://www.accessexcellence.org/AE
/AEC/CC/DNA_structure.html
2. http://www.johnkyrk.com/DNAanato
my.html
3. http://molvis.sdsc.edu/dna/index.ht
m
4. http://www.moleculesinmotion.com/
5. http://www.pwc.k12.nf.ca/wadey/biot
ech/dna1.swf
6. http://www.rothamsted.bbsrc.ac.uk/n
otebook/courses/guide/dnast.htm
7. http://www.ncc.gmu.edu/dna/index.h
tm
8. http://www.dnaftb.org/dnaftb/
a. Write an essay on restriction enzymes and their
applications in recombinant DNA technology.
b. Write on the applications of DNA denaturation
in molecular biology.
I. Short Questions:
1. List the different characteristics of
the secondary
structure of DNA.
2. Give an account about nucleases
and their applications.
3. What is meant by DNA denaturing.
4. Define each of the following:
a. DNA denaturation.
b. The melting point of DNA.
c. Exonucleases.
5. List three causes of DNA
denaturation.
6. List forces affecting DNA double
179
helix stability.
II. MCQs:
1. Which statement is true about the double
helix:
a. Heating causes the strands to separate
(denature).
b. GC pairs involve three hydrogen bonds.
c. Purine pairs with pyrimidine.
d. All of the above.
2. If a DNA molecule is composed of 40%
(T) what percentage of guanine would be
expected:
a. 10%.
b. 20%.
c. 40%.
d. 80%.
3. All of the following are true about DNA
EXCEPT:
a. Guanine usually pairs with cytosine and
thymine with adenine.
b. A double helix formed of two antiparallel
strands.
c. The sugar-phosphate backbone is
positively charged.
d. Base stacking stabilizes the double helix.
4. Nucleases are enzymes that catalyze
cleavage of:
a. Peptide bond.
b. Glycosidic bond.
c. Hydrogen bond.
d. Phosphodiester bond.
5. All of the following statements regarding
the Watson-Crick
"B" form of DNA are true EXCEPT:
180
a. Two chains are coiled around a common
axis forming a righthanded helix.
b. The bases are found on the outside of
the helix and the sugar
phosphate backbone on the inside.
c. The two chains run in opposite
directions.
d. Adenine is always paired with thymine,
guanine with cytosine.
III. True / False
3. In DNA double helix, the alternating
sugar phosphate units form the
backbone while the nitrogenous bases
are projecting to the outside.
4. Exonucleases cleave phosphodiester
bonds located in the interior of
polynucleotides.
5. The two strands of DNA double helix
are held together by the
complementary base pairing through
specific hydrogen bonds.
6. Melting Temperature (Tm) is the
temperature at which the two strands
of DNA double helix is completely
ruptured and separated.
5. Each DNA strand has two terminals
one end has a free
phosphate group attached to 5`hydroxyl group of the
terminal pentose and the other end has
a free 3`-hydroxyl
group.
181
LECTURE # 39: Organization of eukaryotic chromatin
Student Notes:
DEPARTMENT: Clinical Biochemistry
.
TUTOR:
TEACHING LOCATION: Auditorium
By the end of this lecture you will be
able to:
1- Define genome structure.
2- State the differences between viral,
prokaryotic and eukaryotic genome
structures.
3- Describe the role of histones in DNA
packaging.
4- Describe nucleosome structure.
5. Demonstrate the different levels of DNA
packaging.
 Genome structure in different
species.
 Genome structure of viruses.
 Genome structure of prokaryotes
 Genome structure of eukaryotes.
 Human genome.
 Organization of eukaryotic DNA.
 Role of histones in packaging of
DNA.
 Nucleosomes and polynucleosomes.
 Different levels of organization of
eukaryotic DNA.
DNA is usually much larger than the size of the
cell containing the DNA. For example, a single
diploid human cell contains 6X109 bp of
182
chromosomal
DNA
packaged
chromosomes. The counter length of
approaches 2 meters, all of which is
within a nucleus, about 10 m in
Hence, the DNA of all organisms
exquisitely packaged.
in
46
this DNA
contained
diameter.
must be
1.
Required Texts And Resources:
Lippincott Illustrated Reviews, 3rd
edition, Champe & Harvey
2. Textbook of Biochemistry with Clinical
Correlations, Thomas M. Devlin, 5th
edition, Wiley-Liss



You have the opportunity to watch the CDROM about Packaging of DNA You can
access the CD-ROM during your spare
time.
1. http://www.dnaftb.org/dnaftb/
2.
http://learn.genetics.utah.edu/units/basics/
tour/
3- http://www.biologie.unihamburg.de/b-online/library/catremoved/u4aos1p2.html
4- http://www.biologie.unihamburg.de/b-online/library/catremoved/u4aos1p2.html
5.http://www.sciencemuseum.org.uk/ex
hibitions/lifecycle/152.asp
6.http://pulse.pharmacy.arizona.edu/10t
h_grade/dawn_new/science/dna_genes.
html
7.http://morgan.rutgers.edu/MorganWe
183
bFrames/Level1/Page1/p1.html
8.http://www.ndsu.nodak.edu/instruct/
mcclean/plsc431/eukarychrom/eukaryo
3.htm
I. Short Questions:
1. Define each of the following:
a. Histones.
b. Nucleosome structure.
2. List the different levels of DNA
packaging.
II. MCQs:
1. All of the following are true about
eukaryotic genes EXCEPT:
a.
Most of eukaryotic genes are
discontineous.
b. They are always overlapping.
c. Coding sequences are unique and non
repetitive.
d. They contain a regulatory sequence and a
coding sequence.
2. Regarding nucleosome structure, which
of the following
statements is correct?
a. Nucleosomes are spherical structures
comprised of RNA,
nonhistone proteins and histone
proteins.
b. The major histones comprising
nucleosomes are H1and H4.
c. Nucleosomes permit efficient packing of
DNA to about one seventh its normal
length.
d. The histone associated with the DNA in
the linker region holding nucleosomes is
called H2A.
e. All of the above.
184
3. The following statements describes both
human and bacterial
DNA EXCEPT:
a. The DNA occurs physiologically as
nucleosome complexes.
b. The DNA contains major and minor
grooves.
c. The DNA consists of an antiparallel
duplex.
d. The DNA contains equal molar fractions
of adenine and thymine.
e. The DNA contains equal molar fractions
of guanine and cytosine.
4. Histones are small basic proteins that:
a. Nucleosome core consists of spherical
structures comprised of
DNA surrounded by H3.
b. The major histones comprising
nucleosomes are H1and H4.
c. Permit efficient packing of DNA to
about one seventh its normal length.
d. The histone associated with the DNA in
the linker region holding nucleosomes is
called H2A.
e. All of the above.
5. The third level of DNA packaging:
a. Nucleosomes, joined by “linker” DNA
in presence of H1 form a
polynucleosome.
b. It is by coiling the 30 nm fiber into
twisted-looped structure
attached to a protein scaffold in the form
of rosettes.
c. It is by formation of nucleosomes in
which a segment of the DNA
double helix is wound nearly twice
around a histone core.
d. The histone core consists of two
molecules each of H2A, H2B,
H3, and H4.
e. All of the above.
185
III. True / False:
1. Human immuno-deficiency virus
(HIV) is RNA virus; its genome is
formed of two copies of dsRNA.
2. Prokaryotic genome consists of one
single double-stranded supercoiled
circular chromosome
3. Plasmid DNA is small and circular
extra chromosomal DNA molecules that
present in bacteria and undergoes
replication that is always synchronized
to chromosomal division.
4. Human genome consists of 46
chromosomes that contain about 120,000
genes coding for about 120,000 proteins.
5. Most of the eukaryotic genes are
continuous sequences and genes
are usually overlapping.
186
LECTURE # 40 : DNA sequence and function
DEPARTMENT: Clinical Biochemistry
TUTOR:
TEACHING LOCATION: Auditorium
By the end of this lecture you will be
able to:
Compare between prokaryotic
genes and eukaryotic genes.
1-
2- Differentiate between the different
types of eukaryotic DNA sequences.
3. Identify functions of different
types of eukaryotic DNA sequences.







Prokaryotic gene structure.
Eukaryotic gene structure.
Single-copy DNA.
Repeated DNA sequences:
Moderately reiterated DNA.
Highly reiterated DNA.
Inverted repeat DNA.
The size and average base composition of DNA
vary widely between species. The property that
makes the DNA of a species unique is the
nucleotide sequence.
The human genome
project offers a complete sequence of human
genome. In contrast to prokaryotic genome,
eukaryotic genome contains repetitive sequences
that are repeated anywhere from a few times, for
certain coding genes, to million of times per
187
Student Notes:
.
genome for certain simple, relatively short,
sequences.
1.
Required Texts And Resources:
Lippincott Illustrated Reviews, 3rd
edition, Champe & Harvey
2. Textbook of Biochemistry with Clinical
Correlations, Thomas M. Devlin, 5th
edition, Wiley-Liss
3. Human Molecular Genetics, Strachan
T. & Read, A.P. BIOS Scientific
Publishers
Limited.



You have the opportunity to watch the CDROM about DNA Sequence and Function.
You can access the CD-ROM during your
spare time.
1- http://www.webbooks.com/MoBio/Free/Ch3G.htm
2http://www.neuro.wustl.edu/NEUROMUSC
ULAR/mother/dnarep.htm#gengenom
3- http://library.lanl.gov/cgibin/getfile?00418723.pdf
4http://www.math.umd.edu/~ssindi/mainthe
sis.pdf
5http://www.pubmedcentral.nih.gov/articler
ender.fcgi?artid=324220
6.
http://en.wikipedia.org/wiki/Alu_sequence
7.
http://en.wikipedia.org/wiki/Category:Repe
188
titive_DNA_sequences
I. Short Questions:
1. List the different classes of eukaryotic
repeated DNA sequences.
2. List different types of single copy DNA
sequences.
II. MCQs:
1. The unique sequence DNA includes
all the following EXCEPT:
a. Alu repeats.
e. Most coding genes.
f. Pseudogenes.
g. Regions flanking genes.
f. Introns.
2. The Alu repeat :
a. Involves most genes.
b. Is 300 base pairs long, present in about
500,000 copies per haploid genome
c. Is found only within genes in introns.
d. Is the main component of Pseudogenes.
h. Present mainly in centromeres of
chromosomes.
e. Present mainly in telomeres.
3. Microstellit sequences :
a. Sequences of 2-5 base pairs repeated up
to 50 times.
b. Exists as both dispersed and grouped
tandem arrays.
c. Most commonly found as dinucleotide
repeats of AC.
d .The GT repeats range in size from about
20 to 60 base pairs.
e. All of the above.
189
III. True / False
1. Most of the prokaryotic genes are
continuous sequences and genes are usually
overlapping.
2. Eukaryotic genes consist of coding
sequences (exons) interrupted by
intervening
sequences (introns).
3. Pseudogenes are sequences of DNA that
have significant nucleotide homology to
a functional gene but that contain
mutations that prevent gene expression.
4. As distinct from eukaryotes, the DNA of
prokaryotes contains multiple copies of
repetitive sequences.
5. In human DNA, at least 25-35% of the
genome consists of repetitive sequences.
190
LECTURE # 41 : Replication of DNA (DNA Synthesis)
Student Notes:
DEPARTMENT: Clinical Biochemistry
.
TUTOR:
TEACHING LOCATION: Auditorium
By the end of this lecture you will be able
to:
6- State the role replication in transfer of
genetic information.
7- List the common features of replication.
8- List the different
replication.
components
of
9- Define replication fork and its role in
replication.
10- Explain
the
replication.
different
steps
of
11- Distinguish between prokaryotic and
eukaryotic replication.
12- List the different activities of DNA
polymerases.
13- State the different DNA polymerase and
their role in replication in both
prokaryotes and eukaryotes.
14- Explain the mechanism of DNA
proofreading of newly synthesized DNA
strands.
15- Discuss the role of topoisomerases
during replication.
16- Explain the role of telomerases in
replication.
17- List the
different inhibitors
replication and their site of effect.
 Principles of replication.
 Components of DNA replication.
191
of
 Origin of replication.
 Prokaryotic replication:
H. Single origin of replication.
I. Proteins required for DNA
separation.
J. Prokaryotic DNA polymerases.
K. Synthesis of Leading and
Lagging strands.
 Eukaryotic replication:
L. Multiple origin of replication.
M. Eukaryotic DNA polymerases.
N. Synthesis of Leading and
lagging strands.
 Proofreading of newly synthesized
DNA strands.
 DNA Topoisomerases.
 Telomerases.
 Inhibitors of replication.
Remember that DNA, the storehouse of
genetic information, is required for the storage
and expression of genetic information. This
genetic information is copied and transmitted
to daughter cells through DNA replication.
The DNA contained in a fertilized egg
encodes the information that directs the
development of an organism.
This
development may involve the production of
billions of cells. Each cell is specialized,
expressing only those genes that are required
its function. Therefore, DNA must be able to
not only replicate precisely each time a cell
divides, but also to have the information that it
contains be selectively expressed.
1.
Required Texts And Resources:
Lippincott Illustrated Reviews, 3rd
edition, Champe & Harvey
2. Textbook of Biochemistry with Clinical
Correlations, Thomas M. Devlin, 5th
192
edition, Wiley-Liss



You have the opportunity to watch the CDROM about Replication of DNA. You can
access the CD-ROM during your spare
time.
21- http://www.biostudio.com/d_%20Replic
ation%20of%20a%20Chromosome.htm
22- http://www.biostudio.com/d_%20DNA%
20Replication%20Nucleotide%20Polym
erization.htm
23- http://www.biostudio.com/d_%20DNA%
20Replication%20Coordination%20Lea
ding%20Lagging%20Strand%20Synthe
sis.htm
4- Inhibitors of DNA replication are
used clinically for treatment of
different diseases. In the light of the
above, deduce the difference
between inhibitors of prokaryotic
replication and eukaryotic
replication in clinical applications.
Clinical Question
I. Short Questions:
1. List different characteristics of DNA
replication.
193
2. List different types of eukaryotic DNA
polymerases and their functions.
3. Define:
a. Origin of replication.
b. Semiconservative replication.
4. Give function of the following:
a. Helicase.
b. Single strand DNA-binding proteins.
c. DNA-derpendent DNA polymerase.
5. List different characteristics of origin of
replication.
6. Compare between prokaryotic DNA
polymerases.
7.
List the steps of eukaryotic DNA
replication.
8. List three inhibitors of DNA replication.
II- MCQs:
1. All of the following are true about
eukaryotic DNA replication EXCEPT:
a. It is semiconservative.
b. It occurs in the 35 direction.
c.
Both strands act as a template
simultaneously.
d. It is bidirectional.
2. Which statement is TRUE about DNA
replication:
a. It occurs on one strand only
b. It is catalyzed by RNA polymerase.
c. It occurs in the 35 direction.
d. It is semiconservative
3.
DNA replication requires all the
following EXCEPT:
a. RNA polymerase
b. A short RNA primer.
c. Deoxynucleoside triphosphates.
d. DNA template.
4. In replication, separation of the double
194
strands of DNA is catalyzed by:
a. Helicase.
b. Primase.
c. DNA polymerase.
d. RNA [polymerase.
5. Single stranded DNA (ssDNA) binding
proteins play a role in the following
EXCEPT:
a. Packaging of DNA.
b. Bind to ssDNA
c. Keep the two DNA strands separated.
d. Protects ssDNA from digestion by
nucleases.
6. During DNA replication, the sequence 5′TpApGpAp-3′ would produce which
of the following complementary
sequence:
a. 5′-TpCpTpAp-3′.
b. 5′-ApTpCpTp-3′.
c. 5′-UpCpUpAp-3′.
d. 5′-GpCpGpAp-3′.
III. True / False
7- Replication process involves
replication of certain genes of DNA.
8- Ligase enzyme plays a major role in
the separation of the two DNA
strands for replication.
9- In prokaryotes, replication starts at
multiple sites that are rich in AT
sequences.
10Single Stranded DNA binding
proteins bind to the single stranded
DNA keeping the 2 strands
separated.
11DNA polymerases utilizes
ribnucleoside triphosphates for the
synthesis of the new strands.
195
LECTURE # 42 : DNA Repair
DEPARTMENT: Clinical Biochemistry
TUTOR:
TEACHING LOCATION: Auditorium
By the end of this lecture you will be able
to:
1- Define gene mutations.
2- List the different causes of mutations.
3- Specify the different types of mutations.
4- Describe the mechanism of DNA repair.
5-Indicate the consequences of defective DNA repair
mechanism.





Gene mutations.
Causes of mutations.
Types of mutations.
DNA repair mechanism.
Examples of defective DNA repair
mechanism.
Remember that despite the elaborate
proofreading system employed during DNA
synthesis, mutations can occur. In addition,
DNA is constantly being subjected to
environmental insults that cause the alteration
or removal of bases. Bases are also altered
or lost spontaneously from mammalian DNA.
If the damage is not repaired, a permanent
mutation may be introduced that can result in
any of a number of deleterious effects.
Luckily, cells are remarkably efficient at
repairing the damage done to their DNA.
196
Student Notes:
.
1.
Required Texts And Resources:
Lippincott Illustrated Reviews, 3rd
edition, Champe & Harvey
2. Textbook of Biochemistry with Clinical
Correlations, Thomas M. Devlin, 5th
edition, Wiley-Liss



You have the opportunity to watch the CDROM about DNA Repair. You can access
the CD-ROM during your spare time.
1-
Clinical Question:
a) Clinical Case:
I. Short Questions:
1. List different types of mutations.
2. DNA repair is an important process:
a.
List the different causes of
mutations.
b. Outline steps of DNA repair.
II. MCQs:
1. What will be the effect of a single base
pair deletion in the middle of a DNA
sequence coding for a certain protein?
197
a. A protein with a single amino acid
substitution in its centre.
b. The gene will not be transcribed and no
protein will be produced.
c. The amino half of the protein will have a
normal sequence.
d. The carboxyl half of the protein will
have a normal sequence.
e.
DNA polymerase will repair the
damage.
2. Which one of the following enzymes
catalyzes the elimination of nicks or
discontinuities in DNA that occur during
DNA repair or in the linking together of
Okazaki fragments?
a. AP exonuclease.
b. DNA gyrase.
c. DNA ligase.
d. Topoisomerase I.
e. Topoisomerase II.
3. Xeroderma pigmentosum results from a
deficiency in:
a. Collagen synthesis.
b. DNA replication.
c. DNA repair.
d. Bilirubin conjugation.
e. A tumor suppressor.
III. True / False
1. Mutations are permanent changes in a
DNA sequence.
2. Frame shift mutation results from a
single base substation.
3. Xeroderma Pigmentosum is a rare
autosomal recessive disease due to
defective repair.
4. The DNA repair mechanism involves
recognition of the lesion by an
exonuclease, which cleaves the
damaged strand to form a nick.
5. Excision of damaged DNA is catalysed
198
by an excision “3′  5′ ”
exonuclease.
199
LECTURE # 43 : Structure of Ribonucleic Acid (RNA)
Student Notes:
DEPARTMENT: Clinical Biochemistry
.
TUTOR:
TEACHING LOCATION: Auditorium
By the end of this lecture you will be able
to:
1- Identify the structural components of
234567-
ribonucleic acid (RNA).
List the different types of RNA.
Explain the structural characteristics of
rRNA.
Explain the structural characteristics of
tRNA.
Explain the structural characteristics of
rRNA.
Differentiate between the functions of
different types of RNA.
Illustrate the importance of interaction
between the three different RNAs in
protein synthesis.
 Structure of Ribonucleic Acid (RNA).
 Types of RNA:
O. Ribosomal RNA.
P. Transfer RNA.
Q. Messenger RNA.
R. Nuclear RNA.
S. Mitochondrial RNA.
RNA molecules play different roles in
cellular information transfer. All three types of
RNA; ribosomal RNA, transfer RNA and
messenger RNA interact together for the
process of protein synthesis. Ribosomes
carry out protein synthesis. Transfer RNAs
200
transfer specific amino acids to ribosomes.
Messenger RNAs carry information from the
DNA to the cellular protein synthetic
machinery. Other RNAs in the cell are
important in RNA processing and in protein
export from the cell.
1.
Required Texts And Resources:
Lippincott Illustrated Reviews, 3rd
edition, Champe & Harvey
2. Textbook of Biochemistry with Clinical
Correlations, Thomas M. Devlin, 5th
edition, Wiley-Liss



You have the opportunity to watch the CDROM about RNA Structure. You can
access the CD-ROM during your spare
time.
1a)
Clinical Question
2-
Clinical Case
I. Short Questions:
1.
Enumerate the major differences
201
between DNA and RNA.
2. List the different characteristics of tRNA
and function of each.
3. List the structural features of mRNA.
II. MCQs:
1. RNA is found mainly in:
a. Cytoplasm.
b. Nucleus.
c. Mitochondria.
d. Lysosomes.
2. The sugar present in RNA is:
a. Ribose.
b. Ribulose.
c. Deoxyribose.
d. Glucose.
3.
RNA has the following features
EXCEPT:
a. Contains purine bases.
b. Contains pyrimidines bases.
c. Contains phosphate.
d. Is double stranded helix.
4. All of the following are present in RNA
EXCEPT:
a. Deoxy ribose.
b. Ribose.
c. Adenine.
d. Cytosine.
5. The DNA & RNA share the following
features EXCEPT:
a. Both contain purine bases.
b. Both contain pyrimidines bases.
c. Both contain phosphate.
d. Both are double stranded helix.
202
6. If a sample of mRNA is 30 mole % G, the
mole % A:
a. is greater than 30.
b. is less than 30.
d. cannot be ascertained from this
information.
e. is also 30.
7. Acceptor arm of tRNA is characterized
by the following:
a. Contains three specific bases
(anticodon) that is complementary to mRNA.
b. contains from 3 to 12 bases and it is the
major site for variation in tRNA.
c. It terminates at its 3` OH end by a
specific sequence formed of CCA.
d. Contains the unusual base dihydrouracil
so termed the D-loop.
e. Contains the unusual thymine and
pseudouridine bases.
III. True / False
1. The main function of mRNA is the
transport of amino acids to the ribosome
for synthesis of proteins.
2. The anticodon loop of tRNA plays a key
role in translation by pairing with the
complementary codon of mRNA.
3. Each mRNA molecule carries a
message to represent the genetic
information
of a specific gene for the synthesis of a
specific protein.
4. RNA molecules are synthesized in a
process termed replication where the
sequence of bases in each RNA
molecule is controlled by base sequence
in
both strands of DNA.
5. Eukaryotic 80S ribosomes are formed
mainly of two main nucleoprotein
subunits of unequal size, the 60S
subunit and the 40S subunit.
203
204
LECTURE # 44 -a : Transcription of DNA (RNA Synthesis)
Student Notes:
DEPARTMENT: Clinical Biochemistry
.
TUTOR:
TEACHING LOCATION: Auditorium
By the end of this lecture you will be able
to:
1.
State the role transcription
expression of genetic information.
in
2.
State the
transcription.
of
general
principle
3.
List the different components of
transcription.
4. Explain structure and functions of RNA
polymerase.
5. State the functions of different types of
RNA polymerases.
6.
Explain
transcription.
the
different
phases
of
7. Discuss the steps of eukaryotic mRNA
synthesis.
8. State the role of promoter sequence in
transcription.
9. Explain the role of transcription factors
in transcription.
10. List the different inhibitors of
transcription and their site of effect.






General principles of transcription.
Eukaryotic transcription.
Components of transcription.
RNA polymerases.
Types of RNA polymerases.
Transcription phases:
T. Initiation.
205
U. Elongation.
V. Temination.
 Synthesis of mRNA.
 Transcriptional gene regulatory
elements.
 Inhibitors of transcription.
Remember that gene expression involves
both transcription and translation processes.
Transcription is the process by which the
information stored in DNA for certain protein
sequence is copied from one strand of a
template sequence into the sequence of
mRNA.. This mRNA then acts as a template
for the synthesis of proteins. The sequence of
nucleotides on DNA specifies the sequence of
nucleotides on mRNA, which in turn specifies
the sequence of amino acids in proteins.
1.
Required Texts And Resources:
Lippincott Illustrated Reviews, 3rd
edition, Champe & Harvey
2. Textbook of Biochemistry with Clinical
Correlations, Thomas M. Devlin, 5th
edition, Wiley-Liss



You have the opportunity to watch the CDROM about Transcription. You can
access the CD-ROM during your spare
time.
206
1. www.uhmc.sunysb.edu/som/courses/mgac/Lects.%20
16&.
2. www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb2/part1/26transl.ppt
3. http://www.biostudio.com/d_%20Transcription.ht
m
4. http://207.207.4.198/pub/flash/26/transmenu_s.s
wf
5.
Clinical Question:
1- Clinical Case
I. Short Questions:
1. Tabulate the similarities and differences
between eukaryotic replication and
Transcription (function, site, enzyme,
direction, requirements).
2. In a tabular form compare between
DNA-polymerase and RNA-polymerase
(function, activity, requirements).
3. List the function of  subunit of RNA
polymerase.
4. List different types of RNA polymerases
and their functions.
II. MCQs:
1. Transcription of a gene in human cells:
a. Always begins at an AUG (codon which
codes for methionine).
b. Does not require local unwinding of two
DNA strands.
c. Always “reads” the DNA template
207
strand in the 3′ to 5′ direction.
d. Occurs on both strands simultaneously.
2. Synthesis of RNA from a DNA template
requires:
a. ddA, ddC, ddG and ddT nucleotides.
b. A, C, G and U triphosphate nucleotides.
c. Reverse transcriptase.
d. dA, dC, dG and dT triphosphate
nucleotides
e. Restriction endonucleases.
3. All of the following is true about RNA
polymerase EXCEPT:
a. It requires a primer.
b. It has a 35 polymerase activity.
c. It utilizes ribonucleoside triphosphates.
d. Is a polymeric enzyme.
4. TATA box is recognized by the following
subunit of RNA polymerase:
a. α subunit.
b. β subunit.
c. Core enzyme.
d.  subunit.
5. TATA box:
a. Determines the start of trascription.
b.
Determines the frequency of
transcription.
c. Occurs down stream of the structural
gene.
d. consists of 20 bases.
6. The  subunit of RNA polymerase:
a. Enables RNA polymerase to recognize
and bind to the promoter.
b. Determines which strand is copied.
c. Determines the start of transcription.
d. All of the above.
7. During RNA synthesis, the DNA template
sequence 5′-ApTpGpCp-3′
208
would be transcribed to produce which
of the following RNA sequences:
a. 5′-TpApCpGp-3′.
b. 5′-GpCpApTp-5′.
c. 5′-ApUpCpGp-3′.
d. 5′-GpCpApUp-3′.
8. Concerning TATA box (Hogness box):
a. It encodes repressor protein.
b. It binds to anticodon.
c. It regulates translation.
d. It binds to RNA polymerase.
9. All of the following are true for both
DNA polymerase and RNA polymerase
EXCEPT:
a. Both require a template.
b. Both reactions produce pyrophosphate
as a product.
c. Both add 5' nucleotides to 3' hydroxyl
groups.
d. both utilize nucleotide triphosphates as
substrates.
e. Both require a primer.
III. True / False
1. The first step in mRNA synthesis is
the binding of the TF IID to the TATA
Box.
2. The CAAT box and the GC box
determine the frequency of
transcription.
3. The complex of RNA polymerase,
DNA template and new RNA transcript
is called transcription bubble.
4. In transcription, RNA polymerase
utilizes deoxyribonucleoside
triphosphate and releases
pyrophosphate.
5. Initiation of transcription involves
the binding of RNA polymerase to the
promoter regi
LECTURE # 44-b : Posttranscriptional processing and Regulation of
209
Gene Expression
DEPARTMENT: Clinical Biochemistry
TUTOR:
TEACHING LOCATION: Auditorium
By the end of this lecture you will be able to:
1. List postranscriptional processing of RNA.
2. Explain postranscriptional processing of
mRNA.
3. List the different levels of regulation of
eukaryotic gene expression.
4. Differentiate between the different levels of
regulation of gene expression.
5. Identify the basal expression elements and
their role in regulation of gene
expression.
6. Identify the regulated expression elements
and their role in regulation of gene
expression.
7. Explain the role of alternative splicing in
regulation of gene expression.
8. Explain the role of polyadenylation in
regulation of gene expression.
 RNA processing.
 mRNA processing.
 Levels of eukaryotic Gene Expression
Regulation:
a.
Alteration of Gene Content:
i. Gene Amplification.
ii. Gene Diminution.
iii. Gene Rearrangement or
Recombination.
b.
Transcriptional regulation:
i. Chromatin Remodeling.
210
Student Notes:
.
ii.
DNA Regulatory Region:
- Basal Expression
Elements: TATA box, and CAAT box or
GC
box.
- Regulated Expression
Elements: Enhancers, Silencers and
other regulatory elements.
iii. DNA Regulatory Factors.
c.
Posttranscriptional Regulation:
i. Alternative Splicing.
ii. Regulation of RNA Stability.
The process of transcription involves
transcription of the whole gene to give primary
transcript. However, most eukaryotic genes are
interrupted by introns that are not coding for
proteins. Posttranscriptional modification of RNA
involves many chemical modifications along with
excision of primer sequences and ligation of the
exons (coding sequences) together to give
mature mRNA ready to be transferred to the
cytoplasm where protein synthesis occurs on
ribosomes.
While the whole set of chromosomes are present
in every cell, genes expression in different cell
types vary widely according to the activity of
individual cells. Hence, gene expression is finely
controlled through different mechanisms of gene
regulation.
1. Required Texts And Resources: Lippincott
Illustrated Reviews, 3rd edition, Champe &
Harvey
2. Textbook of Biochemistry with Clinical
Correlations, Thomas M. Devlin, 5th edition,
Wiley-Liss


211

You have the opportunity to watch the CDROM about RNA processing. You can
access the CD-ROM during your spare time.
1- http://highered.mcgrawhill.com/sites/007243
7316/student_view0/chapter15/animations.h
tml#
2- http://207.207.4.198/pub/flash/26/transmenu
_s.swf
3-
1. Clinical Question:
2. Clinical Case
I. Short Questions:
1. List the different posttranscriptional
modifications of RNA.
2. List the different posttranscriptional
modifications of mRNA.
3. Define the following and give function:
a. The TATA box.
b. Capping of mRNA.
c. Polyadenylation of mRNA.
d. Regulated expression elements.
4. List the different levels of regulation of
eukaryotic gene expression.
5. Define:
a. Basal regulatory elements.
b. Enhancer.
c. Silencer.
212
II. MCQs:
1. Regulation of eukaryotic gene expression
involves:
a. Alteration of gene content.
b. Transcriptional regulation.
c. Posttranscriptional regulation.
d. All of the above.
e. None of the above.
2. Gene expression:
a. Shows no relation with the tissue activities.
b. Is the same in all tissues due to the same
chromosome structure.
c. Involves replication of the whole genome.
d. Differ in different tissues due to the
different chromosome structure.
e. Differ in different tissues according to the
different tissue activities.
3. Basal expression elements involves:
a. TATA box.
b. Enhancers.
c. Silencers.
d. Other regulatory elements.
e. Poly A tail.
4. Histone acetylation at their N-terminal
(lysine):
a. Increases the histone positive charges and
decreases the binding affinity of
histones with the negatively charged DNA.
b. Increases the histone positive charges and
increases the binding affinity of
histones with the negatively charged DNA.
c. Reduces the histone positive charges and
decreases the binding affinity of histones
with the negatively charged DNA.
d. Reduces the histone positive charges and
increases the binding affinity of histones
with the negatively charged DNA.
e. None of the above.
213
III. True / False
1. Methylation of cytosine of DNA converts the
active euchromatin into inactive
heterochromatin.
2. Enhancers interact with gene regulatory
proteins or trans-factors and decrease
the rate of expression.
3. Basal expression elements contains TATA
box and CAAT box or GC box.
4. TATA box specify the frequency of
initiation.
5. The length of poly A tail determines the half
life time of mRNA.
214
LECTURE # 45 : Translation of RNA (Protein Synthesis)
Student Notes:
DEPARTMENT: Clinical Biochemistry
.
TUTOR:
TEACHING LOCATION: Auditorium
By the end of this lecture you will be able
to:
1. State the principle of translation (protein synthesis).
2. Define genetic code.
3. Explain the relation between genetic code and amino
acid sequence in the process of protein
synthesis.
4. Define initiation codon and stop codons.
5. List the steps involved in protein synthesis.
6. Describe activation of amino acids (synthesis of
amino acyl-tRNA).
7. Discus the steps of polypeptide chain synthesis.
8. Define the role of different initiation factors in the
initiation of protein synthesis.
9. Describe the interaction between different types of
RNA in the process of protein synthesis.
10. Define the role of different elongation factors in the
elongation of polypeptide chain.
11. State the role of peptidyl transferase in the process
of protein synthesis.
12. Discus the process of termination of protein
synthesis and its regulation.
13. Explore the role of polyribosome in enhancing the
synthesis of protein.
14. List the different posttranslational modifications of
proteins.
215
 Principle of Protein Synthesis.
 Genetic Code.
 Protein Synthesis:
I. Synthesis of Aminoacyl-tRNA
(Activation of Amino Acids).
II. Synthesis of Polypeptide Chain
(translation):
1.
Initiation:
1) Ribosomal
Dissociation.
2) Formation of the 43S
Preinitiation Complex.
3) Formation of 48S
Initiation Complex.
4) Formation of the 80S
Initiation Complex.
- Regulation and
Control of Initiation.
2.
Elongation:
1) Binding of aminoacyltRNA to the A Site.
2) Peptide Bond
Formation.
3) Translocation.
3.
Termination
 Polyribosomes.
 Posttranslational Processing of
Proteins:
iii. Trimming.
iv. Covalent Alteration.
Translation is the second step by which gene
expression leads to protein synthesis.
Protein synthesis involves interaction of the
three main types of RNA. The sequence of
codons in mRNA specifies the order of amino
acids in a protein. Protein synthesis takes
place on the ribosomes by the aid of tRNA. This
process involves activation of amino acids then
synthesis of polypeptide chain. In addition,
216
many
proteins
requires
posttranslational
modifications to give rise to the functional
protein.
1.
Required
Texts
And
Resources:
Lippincott
Illustrated
Reviews,
3rd
edition, Champe & Harvey
2. Textbook of Biochemistry with Clinical
Correlations, Thomas M. Devlin, 5th
edition, Wiley-Liss



You have the opportunity to watch the CDROM about Translation. You can access
the CD-ROM during your spare time.
1.http://highered.mcgrawhill.com/sites/007243
7316/student_view0/chapter15/animations.ht
ml#
www.uhmc.sunysb.edu/som/courses/mgac/Lect
2.1&s.%2016
3.http://www.biostudio.com/demo_freeman_p
rotein_synthesis.htm
4.
http://207.207.4.198/pub/flash/26/transmenu_s
.swf
Clinical Question:
217
Clinical Case
I. Short Questions:
1. Enumerate the steps of protein
synthesis.
2. List different initiation factors of
protein synthesis and their function.
3. List the posttranslational modifications
of proteins.
II. MCQs:
1. A codon consists of :
a. One molecule of aminoacyl-tRNA.
b. Three successive bases.
c. Four individual nucleotides.
d. Two complementary base pairs.
2. All of the following are requirements for
protein synthesis EXCEPT:
a. Ribosomes.
b. mRNA.
c. Aminoacyl-tRNA.
d. Carbamoyl phosphate synthetase I.
3. All of the following are required for
protein synthesis EXCEPT:
a. Ribosomes.
b. mRNA.
c. Aminoacyl-tRNA.
d. Primer protein.
4. Activation of amino acids means:
a. Synthesis of peptide bond.
b. Translocation of peptidyl-tRNA.
c. Synthesis of aminoacyl-tRNA.
d. Ribosomal dissociation.
e. Hydrolysis of GTP.
5. All of the following is required for protein
218
synthesis EXCEPT:
a. mRNA.
b. Aminoacyl tRNAs.
c. Ribosomes.
d. DNA template.
e. Peptidyl transferase.
6. Which one of the following choices best
completes the following
sentence?
Transfer RNA……..
a. Contains the information necessary for the
synthesis of a specific protein.
b. Must exist in at least 20 different forms,
one for each amino acid.
c. Is the largest of RNA species.
d. Has little or no secondary structure.
7. Initiation of eukaryotic peptide synthesis
requires:
a. The initiation factors.
b. The enzyme RNA polymerase.
c. The enzyme peptidyl transferase.
d. The enzyme translocase.
8. Which one of the following statements
about messenger RNA is
INCORRECT?
a. The sugar moiety of mRNA is D-ribose.
b. The polynucleotde chain at mRNA is
longer than that of DNA.
c.
mRNA exists as single-stranded
molecules.
d. mRNA has a 7′-methylguanosine “cap” at
its 5′-end.
9. During the process of peptide chain
elongation, the growing peptide chain:
a. Is linked to the mRNA.
b. Is linked to the ribosomal RNA.
c. Is not linked at all to any RNA.
d. Is linked to template DNA.
219
e. Is linked to the 3'-OH of the adenosine
terminal nucleoside of tRNA.
III. True / False
1. Different proteins are synthesized in
different tissues due to the different
chromosome structure.
2. Phosphorylation of IF-2 prevents formation
of 43S preinitiation complex and
blocks protein synthesis.
3. A site is the ribosomal site where tRNA
carrying the growing polypeptide chain
binds.
4. Elongation of protein synthesis is a cyclic
process and involves synthesis of
Aminoacyl-tRNA.
5. A codon is formed of three specific
nucleotides ( or three nitrogenous bases).
220
Lectures #(46) : Recombinant DNA Technology
DEPARTMENT: Clinical Biochemistry
Tutor: Dr.
TEACHING LOCATION: Auditorium
By the end of this topic the student shall
be able to:
1.
Describe the basic techniques
utilized in recombinant DNA.
2. Know the utility of these techniques
in diagnosis and research.
 Introduction.
 Hybridization.
 Methods used in labeling nucleotide
proteins.
 DNA storage.
 DNA amplification and cloning.
 Cell-based cloning.
 Polymerase chain reaction-based
DNA cloning.
 Specific methods used in the
analysis of DNA.
 PCR-based methods.
 Other methods for detection of
variation in DNA.
 DNA sequencing
The rapid development of techniques in
the field of molecular biology is
revolutionizing the practice of medicine.
221
Student Notes:
.
The potential uses of these techniques for
the diagnosis and treatment of diseases
are vast. Techniques of molecular biology
are used in the prevention and treatment
of diseases. For example, recombinant
DNA techniques provide human insulin for
the treatment of Diabetes. In these 2
lectures some of recombinant DNA
techniques will be described as Methods
of isolation, amplification and manipulating
DNA involve the use of restriction
enzymes, cloning vectors, and PCR.
Lippincott Illustrated Reviews, 3rd
edition, Champe & Harvey
2. Reading Handouts will be distributed
3- Lectures and power point presentation
1.
will be published on department website:
www.kaau.edu.sa/faculties/medicine/dcbcweb
You have the opportunity to watch the CDROM about Extracellular matrix You can
access the CD-ROM during your spare time.
As
a process of
Self
Directed
Learning (SDL) search in the internet
for web sites related to this subject and
write them down:
1-
222
2-
3-
A 70-year-old man presented with back pain and
Joss of weight. Although a non-smoker, he had
had several recent chest infections and was
increasingly short of breath on exercise. On
examination, he was anaemic but there were no
other obvious abnormalities.
Investigations
Sodium130 mmol/L
urea 15.3 mmol/L
creatinine 212umol/L
calcium 2.75 mmol/L
total protein 85g/L
albumin 30g/l
urate 0.51 mmol/L
ESR >100mm/h
haemoglobin8.5 g/dL
A blood film showed normochromic, normocytic
anaemia; rouleaux were present on the blood film
and there was increased background staining.
Serum protein electrophoresis revealed a
paraprotein in the ^globulin region [Fig. 13.4,
pattern b); this was typed by immunofixation and
shown to be IgG-K. There was a decrease in the
normal yglobulin band. Bence Jones protein was
present in the urine and identified as k in type.
Radiological examination showed the typical
punched-out lytic lesions of myeloma in the
lumbar vertebrae, ribs and pelvis.
What is your comments on this case?
Make
internet
search
about
gene
223
therapy. With the aid of figure write 3
to 4 pages on the principles of gene
therapy and its applications in human
diseases.
I- Short Questions:
1- What are the methods of DNA
amplification.
2- Enumerate Medical applications of
PCR
3- What is meant by DNA finger printing?
II- MCQ:
1- All of the following are desirable features
of a good vector EXCEPT:
A. An origin of replication
B. A gene for selectable marker
C. A restriction enzyme site for insertion of
targets DNA
D. The ability to prevent lysis of the host
cell.
III- True / False
a- Restriction enzymes are best described by
conferring a selective advantage on invading
bacteriophage
b- Restriction fragment polymorphism analysis
isolate a gene that causes an inherited disease.
PRACTICALS
224
Practical (1) : Enzymes: Amylase activity in serum
Department: Biochemistry
Teaching location: Classroom
By the end of this practical the student will be able to:
o Determine the optimum temperature for enzyme activity
o Estimate serum amylase activity in the provided sample
o Explain the function of serum amylase
o Discuss the diagnostic importance of serum amylase

Determination of serum amylase

Explaining the effect of temperature on enzyme activity

Discuss the role of measurement of serum amylase in disease condition

Evaluating the role of amylase in GIT digestion of nutrients
Transferable skills:

Interrelate laboratory data with clinical findings
READING: Laboratory Handouts will be distributed
225
Practical (2) : Enzymes: Estimation of serum alkaline phosphatase
Department: Biochemistry
Teaching location: Classroom
By the end of this practical the student will be able to:
o Determine serum alkaline phosphatase
o Evaluate the effect of enzyme inhibitors on enzymatic activity
o Define Km and Vmax
o Show how the Lineweaver-Burk plot can be used to evaluate Km and
Vmax

Determination of serum alkaline phosphatase

The definition of Km and Vmax and the effect of enzyme inhibitors on both of
them

Plotting of Lineweaver-Burk plot and its utilization for evaluation of Km and
Vmax

Clinical importance of measurement alkaline phosphatase
Transferable skills:

Interrelate laboratory data with clinical findings

Serum alkaline phosphatase as marker for bone and liver diseases
READING: Laboratory Handouts will be distributed
226
Practical (3) : Enzymes: Serum CK isoenzymes
Department: Biochemistry
Teaching location: Classroo‫ة‬
By the end of this practical the student will be able to:
o Define what is meant by isoenzymes
o Separate the different CK isoenzymes using electrophoresis
o Evaluate the role of CK in tissues
o Discuss the role and importance of measuring CK isoenzymes in different
diseases conditions

Separation of serum CK isoenzymes

Function of Ck in different tissues

The different isoenzymes of CK and relation to different diseases
Transferable skills:

Interrelate laboratory data with clinical findings

How to use CK isoenzymes in evaluating cardiac and muscle
diseases
READING: Laboratory Handouts will be distributed
227
Practical (4) : Serum lactate
Department: Biochemistry
Teaching location: Classroom
By the end of this practical the student will be able to:
o Determine blood lactate
o Evaluate the importance of determination of serum lactate
o To discuss how one enzyme affects different metabolic pathways

Determination of serum lactate

The importance of measurement blood lactate in evaluating children with
hypoglycemia

The relation of lactic acidosis to enzyme deficiency such as glucose 6-phosphatase
deficiency
Transferable skills:

Interrelate laboratory data with clinical findings
READING: Laboratory Handouts will be distributed
228
Practical (5) : Serum lactate dehydrogenase isoenzymes
Department: Biochemistry
Teaching location: Classroom
By the end of this practical the student will be able to:
o Use electrophoresis for separation of LDH isoenzymes
o Differentiate between the different LDH isoenzymes (sources and function)
o Evaluate the role of LDH isoenzyme in disease diagnosis

Determination of serum LDH isoenzymes using cellulose electrophoresis

The role of LDH in different metabolic pathways

The sources of LDH isoenzymes and its role in diagnosis
Transferable skills:

Interrelate laboratory data with clinical findings

How to use LDH isoenzymes in evaluating cardiac cases
READING: Laboratory Handouts will be distributed
229
Practical (6) : Liver glucose-6-phosphatase deficiency
Department: Biochemistry
Teaching location: Classroom
By the end of this practical the student will be able to:
o Determine glucose-6-phosphatase in tissue extract
o Discussing the different changes in blood glucose, lactate, pyruvate, fatty
acids, ketone bodies and uric acid found in this case
o Explaining the basis of other glycogen storage diseases

Determination of glucose-6-phosphatase activity in liver tissues
Transferable skills:

Interrelate laboratory data with clinical findings

Correlation of lactic acidosis with glucose-6-phosphatase deficiency
READING: Laboratory Handouts will be distributed
230
Practical (7) : Plasma glucose estimation & Oral glucose tolerance curve
Department: Biochemistry
Teaching location: Classroom
By the end of this practical the student will be able to:
o Estimate plasma glucose
o Differentiate between the different methods for measuring plasma glucose
o Utilize the result of plasma glucose to diagnose a case of hyperglycemia
o Discuss how to monitor a diabetic patient
o Draw glucose tolerance curve
o Utilize this curve in diagnosis of hyperglycemic case
Blood Ammonia Determination
a- Principle
b- Specimen
c- Reagents
d- Procedures
e- Calculation
4. Case discussion

Determination of plasma glucose

Difference between blood glucose and plasma glucose

WHO classification of hyperglycemia

Drawing the curve using different glucose concentration

Estimation of the different samples (fasting, 60 minutes, 90 minutes and 120
minutes)

The difference between oral glucose and intravenous glucose tolerance curve

Monitoring of diabetic patient
Transferable skills:
231

Interrelate laboratory data with clinical findings

How to utilize plasma glucose for diagnosis and monitoring diabetic
patients
READING: Laboratory Handouts will be distributed
232
Practical (8) : Lipid Estimation of plasma total cholesterol & Triacylglycerol
Department: Biochemistry
Teaching location: Classroom
By the end of this practical the student will be able to:
o Estimate plasma cholesterol using cholesterol oxidase method
o Correlate plasma cholesterol level with cardiac diseases
o Utilize biochemical knowledge in treating this patient
o Estimate plasma triacylglycerol
o Evaluate the role of lipoprotein lipase in lipid metabolism
o Differentiate between the different types of hyperlipidemia

Measurement of plasma total cholesterol

Different types of hyperlipidemia

Classification of hypercholesterolemia according to Adult Treatment Panel III
(ATP III) provided by National Cholesterol Education Program (NCEP)

Different types of hyperlipidemia

Classification of hyperlipidemia according to Adult Treatment Panel III (ATP III)
provided by National Cholesterol Education Program (NCEP)
Transferable skills:

Interrelate laboratory data with clinical findings

Approach a case of hypercholesterolemia

Approach a case of hyperlipidemia
READING: Laboratory Handouts will be distributed
233
Practical 9: Serum Urea & Ammonia Determination
Department: Biochemistry
Teaching location: Classroom & Biochemistry Laboratory
By the end of this topic the student shall be able to:
1. Knowing the causes of changes in Blood Urea.
2. Determine urea by diacetyl monoxime method
3.determine ammonia by Brthelot reaction
4.Know what is meant by hyperammonemia
1-
Introduction.
2. Case History
3. Blood Urea & Ammonia Determination
a- Principle
b- Reagents
c- Procedures
d- Calculation
Transferable skills:
1.Acquire manual skills in handling laboratory equipments
2.Correlate the laboratory findings with theoretical knowledge
READING: Handouts will be distributed before the class
234
Practical 10 : Serum and urinary creatine and creatinine
Department: Biochemistry & Biochemistry Laboratory
Teaching location: Classroom
By the end of this topic the student shall be able to:
1. Determine creatine and creatinine in serum and urine
2. Understand the role of creatine phosphate in muscle
3. Correlate creatine and creatinine level to disease states
1-
Introduction.
2. Case History
3. Serum and urinary creatine and creatinine
a- Priniciple
b- Reagents
c- Procedures
d- Calculation
4. Case discussion
Transferable skills:
1.Acquire manual skills in handling laboratory equipments
2.Correlate the laboratory findings with theoretical knowledge
READING: Handouts will be distributed before the class
235
Practical 11 : Serum Alanine aminotransferase (ALT) & Serum
aminotransferase (AST)
Aspartate
Department: Biochemistry
Teaching location: Classroom & Biochemistry Laboratory
By the end of this topic the student shall be able to:
1. Understand the mechanisms involved in the development of liver
damage related to chronic liver disease
2. Understand the principle of the common methods for the measurement
of Alanine aminotransferase
3. Learn how to interpret biochemivcal data in relation to a disease state
(in this case chronic liver disease)
1-
Introduction.
2. Case History
3. Determination of ALT
a- Priniciple
b- Reagents
c- Procedures
d- Calculation
4. Case discussion
Transferable skills:
1.Acquire manual skills in handling laboratory equipments
2.Correlate the laboratory findings with theoretical knowledge
READING: Handouts will be distributed before the class
236
Practical 12 : Inborn error of metabolism
Department: Biochemistry
Teaching location: Classroom & Biochemistry Laboratory
By the end of this topic the student shall be able to:
1. Appreciate the concept of screening
2. Utilize screening test for identification of suspected cases of inborn
errors
3. Understand the biochemical basis of such diseases
1-
Introduction.
2. Case History ( 3 cases)
3. Aminoaciduria
4. Qualitative screening of urine
5. Different tests used in screening:
a-Ferric Chloride test
b- Dinitrophenylhdrazine
c-Cyanide Nitroprusside reaction and test
d- Nitroosonapthol test
e- P- Nitroaniline reaction
6. Cases Discussion
Transferable skills:
1.Acquire manual skills in handling laboratory equipments
2.Correlate the laboratory findings with theoretical knowledge
READING: Handouts will be distributed before the class
237
Practical 13 : Serum Uric Acid
Department: Biochemistry
Teaching location: Classroom & Biochemistry Laboratory
By the end of this topic the student shall be able to:
1. Determine uric acid in serum by spectrophotometric method
2. Correlate the biochemical defect to physical properties of uric acid, to
clinical picture of gout
3. Utilize an enzyme inhibitor as a drug
1-
Introduction.
2.Case History
3. Blood Uric Determination
a- Priniciple
b- Reagents
c- Procedures
d- Calculation
4. Case discussion
Transferable skills:
1.Acquire manual skills in handling laboratory equipments
2.Correlate the laboratory findings with theoretical knowledge
READING: Handouts will be distributed before the class
238
Practical 14 : Molecular Diagnosis of Genetic Defects (Sickle cell disease)
Department: Biochemistry
Teaching location: Classroom
By the end of this topic the student shall be able to:
1. Understand the basic principles of molecular diagnosis
2. Appreciate the ability of these techniques to diagnose families at risk
for sickle cell anaemia
1-
Introduction.
2.
Case History
3. Genetic diseases
4. Molecular diagnosis of sickle cell anaemia
a- Isolation of DNA
b- Digestion of DNA by restriction enzyme
c- Separation of restriction fragments by electrophoresis
d- Transfer of separated fragments to nitrocellulose (blotting)
5. Polymerase chain reaction (PCR)
6. DNA Preparation from blood in EDTA
Transferable skills:
1.Acquire manual skills in handling laboratory equipments
2.Correlate the laboratory findings with theoretical knowledge
READING: Handouts will be distributed before the class
239
Practical (15) : OSPE TRAINING
Department: Biochemistry
Teaching location: Classroom
By the end of this practical the student will be able to:
o Be familiar with the OSPE

8-9 stations will be included, two of them will be related to the previously
mentioned tests (determination of the analytes), the other will include questions
to evaluate the student benefits of the information given in these practicals.
Transferable skills:

Accuracy of performing the test

Utilization of data in the different stations for interpretation of clinical
cases
READING: Laboratory Handouts will be distributed
240