MEDICAL BIOCHEMISTRY AND MOLECULAR BIOLOGY DEPARTMENT

FIRST YEAR STUDENT LOG BOOK

2012-2013

ال

OUR MISSION IS

-To prepare a graduate having competitive skills on the

national and local levels, capable of teaching, learning and

training for life and is committed to the standards of

medical service and professional ethics.

-The College also seeks continued development of programs

and courses, supports and develops scientific research

with the expansion of applied scientific research and

health care programs to serve the needs of society and

environment development.

-The College also aims to provide excellent academic staff

and research faculty members, to support the upgrading of

administrative and institutional systems and to provide its

own resources in order to achieve the goals and objectives.

OUR VISION IS

-To be the first in the Middle East to produce doctors with a

competitive edge and lead the development of medical

education.

OUR VALUES

-We carry out our job aiming at excellence and not just

performance, we practice honesty in everything we do, we

always strive to achieve equality of rights and the balance

between the right and duty, with mutual respect and we

work together for the benefit of one and all.

MEDICAL BIOCHEMISTRY AND

MOLECULAR BIOLOGY DEPARTMENT

MB 303

LOG BOOK OF FIRST YEAR STUDENTS

(2012-2013)

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Names of The Department Staff Members مـــــقسالة التدريس بــــــــاء هيئـــــعضاء أــــــمـــاس

ا.د هناء الطيب ناصر

Prof. Dr Nora Al Kholy ا.د نورا عبد الواحد الخولى

Prof. Dr Sanaa Eissa سناء عيسى محمد ا.د

Prof. Dr AbdelRhman ا.د عبد الرحمن محمد صالح

Prof. Dr Samar Kassim ا.د سمر كمال قاسم

Prof. Dr Heba Said ا.د هبة اللة سعيد

Prof. Dr Aza Abo-Ghalya ا.د عزة حسن ابو غالية

Prof. Dr Randa Ali- Labib ا.د راندا على لبيب

Prof. Dr Maha Salam ا.د مها محمد سالم

Prof. Dr Fayda Ibrahim ا.د فايدة ابراهيم عبد المطلب

Prof. Dr Farid Al asmar ا.د فريد االسمر

Prof. Dr Mofeda Salah ا.د مفيدة محمد صالح

Prof. Dr Fawzya Khalil ا.د فوزية خليل ابراهيم

Prof. Dr Fathy Tash ا.د فتحى محمد طاش

Prof. Dr Sabha Hodhod ا.د صابحة صبحى هدهد

Prof. Dr Emtiyaz AbdelKawy ا.د امتياز عبد القوى

Prof. Dr Rashwan Farag ا.د رشوان محمد فرج

Prof. Dr Nahed Swelam ا.د ناهد زكى سويلم

Dr Magda Nagaty ا.د ماجدة محمد نجاتى

Prof. Dr Hany Halem ا.د هانى يوسف حليم

Ass. Prof. Dr Hanan Shehata ا.م حنان حسين شحاتة

Ass. Prof. Dr. Amal Mansour امل منصور ا.م

Dr Ayman Besheer ايمن رجاء بشير .د

Dr Manal Louka د. منال لويس لوقا

Dr Enas Samir د. ايناس سمير نبية

Dr.Haidy Habib د. هايدى زكريا حبيب

Dr Walid Said سعيد زكىد. وليد

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Biochemistry and

Molecular Biology

MB 303

Basic Information

Program Title Bachelor of Medicine and Surgery; MB, BCh

Department Offering the Course Medical Biochemistry and Molecular Biology

Department

Academic Year / Level First Year

Date of Specification Approval 4 / 7 / 2012

Total Teaching Hours

150 hour

Theoretical: 90

Practical: 60

Allocated Marks 150 marks

Allocated Duration September through May (as per student)

Course Director Prof Hanaa Eltayeb Nasser

Head of Department

Teaching Staff (17) Professors

(2) Assistant Professors

(5) Lecturers

(9) Assistant lecturers

(11) Demonstrators

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Professional Information

1- Overall Aims of Course

Biochemistry Course Provides Students with:

Aim 1

Basic knowledge of the structure and function of the human body at

the molecular level with a fundamental understanding of chemistry of

biological processes involved in normal and disease states.

Aim 2

Understanding of the storage, transfer and expression of genetic

information with correlation to medical problems and applied

techniques in molecular biology.

2- Intended Learning Outcomes of Course (ILOs)

A. Recall of Knowledge and Understanding:

By the end of the course, students will be able to:

Course ILO Program

ILO

a1 Describe the structure, classifications, and properties of lipids,

amino acids and protein. A1

a2

Relate molecular structures and chemical properties of

macromolecules to their functions including; enzymes,

hemoglobin, myoglobin, collagen, elastin, plasma protein, and

immunoglobulins.

A1

A6

a3 Describe biochemical membrane architecture. A1

a4 Describe structure and function of extracellular matrix. A1

a7 Describe the molecular mechanism of blood coagulation,

anticoagulation and fibrinolysis.and role of vitamin K in them. A1

a8 Describe nucleotides, DNA and RNA structure. A2

a9

Describe the molecular process of replication, transcription,

reverse transcription, posttranscriptional modifications, translation

and posttranslational modifications. A2

a10 Define genetic code and its features. A2

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a11 Identify mutation and classify its types. A2

a12 Describe DNA repair mechanisms A2

a13 Describe the pathway of nucleic acid metabolism. A2

a14 Explain the molecular mechanisms of cancer. A2

a15 Describe the molecular biology techniques A2

a16 Explain end replication problem and molecular mechanism of

aging. A5

B. B. Intellectual Skills

C. By the end of the course, students will be able to:

Course ILO Program

ILO

b1 Correlate biochemical molecular facts to clinical data. B1

b2 Explain causes, detection and consequences of genetic defect(s). B2

b3 Correlate biochemical alterations with clinical data to reach

etiology, diagnosis and treatment. B2

b4 Utilize problem solving skills in a variety of situations. B4

C. Professional and Practical Skills

By the end of the course, students will be able to:

Course ILO Program

ILO

c1 Apply different methods for expression of concentration and

calculation of the dilution of solution. C1

c2 Extract DNA, measure its concentration and interpret the results. C1

c3 Interpret electrophoresis results for serum proteins and

hemoglobin. C1

c5 Interpret results of DNA electrophoresis and DNA fingerprinting. C1

c6 Practice basics of safety in the laboratory. C6

c7 Identify lab instruments, apparatuses and glass wares and their

uses in practice. C1

c8 Identify different separation processes, different tonic and pH

solutions. C1

c9 Identify bio-molecules and enzymes. C1

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D. General and Transferable Skills

By the end of the course, students will be able to:

Course ILO Program

ILO

d1 Respect superiors and colleagues. D3

d2 Gather, organize and appraise information including the use of

information technology where applicable. D4

d3 Present the medical information in written, oral and electronic

forms. D6

d4 Communicate ideas and arguments effectively. D7

d5 Be prepared for the lifelong learning needs of the medical

profession. D8

d6 Work constructively and cooperatively within a team. D9

d7 Manage time effectively. D11

DETAILED CONTENTS OF 1ST

YEAR MEDICAL

BIOCHEMISTRY & MOLECULAR BIOLOGY COURSE

2012/2013 I. Introduction of Biochemistry:

1. Chemistry of amino acids and protein structure

1.1. Amino acids (AAs)

1.2. Definition.

1.3. General structure of AAs.

1.4. Classification of AAs:

1.4.1. Chemical classification

1.4.2. Classification of Aas according to polarity

1.4.3. Biological classification of AAs.

1.4.4. Metabolic classification of AAs.

1.5. Abbreviations and symbols for AAs.

1.6. AAs properties.

1.6.1. Solubility in water (polarity).

1.6.2. Optical property.

1.6.3. Amphoteric property.

1.6.4. Amino acids can act as buffers.

2. Protein structure

2.1. Peptide bond:

3- Course Contents

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2.1.1. Formation

2.1.2. Properties (rigid, planar, trans, polar, angles)

2.1.3. Peptides.

2.1.4. Orientation of the polypeptide chain.

2.1.5. Naming of peptides (lysyl – valinyl- cysteine)

2.1.6. Biologically active peptides, examples: GSH & oxytocin

2.2. Primary structure of proteins.

2.3. Secondary structure of proteins:

2.3.1. helix.

2.3.2. sheet.

2.3.3. -turns.

2.3.4. Supersecondary structures (motifs).

2.4. Tertiary structure of proteins:

2.4.1. Domains.

2.4.2. Interactions and bonds stabilizing tertiary structure.

2.4.3. Fibrous and globular proteins

2.5. Quaternary structure of proteins (examples: Hb, CK)

2.6. Classification of proteins according to:

2.6.1. Solubility and its relation to function.

2.6.2. Shape.

2.6.3. Chemical structure

2.6.4. Simple proteins: example albumin

2.6.5. Conjugated proteins: types and one example for each.

2.7. Denaturation of proteins

2.8. Properties of proteins

2.9. Protein folding

2.10. Protein misfolding: Prion D, Alzheimer D, α1-antitrypsin deficiency

3. Enzymes

3.1. Definitions

3.1.1. Enzymes as biological catalysts

3.1.2. Cofactors

3.1.3. Apoenzyme, holoenzyme

3.1.4. Active site

3.2. Nomenclature of enzymes

3.3. The six major classes of enzymes

3.4. Enzyme Specificity

3.5. How enzymes work:

3.5.1. Reaction progress curve

3.5.2. Enzymes decrease activation energy

3.6. Factors affecting reaction velocity

3.7. Enzyme kinetics

3.7.1. Michaelis-menten equation

3.7.2. Importance of km

3.7.3. Lineweaver-Burk plot curve

3.7.4. Inhibition of enzyme activity

3.7.5. Competitive inhibition (

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3.7.6. Non-competitive inhibition

3.7.7. Irreversible inhibition (enzyme Poisons)

3.8. Regulation of enzyme activity 3.8.1. Properties of regulatory enzyme

3.8.2. Regulation of absolute quantity of enzyme

3.8.3. Regulation of enzyme activity (Short term regulation)

3.8.4. Allosteric regulation

3.8.5. Reversible covalent modification

3.8.6. Irreversible covalent modification[proteolytic cleavage]

3.8.7. Regulatory proteins (calmodulin)

3.8.8. Enzyme Compartmentation

3.8.9. Multienzyme complex

3.9. Clinical enzymology

3.9.1. Functional and nonfunctional plasma enzymes

3.9.2. Enzymes specific to one organ e.g PAP

3.9.3. Multiple enzymes for one organ e.g AST,ALT for liver,

3.9.4. Isoenzymes as a diagnostic tools: examples: LDH, CK, ALP

3.10. Enzymes as a therapeutic agent e.g streptokinase, asparginase.

4. Chemistry of Lipids

4.1. Definition and classification

4.2. Fatty acids: General nomenclature and properties

4.3. Structure of fatty acids: monocarboxylic,straight chain, even no. of C atoms.

4.3.1 Saturated or unsaturated. Cis-trans isomers

4.3.2 Δ-numbering, ω-numbering, and Greek lettering of fatty acids.

4.3.3 Essential fatty acids

4.4. Triacylglycerol - Phospholipids- Glycolipids- Steroids

5. Biological Membranes

5.1. Characteristics of cell membrane

5.2. The composition and Structure of cell membrane

5.2.1. Membrane lipids

5.2.2. Membrane proteins

5.2.3. Membrane carbohydrates

5.3. Membrane asymmetry

5.4. Membrane fluidity and factors affecting it

5.5. Transport across membranes:

5.5.1. Transport of small molecules

5.5.2. Transport of macromolecules

6. Signal Transduction

6.1. Definition and features of signal transduction systems.

6.2. Hormone receptors:

6.2.1. Definition and structure,

6.2.2. Types of receptors: membrane-associated and intracellular receptors

6.2.3. Regulation of receptor number

6.3. Classification of hormones:

6.3.1. According to the distance at which hormones exert their effects

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6.3.2. According to their chemical structure

6.3.3. According to their solubility: hydrophilic and lipophilic hormones

6.4. Mechanism of action of hormones:

6.4.1. Hydrophilic hormones bind to different types of membrane receptors:

6.4.1.1. Receptor coupled to adenyl cyclase

6.4.1.2. Receptor coupled guanyl cyclase

6.4.1.3. Receptor coupled to phospholipase C

6.4.1.4. Tyrosine kinase receptors and tyrosine kinase associated receptors

6.4.2. Lipophilic hormones traverse cell membrane and bind to intracellular receptor.

7. Extracellular Matrix

7.1. The 3 major classes of biomolecules in ECM

7.1.1. Collagen.

7.1.1.1. Structure of collagen

7.1.1.2. Types of collagen.

7.1.1.3. Degradation.

7.1.1.4. . Diseases: Osteogenesis imperfecta (OI).

7.1.1.5. Scurvy (vitamin C deficiency)

7.1.2. Elastin.

7.1.2.1. Structure of elastin.

7.1.2.2. Role of 1-antitrypsin 1-AT) in elastin degradation.

7.1.2.3. Deficiency of 1-antitrypsin results in emphysema.

7.1.3. Proteoglycan

7.1.4. Laminin and Fibronectin

7.1.5. Medical importance of ECM

II- Blood:

1. Protein structure-function relationship

1.1. Globular proteins.

1.1.1. Structure of heme.

1.1.2. Structure and function of myoglobin.

1.1.1.1. -helical content.

1.1.1.2. Location of polar and nonpolar AAs.

1.1.1.3. Binding of heme group.

1.1.3. Structure and function of hemoglobin.

1.1.3.1. Quaternary structure of hemoglobin.

1.1.4. Binding of oxygen to myoglobin and hemoglobin.

1.1.4.1. Oxygen dissociation curves of myoglobin and hemoglobin.

1.1.5. Allosteric effects.

1.1.5.1. Cooperativity (Heme-heme interactions).

1.1.5.1.1. Loading and unloading oxygen.

1.1.5.1.2. Significance of the sigmoidal O2-dissociation curve.

1.1.5.2. Allosteric effectors.

1.1.5.2.1. PH.

1.1.5.2.2. Effect of 2,3-BPG.

1.1.5.2.2.1. Binding of 2,3-BPG to deoxy-Hb.

1.1.5.2.2.2. Binding site of 2,3-BPG.

1.1.5.2.2.3. Effect of 2,3-BPG on O2-dissociation curve.

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1.1.5.2.2.4. Response of 2,3-BPG to chronic hypoxia or anemia.

1.1.5.3. Role of 2,3-BPG in transfused blood.

1.1.5.4. Binding of CO2.

1.1.6. Minor Hbs.

1.1.6.1. Fetal hemoglobin (HbF).

1.1.6.1.1. Binding of 2,3-BPG to HbF.

1.1.6.2. Hemoglobin A2.

1.1.7. Organization of globin genes.

1.1.7.1. -gene cannot be compensated.

1.1.7.2. . Gene can be compensated.

1.1.8. Hemoglobinopathies.

1.1.8.1. Sickle cell anemia (HbS disease).

1.1.8.1.1. Amino acid substitution in HbS -chains.

1.1.8.1.2. Sickling causes tissue anoxia.

1.1.8.1.3. Factors that increase sickling.

1.1.8.1.4. Possible selective advantage of the heterozygous state.

1.1.8.2. Methemogloinmemias.

1.1.8.3. Thalassemias.

1.1.8.3.1. -Thalssemias.

1.1.8.3.2. -Thalassemias.

1.2. Plasma proteins 1.2.1. Types and Functions

1.2.2. Separation of different components of plasma proteins

1.2.3. Normal values and composition of electrophoretic fractions

1.2.4. Hypoalbuminemia

1.3. Immunoglobulins (IGs)

1.3.1. Basic structures of immunoglobulins

1.3.2. Immunoglobulin classes and functions

1.4. The molecular mechanism of blood coagulation,

1.4.1. Anticoagulation and fibrinolysis

1.4.2. Role of vitamin K

1.4.3. Conversion of fibrinogen to fibrin

1.4.4. Generation of thrombin

1.4.5. Comparison of intrinsic to the extrinsic system of blood coagulation

1.4.6. Vitamin K-dependent factors

1.4.7. Physiological anticoagulants

1.4.8. In vitro anticoagulation

1.4.9. The fibrinolytic system

III. Molecular Biology:

A- Basics

1. Nucleotides and Nucleic acid chemistry

1.1 Nucleotide structure

1.2 Purines and pyrimidines

1.3 Nucleotides and nucleosides

1.4 Phosphodiester bond

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1.5 Exonuclease and endonuclease

1.6 Examples for adenosine derivatives and guanosine derivatives

1.7 Nucleotide analogs: antiviral agent and antitumor agents

2. DNA Structure and Replication:

2.1 The flow of genetic information (central dogma)

2.2 DNA structure

2.2.1 DNA as a nucleic acid

2.2.2 DNA double helix

2.2.2.1 Base pairing

2.2.2.2 Separation of the 2 DNA strands (DNA denaturation) and renaturation

2.2.2.3 Structural forms of double helix (A, B,Z)

2.2.2.4 Features of Watson and Crick form (B)

2.2.3 Circular DNA

2.2.4 Organization of eukaryotic DNA

2.2.4.1 Histones

2.2.4.2 Nucleosomes and higher order of organization

2.2.4.3 Fate of nucleosomes during replication

2.2.4.4 Gene ,genome and chromosome

2.3 Steps in prokaryotic DNA synthesis

2.3.1 Direction of replication

2.3.2 Separation of the two DNA strands

2.3.3 Formation of the replication fork

2.3.3.1 Proteins required for DNA strand separation

2.3.3.1.1 DnaA protein

2.3.3.1.2 SSBP

2.3.3.1.3 helicases

2.3.3.2 Solving the problem of supercoils

2.3.3.2.1 Topoisomerase I

2.3.3.2.2 Topoisomerase II (gyrase)

2.4 DNA synthesis by polymerases

2.4.1 Characteristics of DNA polymerases

2.4.1.1 DNA synthesis from 5’ to 3’ direction

2.4.1.2 need primer

2.5 RNA primer synthesis

2.5.1 Primase

2.5.2 Primosome

2.6 Chain elongation in leading strand

2.6.1 DNA pol III

2.7 Chain elongation in lagging strand

2.7.1 DNA pol III

2.7.2 Excision of RNA primers & replacement by DNA

2.7.2.1 DNA pol I polymerase activity from 5’ to 3’

2.7.2.2 DNA pol I exonuclease activity from 5’ to 3’

2.7.3 DNA ligase

2.8 post replication methylation

2.9 Proofreading of newly synthesized DNA

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2.10 Eukaryotic DNA replication

2.10.1 Phases of eukaryotic cell cycle

2.10.2 Eukaryotic DNA polymerases are different and more specific

2.10.3 Multiple origin of replication

2.10.4 Nucleosome in replication

2.11 Inhibition of DNA synthesis by nucleoside analogs e.g antiviral and antitumor agent.

3. DNA repair

3.1. Strand directed mismatch repair system

3.2. Repair of damage caused by ultraviolet

3.2.1. thymine dimmers

3.2.2. recognition and excision of dimmers by UV-specific endonuclease

3.2.3. UV radiation and cancer (xeroderma pigmentosum)

3.3. Base excision repair

3.3.1. Alteration of DNA bases

3.3.2. Removal of abnormal base

3.3.3. Recognition and repair of an AP site

3.4. Nucleotide excision repair

4. RNA structure and Synthesis

4.1. RNA structure

4.1.1. rRNA

4.1.2. tRNA

4.1.3. mRNA

4.1.4. snRNA

4.2. Transcription of prokaryotic genes

4.2.1. Properties of RNA polymerase 4.2.1.1. Core enzyme

4.2.1.2. Holoenzyme

4.2.1.3. Termination factor

4.2.2. Steps in RNA synthesis

4.2.2.1. Initiation (promoter and basal initiation factors)

4.2.2.2. elongation

4.2.2.3. termination (Rho dependent and independent)

4.2.2.4. Action of antibiotics (rifampcin)

4.3. Transcription of Eukaryotic genes

4.3.1. Nuclear RNA polymerases

4.3.2. Mitochondrial RNA polymerase

4.3.3. Regulation of initiation of transcription

4.3.3.1. Chromatin remodling,

4.3.3.2. Sequences control gene transcription (promoter, enhancer and silencer) and

transcription factors (general and specific transcription factors)

4.4. Posttranscriptional modification of RNA

4.4.1. rRNA

4.4.2. tRNA

4.4.3. mRNA

4.4.3.1. Capping

4.4.3.2. Poly A tail

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4.4.3.3. Removal of introns

4.4.3.3.1. snRNA

4.4.3.3.2. intron excision mechanism

4.4.3.3.3. Effect of splice site mutations

4.4.3.4. Alternative splicing

4.5. Reverse transcription

4.5.1. reverse transcriptase

4.5.2. telomerase

4.5.3. retroviruses

5. Genetic code and Protein Synthesis

5.1 The genetic code

5.1.1 Codons

5.1.1.1 How to translate a codon

5.1.1.2 Termination codons

5.1.2 Characteristics of the genetic code

5.1.2.1 Specificity

5.1.2.2 Universality

5.1.2.3 Redundancy

5.1.2.4 Nonoverlapping and commaless

5.1.3 Consequences of altering the nucleotide sequence:

5.1.3.1 Silent mutation

5.1.3.2 Missense mutation

5.1.3.3 Nonsense mutation

5.1.3.4 Tri nucleotide repeat expansion

5.1.3.5 Splice site mutation

5.1.3.6 Frame shift mutation

5.2 Components required for translation

5.2.1 Aminoacyl tRNA synthetase

5.2.1.1 recognition of a specific amino acid

5.2.1.2 mechanism of action

5.2.2 mRNA

5.2.3 ribosomes

5.2.4 amino acids

5.2.5 Protein factors

5.2.6 ATP and GTP

5.3 Codon recognition by tRNA

5.3.1 Antiparallel binding between codon and anticodon

5.3.2 Wobble hypothesis

5.4 Steps in protein synthesis

5.4.1 Initiation

5.4.1.1 Shine Dalgarno sequence

5.4.1.2 Initiation codon

5.4.2 Elongation

5.4.3 Termination

5.4.4 Polysomes

5.4.5 Regulation of translation

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5.5 Posttranslational modification of polypeptide chains

5.5.1 Trimming e.g zymogen

5.5.2 Covalent alterations e.g. phosphorylation, hydroxylation, glycosylation

B- Metabolism

Metabolism of Nucleic acids

1. Digestion of Dietary nucleic acids

2. Purine metabolism:

2.1 Sources of individual atoms in purine ring

2.2 Biosynthesis:

2.2.1 De novo synthersis and its regulation (1st two reactions, last two reactions)

2.2.2 Salvage pathway

2.2.3 Lesch nyhan syndrome

2.2.4 Synthesis of deoxyribonucleotides

2.3 Catabolism of puirnes

2.3.1Disorders of purine Catabolism:

2.3.1.1 Gout and allopuranol

2.3.1.2 Immunodeficiency Diseases (ADP deficiency)

3. Pyrimidine metabolism

3.1 Biosynthesis:

3.1.1 Denovo synthesis and its regulation (1st reaction)

3.1.2 dTMP synthesis and FH4 inhibitors

3.1.3 Salvage pathway

3.2 Catabolism of pyramidine (ended by sol products without details)

C-Cancer

The molecular biology of cancer:

1. Definition

2. Molecular mechanisms:

2.1 Cell proliferation

2.1.1 Oncogenes:

2.1.1.1 Role of proto oncogenes in normal growth

2.1.1.2 Activation of proto oncogenes to oncogenes by amplification, point

mutation, viral integration

2.1.1.3 Examples

2.1.2 Tumor suppressor genes

2.1.2.1 cell cycle

2.1.2.2 check point G1/S

2.1.2.3 Rb inhibition of check point

2.1.2.4 P53 inhibition of check point

2.2 Cell loss

2.2.1 Apoptosis

2.2.1.1 Definition

2.2.1.2 Physiological examples ( embryonic, involution of pregnant uterus and

lactating mammary gland)

2.2.1.3 Molecular mechanism ( caspases regulated by bcl-2)

2.2.2 Telomerase and telomere

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D-Techniques-

1. Molecular Biology techniques:

1.1. Invitro Amplification (PCR)

1.1.1. Definition, PCR principle (imitation of replication)

1.1.2. Steps ( denaturation, annealing, extension )

1.1.3. Requirements ( DNA template, Taq pol, primer, dNTPs)

1.1.4. RT-PCR, Uses of PCR

1.2. Invivo DNA amplification (cloning): Definition, Tools, Restriction endonculeases, Vectors,

Liagse, Host, Uses.

2. Gene therapy:

2.1. Principal gene replacement therapy

2.2. Examples of gene therapy

Practical Topics:

Laboratory Safety

Laboratory Instruments and Apparatuses

Solutions, Diffusion, Dialysis and Osmosis

Methods of Expressing the Concentration of a Solution

pH and Buffers

Biological Molecules Laboratory Investigations

Electrophoresis Fractionation

DNA Extraction and detection

DNA Fingerprinting

Bioinformatics

4- Teaching and Learning Methods

Teaching/

Learning

Methods

Recall of

Knowledge/

Understanding

Intellectual

skills

Professional/ Practical

GTS

4.1-Lectures a1-a4,a7-a16 b1-b4

4.2- Tutorials/

small group

discussion

a1-a4,a7-a16 b1-b4 d1 - d7

4.3-Practical

Classes c1-c3,c5-c9 d1-d7

*4.4-

E-learning

Classes

a1-a4,a7-a16 b1,b2,b3 d1,d2,d6

**4.5-

Directed Self

Learning

d1 - d7

GTS: general transferable skills

* Bioinformatics laboratory, online lectures and discussion through forum. **Projects and homework assignments

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Facilities Required for Teaching and Learning

Halls for tutorials

Computer laboratory for e-learning classes and e-exams

Audiovisuals

5- Teaching and learning methods for students with learning

difficulties

The following process is carried out by the medical biochemistry student support team in

the department as follow:

1- Identification of students with learning difficulties by formative quizzes and

continuous assessments quizzes

2- Organization of meetings with these students to discuss their problems

3- Organize extra lectures outside the schedule to support them

4- Organize extra quizzes to evaluate their needs.

5- Close follow up of these students

6- Student Assessment Methods

6.1 Methods:

Type Time Assessment Method ILOs Measured

Formative

Assessment

Weekly Assessments in

Tutorials and lectures a1-a4,a7-a16

b1-b4 Online Quizes (MCQs)

Home Assignments a1-a4,a7-a16

b1-b4

Summative

Assessment

Continuous

Assessment

Quiz1

Written

[MCQ]

a1-a4,a7-a16

b1-b4

Quiz2

Written

[MCQ]

a1-a4,a7-a16

b1-b4

Final

WRITTEN EXAM a1-a4,a7-a16

b1-b4

PRACTICAL EXAM c1-c3,c5-c9d

ORAL EXAM a1-a4,a7-a16

b1-b4

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6.2 Time Schedule

Week Method

Weeks 2-12

Weeks 17-27

Available to students

all through the year

Formative Assessment:

Assessments in Tutorials and lectures

Online Quizes (MCQs)

All through the year Home Assignments

All through the year Clinically Oriented Small Group Discussion

Week 12

Week 24 Continuous Assessment

END of YEAR

Practical (check list, OSPE and E-learning exam)

Written Exam:

Multiple Choice Questions

Short

Long Essay

Complete

True And False with Explanation

Cross Matching

Case Studies

Oral exam

Weighing of Assessments

Method Weight %

Continuous

Assessment

20%

Quizzes 0 % (Mark)

Written

[MCQ]

Mid-term 1

10% (15 Mark)

Written Exam

[MCQ]

Mid-term 2

10% (15 Mark)

Final 80%

Written Exam 50 % (75 Mark)

Oral Exam 6. 6% (10 Mark)

Practical Exam 20% (30 Mark)

Clinically Oriented Small

Group Discussion 3.4 % (5 Mark)

Total 100% 150 Mark

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7- List of References

7.1 Course Department Notes

-Comprehensive Notes In Medical Biochemistry & Molecular Biology By Staff

Members

-Medical Biochemistry And Molecular Biology First Year Practical Guide Notes

7.2 Essential Books (Text Books) (Available at department and faculty library)

Harper's Biochemistry (28th edition) Robert K. Murray , Daryl K. Granner , Peter A.

Mayes , Victor W. Rodwell Textbook of Biochemistry with Clinical Correlations (8th edition)

Thomas M. Devlin

Lehninger Principles of Biochemistry (6th edition) David L. Nelson, Michael M. Cox

Biochemistry (3rd Edition) Christopher K. Mathews , Kensal E. van Holde, Kevin G.

Ahern

7.3 Recommended Books

Lippincott's Illustrated Reviews: Biochemistry (4th edition)

Richard A. Harvey, Denise R. Ferrier

7.4 Periodicals, Web Sites, etc

www.dentistry.leeds.ac.uk/biochem/thcme

http:// mic2.shams.eg (Faculty web site)

7.5 Others

Course Coordinator: Prof.Sanaa Eissa

Head of the Department: Prof Hanaa El-Tayeb

Date of Department Council approval: 4/7/2012

Important Instructions and Rules

وقواعد تعليمات هامة Every student has to attend at least

75% of the lab sessions to be to permit

the final exam.

من75 ال يقل عن ما الحضور على كل طالب ٪

متحان ح له بحضور االحتى يسم حصص المعمل

.النهائي

In case of documented excuses for

accredit reasons for any exam (e.g.

assessments…etc.) marks will be

recorded according to university rules.

• في حال وجود األعذار الموثقة ألسباب معتمدة

سيتم تسجيل )الخ ...متحان )مثل التقييمات ألي ا

.العالمات وفقا لقواعد الجامعة

Exam Marks will be distributed on the

following:

a. Assessment Exams(MCQ)

b. Final Exam(MCQ-Assay and cases

questions)

c. Practical Exam(check list practical

experiment -electronic exam of

bioinformatics-OSPE)

• على ما يلي•سيتم توزيع درجات االمتحان:

امتحانات التقييم )اختيار من متعدد( .أ

اسئلة -امتحان النهائي) اختيار من متعدد .ب

وأسئلة الحاالت( -مقالية

امتحان العملي التجربة العملية بقائمة .ج

االمتحان االلكتروني على المعلوماتية -المالحظة

.الموضوعىو االمتحان العملي الحيوية

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Communication with students التواصل مع الطلبة

استفسارات و ان القسم سيقوم بالرد على

التواصل المستمر من خالل شكاوى الطالب

يتواصل قسم الكيمياء الحيوية الطبية س معهم.

خالل: الطالب من مع

The Department Will respond to inquiries and

complaints from students through continuous

communication with them. Department of

Biochemistry will communicate with medical

students through:

.A. Website الموقع االلكترونى. - أ

صندوق الشكاوى و اقتراحات الطالب - ب

. )فى المعمل(

B. Student complaints and suggestions box (In the

LAB).

ان فريق الكيمياء الحيوية الطبية لدعم - ت

قسم دوره كالتالىال الطالب في

تحديد الطالب ذوي صعوبات التعلم عن .1

ة.طريق مسابقات والتقييمات المستمر

تنظيم لقاءات مع هؤالء الطالب لمناقشة - .2

.مشاكلهم

إضافية خارج الجدول تنظيم محاضرات - .3

.لدعمهم

.تنظيم مسابقات إضافية لتقييم احتياجاتهم - .4

.قربعن متابعة هؤالء الطالب - .5

C. Medical biochemistry student support team in

the department role is as follows:

1- Identification of students with learning

difficulties by formative quizzes and

continuous assessments quizzes

2- Organization of meetings with these students

to discuss their problems

3- Organize extra lectures outside the schedule to

support them

4- Organize extra quizzes to evaluate their needs.

5- Close follow up of these students.

الساعات المكتبية مع السادة اعضاء - ث

هيئة التدريس .

D. Office hours with Department staff members.

مسئول التواصل مع الطالب لتلقى - ج

شكاوى و استفسارات الطالب و كذلك

مقترحات الطلبة فيما يخص منهج

الكيمياء الحيوية الطبية و حضور

المعامل و المحاضرات .

أ.د سناء عيسى منسق المقرر:

رئيس القسم: أ.د هناء الطيب

E. Official communication with students and also

complaints and inquiries will be done through

F. Course coordinator: Prof .Dr. Sanaa Eissa

Head of the Department: Prof. Dr. Hanaa El-Tayeb

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Instructions for security and safety in Lab إرشادات االمن والسالمة في المختبر

الدخول والخروج اتباع النظام اثناء يجب .1

اإلرشادية العالماتوحسب وذلك والتواجد بالمختبر

.قهايعمل على تطبلامع الموجودة

1. Must follow the rules during going in and

out and during the presence in lab according

to the guiding signs and existing work for

application. عدم سد الطرقات والممرات باألجهزة يجب . .2

واألدوات ، خاصة منافذ الخروج االضطرارية ، والتي

.يجب أن يكون الوصول إليها سهال وسريعا

2. You should not fill the passages and lanes

with devices and tools, especially the forced

exit ports, which should be easily accessible.

يجب اتباع القواعد الخاصة بسالمة المعمل .3

والموضحة اثناء الممارسة العملية والمبينة باللوح

التوضحية واالرشادات المختلفة

3. Must follow the rules for Lab safety

described during the practice and set out on

guiding posters and the other various

instructions

معرفة مكان التالي: يجب .4

مخارج المعمل والمبنى

تيليفون الطوارىء

طفاية الحريق

بطانية الحريق

االسعافات االولية

دش سيل الماء للسالمة

4. Must know the place the following:

• Exits of Lab and building

• Emergency Telephone

• Fire extinguisher

• Fire blanket

• First Aid

• Deluge safety shower

عند حدوث اي حادث او طاريء يتم عمل .5

التالي: ابالغ المشرف المسئول فورا اتباع اجراءات الطوارىء المجهزة لهذا الشأن المختبر او المبنى اذا التزم االمر من اخالء

اقرب منفذ خروج

5. In the event of any accident or emergency

is to do the following:

• immediately inform the supervisor in charge

• follow the emergency procedures fitted for

this purpose

• Evacuate the laboratory or the building if it

is needed from nearest port of exit

يجب أن يتأكد محضر المختبر من فصل .6

الكهرباء وإغالق الغاز والمـاء عند انتهاء العمل

بالمختبر يومياً ما لم يكن هناك أجهزة تلزمها الكهرباء

باستمرار مثل الثالجات أو أجهـزة تكييف الهــواء

لظروف معينة

6. The lab technician must ensure to separate

electricity, gas and water close at the end of

the laboratory work every day unless there

are devices constantly obliges electricity such

as refrigerators or air conditioners in

particular circumstances

محضر المختبر إجراء التفتيش علىيجب .7

الدوري على توصيالت الغاز والمياه والمجاري

والكهرباء للتأكد من سالمتها واإلبالغ عن أي خلل بها

اكتشافه.فور

7. The lab technician must conduct periodic

inspection of gas connections, water, sewage

and electricity for safety and to report any

defect immediately after it is detected.

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السنة االولى الطالب استبيان

االنتهاء من بعد يمأل

يسلم الجزيئية وكيمياء الحيوية والبيولوجيا من دراسة العملي لل

االمتحان من في آخر يوم :في هذا االستبيان

أو سيئة سيئة للغاية،=ال، 1

طوس أو ملتبسة =2

أو جيد جدا قوية جدا،، =نعم 3 التصنيف قييمالتنقاط م

1 2 3

مصادر التعليم والتعلم

لعدد الطالب مناسبة مساحة المعمل 1

المعمل نظيف ومنظم 2

االجهزة المعملية كافية للتجارب المعملية 3

الدروس االكترونية لمقرر العملى مفيدة 4

التدريس والمدرسين المساعدين والمعيدين كاف عدد اعضاء هيئة 5

.لتحقيق اهداف المقرر

اعضاء هيئة التدريس والمدرسين المساعدين مدى التزام 6

والمعيدين بالتواجد فى الدروس العملية.

طرق التعليم

طرق العملى والتدريب متنوعة 7

Bioinformaticsمدى االستفادة من معمل ال 8

نشطة التفاعلية من خالل شبكة االنترنتمدى االستفادة من األ 9

مدى الستفادة من مراجعات العملى 11

المقرر

؟هل اهداف التعليمية لدروس العملى واضحة 11

؟هل وقت درس العملى كاف لتحقيق هذه االهداف 12

االمتحان

العملى؟رر قمهل تم تقييم ماتحقق من اهداف ال 13

هل تم التقييم بطريقة موضوعية ومتكافئة لجميع الطالب؟ 14

مقترحات

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Students Questionnaire To be filled after completion of the

First Year practical course of Biochemistry and Molecular Biology and

delivered on the last day of your exam.

In this questionnaire:

1-Stand for: no, very poor, or bad

2-Stands for: equivocal or intermediate

3- Stand for: yes, very strong, or very good Rating Points to evaluate No

3 2 1

Sources of teaching and learning

Laboratory space suitable for the number of students 1

Clean and orderly lab 2

Adequate laboratory equipment for laboratory experiments 3

Electronic lessons useful for practical course 4

The number of faculty members, assistant lecturers and demonstrators

enough to achieve the ILOs of the course.

5

The commitment of faculty members, assistant lecturers and

demonstrators to co-exist in practical lessons.

6

Teaching methods

Practical tools and training varieties 7

To what extent was the Bioinformatics Lab useful 8

To what extent were the interactive activities through the internet useful 9

The benefit of practical revisions 10

Course

Were the practical courses ILOs clear 11

Was the time allocated sufficient for these ILOs 12

Student's assessment:

Did your final exam evaluate all your practical courses ILOs? 13

Did the final exam evaluate all students by same criteria (objective exam)? 14

Suggestions: