University: Suez Canal UniversityFaculty of Medicine

Course SpecificationsProgramme on which the course is given: PhD Degree in MedicalBiochemistry & Molecular BiologyMajor or Minor element of programmes: MajorDepartment offering the programme: Medical Biochemistry DepartmentDepartment offering the course: Medical Biochemistry DepartmentAcademic year / Level: Second partDate of specification approval by the Faculty Council: October 2009

A- Basic Information

Title: Medical Biochemistry & Molecular Biology Code: MBC2Credit Hours: NA Lecture: 197 Practical: 230 Tutorials: 97 Total: 524

B- Professional Information1 - Overall Aims of Course:

1- To prepare students for productive careers in biochemistry and molecularbiology as both researchers and educators.2- To provide students with a deep understanding of the chemical principlesgoverning the workings of biological macromolecules.3- To give students a substantial understanding of the chemical and molecularevents in biological processes.4- To enable students to develop skill in the recognition of meaningful problems and questions for research in Biochemistry and Molecular Biology.5- To enable students to possess technical skills in lab manipulation.6- To help students to acquire oral, written, and visual communication skills.7- To enable candidate to demonstrate skill in designing experimental protocols and in conducting productive independent research.

2 - Intended Learning Outcomes of Course (ILOs)A. Knowledge and Understanding:By the end of the course the student should be able to:

A1 Life, Water& Acid Base Balance: 1. Explain the structure of an atom, molecules and define isotopes and showhow they are used for diagnosis of diseases .2. Recognize the essential elements required for life.2. Discuss the different types of chemical bonds.

4. List the major biomolecules that exist in nature and describe them in terms of structure and function.5. List the differences between the prokaryotic and eukaryotic cells.6. Discuss the components of cells, the function of each and methods of their separation.7. Describe the functional groups important in biochemical reactions and the different types of isomerism.8. Explain the chemical structure of water molecule and discuss the thermal and solvent properties of water.9. Explain the terms; dipolar, ionic, electrolytes, hydrophilic, hydrophobic, amphipathic and micelle.10. Describe the classification of solutions and define the terms: osmotic pressure, viscosity, surface tension, hydrotropy, adsorption, elution and colloids.11. Explain dissociation of pure water.12. Define the terms; acid, base and explain the difference between strong and weak acid or base.13. Define pH, give its range in solutions and define Keq, Kw pK, pi, zwitterions, ampholyte, polyampholyte, Bohr effect and chloride shift.14. Define the Henderson Hasselbalch equation and mention its usage.15. Identify the normal blood pH and illustrate why it is important to keep it in a narrow range.16. Define a buffer, and discuss its composition and mechanism of action.17. List the physiological buffers and discuss why Carbonic acid/Bicarbonate system is the most important buffer in the body.18. Discuss acid-base disturbances and compare between them; Demonstrate their common causes and describe the role of lung and kidney in adjusting blood pH.

A2 Enzymes: 1. Define enzymes and explain the chemical structure of them. 2. List the six major categories of enzyme activity and give an example of each.3. Explain the EC number according to the international union of biochemistry and molecular biology (IUBMB).4. Describe how enzymes act as catalysts; how they affect the energy of activation? and define the transition state?5. Contrast the induced-fit theory of enzyme catalysis with the lock-and-key theory.6. Identify the properties of the enzyme active site that determine substrate specificity. Explain why enzymes have an optimum temperature and pH for their activity.7. Define Vmax, Km, kcat and turnover number and Describe the graphical representation of the Michaelis-Menten equation.8. Identify the Lineweaver-Burke plot and explain how Vmax and Km can be determined from this plot.9. Explain the fate of the enzyme-substrate complex.10. Define inhibitor and differentiate between reversible and irreversible inhibition.11.List the types of reversible inhibition and describe the effects on Km and Vmax for each.12. Describe the change in the Lineweaver-Burke plots for each of the reversible inhibitors.13. Discuss the different mechanisms for regulation of enzyme activity.14.Describe allosteric regulation of enzyme activity and describe the substrate vs. velocity curve.15. Describe the covalent modification and illustrate its effect on the enzyme activity16. Explain zymogen and explain its significance.17. Define isozymes and their clinical relevance using examples.18.Define a coenzyme. Compare the two types of coenzymes, cofactors and prosthetic groups and differentiate between a holoenzye and apoenzyme .

A3 Bioenergetics, Biologic Oxidation and Oxidative phosphorylation1. Define the terms: free energy, entropy, enthalpy and discuss the first and second laws of thermodynamics.2. Compare an endergonic with an exergonic reaction and explain the general features of catabolic and anabolic pathways in metabolism3. Explain the concept of coupled reactions and the meaning of high-energy phosphate compound.4. Explain how is the structure of ATP compared with the other high-energy phosphate compounds.5. Explain the term 'energy charge.' and define the ATP/ADP ratio of a healthy cell.6. Determine the enzyme that maintains the equilibrium between all three adenine nucleotides.7. Describe how the other nucleoside triphosphates are formed and give examples of their metabolic function.8. List the major redox cofactors (coenzymes) and give the vitamins that they contain.9. Discuss the principals of Reduction/Oxidation Reactions.10. Discuss the relationship between the redox potential difference (AEo) and the free energy of a reaction (AGo).11. Name the classes of enzymes involved in oxidation and reduction reaction and describe the role of each class in biologic oxidation.12. Identify the components, location and the process of the electron transport chain.13. Identify how reducing equivalents produced by different sources are used in the ETC.14. Recognize how the chemiosmotic hypothesis explains the process of oxidative phosphorylation and production of ATP.15.Describe ATP synthase in terms of its location, its composition, and its function.16. Define the P/O ratio and respiratory control.17.Describe the role of the NADH shuttle systems (a-glycerol phosphate; malate-aspartate) in producing energy during aerobic glycolysis.18. Compare the effects and discuss the mechanism of action of uncouplers and inhibitors of oxidative phosphorylation19.Define the types of free radicals that are produced as a by product of metabolism and list cellular molecules damaged by free radical attack.20.Name the chemical species that neutralize free radicals and identify which ones are vitamins.21. Describe the enzyme systems that neutralize free radicals.

A4 Tricarboxylic acid cycle

1. List all of the possible sources and fates of acetyl-CoA.2. Identify the cellular location of the TCA cycle.3. List steps of TCA cycle, Identify the enzymes, coenzymes, intermediates and estimate how many ATP (GTP) are produced from one molecule of acetyl-CoA.4. Discuss regulation of TCA cycle.5. Name the TCA cycle intermediates that can also be derived from amino acids and be converted into precursors for other metabolicproducts.6. Discuss the effect of vitamins deficiencies on the TCA cycle.

A5 Carbohydrates Structure and Metabolism1. Define Carbohydrates, Monosaccharides, Oligosaccharides and Polysaccharides2. Describe classifications, structure, properties of monosaccharides, disaccharides, and polysaccharides and their biological importance.3. Define glycosidic bond, epimers, isomers, reducing and non-reducing sugars.4. Describe and compare the structure and classification of glycosaminoglycans and

glycoproteins and discuss their function.5. Describe the digestion and absorption of carbohydrates and explain how may defects in these processes may lead to disease.6. Carbohydrate metabolism: For each of the following pathways demonstrate in details using formula: substrate, steps, enzymes, coenzymes, intermediates, products and their fate, energy consumption or yield, purpose, site, importance and regulation of glycolysis, pentose phosphate pathway, gluconeogenesis, glycogenesis, glycogenolysis and uronic acid pathway.7. Relate carbohydrate metabolism to the functioning Krebs cycle.8. List the steps that transform pyruvate to acetyl-CoA and NADH, identify the coenzymes that participate and name their associated enzyme.9. Estimate the medical importance of the defects in the carbohydrate metabolism.10. Describe the role of different organs and hormones in the regulation of the blood glucose level and the causes of hyperglycemia and hypoglycaemia.11. Discuss diabetes mellitus, its causes, diagnosis, associated metabolic disturbances and complications.

A6 Amino Acids and Proteins and their metabolism1. Describe the structure of amino acids and draw the 20 amino acids found in proteins.2. Recognize the properties of the protein amino acids (acidic, basic, neutral,amphoteric, polar, nonpolar, essential, and optical) and give their classification.3. Explain the formation of peptide bond and list its characteristics.4. Define the four basic structural levels of proteins (primary, secondary, tertiary and quaternary structures), list the four types of weak chemical bonds that control their structure, and demonstrate the clinical significance of proper protein structure.5. Regarding protein structure: define the direction of reading polypeptide structure, differentiate between alpha-helix and beta-pleated sheet structures, explain the relationship between a domain and tertiary structure and explain the role of amino acid sequence in the conformation of a protein.6. Describe the classification of proteins and the characteristic of each type.7. Describe the different techniques used to study protein structures e.g. protease digestion, dialysis, electrophoresis, chromatography and sequencing.8. Describe how are the proteins digested and absorbed and describe defects in these processes may lead to disease.9. Explain how insulin and glucocorticoids contribute to protein and nitrogen balance.10. Describe in details and with formulas the following reactions including their cofactors and their relationship to the removal of nitrogen waste in the body: transaminase, glutamate dehydrogenase, glutamine synthetase and glutaminase.11. In relation to the urea cycle: Describe in details using formula: substrate, steps, enzymes, coenzymes, intermediates, products and their fate, energy. consumption or yield, purpose, site, importance, regulation and disorders.12. Discuss possible mechanisms by which excess ammonia might cause neurologic defecit .13. Describe the overall metabolism of nitrogen as well as the states of positive balance , negative balance and equilibrium of nitrogen.14. Differentiate the difference between various proteins to maintain the body in nitrogen equilibrium.15. Describe how the nonessential amino acids are synthesized by humans and how are active amines and other important metabolites formed from amino acid.16. Describe how are individual amino acid metabolized through specific pathways so as to estimate the different types of inborn errors of metabolism resulting from defects in the metabolism of these amino acids.

A7 Porphyrins & Bile Pigments

1. Describe structure and properties of porphyrin compounds.2. List steps of heme synthesis.3.Explain the mechanisms and types of Porphyrias.4.Discuss heme catabolism and different types of Jaundice.

A8 Structure function relationship of proteins: 1. Describe the structure and the role of the heme prosthetic group and List important structural similarities and differences between myoglobin and hemoglobin.2. Contrast and explain the oxygen binding curves for myoglobin and hemoglobin.3. List the major hemoglobins present in the adult and the fetus.4. Identify the difference between normal Hb and methemoglobin.5. Identify the site and compare Hb binding with O2, CO2 and CO6. Contrast the tense and relaxed forms of hemoglobin.7. Compare between homotropic and heterotropic effects.3. Describe the molecular genetic basis of sickle cell disease and thalassemia, and the aberrant hemoglobins that are produced in these diseases.

A9 Lipids and their metabolism1. Describe the classifications, structure, properties and important derivatives of different lipids present in the body (simple lipids, complex lipids precursor and derived lipids) and describe their biological roles.2. Identify the structure of fatty acids and describe their classifications according to chain length and saturation and explain how this relate to their physical properties3. Estimate the difference between depot and tissue fat4. Discuss lipid peroxidation as a source of free radicals4. Discuss lipid digestion and absorption and explain how defects in these processes may lead to disease.6. Lipid metabolism: For each of the following pathways discuss in details using formula: substrate, steps, enzymes, coenzymes, intermediates, products and their fate, energy consumption or yield, purpose, site, importance and regulation of Lipogenesis, Lipolysis, fatty acid synthesis, fatty acids oxidation, ketogenesis and ketolysis.7. Discuss in details glycerol metabolism.8. Identify essential fatty acids and describe the synthesis of unsaturated fatty acids.9. Define eicosanoides and list the related compounds of physiological importance.10. List steps of cyclooxygenase and lipooxygenase pathways and differentiate the biochemical actions of: anti-inflammatory glucocorticoids and nonsteroidal anti-inflammatory drugs (NSAIDs).11. Determine the clinical relevance of co3 fatty acids and the corresponding 3-series prostaglandins.12. Identify the major component of lung surfactant, the mechanism by which it works, and its relationship to evaluating and treating respiratory distress syndrome.13. Describe steps of phospholipids synthesis and degradation and the role of different phospholipases and LCAT.14. Describe synthesis of sphinolipids and glycolipids.15.Identify the jtefe symptom associated with sphingolipidoses16. Explain how free fatty acids are transported in the blood.17. Define lipoprotein and describe its core structure.18. For each of the major lipoprotein classes: chylomicron, very low density lipoprotein (VLDL), low density lipoprotein (LDL), high density lipoprotein (HDL):a. Identify the site of synthesis.b. Compare their relative compositions of protein:lipid, and identify the major lipid(s) transported by eachc. Identify the major apolipoproteins associated with the nascent and mature forms and their functions.d. Discuss their pathways of transport from intestine or liver to sites of utilization and ultimate

clearance.19. Define the functions of lecithin cholesterol acyl transferase (LCAT), acylCoA cholesterol acyl transferase (ACAT) and lipoprotein lipase (LPL)20. Compare the exogenous and endogenous transport pathways for triacylglycerol and cholesterol ester.21. Define the steps for the receptor-mediated endocytotic uptake of LDL into target cells and recycling of receptors to the cell surface22. Determine the steps of the extraction of cholesterol from cells by HDL ("reverse cholesterol transport").23. Interpret the relative importance to total body cholesterol of exogenous (dietary) vs. endogenous (biosynthesized) sources.24. Identify the key intermediates (i.e., HMG-CoA, mevalonate, active isoprenoids, squalene and lanosterol) and the primary cofactor (NADPH) of the pathway of cholesterol biosynthesis.25. Discuss regulation of cholesterol synthesis and utilization26. Describe the fates of cholesterol in the tissues of the body27. Identify the composition and function of bile and describe the steps of formation of bile acids and its regulation28. List the dietary sources of monounsaturated, polyunsaturated, and trans-fatty acids and compare their effects on cholesterol metabolism with the effects of saturated fatty acids29. Explain the role of liver in lipid metabolism and its relation to the causation of fatty liver30. Discuss the primary disorders of plasma lipoproteins including their proposed molecular defect(s) in each case.31. Describe the relationship between circulating lipoproteins and the pathogenesis of atherosclerosis and indicate lipid-lowering drugs (i.e., statins, cholestyramine) and dietary measures that can be used to combat atherosclerosis and, if known, describe the mechanism of action of these agents.

A 10 Interrelationships of the Major Organs and Integration of Metabolism 1. Describe the pathways involved in the storage of energy in the liver in the well-fed

state, the main output of the liver during starvation and discuss how these pathways are regulated.

2. Discuss the roles of insulin, glucagon and cortisol in the pattern of changes in the major source(s) of fuel during the transition from the well-fed state to prolonged starvation.

3. Describe the metabolism in well-fed versus fasting states in muscle ,brain, heart and adipose tissue and mention the source of energy for each organ in both conditions.

4. Describe the mechanism(s) for mobilizing fuels in response to stress, trauma aerobic and anaerobic exercises, and diabetes mellitus.

A11 Genes: Replications and Expression 1. Describe the structure of a nucleotide and define nucleoside.2. Compare the structure of a purine base with a pyrimidine base, give examples for each and

identify those found in nucleic acids3. Describe the source of nucleotides in the body.4. List the various functions of nucleotides other than their role as components of DNA and

RNA.5. Describe the formation of PRPP.6. Describe the steps of de novo synthesis of purine nucleotides.7. Describe the regulatory mechanisms that produce AMP and GMP in balanced amounts and

in sufficient quantity.8. Discuss the steps of de novo synthesis of pyrimidine nucleotides.9. Describe the regulation of pyrimidine synthesis.10. Describe the synthesis of deoxyribonucleotides for the synthesis of DNA.11. Explain how the free purine and pyrimidine bases that are produced from normal

degradation of cellular nucleic acids are salvaged for reuse.12. Describe the degradation of purines13. Describe Lesch-Nyhan syndrome and identify the defective enzyme in this syndrome14. Describe the symptoms that accompany adenosine deaminase (ADA) deficiency.15. Define gout and determine the biochemical causes and effect of hyperuricemia16. Assess the rationale for allopurinol in the treatment of gout and define its effect on

xanthine and hypoxanthine concentrations17. Discuss the degradation of pyrimidines. 18. Describe the metabolism of dietary folic acid and identify the specific THF cofactors

that are required for the synthesis of purine bases and thymidine.19. Discuss nucleotide analogs and its uses.20. Describe the mechanisms by which methotrexate and 5-fluorouracil, chemotherapeutic

agents, can disrupt DNA formation by limiting the synthesis of thymidine monophosphate.

21. Describe the primary (linear) structure of RNA and DNA with respect to polarity, the sugar-phosphate backbone and the purine and pyrimidine bases.

22. Describe the secondary (helical) structure of DNA and define how it is stabilized23. Explain the concept of base complementarities.24. Compare the structures of the A-form, B-form, and Z-form of DNA and define which

one is found in the cell25. Describe the denaturation of DNA; factors affecting it and how it is measured26. Define Tm and explain how it depends on the GC content of DNA and describe the

renaturation of DNA.27. Define hybridisation and created.28. Describe histone proteins, nucleosomes and explain their contribution to chromatin

structure29. Differentiate between the two major categories of chromatin (heterochromatin and

euchromatin)30. Describe the levels of chromosume organization.31. Explain the semiconservative concept of replication and describe the relationship

between a replication fork and an origin of replication.32. Name the components, substrates and enzymes needed for DNA replication and describe

their function.33. Compare leading strand synthesis with lagging strand synthesis.34. Explain how proofreading works and why it is necessary.35. Identify the different types of DNA damage and their causes36. Describe the different types of DNA repair mechanisms with emphasis on mismatch,

base excision, nucleotide excision and double-strand break repair and give examples of diseases associated with defects in DNA repair.

37. Define an allele, dominant and recessive inheritance and Compare heterozygosity with homozygosity.

38. Identify the concept of mutation and discuss its different types and consequences .39. Describe the different forms of RNA and their functions.40. Define transcription, and name the components, substrates, factors and enzymes

needed for transcription and describe their function.41. Explain the structure and function of the prokaryotic promoter.42. Define the template and coding strands and mention which of these is antisense

and which is the sense strand43. Compare DNA polymerase and RNA polymerase.44. Recognize the major mRNA processing events45. Describe the synthesis of the ribosomal RNA's and transfer RNA.46. Define the four major features of the genetic code, and List out the codons that terminate

protein synthesis and the codon that starts protein synthesis.47. Define the process of translation; name and describe in details the three steps of

polypeptide synthesis including components, factors ancj enzymes.

48. List types of posttranslational modifications of proteins that make them biologically active.

49. List the antibiotics which inhibit protein synthesis.50. Describe the major mechanism for control of gene expression in prokaryotes and

eukaryotes.51. Discuss recombinant DNA methodology and technologies and describe modern

cloning strategies and their application in the production of recombinant proteins.52. Compare between the construction and use of cDNA and genomic libraries.53. Identify and determine the methodologies and ethical considerations of gene therapy and

genetically engineered (transgenic) animals.

A12 Membrane structure and function 1. List and explain the major functions of membranes in biological systems1. Describe the role of lipids, proteins, and carbohydrates in the structure of membranes.2. List the different types of lipids characteristics and arrangement within the membrane.2. Describe how are proteins and carbohydrates arranged in the lipid bilayer3. Describe the type of interactions hold membranes together4. Explain what is meant by the asymmetric property of membranes3. Discuss fluidity of membranes and explain how does flip-flop diffusion compare to lateral diffusion5. Explain what is meant by self-assembly of membrane structure?4. Describe the organization and role of proteins in membrane structure and function.5. Define an integral membrane protein and compare it with a peripheral membrane protein6. List the diseases caused by mutation affecting membranes proteins.7. List the properties of membranes that are explained by the fluid mosaic model of membrane structure.8. Describe the permeability of membranes to various types of solutes.9. List and describe the different methods of membrane transport10. Describe the general characteristics of transport proteins.11. Discuss the classification of transporter proteins, describe how each works, and give an example of each.12. Contrast facilitated diffusion with active transport

A13 Intracellular Traffic & Sorting of Proteins 1. Discuss the role of signal sequences in protein targeting to its correct destination.2. Describe the synthesis and targeting of mitochondrial proteins.3. Discuss the transport of macromolecules in & out of the nucleus.4. Describe the different routes proteins follow to be inserted into or attached to the membranes of the endoplasmic reticulum.5. Define chaperones and their role in proper protein folding & prevention of unproductive interactions of other proteins.6. Discuss endoplasmic reticulum-associated degradation of misfolded protein.7. Identify the role of ubiquitin in protein degradation and explain how and where the ubiquitinated proteins are degraded.8. Discuss the role of transport vesicles in intracellular protein traffic.

A14 Endocrine system and Signal transduction 1. Explain the target cell concept and discuss the general structure of hormone receptors.2. Identify the biochemical properties of hormones and list the chemical classes in which they can be categorized.3. Discuss the different mechanisms of hormone action.

4. For the following endocrine glands: hypothalamus, pituitary, thyroid, parathyroid, adrenal gland, gonads, placenta, pancreas and gasterointestinal tract; Describe the hormones secreted and their structure, synthesis, mechanism of action, transport and metabolism, and discuss disorders resulting from their abnormal secretion.5. Explain the basis of a cascade signalling mechanism.6. Describe the classifications of signal transducing receptors.7. Describe protein kinases with respect to the residues phosphorylated, the reversal of their effects, and their specificity for a target protein.8. Define the physical characteristics of a G-protein and its linked receptor.9. Describe the sequence of events that take place when a hormone signal binds to a G-protein linked receptor and explain how continuous reactivation of a G-protein is avoided.10. Describe the cycle of synthesis and degradation of cAMP.11. Describe how protein kinase A recognizes its target and how it is regulated.12.Compare phospholipase C to adenylate cyclase in terms of its function, mechanism of action and products.13. Describe the actions of IP3 and DAG as second messenger.14. Describe the characteristics, mechanism of action, and the substrates for tyrosine kinases.15. Describe the structure and function of guanylate cyclase receptors.

A15 Micronutrients: Vitamins & Minerals 1. Identify the characteristics and classification of vitamins.2. For each vitamin: List the sources, describe the structure, absorption, active form, the biochemical function, recommended dietary intake and manifestations of deficiency.3. Define macrominerals and microminerals4. For each mineral: Describe the metabolism, functions and effect on metabolic processes of excess or deficiency of each mineral.

A16 Glycoproteins and Extra-cellular matrix 1 .Describe the functions of glycoproteins and list the roles played by oligosaccharide chains of them.2. Discuss the three major classes of glycoproteins and their synthesis.3. Describe the processing of the oligosaccharide chains.2. Discuss factors regulating glycosylation of glycoproteins and disease resulting from abnormal synthesis or degradation of glycoproteins.3. Describe the structure, types and functions of proteoglycans & glycosaminoglycans.4. Describe the structure and properties of collagen.4. List the different post-translational modifications of amino acid residues in collagen that occur during maturation. Identify the cofactors required for these modification reactions.5. List the steps in collagen maturation and where they occur in (or out of) the cell.6. Describe the molecular etiology of Osteogenesis Imperfecta, Scurvy and Ehlers Danlos Syndromes.7. Discuss the function and location of elastin and give the cause of Marfan syndrome.8. Describe the structure and properties of Fibronectin, Laminin, Fibrillin.

A17 Molecular Motors1. Relate the microscopic structure of the sarcomere to its protein components.2. Describe the structure of muscle proteins and their function3. List the steps that occur in one contraction cycle.4. Describe the role of creatine phosphokinase in the storage of high energy phosphate bonds .5. Differentiate between skeletal and cardiac muscle .6. Explain the control of smooth muscle contraction by phosphorylation of myosin light chains.7. Describe The Cytoskeleton Proteins and their Functions,8. Discuss in molecular basis Duchenne Muscular Dystrophy

A18 Plasma proteins , Immunoglobulins and Blood coagulation : 1. Discuss the general characteristics and synthesis of plasma proteins2. Discuss the specific functions of albumin, haptoglobin, transferring, ferritin, ceruloplasmin, a1-antiproteinase and a2-macroglobulin.3. Describe diseases resulting from deficiency of individual plasma proteins4. Describe the structure of immunoglobulin5. Describe the different classes of immunoglobulin and differences between them.6. Describe cytokine production and the role of these peptide hormones in the immune response.7. List and discuss the steps of platelet activation.8. Design and discuss the intrinsic, extrinsic, and common pathways of blood coagulation.9. Illustrate the vitamin K cycle and describe its role in the blood coagulation cascade and their requirement for Ca2+ and phospholipids10. List common causes of vitamin K deficiency, and a pharmacological intervention that reduces vitamin K activity.11. Explain the process of fibrinolysis.12. Discuss each of the following and describe their actions in modulating clotting:TFPI, thrombomodulin (with proteins C and S), antithrombin, t-PA, urokinase and coumarins.13. Describe the clinical utility and mechanism of heparin, t-PA, urokinase and streptokinase and the normal regulation of the affected pathway by a2antiplasmin.14. List the factors "tested for" by the prothrombin time (PT); by the activated partial thromboplastin time (aPTT).15. Identify the defects in hemophilia types A and B and in von Willebrand disease and the signs and symptoms of these diseases.

A19 Metabolism of Xenobiotics 1. Identify xenobiotic and explain the term xenobiotic metabolism.1. Compare between Phase I and Phase II reactions.2. Define the site of xenobiotic metabolism at organ and cellular level.2. List types of Phase I reactions and enzymes responsible for it.3. Discuss the function of cytochrome P450 and its regulation.4. List types of Phase II (conjugation) reactions.

A20 Cell cycle, carcinogenesis, apoptosis 1. Describe the eukaryotic cell cycle and the purpose of checkpoints.1. Describe the role of cyclins and cyclin-dependent kinases in cell cycle progression.2. Identify the characteristic of cancer cell3. Explain immortalization and transformation and describe the morphological and biochemical changes occur upon malignant transformation.4. Discuss the various carcinogenes.5. Explain the multi-step hypothesis of cancer.6. Discuss the biochemical aspects of cancer.7. Describe the three classes of growth factors and their receptors. Identify common elements and differences.8. Describe the type of signalling activity of most growth factor receptors.9. Define each of the following terms: oncogene, proto-oncogene, tumour suppressor gene.10. Describe the different types of proto-oncogenes and their mechanisms of activation to oncogenes.11. Discuss in brief the role of oncogenes in carcinogenesis12. Discuss the feature and role of tumour suppressor genes13. Discuss the concept of Loss of Heterozygosity (LOH) in the tumour suppressor genes.14. Describe the different types of tumour suppressor genes and describe their role in

oncogenesis (e.g. Rb, WT1, NF-1, APC, DCC, and p53).15. Describe the central role of p53 in signalling DNA damage and its squelae for cell cycle arrest and DNA repair.16. Explain in biochemical terms the process of metastasis including extravasation and colonization.17. Define tumour markers and identify the characteristics of an ideal tumour marker.18. Give a classification of tumour markers19. Explain the clinical value of tumour markers and their role in management of cancer, and give examples of markers routinely used in practice.20. Describe structure and function of telomerase and its biomedical importance.21. Define apoptosis and list its biological roles in development and in the adult.22. Differentiate between Caspases on the basis of their structure, substrate specificities and describe different Caspase activation mechanisms.23. Describe the signalling of apoptosis initiated by binding of FasL to its receptor.24.Describe the role of the Caspase and the Bcl-2 family of proteins in regulating apoptosis

A21 Neurotransmitters and biochemical basis of certain neuro-psychiatric disorders 1. List the properties of neurotransmitters1. Discuss the major neurotransmitter types, their synthesis , receptors , transporters, function and localisation in the brain.2. Discuss synaptic transmission, neuromuscular transmission and neurotransmitter receptors.3. Describe the molecular basis of neurotransmitter release and the function of the key proteins involved in this process.4. Explain in detail neurotransmission by acetylcholine, serotonin, glutamate and GAB A.5. Identify key defects in neurotransmitter signalling that lead to brain malfunction

A22 Special Topics In this part selected topics in biochemistry and molecular biology will be analyzed in depth with emphasis on group discussion of papers from the recent research literature. Topics change yearly. Recent topics have included the following titles:Epigenetic1. Define the term epigenetics and discuss its molecular basis2. Discuss mechanisms of epigenetics3. Discuss functions and consequences of epigenetic mechanisms.Stem cell- Scientific progress and applications in Medicine1. Define stem cells and list the_unique properties of all stem cells.2. Explain different types of stem cells.1. Discuss the similarities and differences between embryonic and adult stem cells.3. Illustrate the potential uses of human stem cells.2. Identify the obstacles that must be overcome before these uses can be realized.4. List the risks associated with stem cell therapy.

b- Intellectual Skills

By the end of the course the student should be able to:1. Analyze and solve biochemical problems.2. Integrate and evaluate information.3. Correlate between signs and symptoms of some diseases with the presence of certain biochemical defects.4. Formulate and test hypotheses using appropriate experimental design and statistical analysis of data.5. Comprehend, analyze and criticize published information in biochemistry and Molecular biology.6. Use integrated approaches to problem solving.

c- Professional and Practical Skills By the end of the course the student should be able to:1. Demonstrate the different laboratory safety measures.2. Identify hazards related to handling chemicals, biologic specimens, and radiological materials and choose appropriate personal protective equipment when working in the laboratory.3. Demonstrate competence in preparation of solutions and biochemical reagents.4. Estimate different ways of expression of concentrations of substances and show the ability to convert one form to other.5. Describe and efficiently use all common laboratory instruments used in biochemical research e.g. different types of pipettes, centrifuge, analytical balance, vortex, shaker, pH meter, autoclave, spectrophotometer, chromatograph.6. Identify and describe the types of samples used in clinical chemistry and Molecular biology.7. Describe the typical specimen collection, transport, and storage requirements for Biochemistry and Molecular biology testing8. Outline the general steps for processing blood samples.9. Identify the pre-analytical , pre-collection ,collection and post collection variables that can adversely affect laboratory results10. Illustrate the different techniques used in the separation, purification and characterization of important biochemical compounds: electrophoresis, chromatography , precipitation, ultracentrifugation and dialysis.11. Perform calculations on and analysis of laboratory data.12. Calculate the following: Mean , median, range, variance, and standard deviation.13. Understand the fundamentals of core biochemical methods and techniques covered by the course .14. Understand the merits and limitations of each of them in studying biological objects and bio-molecules15. Demonstrate how to determine and adjust the pH of different solutions16. Illustrate the presence of some types of carbohydrates in a sample.17. Illustrate the presence of some amino acids in protein sample.18. Describe the principles and practice the analysis of glucose and ketones in various body fluids, including commonly encountered sources of analytical interferences and estimate the clinical significance of determination of their plasma levels.19. Assess glucose tolerance by glucose tolerance test and distinguish the different types of abnormality of pathological glucose tolerance curve.20. Describe the principles and practice the analysis of total cholesterol , triglycerides, LDL & HDL tests, and interpret the commonly encountered sources of analytical interferences.21. Describe testing for cardiac function: troponin T and I, total CK, CK isoenzymes & isoforms, total LD, LD isoenzymes, myoglobin, hs-CRP, and homocysteine.22. Describe the principles of alanine and aspartate transaminase, alkaline phosphatase, gamma glutamyl transferase, 5- nucleotidase ammonia, total and direct bilirubin, urobilinogen, total serum protein, and albumin analyses in terms of key reagents and their roles and practice their estimation in different body fluids.23. Perform renal function tests: urea, creatinine, creatinine clearance, uric acid and complete urine analysis.24. Provide appropriate criteria for interpreting renal function and electrolyte laboratory test results.25. Practice a densitometric scan of a serum protein electrophoresis using the routine method (five zones) and, recognize and name the fractions, interpret any abnormality in the sample, and associate these patterns with common disease states.26. Practice a densitometric scan of Hb electrophoresis, recognize and name the different types of bands, identify presence of any abnormal HB and correlate the findings with the

clinical state of the patient if available.27. Compare advantages and disadvantages of current immunoassay methods and include principle of analyses, specimen requirements, specificity, and sources of interferences.28. Practice a chemiluminescence's detection of some tumour markers and discuss common pre-analytical errors resulting from improper specimen collection and handling and explain sources of interference in their estimation.29. Discuss the principals of ELISA technique and practice estimation of some hormones by this technique.30. Isolate Nucleic acids (DNA & RNA ) from different biological samples : serum and whole blood.31. Calculate the concentration and purity of DNA or RNA solution using spectrophotometer.32. Perform Polymerase Chain Reaction (PCR) starting from DNA or RNA templates; examples Detection of HCV and HBV33. Perform restriction digestion of DNA segments (RFLP) 34. Perform agarose gel electrophoresis for DNA separation.35. Correlate between signs and symptoms of some diseases with the presence of certain biochemical defects and interpret the biochemical laboratory findings of some metabolic disorders.36. Write scientific abstracts, articles and reports

d- General and Transferable Skills

By the end of the course, student should be able to:1. Organize his work and time.2. Demonstrate an ability to use information technology, including the use of databases, word processing, spreadsheets, statistical software.3. Work professionally with superiors, peers and assistants.4. Communicate ideas and experiments to others and debate relevant scientific and or ethical issues.5. Teach effectively using available presentation aids (e.g. overhead projectors or data show) to present clearly and effectively a scientific topic and act as mentor to others6. Use web-based resources, textbooks to find up to date information on related topics.7. Apply the principles of scientific research

3- ContentsTopic No. of hours Lecture Tutorial PracticalLife, Water & Acid Base Balance 33 8 10 15Enzymes 29 8 6 15Bioenergetics, Biologic Oxidation and Oxidative phosphorylation

27 10 8 9

Tricarboxylic acid Cycle 5 3 2Carbohydrates Structure and Metabolism

43 18 5 20

Proteins and their Metabolism 47 21 6 20Porphyrins & Bile Pigments 10 3 2 5Structure function relationship of Proteins

7 3 2 2

Lipids and their metabolism 50 24 6 20Interrelationships of the Major Organs and Integration of Metabolism

14 6 3 5

Genes: Replications and Expression

90 30 10 50

Membrane structure and function 8 3 3 2Intracellular Traffic & Sorting of Proteins

6 3 3

Endocrine system and Signal transduction

38 12 6 20

Micronutrients : Vitamins & Minerals

21 9 3 9

Glycoproteins and Extracellular matrix

11 6 2 3

Molecular Motors 5 3 2Plasma Proteins, Immunoglobulins and Blood coagulation

31 9 2 20

Metabolism of Xenobiotics 11 3 2 6cell cycle 21 9 3 9Neurotransmitters and biochemical basis of certain neuropsychiatric disorders

5 3 2

Special Topics; Epigenetics & Stem cell

12 3 9

4- Teaching and Learning MethodsLecturesPractical (Department lab ,Oncology Diagnostic Unit)Tutorials: Group discussion in specified subjectsInformation collection from different sources (library, Web ,..)

5- Student Assessment MethodsWritten exam: to assess recall, analysis & interpretation of knowledge.Oral exam: to assess knowledge , recall, Comprehension , intellectual and general skills.Practical exam: to assess practical, professional , intellectual and general

skills.

Assessment Schedule

Assessment 1: Written Exam., at the end of the course 2 papers (3 hours each) on two different daysAssessment 2: Oral Exam., at the end of the courseAssessment 3 : Practical Exam., at the end of the course

Exam includes:- Essay questions (short and long).- Oral exam. - Practical exam.

Weighting of AssessmentsWritten exam 200Oral exam 100Practical examination 100

Total 400

6- List of References6.1- Course Notes: Lectures Handouts

6.2- Essential Books (Text Books)Harper's illustrated Biochemistry, 29Edition, Robert K. Murray, Daryl K .Granner, Victor W. Rodwell, Lange Medical books / Me Graw-Hill Biochemistry: Lubert Stryer, W.H. Freeman and company N .Y .Fundamentals of Biochemistry: Life at the Molecular Level, 3rd Edition, 2008 Donald J. Voet, Judith G. Voet, Charlotte W. Pratt WileyTietz text Book of clinical biochemistry. Carl A and Edward R ( .B.Saunders company N.Y.).

6.3- Recommended Books

Principle and techniques of biochemistry and Molecular Biology, 6th Edit ion,2005 . Wilson K and Walker J Cambridge University Press Varley's Practical Clinical Biochemistry, 6th edition CBS

Clinical chemistry: Principles, Procedures, Correlations 5th edition. Michael L Bishop, Edward P. Fody, Larry Schoeff.

6.4- Periodicals, Web Sites , ... etcJournal of Biological Chemistry (JCB) Science (Journal) Nature (Journal)www.aacc.org , http://www.lcusd.net/lchs/mewoldsen/Ebiolink.htm Course coordinator:Assisstant professor/ Moushira Abdel-Wahab Mahmoud

Head of the Department:

Professor/ Samir M Abdel Moneim