University: Suez Canal University
Faculty of Medicine
Course Specifications
Programme on which the course is given: PhD Degree in Medical
Biochemistry & Molecular Biology
Major or Minor element of programmes: Major
Department offering the programme: Medical Biochemistry
Department
Department offering the course: Medical Biochemistry Department
Academic year / Level: Second part
Date of specification approval by the Faculty Council: October 2009
A- Basic Information
Title: Medical Biochemistry & Molecular Biology Code:
MBC2
Credit Hours: NA
Lecture: 197
Practical: 230
Tutorials: 97
Total: 524
B- Professional Information
1 - Overall Aims of Course:
1- To prepare students for productive careers in biochemistry and molecular
biology as both researchers and educators.
2- To provide students with a deep understanding of the chemical principles
governing the workings of biological macromolecules.
3- To give students a substantial understanding of the chemical and molecular
events 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 show
how 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 activity
16. 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 phosphorylation
1. 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 metabolism
3. 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; malateaspartate) in producing energy during aerobic glycolysis.
18. Compare the effects and discuss the mechanism of action of uncouplers and inhibitors of
oxidative phosphorylation
19. 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 metabolic
products.
6. Discuss the effect of vitamins deficiencies on the TCA cycle.
A5 Carbohydrates Structure and Metabolism
1. Define Carbohydrates, Monosaccharides, Oligosaccharides and Polysaccharides
2. 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 metabolism
1. 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 CO
6. Contrast the tense and relaxed forms of hemoglobin.
7. Compare between homotropic and heterotropic effects.
8. 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 metabolism
1. 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 properties
3. Estimate the difference between depot and tissue fat
4. Discuss lipid peroxidation as a source of free radicals
5. 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 sphingolipidoses
16. 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 each
c. 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 surface
22. 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 utilization
26. Describe the fates of cholesterol in the tissues of the body
27. Identify the composition and function of bile and describe the steps of formation of
bile acids and its regulation
28. List the dietary sources of monounsaturated, polyunsaturated, and trans-fatty acids and
compare their effects on cholesterol metabolism with the effects of saturated fatty acids
29. Explain the role of liver in lipid metabolism and its relation to the causation of fatty liver
30. 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 acids
3. 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.
Describe the degradation of purines
Describe Lesch-Nyhan syndrome and identify the defective enzyme in this syndrome
Describe the symptoms that accompany adenosine deaminase (ADA) deficiency.
Define gout and determine the biochemical causes and effect of hyperuricemia
Assess the rationale for allopurinol in the treatment of gout and define its effect on
xanthine and hypoxanthine concentrations
17. 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 stabilized
23. 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 cell
25. Describe the denaturation of DNA; factors affecting it and how it is measured
26. 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
structure
29. 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 causes
36. 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 strand
43. Compare DNA polymerase and RNA polymerase.
44. Recognize the major mRNA processing events
45. 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.
12.
13.
14.
15.
16.
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 systems
2. Describe the role of lipids, proteins, and carbohydrates in the structure of
membranes.
3. List the different types of lipids characteristics and arrangement within the membrane.
4. Describe how are proteins and carbohydrates arranged in the lipid bilayer
5. Describe the type of interactions hold membranes together
6. Explain what is meant by the asymmetric property of membranes
7. Discuss fluidity of membranes and explain how does flip-flop diffusion compare to
lateral diffusion
8. Explain what is meant by self-assembly of membrane structure?
9. Describe the organization and role of proteins in membrane structure and function.
10. Define an integral membrane protein and compare it with a peripheral membrane
protein
11. List the diseases caused by mutation affecting membranes proteins.
12. List the properties of membranes that are explained by the fluid mosaic model of membrane
structure.
13. Describe the permeability of membranes to various types of solutes.
14. List and describe the different methods of membrane transport
15. Describe the general characteristics of transport proteins.
16. Discuss the classification of transporter proteins, describe how each works, and give an
example of each.
17. 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 Gprotein 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 microminerals
4. 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.
4. Discuss factors regulating glycosylation of glycoproteins and disease resulting from
abnormal synthesis or degradation of glycoproteins.
5. Describe the structure, types and functions of proteoglycans & glycosaminoglycans.
6. Describe the structure and properties of collagen.
7. List the different post-translational modifications of amino acid residues in collagen that
occur during maturation. Identify the cofactors required for these modification reactions.
8. List the steps in collagen maturation and where they occur in (or out of) the cell.
9. Describe the molecular etiology of Osteogenesis Imperfecta, Scurvy and Ehlers Danlos
Syndromes.
10. Discuss the function and location of elastin and give the cause of Marfan syndrome.
11. Describe the structure and properties of Fibronectin, Laminin, Fibrillin.
A17 Molecular Motors
1. Relate the microscopic structure of the sarcomere to its protein components.
2. Describe the structure of muscle proteins and their function
3. 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 proteins
2. Discuss the specific functions of albumin, haptoglobin, transferring, ferritin, ceruloplasmin,
a1-antiproteinase and a2-macroglobulin.
3. Describe diseases resulting from deficiency of individual plasma proteins
4. Describe the structure of immunoglobulin
5. 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 phospholipids
10. 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.
2. Compare between Phase I and Phase II reactions.
3. Define the site of xenobiotic metabolism at organ and cellular level.
4. List types of Phase I reactions and enzymes responsible for it.
5. Discuss the function of cytochrome P450 and its regulation.
6. List types of Phase II (conjugation) reactions.
A20 Cell cycle, carcinogenesis, apoptosis
1. Describe the eukaryotic cell cycle and the purpose of checkpoints.
2. Describe the role of cyclins and cyclin-dependent kinases in cell cycle progression.
3. Identify the characteristic of cancer cell
4. Explain immortalization and transformation and describe the morphological and biochemical
changes occur upon malignant transformation.
5. Discuss the various carcinogenes.
6. Explain the multi-step hypothesis of cancer.
7. Discuss the biochemical aspects of cancer.
8. Describe the three classes of growth factors and their receptors. Identify common
elements and differences.
9. Describe the type of signalling activity of most growth factor receptors.
10. Define each of the following terms: oncogene, proto-oncogene, tumour suppressor
gene.
11. Describe the different types of proto-oncogenes and their mechanisms of activation to
oncogenes.
12. Discuss in brief the role of oncogenes in carcinogenesis
13. Discuss the feature and role of tumour suppressor genes
14. Discuss the concept of Loss of Heterozygosity (LOH) in the tumour suppressor
genes.
15. Describe the different types of tumour suppressor genes and describe their role in
oncogenesis (e.g. Rb, WT1, NF-1, APC, DCC, and p53).
16. Describe the central role of p53 in signalling DNA damage and its squelae for cell cycle
arrest and DNA repair.
17. Explain in biochemical terms the process of metastasis including extravasation
and colonization.
18. Define tumour markers and identify the characteristics of an ideal tumour marker.
19. Give a classification of tumour markers
20. Explain the clinical value of tumour markers and their role in management of cancer, and
give examples of markers routinely used in practice.
21. Describe structure and function of telomerase and its biomedical importance.
22. Define apoptosis and list its biological roles in development and in the adult.
23. Differentiate between Caspases on the basis of their structure, substrate specificities and
describe different Caspase activation mechanisms.
24. Describe the signalling of apoptosis initiated by binding of FasL to its receptor.
25. 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 neurotransmitters
2. Discuss the major neurotransmitter types, their synthesis , receptors , transporters,
function and localisation in the brain.
3. Discuss synaptic transmission, neuromuscular transmission and neurotransmitter receptors.
4. Describe the molecular basis of neurotransmitter release and the function of the key
proteins involved in this process.
5. Explain in detail neurotransmission by acetylcholine, serotonin, glutamate and GAB A.
6. 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:
Epigenetic
1. Define the term epigenetics and discuss its molecular basis
2. Discuss mechanisms of epigenetics
3. Discuss functions and consequences of epigenetic mechanisms.
Stem cell- Scientific progress and applications in Medicine
1. Define stem cells and list the_unique properties of all stem cells.
2. Explain different types of stem cells.
3. Discuss the similarities and differences between embryonic and adult stem cells.
4. Illustrate the potential uses of human stem cells.
5. Identify the obstacles that must be overcome before these uses can be realized.
6. 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 testing
8. 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 results
10. 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-molecules
15. Demonstrate how to determine and adjust the pH of different solutions
16. 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 HBV
33. 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 others
6. Use web-based resources, textbooks to find up to date information on related topics.
7. Apply the principles of scientific research
3- Contents
Topic
Life, Water & Acid Base Balance
Enzymes
Bioenergetics, Biologic Oxidation
and Oxidative phosphorylation
Tricarboxylic acid Cycle
Carbohydrates Structure
and
Metabolism
Proteins and their Metabolism
Porphyrins & Bile Pigments
Structure function relationship of
Proteins
Lipids and their metabolism
Interrelationships of the Major
Organs and Integration of
Metabolism
Genes: Replications and
Expression
Membrane structure and function
Intracellular Traffic & Sorting of
Proteins
Endocrine system and Signal
transduction
Micronutrients : Vitamins &
Minerals
Glycoproteins and Extracellular
matrix
Molecular Motors
Plasma Proteins, Immunoglobulins
and Blood coagulation
Metabolism
of Xenobiotics
cell cycle
Neurotransmitters and
biochemical basis of certain
neuropsychiatric disorders
Special Topics; Epigenetics & Stem
cell
No. of hours
33
29
27
Lecture
8
8
10
Tutorial
10
6
8
Practical
15
15
9
5
43
3
18
2
5
20
47
10
7
21
3
3
6
20
2
2
5
50
14
24
6
6
3
20
5
90
30
10
50
8
6
3
3
3
3
2
38
12
6
20
21
9
3
9
11
6
2
3
5
31
3
9
2
2
20
11
21
5
3
9
3
2
3
2
12
3
9
2
6
9
4Teaching and Learning Methods
Lectures
Practical (Department lab ,Oncology Diagnostic Unit)
Tutorials: Group discussion in specified subjects
Information collection from different sources (library, Web ,..)
5- Student Assessment Methods
Written 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 days
Assessment 2: Oral Exam., at the end of the course
Assessment 3 : Practical Exam., at the end of the course
Exam includes:
- Essay questions (short and long).
- Oral exam.
- Practical exam.
Weighting of Assessments
Written exam
Oral exam
Practical examination
200
100
100
Total
400
6- List of References
6.1- 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 Wiley
Tietz text Book of clinical biochemistry. Carl A and Edward R ( .B.Saunders
company N.Y.).
6.3- Recommended Books
P ri nci pl e and t echniques of bi ochemi st ry and Mol ecul ar Bi ol ogy, 6 t h
Editi on,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 , ... etc
Journal 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