The University of Jordan - Doctor 2018



The University of JordanFaculty: MedicineDepartment: Physiology and BiochemistrySemester: SummerAcademic Year: 2013-2014Course Name:IntroductoryCourse Number: 0501118Biochemistry and molecular biology (for medical students)-----------------------------------------------------------------------------------------------------------Credit hours2Level1PrerequisiteNoneCoordinator/ LecturerProf. Mamoun AhramDr. Diala Abu HassanOffice numberOffice phoneCourse websiteE-mailPlaceOffice hoursDay/TimeSundayMondayTuesdayWednesdayThursdayTBDTBDTBDTBDTBDIntroduction Biochemistry as the name implies is the chemistry of life. It is the alphabets and language of biology. The study of biochemistry is essential to understand the structure and functioning of cells at the molecular level. Biochemistry is perhaps the most rapidly developing subjects in medicine. No wonder the major share of Nobel prizes in medicine has gone to research workers engaged in biochemistry. Course DescriptionThis three-credit hour course is mandatory for first-year medical students. The course is designed to introduce medical students to biochemistry and molecular biology via covering the basic concepts of structures and functions of macromolecules. A large portion of the course will also cover detailed information of enzymes, their mechanisms of action, their regulation, and their uses in biology and medicine with an emphasis to molecular biology, cofactors critical for enzyme function and mechanism of actions, clinical enzymology, and isoenzymes. Basic and advanced biochemical and molecular techniques used in research will be discussed. Learning Objectives-Understand strong and weak acids and bases-Metabolic sources of acids and bases-The concept of pH and pKa-Regulatory mechanism against changes of pH-Main physiological buffers and their actions-Describe the chemical structures of carbohydrates, lipids, amino acids and proteins , enzymes, co-enzymes and vitamins-Explain the chemical structures in relation to function of the macromolecules-Appreciate the specificities and catalytic power of enzymes, understand the mechanisms of their actions and identify factors that affect their activity-Know the principles and applications of different biochemical techniques used in biological researchIntended Learning Outcomes (ILOs):Successful completion of the course should lead to the following outcomes:A. Knowledge and Understanding: Student is expected toDifferentiate the types and characteristics of non-covalent interactionspH and buffers : Recall the concepts of acids, bases, amphoteric molecules, and ionization of water and weak acidsApply the molecular expressions: molarity, normality, equivalence, pH, and pKa.Know the chemical concept of different types of buffers, buffering capacity, midpoint, and titration.Apply the Henderson-Hasselbalch equation and mechanisms of buffer actions. List of physiological buffers and translate knowledge in normal and abnormal condition.Review of basic organic chemistry and functional groups in biomolecules.Definition of Carbohydrates Chemistry of CarbohydratesImportance of CarbohydratesClassification of Carbohydrates (e.g. mono and diasaccharides) Important diasaccharides and polysaccharides Differentiate proteoglycans and glycoprotiens and carbohydrates linked to blood groups.Define lipids and importance of lipids.Identify the classifications, drawing, structure, and function of lipids (fatty acids, triglycerides, waxes, phiospholipids, glycolipids, and steroids.Differentiate the basic mechanism of lipid transport in bloodRecall the complex structure of cell membranes Define proteinsList amino acidsDifferentiate the structure, isomerism, classes of amino acidsIdentify the ionization states of amino acidsKnow the concept of isoelectric pointList modified and specialized amino acidsRecall of features of peptide bondApply the concept isoelectric point of amino acids to polypeptides Recall the four levels of protein structureDifferentiate the different secondary structures of proteins and their structural significanceUnderstand the formation of tertiary structure of proteinsDefine quaternary structureKnow the concept of complex protein structures (glycoproteins, lipoproteins, phosphoproteins)Apply the concepts of denaturation and renaturation to protein structure and functionApply the previous information to pathological defects in protein formationRecognize the different classes of proteins (fibrous, globular)Discuss different proteins from each class I(mainly collagen, myoglobin, hemoglobin, and immunoglobulins) in connection to their function in light of previous knowledgeDefine enzymesRecall the general properties and functions of enzymes, ribozymes.List the classes of enzymes and differentiate the reactions they catalyzeRecall the major features of active sitesRecall the concept of free energy and activation energy, transition state, abzymes.Differentiate between holoproteins and apoproteinsDifferentiate classes of cofactorsDefine and list vitamins and understands their contribution in enzymatic reaction (coenzymes) Identify the role of metals in enzyme activity of metal-activate enzymesDefine enzyme kineticsApply the concept of Vo, Vmax, and KM, and their biological significanceApply the above terms to the Michaelis-Menten equationApply the enzyme units to understand the following terms: (rate of reaction (Vo), Vmax, specific activity, turnover number).Link the mechanisms of action of the different classes of inhibitors in relation o the Lineweaver-Burk or double-reciprocal plotDescribe how enzyme activity can be regulated by physiological and pharmacological inhibitorsRecall the concept of allosteric regulationIdentify the role of small and large enzyme regulatory moleculesIrreversible inhibition and suicide inhibition. Define the various modes of enzyme regulation.Discuss the effect of nonspecific inhibitors (temperature, pH) on protein structure and functionDefine isoenzymes and know their biological and clinical significance (Clinical enzymology).Principles and applications of dialysis.Various types of chromatography techniques: gel filtration chromatography ion exchange chromatography, affinity chromatography, HPLC. Vertical protein electrophoresis and isoelectric focusing.Immunological techniques (ELISA, immunoblotting, immunoprecipitation, proteomics – mass spectrometry, protein arrays, cell fractionation).Advanced molecular techniques (restriction endonucleases for DNA cloning and recombinant DNA technology, PCR, DNA sequencing, DNA microarrays, RNA-seq, CRISPR-CAS9) B. Intellectual Analytical and Cognitive Skills: Student is expected toCalculate pH and changes in pH according to different variablesPredict changes in blood pH according to equilibrium of bicarbonate buffering systemDifferentiate between the various sugar molecules, lipids, and amino acidsCalculate isoelectric point of small polypepidesPredict changes in enzyme kinetics according to inhibitor typeCalculate enzyme units Determine enzyme class according to catalyzed reaction and involved cofactorTurnover number and specific activity. Interpretation of technical results.Teaching/Learning MethodsTeaching MethodILO/sLectures and Discussions: Homework and Assignments: Projects: PresentationCourse ContentsTopicNo. of lecturesWeekReferenceILOsIntroduction11Campbell Chapter 1 1-5A1Acids, bases, pH, and buffers51,2,3Campbell Chapter 2 35-57A2-6Carbohydrates33,4Campbell Chapter 16451-477A7-13Lipids35,6Boyer Chapter 8231-258A14-17Amino acids26,7Campbell Chapter 361-79A18-23Polypeptides and protein structure27,8Campbell Chapter 3,483-117A24-30Protein structure-function relationship (part I: fibrous proteins)19Campbell Chapter 3,483-117A31-34Protein structure-function relationship (part II: globular proteins)19Campbell Chapter 3,483-117A31-34Protein structure-function relationship (part III: immunoglobulins)16A31-34Enzymes (introduction)210Marks Chapter 8112-133A35-40Enzymes (cofactors)211Marks Chapter 8112-133A41-43Enzymes (kinetics)212Marks Chapter 9112-133A44-48Enzymes (mechanism and regulation)113Marks Chapter 9112-133A49-55Biochemical techniques 313Campbell Chapter 5117-135A56-59Molecular techniques6Cooper, Ch. 4 (126-135; 148-149), Ch. 5 (164-172)A60Learning MethodologyLectures and homeworkProjects and Assignments NoneEvaluationEvaluationPoint %DateMidterm Exam40%Project0%Assignments0%Quizzes10%Final Exam50%Main References:Biochemistry; Mary K. Campbell and Shawn O. Farrell, Brooks Cole; 7th edition.The Cell: A Molecular Approach, Geoffrey M. Cooper and Robert E. Hausmann, 7th edition, Sinauer Associates, 2018.Mark's Basic Medical Biochemistry by M. Lieberman of A. Marks, Lippincott, Williams and Wilkins, 2013. 4th edition, Concept in Biochemistry by R.BoyersReferences:-NCBI Bookshelf:()-The Medical Biochemistry Page: ()-Biochemistry, Garret and Grishan, Second Ed.: Grading Scale 0-39F45-49D-50-54D54-69D+60-64C-65-69C70-73C+74-76B-77-80B81-84B+85-89A-90-100ANotes: Concerns or complaints should be expressed in the first instance to the module lecturer; if no resolution is forthcoming, then the issue should be brought to the attention of the module coordinator (for multiple sections) who will take the concerns to the module representative meeting. Thereafter, problems are dealt with by the Department Chair and if still unresolved the Dean and then ultimately the Vice President. For final complaints, there will be a committee to review grading the final exam. For more details on University regulations please visit: ................
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