Medical Biochemistry, Molecular and Cell Biology I. 2014/15, spring semester Information on the course and examinations

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1 Medical Biochemistry, Molecular and Cell Biology I. 2014/15, spring semester Information on the course and examinations Name of the Department: Department of Medical Biochemistry, Faculty of Medicine, Semmelweis University Name of the course: Medical Biochemistry, Molecular and Cell Biology I. Neptun code: AOKOBI001_1A Credits: 7 Director of the course: Prof. László Tretter M.D., Ph. D., D. Sc. Description of the curriculum The principal aim of the course is to provide an insight into the structure and function of biologically important molecules including amino acids, carbohydrates, lipids and nucleotides as well as proteins, enzymes and nucleic acids. This module is a prerequisite to the understanding of the intermediary metabolism of the cell that is introduced by the module of bioenergetics and mitochondrial ATP production. The cell biology unit describes the principles of organization of cells as well as the function of subcellular organelles. The molecular biology module aims at highlighting the storage and expression of genetic information throughout replication, transcription and translation as well as our current understanding of the regulation of gene expression, followed by an up-to-date summary of currently used methods in molecular biotechnology. Module I. Biologically important molecules and macromolecules I/1. Amino acids, peptides, proteins Amino acids. Amino acids as electrolytes. Structure and chirality of amino acids. Reactions of amino acids. Proteins. The peptide bond. Structure levels in proteins. Primary structure of proteins. Steric structure of globular proteins. Conformation of proteins. Purification of proteins. Structural characteristics of fibrous proteins. Collagen. Myoglobin and hemoglobin. I/2. Enzymology Enzymes. Enzymes as biocatalysts, enzyme activity. Isoenzymes. Coenzymes. Enzyme kinetics: the Michaelis-Menten model. Mechanism of action of some important enzymes (serine proteases). Reversible and irreversible inhibition of enzymes; competitive, noncompetitive and uncompetitive inhibitors. Regulation of enzyme activity. Allosteric enzymes. I/3. Carbohydrates, lipids, nucleotides

2 Structure and function of essential building blocks of living cells. Module II. Bioenergetics and mitochondrial ATP production Group transfer potential. Bonding types of high group transfer potential. Principle and examples of coupled reactions in the metabolism. The phosphoryl transfer. Role of high energy phosphates in the intermediary metabolism. Synthesis of ATP by substrate level phosphorylation. Mitochondrial membranes and their permeability. Mitochondrial transporter systems. The respiratory chain: components, organization, function, inhibitors. Respiratory control, P/O ratio, uncoupling of oxidative phosphorylation. Mitochondrial ATPase. (F o F 1 -ATP-ase): structure, function, inhibitors. Mechanism of oxidative phosphorylation. Chemiosmotic hypothesis. Module III. Cell biology Compartmentation in eukaryotic cells. Membrane structure. Intracellular membranes. Cell nucleus. Movement of cellular organelles. Cytoskeleton, microfilaments, microtubuli, actomyosin. Mechanism of vesicular transport. Metabolism and transport, the principle of metabolom. Metabolic profile of various organelles (endoplasmic retikulum, peroxisomes, lysosomes, mitochondria). Module IV. Molecular Biology IV/1. DNA, RNA and protein synthesis (storage and expression of genetic information) Nucleic acids structure and function. Bases, nucleosides, nucleotides, DNA structure, DNA denaturation, hybridization. DNA replication. Replication in prokaryotes, leading and lagging strand. Okazaki fragments. DNA-dependent DNA polymerases. DNA ligase. Telomerase. topoizomerases. Replication in eukaryotes. Structure of eukaryotic chromosomes. Mitochondrial DNA. Nucleosome structure. DNA repair. Types of DNA damage; mutations, frameshift, nonsense mutations, mismatch repair. Coordination of repair and replication. Transcription in procaryotes. Structure of RNA; t-rna, r-rna, m-rna, differences between the procaryotic and eucaryotic genomes. Transcription complexes, initiation, elongation, termination in procaryotes. Transcription in eucaryotes, RNA polymerases, promoters, enhancers, silencers. Processing of mrna, mechanism of splicing. Alternative splicing, mrna editing. The genetic code. Activation of trna. Mechanism of translation, initiation, elongation, termination. Antibiotics. Posttranslational modification of proteins. Protein folding, sorting, quality control and transport into intracellular compartments. Ubiquitination and intracellular proteolysis. IV/2. Regulation of gene expression Regulation of gene expression in prokaryotes. The operon model. Positive and negative regulation in the lac operon. Regulation of gene expression in eukaryotes at the transcriptional level. Role of chromatine structure; covalent and non-covalent chromatin modifying activities and DNA methylation (epigenetics). Post-transcriptional regulation in eukaryotes. Regulation of mrna stability; micrornas. Translational regulation. IV/3. The eukaryotic cell cycle and its regulation

3 Cell cycle in eukaryotes. Cyclins and cyclin dependent protein kinases. Proteases in the cell cycle. Regulation of G0/G1, G1/S and G2/M transitions. Integration of DNA repair into the cell cycle. Module V. Methods in molecular biology and gene technology Principles of recombinant DNA technology: molecular cloning, restriction endonucleases. Genomic and cdna libraries. Blotting techniques (Southern, Northern, Western) and their utilization. DNA microarrays. PCR and its application in molecular biology. Recombinant vectors (reporter and expression vectors); synthesis of recombinant proteins. Transgenic, knock-out and knock-in animals in medical research. Human gene therapy. The Human Genome Project and its results: organization and polymorphic nature of the human genome; implications for human traits and diseases. Genotyping methods (PCR-RFLP, PCR-ASA). Application of bioinformatics in biological and medical research. Requirements 1. Participation in the laboratory practicals, consultations and seminars is obligatory; students have to sign the attendance sheets at the end of every lesson. In case of more than three absences from the practical lessons for any reason, the semester will not be acknowledged and the student is not allowed to sit for the semifinal exam. Missed practicals can be completed only in the same week at another group; certificate from the host teacher should be presented by the student to his/her own teacher. The schedule of practical lessons, consultations and seminars can be downloaded from the official homepage of the Institute. 2. Both midterm examinations have to be passed before the commencement of the examination period (see next paragraph). Lectures and practical lessons Two lectures and a laboratory lesson (practical) are held every week; schedules can be found in separate uploaded files. Students are expected to keep records and write protocols on the performed experiments (suggested structure: aim of the experiment, applied methods/devices/reactions, results and evaluation). Hand-written protocols might be presented either at the end of the lab lesson or at the beginning of the next practical to the lab teacher. Students might get max. two points for each acceptable protocol, and points collected this way are added to the total score they achieve in the corresponding midterm exams. Thus, bonus points collected in weeks 2, 3 and 5 (at most 6) are added to the scores of midterm I and those obtained in weeks 8 11 (at most 8) to midterm II, respectively. Importantly, these bonus points not only improve your midterm grades but might help you pass the midterm, too.

4 Midterm examinations Two midterm written examinations will be held during the semester (in weeks 7 and 12 of the semester, respectively), in frame of the regular laboratory practical lessons. As Tuesday and Friday in week 12 are holidays (28th April (University Day) and 1st May), groups having their lab lessons on these days (EM 2-4, 6, 7, and ED 1) are going to write Midterm II in the EOK Szent-Györgyi lecture hall on 27th April (Monday) at 18:05. Midterm tests consist of open questions that might include structures of bioorganic compounds as well as calculations with regard to ph of amino acid solutions, enzyme purification and enzyme kinetics. The material of midterm I covers the subject of lectures and seminars of the first 6 weeks (corresponding chapters from the topic list: Amino acids, peptides, proteins and enzymes: 1-18; Carbohydrates: 1-6; Lipids: 1-7; Bioenergetics and mitochondrial energy production: 1-6). Midterm II is based on the lectures and seminars of weeks 7-11 (corresponding chapters from the topic list: Nucleotides and nucleic acids: 1-8; Cell Biology: 1-11; Molecular Biology: 1-33). Midterm tests will be evaluated and graded by lab teachers (0, 2, 3, 4 or 5 scores). It is compulsory to pass BOTH midterm exams, that is, to acquire at least 2 scores from each of them, as a prerequisite to acknowledgement of the semester (obtaining a signature). These midterm or bonus points are added to the scores achieved at the semifinal exam (see below). Passing both midterms is a prerequisite to acknowledgement of the semester. Failed midterms might be retaken twice. The first retake is written; it should be performed in week 8 (retake of midterm I) and week 13 (retake of midterm II), supervised by the student s own lab teacher. Students having failed the first retake might sit for the second retake in the last week of the semester. The second retake is an oral exam conducted by a two-member examination committee. Students having failed the first retake of both midterms I and II will be examined in the material of both midterms at the same time. Semifinal examination Only those students who successfully completed the semester (requirements: not more than 3 absences from the parcticals and at least 2 scores from each midterm), thus obtained an official electronic Neptun signature, are entitled to sit for the semifinal exam. The semifinal is a written exam that consists of two theoretical parts and the lab exam. First theoretical part: drawing 8 structures selected from the List of obligatory formulas (1 point each), solving a biochemical calculation (amino acids as buffers and enzyme kinetics; 2 points), defining two important terms (1 point each) and providing short answers to open questions (8 points). The list of obligatory formulas is available in a separate document. Important terms will be summarized on the last slide of every lecture file. Second theoretical part: solving 40 multiple choice questions (1 point each). Practical (lab) exam: an essay question on a laboratory experiment performed during the semester (evaluation: 0 = unacceptable; 1 point = minor mistakes; 2 points = clear, detailed

5 and correct). Exact quantities (mass, volume of reagents, incubation times etc.) are not expected here. Accordingly, the available total scores in the semifinal test are = 62. The exam is unsuccessful with - 10 or less points in part 1, OR - 20 or less points in part 2, OR - 0 point from the practical exam. Students having passed both part 1 AND part 2 but failed the practical essay have to retake only the practical essay when they retake the semifinal exam. Those who want a better grade are entitled to rewrite the first 2 parts as well, however, with the risk of performing worse. Students who pass the practical exam but fail either part 1 or part II have to retake both theoretical blocks but not the practical exam. In case of successful exams, i. e. when the theoretical part and the practical exam are successfully completed (at least 11 and 21 points from part I and part II, respectively, and at least 1 from the lab exam), bonus points from the midterms (at least 4, at most 10) are added to the total score collected during the exam. Therefore, successful semifinals will be graded as follows: points = grade 2 (pass) points = grade 3 (satisfactory) points = grade 4 (good) points = grade 5 (excellent). It is possible to write the practical essay in week 14, during the first 15 minutes of the last laboratory practical of the semester (as a matter of course, the lab experiment of week 14 will not be asked on this occassion). Students successfully completing this test (getting 1 or 2 points) are exempted from writing the practical exam at the semifinal exam. It is to note that this is an extra opportunity for passing the practical exam prior to the beginning of the exam period and in case of failure the semifinal exam should proceed as outlined above. Registration and modification of examination dates: electronically, via the Semmelweis University Neptun System. Unsuccessful exams can be repeated after three working days at the earliest. All our examination rules comply with the official examination regulations of the Semmelweis University. Textbooks, manuscripts, handouts: Harper s Illustrated Biochemistry (30th edition) Sasvári: Bioorganic compounds (manuscript) Hrabák: Selected Collection of Chemical Calculations (manuscript) Medical Chemistry and Biochemistry Laboratory Manual (manuscript)

6 Powerpoint files of lectures English, For students, Biochemistry I, authorized pages (username and password can be obtained from lab teachers) Students' own lecture notes