Biotechnology Ang 2

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BIOTECHNOLOGY- programme of the study,Institute of Biochemistry and Molecular Biology

University of Wrocaw

General coursesEnglish

I year winter semester 30 hrs (3 ECTS), passing testI year spring semester 30 hrs (3 ECTS), passing testII year winter semester 30 hrs (3 ECTS), passing testII year spring semester 30 hrs (3 ECTS), egzam, level D,

Seminars in EnglishIII year winter semester 30 hrs (3 ECTS), passing testIII year spring semester 30 hrs (3 ECTS), passing testI year master winter semester 30 hrs (3 ECTS), passing testI year master spring semester 15 hrs (2 ECTS), passing test

The main tasks of the seminars are focused on learning of the actual research trends in theinternational scientific laboratories, based on chosen original research papers; increasing theknowledge of the specialized scientific dictionary and gaining the knowledge of presenting of the workand discussing it in English.

Sport activitiesI year winter semester 30 hrs (0 ECTS), passing testI year spring semester 30 hrs (0 ECTS), passing test

Humanistic Courses

PhilosophyII year master spring semester 15 hrs lectures, 2 ECTSEconomyII year master spring semester 15 hrs lectures, 2 ECTSBioethicsII year master spring semester 15 hrs lectures, 2 ECTSLaw Protection of Intellectual PropertiesII year master spring semester 15 hrs lectures, 2 ECTSEconomics of ProductionII year master spring semester 15 hrs lectures, 2 ECTSEconomy in CompanyII year master spring semester 15 hrs lectures, 2 ECTS

InformaticsINF15 hrs lectures,30 hrs lab coursesII year winter semester4 ECTS

Informatics and computers. Expression of a problem, searching the methods to solve it, constructingthe algorithm and its realisation. Elementary comprehension of informatics. Computer - how does itwork? Data storage and processing. Computer programs, operating system, translators, executableuser programs. Elements of logic and computer arithmetic. Computer languages and compilers. Blockschemes of algorithms. Examples of algorithms and their analysis. Recurent algorithms. Structuring ofthe algorithms. Management in operating system. Operating in Windows. Text and graphic editors.Application of computers in biochemistry. Libraries of software, software packages. Examples of the

software for various applications. Data banks. Using Internet. Net software.Lecturer:dr hab. Jacek Leluk


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BioinformaticsBIOINF15 hrs lecturesI year master spring semester2 ECTS

Analysis and processing of information. The structure of the data base and its use. Access and use ofavailable data bases (PDB, Swiss-Prot, Medline). Comparison of protein and nucleotide sequences;homologies; mutation matrices. Work with Fasta and Blast software. Prediction of protein and nucleicacid structures. Molecular dynamics and quantum mechanics. Computer assisted analysis of theprotein-ligand interactions; application of the Free Energy Perturbation method. Design of drugs.Application of computer methods for NMP and X-ray analyses.Lecturer: dr Daniel Krowarsch

Basic courses

MathematicsMAT15 hrs lectures, 30 hrs lab coursesI year winter semester5 ECTS

Functions of one variable. Maximum and minimum functions of two variables. Integrals of functions ofone variable. Elements of ordinary differential equations. Elements of linear algebra.Lecturer: prof. dr hab. Marek Boejko (Institute of Mathematics)References:F. Leja, Rachunek rniczkowy i cakowy, PWN, Warszawa 1997I. Gelfand, Algebra liniowa, PWN, Warszawa 1977.

Statistics in Analysis and Planning of the ExperimentSTAT15 hrs lectures, 45 hrs lab coursesI year winter semester5 ECTS

Probability calculations and statistics. Methods used for processing of empirical data. Statisticalmethods to determine the "best" equation which fits a set of observations. Comparing sets of empiricaldata; Students t-test, significance of the differences. Relationships between variables, correlations,regression. Deterministic and probabilistic models of chosen processes present in the nature. Modelingof the natural processes.

Physical Methods in BiologyMEFIB30 hrs lectures, 60 hrs lab coursesI year winter semester5 ECTS

Discussion of measuring error, theory of incidental error. Mean values, index dispersion. Interrelationbetween variable, correlation factor, linear regression. Accuracy and repeatability of methods. Physicalbasis and application in biology of absorption and emission spectroscopies, flame photometryrefractometry, polarimetry and mass spectroscopy. Electrochemical methods: potentiometry with pH-metry, polarography, voltamperometry, coulometry, conductometry, basis and application.Electrophoresis in separation of macromolecules. Hydrodynamic methods: sedymentation, physicalbasis and application in fractionation of biological materials using centrifugation, ultracentrifugation andcentrifugation in gradient density.Lecturer: dr hab. prof. Andrzej SzczepaniakReferences:Biofizyka dla biologw, red. M.Bryszewskiej,W. Leyko, 1995, PWN, WarszawaBioenergetyka 2, Nicholls DG, Ferguson SJ, 1995 PWN, Warszawa


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BiophysicsBIOFIZ30 hrs lectures, 60 hrs lab coursesII year winter semester + II year spring semester3 + 5 ECTS

Methods for the studies of biopolymers. Spectroscopic analysis of proteins and nucleic acids. The firstlaw and the second law of thermodynamics, free energy and free enthalpy. Chemical work, electricalwork and chemical potential. Thermodynamics of active transport. Redox reaction in biology, directionof redox reactions, concentration dependence of the oxidation-reduction potential. Factors affecting theredox potential. Biophysics of lipids, liquid crystal structure, phase transition, monolayers, liposomes.Biological membranes, structure and function, integral and peripheral membrane proteins. Transportacross the membrane, diffusion, natural and induced permeability (ionophores, uncouplers). Proteinsmediated transport, symport, uniport, antyport. Symport of sugars and amino acids, periplasmictransport system, transport of macromolecules. The chemiosmotic hypothesis, the tenets of Mitchell,proton circuit, measurement of proton-motive force, studies of proton current. The experiments that areinconsistent with the chemiosmotic theory. Mitochondrial respiratory chain, complexes I, II and III.Cytochrome oxidase, proton translocation. Light reaction in photosynthetic bacteria, connection withrespiratory chain, bacterial photosynthetic reaction center. Photosynthetic electron transport chain inhigher plants, photosystem I, photosystem II, oxygen evolution. Complex b6f, the Q cycle inmitochondria and chloroplast. Photosynthetic antenna, light energy transfer. Bacteriorhodopsin,structure and function. ATP-ase, structure and function, G of ATP hydrolysis. Physical and chemicalproperties of DNA, parameters for description of DNA structure.Lecturer: dr hab. prof. Andrzej SzczepaniakReferences:Biofizyka dla biologw, red. M.Bryszewskiej,W. Leyko, 1995, PWN, WarszawaNicholls DG, Ferguson SJ, 1995 Bioenergetyka 2, PWN, Warszawa

General and Analytical ChemistryCHEM30 hrs lectures, 30 hrs lab courses

I year winter semester6 ECTS

Electron configurations of atoms and the periodic table of elements. Chemical bonding: ionic latticesand the Born-Haber cycle; the covalent , and bond - molecular orbital theory, bonding andantibonding orbitals in homo- and heteronuclear molecules. Polarization of covalent bond.Electronegativity of chemical elements. Geometry of molecules - the theory of valence - shell electron -pair repulsion. Intermolecular interactions. Hydrogen bond. Chemical reactions: chemical equations,definitions of acids and bases, redox reactions. Enthalpy, entropy, Gibbs function and the chemicalequilibrium. Activation energy and catalysis. Acid-base equilibria: pH, hydrolysis, buffer solutions.Solubility equilibria: the solubility product. Problems of chemical qualitative analysis. Redox reactionsand standard electrode potentials. The coordination compounds and their applications in chemicalanalysis. Spectroscopic methods of analysis. The basic properties of chemical elements: -general

trends in chemical properties and position of the element in the periodic table; -geochemical properties;-analytical problems; -character of chemical bonding.Lecturer: prof.dr hab. Adam Jezierski (Institute of Chemistry)References:Sienko M.J., Plane R.A. 1992 Chemia. Podstawy i zastosowania. WN-T, WarszawaChang R. 1991 Chemistry. McGraw-Hill, Inc., New York


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Organic ChemistryCHO45 hrs lectures, 45 hrs lab coursesI year spring semester10 ECTS

The structural theory (chemical bonds, molecular and atomic orbitals, orbital hybridization, polarcovalent bond, inductive effects, homolysis and heterolysis of covalent bond, delocalized bonds andresonance theory, acids and bases in organic chemistry). Molecular structure and physical propertiesof organic compounds. Stereochemistry (chiral molecules, configuration, conformation, stereoisomers,stereospecific reactions). Structure, nomenclature, synthesis and chemical properties ofmonofunctional organic compounds (alkanes, alkenes, alkynes, arenes, haloalkanes, organometaliccompounds, alkohols and phenols, aldehydes, ketones, carboxylic acids and their derivatives,inorganic esters, amines, organosulfur and organophosphor compounds). Natural compounds(nomenclature, structure, isolation, synthesis, biological and chemical properties): amino acids andproteins, carbohydrates, lipids, heterocyclic compounds and their derivatives.Lecturer: prof. dr. hab. Zbigniew Szewczuk (Institute of Chemistry)References:Salomons J. W. G. 1992 Organic Chemistry - 5th ed. John Wiley & Sons. New YorkMastalerz P. 1996 Podrcznik chemii organicznej. Wydawnictwo Chemiczne. Wrocaw

Biophysical ChemistryCHFIZ30 hrs lectures, 30 hrs lab coursesI year spring semester6 ECTS

Thermodynamics: properties of gases, work, heat, laws of thermodynamics, state functions, thermo-chemistry, chemical equilibria. Electrochemistry: solutions of electrolytes, conductivity, electrochemicalcells, electrodes, kinetics of electrode processes. Phase equilibria: phase transitions of puresubstances and simple mixtures, phase rule, two and three components systems. Chemical kinetics:rates of chemical reactions, kinetics of complex reactions, molecular reaction dynamics. Intermolecularinteractions. Introduction to molecular spectroscopy: interaction of the electromagnetic radiation withthe molecule, selection rules, methods of optical and resonance spectroscopy.Lecturer: prof. dr hab. Jacek OtlewskiReferences:L. Sobczyk, A. Kisza, 1985 Chemia fizyczna dla przyrodnikw, PWN Warszawa; Z. Kcki, 1975Podstawy spektroskopii molekularnej, PWN Warszawa; L. Sobczyk, A. Kisza, K. Gatner, A. Koll, 1982Eksperymentalna chemia fizyczna, PWN Warszawa.

Bioprocess EngineeringBIOPRO15 hrs lecturesII year master, winter semester2 ECTS

Reaction kinetics. Determination of kinetic equation. Batch reactor. Continuous stirred tank reactor.Column reactor. Membrane techniques in biotechnology. Membranes in immobilization. Separation,concentration and purification of bioproducts in technical scale. View of apparatus construction.Process monitoring.Lecturer: prof. dr hab. in. Andrzej Noworyta (Institute of Chemistry)References:Aiba S., Humphrey A.E. . Inynieria biochemiczna. Wyd. 2. uzup. WNT Warszawa: 1977.Bailey J.E., Ollis D.F. Biochemical Engineering Fundamentals. 2 ed. McGraw-Hill Book Co.New York: 1986.


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Protein EngineeringINZBK15 hrs lectures, 30 hrs lab coursesI year master, spring semester4 ECTS

Protein engineering and methods used in this field. Protein structure: solvent accessible area, packing

density of protein core, secondary structure of proteins: -helix -sheet and -turn. The role of water indetermining protein structure (surface water and integral water). Additive effects in protein chemistry.Protein - protein recognition: protein proteinase inhibitor-serine proteinase as a model system (bindingof different amino acid side chains in S1 pocket of proteinases), structure of the human growthhormone-growth hormone receptor: alanine scanning, effects of single amino acid substitutions.Antibody-antigen interaction: structure and thermodynamics. Structural stability of proteins: effects ofsingle amino acid substitutions on structure and stability of T4 lysozyme. protein folding problem:

systematic mutagenesis of barnase and CI-2 inhibitor, -analysis, H-D exchange method. Engineeringof subtilisin: the influence of amino acid substitutions on activity, stability and specificity of theproteinase. Phage display approach: protein libraries, minimization of protein structures, generation ofnew activities in proteins.Lecturer: prof. dr hab. Jacek OtlewskiReferences:

Perutz M 1992 Protein Structure, Freeman, New York

Environmental ProtectionOSRO30 hrs lecturesIII year, winter semester3 ECTS

Environmental biology as multidisciplinary science. Concepts in protection of human environment.Ecological education and health protection in Polish law. Ethical and law aspects of animal protection.Global, regional and local aspects of biosphere protection. Participation of physical, chemical andbiological factors in polluting of the environment. Environment and diseases. The role ofmicroorganisms in the protection of environment. The role of lower animals in the environment and

human-environment relationships.Lecturer: present lecturer of the course for BIOLOGY studiesReferences: - as suggested by the lecturer

Methods in Environmental BiotechnologyBIOTESRO15 hrs lectures, 30 hrs lab coursesIII year, spring semester3 ECTS

Circulation of the matter in the nature. Main human-related factors involved in the degradation of theenvironment. Pollution of water and classification of the water sources. Biotechnological processesused for treatment of the sawage. Recycling of the industrial and urban wastes. Cleaning the water.

Biotechnological processes of cleaning and recultivation of soil, air and water.Lecturer: dr Mariusz Olczak

BiologyBIOL30 hrs lectures, 30 hrs lab coursesI year, winter semester4 ECTS

Origin and major events in a history of life on Earth - biological time scale. First photosynthetic organisms.Onset of eucaryotic plant cell and its structure: cytoskeleton, membrane system, plastids, cell wall. Thedevelopment of multicellular organisms -principles of morphogenetic processes in plants. Sources ofbiodiversity. Hardy-Weinberg Law. Agents of evolution. Selection. Specificity of plant speciation -

ecotypes, homeostasis of species, hybridization, polyploidy. Evolutionary trends in a kingdom Plantae:protistian ancestors of plants, land invasion, adaptations to the new environment, organ development,homosporous and heterosporous plants, reduction of gametophyte, the appearance of seeds, flowers andfruits (coevolution with insects).


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Animal world organization - basis of systematics (criteria of homology, population, taxon,category, genotype, phenotype). Characteristic of Chordata. Ewolution of Vertebrates and philogeneticrelations between above mentioned groups. Adaptation to evironment - extraembryonic membranes,water economy, ectothermity and endothermity, locomotion methods, structure of body cover(integumentum). Organogenesis of Vertebrates. Anatomical structure and functions of the skin and itsderivatives, the skeleton, the alimentary canal and its derivatives, the circulatory system, the urogenitalsystem and nervous system. Histology of organs. Biology and ecology of vertebrates.Lecturers: dr hab. Danuta Kwiatkowska, dr Aurelia Pawowska-Indyk (Institute of Botany and Institute ofZoology)References:Hejnowicz Z. Anatomia i histogeneza rolin naczyniowych. PWN, Warszawa, 1985.Szweykowscy A.i J. Botanika. PWN, Warszawa, 1992.Raven P.H., Evert R.F., Eichhorn S.E. 1992. Biology of Plants. 5th Edition. Worth Publishers, NY.Z. Grodziski 1979 Zoologia przedstrunowce i strunowceN. Bobriski, B. Matwiejew, A. Bannikow 1972 Zoologia strunowceH. Szarski 1987 Anatomia porwnawcza krgowcwK. Ostrowski 1988 HistologiaK. Sembrat 1981 Histologia porwnawcza zwierztHejnowicz Z. Anatomia i histogeneza rolin naczyniowych. PWN, Warszawa, 1985.Szweykowscy A. J. Botanika. PWN, Warszawa, 1992.Raven P.H., Evert R.F., Eichhorn S.E. 1992. Biology of Plants. Fifth Edition. Worth Publ. N.Y.

MicrobiologyMIKROB30 hrs lectures, 30 hrs lab coursesII year, spring semester6 ECTS

Size, shape and structure of cells of microorganisms belonging to three domains: Eucaryota, Bacteriaand Archaea. Genome organization and means of genetic information transfer in these groups.Metabolism vast metabolic plasticity, diversity of ecological niches and nutritional types amongprocaryotic microorganisms. Interactions between microorganisms, aerobic and anaerobic trophicchains in ecosystems. C,N, S, P cycles in nature. Microorganisms in biotechnology and large scaleproduction. Chosen aspects of microbial pathogens and microbial diagnostics. Relationship betweenmicroorganisms and human and aninal organisms (intestinal flora). Applications of genetic engineeringin modern biotechnology.Lecturer: dr Dorota Dziadkowiec (Institute of Microbiology)References: Schlegel H.G., 1993, General Microbiology. Cambridge University Press.Kunicki-Goldfinger W.J.H., 1994, ycie bakterii. PWN. WarszawaTrends in BiotechnologyAnnual Review of Microbiology

Structure and Function of Proteins and ShugarsSTRUBIAC30 hrs lectures, 60 hrs lab coursesI year, spring semester9 ECTS

Molecular basis of life. The role of water in biological systems. Thermodynamics in biological systems.Aminoacids. Biological function of proteins. The structures in proteins. Carbohydrates. Enzymes,kinetics, specificity and regulation. Mechanisms of enzymatic activity. Vitamins soluble in water.Lecturer: dr hab. prof. Wiesaw WtorekReferences:L. Stryer, Biochemia, PWN 1997,R. H. Garrett, C. M. Grisham, Biochemistry, Saunders College Publ. 1999, 2000


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Structure and Function of Lipidic CompoundsSTRULIP15 hrs lectures, 15 hrs lab coursesI year, spring semester3 ECTS

Definitions of lipids. Chemical structure of lipidic compounds and their classification. Vitamins solublein fats. Steroids and steroid hormons. Prostaglandins, thromboxanes and leucotrienes. Polyketidecompounds. Amphiphiles. Self-assembly of lipids into the aggregates. Bilayer as one form ofaggregates. Biological membranes, natural and model. Liposomes and black lipid membranes.Lecturer: prof. dr hab. Arkadiusz KozubekReferences:R. H. Garrett, C. M. Grisham, Biochemistry, Saunders College Publ. 1999, 2000CYBERLIPID: www.cyberlipid.org/cyberlip/home0001.htm

Introduction to Nucleic Acid BiochemistryNUCLA15 hrs lectures, 15 hrs lab coursesI year, spring semester3 ECTS

Nucleotides and nucleic acids: structural features, conformational variants of DNA, denaturation andrenaturation, superhelical structures of DNA, types of RNA, posttranscriptional modifications.Lecturer: dr hab. Ryszard RzepeckiReferences:D.Voet/J. Voet, Biochemistry, J. Whiley 1995 rokL. Stryer, Biochemia, PWN 1997 rokR. H. Garrett, C. M. Grisham, Biochemistry, Saunders College Publ. 1999, 2000

Metabolism of Proteins and ShugarsMECUB30 hrs lectures, 60 hrs lab coursesII year, winter semester

6 ECTS

Metabolism general definitions. Glycolysis. Tricarboxylic acids cycle. Transport of electrons andoxidative phosphorylation. Gluconeogenesis, glycogen metabolism, pentose-phosphate pathway.Aminoacid metabolism. Integration of the metabolic processes. Peptide and protein hormones;hormonal regulation of the metabolism. Biosynthesis and degradation of proteins.Lecturer: dr hab. prof. Wiesaw WtorekReferences:L. Stryer, Biochemia, PWN 1997,R. H. Garrett, C. M. Grisham, Biochemistry, Saunders College Publ. 1999, 2000

Metabolism of Lipidic CompoundsMELIP

15 hrs lectures, 30 hrs lab coursesII year, winter semester5 ECTS

Transport of small and macro molecules across biological membranes. Import of proteins byorganelles. Katabolism of triglycerides, phospholipids, fatty acids and steroids. Lipases andphospholipases. Oxidation of fatty acids nonenzymatic and enzymatic; biological activity of products.Synthesis of fatty acids. Polyketide and fatty acid synthases. Biological activity of polyketides.Synthesis of triglycerides and phospholipids. Synthesis of sterols. Steroid hormones and their role insignal transduction.Lecturer: prof. dr hab. Arkadiusz KozubekReferences:R. H. Garrett, C. M. Grisham, Biochemistry, Saunders College Publ. 1999, 2000

D. E. Vance, J. Vance, Biochemistry of lipids, Lipoproteins and Membranes, Elsevier, 1996
http://www.cyberlipid.org/cyberlip/home0001.htmhttp://www.cyberlipid.org/cyberlip/home0001.htm


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Metabolism of Nucleic AcidsMEKWANU15 hrs lectures, 30 hrs lab coursesII year, winter semester5 ECTS

Rules of DNA replication. Structure and types of the replication systems. Bacterial, organelle andeucariotic DNA polymerases. Proteins initiating replication. Regulation of the replication initiationvelocity. Elongation and termination of DNA replication. Topological aspects of DNA replication.Coordination of DNA replication and cellular division. Initiation of transcription -the first step of geneexpression. Bacterial, organelle and eucariotic RNA polymerases. Structure of promotors. Formation ofthe complex initiating transcription in procariota and eucariota. The control of initiation of transcription.Synthesis and processing of mRNA. Synthesis and processing of non-coding RNA. Transport of RNAfrom nucleus to cytosol. Degradation of RNA.Lecturer: dr hab. prof. Hanna JaskaReferences:L. Stryer, Biochemia, PWN 1997,R. H. Garrett, C. M. Grisham, Biochemistry, Saunders College Publ. 1999, 2000

Biochemical TechnologiesBIOTECH30 hrs lectures, 60 hrs lab coursesIII year, winter semester8 ECTS

Microorganisms in biotechnological processes: biology, selection, cultivation, strain improvement,maintenance and storage. Plant and animal cell culture and their technological application inagriculture and industry. Enzyme production - enzymes of plant and animal origin; microbial productionof enzymes. Bio-reactors: batch operation, continuous reactors containing freely suspended bio-massor immobilized bio-mass in suspension, surface and immersing surface reactors, fluidized bedreactors. Flow behavior of fermentation fluids and gas-liquid mass transfer. Downstream processing:cell separation, flocculation and flotation, filtration, centrifugation, cell disruption, extraction, membranefiltration, ion-exchange and adsorption processes, precipitation reactions, purification, drying. The useof enzymes in biotechnological industries; enzymatic reactors. Biotransformation in production of L-amino acids, antibiotics and hormons. Biotechnological production of food and fodder proteins.Lecturer: prof. dr. hab. Antoni PolanowskiReferences:Fundamentals of biotechnology (1987). (ed. P. Praeve i in.) VCH Weiheim, FRG.Chmiel A. 1998. Biotechnologia. Podstawy mikrobiologiczne i biochemiczne. PWN WarszawaBiotechnologia zwierzt (1997). (Praca zbiorowa pod red. L. Zwierzchowski, K. Jaszczak i J.A.Modliskiego) PWN Warszawa.Wybrane zagadnienia biotechnologii rolin (1996). (red. K. Wypijewski) Wyd. Naukowe UAM

Biochemical PreparationsBIOPREP15 hrs lectures, 30 hrs lab courses

III year, winter semester4 ECTS

Selecting the material and establishing of the optimal parameters of the extraction. Clarifying andcondensing of the extracts. Basic principles and techniques of purification and separation of proteins.Classical methods of protein purification: use of salts, organic solvents, ion-exchange chromatography,hydrophobic chromatography, molecular filtration chromatography. Modern techniques of purification:affinity and pseudo-affininy chromatography, affinity sedimentation, chromotofocusing, highperformance liquid chromatography (HPLC) and reversed phase HPLC, application of bi- and tri-phasic aqueous systems. Purification of recombinant proteins. Scalling-up the purification procedures.Application of the protein properties for optimization and rational design of the purification process.Lecturer: prof. dr hab. Tadeusz WiluszReferences:R. K. Scopes, 1987, Protein Purification. Principles and Practice. Springer-Verlag, New York,R. Burgess, 1987, Protein Purification. Micro to Macro. Alan R. Liss. Inc. New YorkG.Piljac i V. Piljac, 1986, Genetic Engineering. Liquid Chromatography. TIZ Cakovec.


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Techniques in Molecular BiologyTEBIOM15 hrs lectures, 30 hrs lab coursesII year spring semester3 ECTS

Isolation and purification of total, nuclear, mitochondrial and chloroplast DNA and RNA. Restrictionendonucleases and their use. Cloning vectors (plasmid vectors, bactriophage-derived vectors, cosmidvectors, yeast cloning vectors, vectors for higher eukaryota). Cloning and subcloning. Introduction ofgenes into cells and whole organism. Construction and screening of genomic and cDNA libraries.Genetic and physical maps. DNA sequencing. Amplification of genes without cloning - PCR technique.Site-directed mutagenesis. Determination of DNA sequences recognized by DNA binding proteins. Inorganellotranslation.Lecturer: dr hab. prof. Hanna JaskaReferences:Sambrook, J., Fritsh E.F., Maniatis, T.(1989) Molecular cloning. A laboratory manual. second edition.Cold Spring Harbour Laboratory Press, New York.current research papers

Molecular Organization of the CellMOK30 hrs lectures, 60 hrs lab coursesIII year, spring semmester7 ECTS

Procaryotic and Eucaryotic cells. How the cells are studied. Preparation of the specimens forlight and electron microscope. Application of antibodies, in situhybridization. Fractionation of cells.Biological membranes. Principles of membrane transport. Exo- and endocytosis. Thecompartmentalization of higher cells. Cytosol. Membrane skeleton. Microfilaments, intermediatefilaments, microtubules. Cell nucleus, nuclear pores, nuclear matrix, transport of macromolecules intoand out of the nucleus. Mitochondria and chloroplasts, structure and transport of proteins. Pe-roxisomes. Smooth and rough endoplasmic reticulum; functions, Membrane biosynthesis. Golgiapparatus and its role in carbohydrate components biosynthesis. Processing of the proteins during theformation of secretory vesicles. Lysosomes. Cell junctions. Extracellular matrix. Cell adhesion. Cellsignaling. Intracellular receptors. Cell surface receptors. Second messengers. Target-cell adaptation.Cell growth and division. Cell cycle and its control. Genes involved in cell cycle control and cancercells.Lecturer: prof. dr hab. Aleksander F. SikorskiReferences:Alberts, Bray, Lewis, Raff, Roberts & Watson, Molecular Biology of the Cell, 1994, Garland Publ.Lodish, Baltimore, Zipursky, Matsudaira & Darnell, Molecular Cell Biology, 1995, Sci. Am. Books

GeneticsGENET30 hrs lectures, 30 hrs lab coursesII year, spring semester

6 ECTS

Classical genetics, including Mendels laws and exclusions; Gene mapping. Molecular genetics(structure, expression, regulation, variability of genes and mutagenesis in bacteria, yeast, plant andanimal cell). Background of the genetic engineering. Human genetics (genetic diseases and theirtreatment) and chosen aspects of immunogenetic. Cancers and mechanisms of their generation.Basic principles of population genetics, Hardy-Wiebergs law and factors affecting the balance,including molecular evolution.Lecturer: prof. dr hab. Stanisaw Uaszewski (Institute of Microbiology)References:Klug W. S., Cummings M. R. Concepts of GeneticsLasota Z. (red), Bilogia molekularna. Informacja genetyczna. PWN 1987,Wgleski P. (red), Genetyka molekularna. PWN 1995


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Genetic BiochemistryBIOCHGEN30 hrs lectures, 60 hrs lab coursesIII year, spring semester7 ECTS

Fundamentals of nucleic acid biochemistry. Two types of DNA libraries.The cell nucleus, nuclearenvelope, nuclear matrix, chromatin and chromosome organization. A nuclear DNA attachment andgene activity.Eukaryotic cell cycle. Methods commonly used to measure the lengths of the phases ofthe cellcycle. Control of the cell cycle in Go, G1, S, G2 and M phases. The correlated changes in thelevels of MPF and cyclin during cell cycle. Regulation of kinases cascade. Control of DNA synthesisgenes by the cell-cycle genes. STARTing the plant cell cycle.Cell cycle control in higherplants.Regulation of cell cycle-dependent gene expression. Transcriptional and posttranscriptionalregulation of plant histone genes.Cell cycle toward cancer.Developmental regulation of the cell cycle.Apoptosis. The components of the apoptosis machinery. The genetic regulation of apoptosis.Proteases and nucleases as therapeutic targets for the control of inappropriate apoptosis.Lecturer: prof. dr hab. Jan SzopaReferences:Alberts B., Bray D., Lewis J., Raff M., Roberts K., Watson J.D.,Molecular Biology of the Cell 1994,Garland Publ.;current scientific papers.

Industrial MicrobiologyMIPRZE30 hrs lectures, 30 hrs lab coursesIII year, spring semester6 ECTS

Biological and biochemical characteristics of chosen groups of microorganisms used in industrialprocesses. Biological aspects of production technology: food products (vine, beer, bread, butter,cheese, yogurt); organic compounds (organic solvents, anibiotics, vitamins). Microorganisms inbiotransformation of chemical compounds and as bio-indicators. Protection against microbialcorrossion.Lecturer: dr Marcin ukaszewicz (Institute of Microbiology)References:Chmiel A. Biotechnologia. 1991. PWN. WarszawaSzewczyk K.W. Technologia biochemiczna. 1997. WPW. Warszawa.Bamforth C. Tap into the art and science of brewing. 1998. Plenum Press New YorkReviews from: Trends in Biotechnology, Current Opinion in Biotechnology, Microbiological Reviews,Biotechnology Progress.

ImmunologyIMMUNO30 hrs lectures, 30 hrs lab coursesIII year, winter semester5 ECTS

Fundamentals of immunology, mechanisms of nonspecific immunology, complement system,phagocytosis, cytokines, role of macrophages. Specific immunity - primary humoral, secondary,immunoglobulins - classes and biologic role types of immunoglobulis, cellular immunity. T lymphocytes- maturation, functions, CD antigen. APC cells system cellular interactions, antigens, immunologicalspecificity immunological memory and toleration MHC antigens immunity connected with alimentarytract and respiratory system anti-infectious immunity.Lecturer: prof. dr hab. Adam Jankowski (Institute of Microbiology)References:Mackiewicz S., Wiktorowicz K. 1990. Immunologia w zarysie. PZWL, Warszawa.


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VirologyWIR30 hrs lecturesIII year, spring semester2 ECTS

Structure and properties of viruses as parameters used in contemporary classification of viruses.Replication of viruses and the relation virus-cell (participation of viruses in cancerogenesis).Immunological processes in viral infections and their importance in its restriction as well as in thedevelopment of autoimmunological diseases. Immunodeficiency in viral infections. Diagnostics of viralinfections.Lecturer: dr hab. Egbert Piasecki (Institute of Immunology and Experimental Therapy PAS)References:Januszkiewicz J., 1992. Zarys kliniki chorb zakanych. PZWL, Warszawa.Katoch M., Blaskovic D. 1991. Wirusologia lekarska. PZWL, Warszawasuggested by the lecturer original scientific papers

Amphiphiles and LipidsALIP15 hrs lecturesII year, spring semester2 ECTS

Definition of amphiphiles. Determination of amphiphilicity: Po/w, P w/o, separating funnels, HPLC isocratic mono and multi solvent systems. Definition of HLB; tables. Examples of amphiphiles.Amphiphiles at the interface forming monolayers and not forming monolayers. Monolayers definitions, surface pressure, phase transitions, methods of determination. Amphiphiles in aqueoussolutions aggregation. Micelle, shapes, aggregation number, CMC methods for determination.Types of aggregates. Solubilization = comicellization. Detergents specific amphiphiles; application inbiochemistry and molecular biology; removal from the samples. Temperature and phase transitions phase diagrams, water and phase transitions. Lipids as amphiphiles. Amphiphilic proteins.Lecturer: prof. dr hab. Arkadiusz KozubekReferences:D. M. Small, The Physical Chemistry of Lipids, Plenum Press, 1986Suggested original scientific articles

Biochemistry of Tissues and OrgansBIONAT15 hrs lecuresII year, spring semester2 ECTS

The lecture will be focused on molecular basis of functioning of chosen human tissues and organs andsome problems related to pathological processes in these tissues and organs. The following topics willbe discussed: biochemistry of the neuronal tissue, structure and function of neurons, action potential,neurotransmitters. Liver, its structure and function, plasma proteins as indicators of liver functioning,

importance of albumins in regulation of water distribution, detoxication of ammonia in the organism,deffence function. Macromolecules of the connective tissue. The structure, function and use ofcollagen. Pathologies of collagen. Biochemistry of vision. Muscle contraction. Biochemistry of actin andmiosin, regulation of the muscle contraction, sources of energy and its transduction. The role of acto-miosin systems in cellular motility. Nefrone functional unit of the kidney, biochemistry of urine,pathology. Characteristics of the cancer cell, comparison to the normal cell. Cytoskeleton in cancercell. Chemical factors inducing cancerogenesis in animal cells.Lecturer: prof. dr hab. Maria Malicka BaszkiewiczReferences:G. Zubay ,Biochemistry, wydane 1993, WCB Brown Publishers;W. M. Southerland, Biochemistry, wydanie 1990, Churchill Livingstone Inc.;D. Voet, J.G. Voet, Biochemistry, wydanie 1995, John Wiley & Sons Inc.


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Plant PhysiologyFIZROS30 hrs lectures, 30 hrs lab coursesII year, winter semester6 ECTS

Physiology of plant cell (osmotic, turgor and water potential and water movement between cells,aquaporins in plant cell, metabolic compartmentation of the cell, energy transformations inbiomembrane systems, solute transport mechanisms in plasma membranes). Water relationships inplant (water availability in soil, pathways of water transport across the cortex of root, transpiration asthe main motion in water uptake and long-distance transport, the role of root pressure in active uptakeof water). Mineral nutrition of plants (nitrogen sources for plants, nitrogen-fixation system, biochemistryof nitrogen fixation, assimilation of NO3

-and NH4

+-incorporation into amino acids, sulfate assimilation,

functions of mineral nutrients in plant metabolism). Photosynthesis (photosynthetic active pigmentsystem of chloroplast, photosynthetic electron and proton transport, structure of PSI and PSII, Q-cycle,PSII and water photolysis, mechanism of photophosphorylation, biochemical reactions ofphotosynthesis in C3, C4 and CAM plants, environmental regulation of photosynthetic activity,molecular basis of photorespiration). Respiratory metabolism (respiratory metabolism of sucrose,metabolism of storage protein, lipid breakdown and regulatory interactions between glyoxylate cycleand gluconeogenesis during fat-seeds germination, CN

-or SHAM sensitive electron transport and ATP

synthesis, the role of alternative electron transport rout). Plant growth and development (basic aspectsof growth and development, synthesis and degradation of plant hormones, mechanism of hormoneaction, photomorphogenesis, mode of phytochrome action in photomorphogenesis, flower formationand photo- and thermoperiodism). Plant movements (types of movements, molecular basis ofphototropism and gravitropism, mechanism of turgor movements). Stress physiology (constitutive andadaptive resistance to water stress, osmoregulators and osmoprotectors in salt stress, resistance toheat and cold stress, biogenic stress and role of jasmonate in induction of disease resistance).Lecturer: dr hab. prof. Grayna Kobus (Institute of Botany)References:Zurzycki J., Michniewicz M. 1986 Fizjologia Rolin. PWRiLTaiz L., Zeiger E 1991 Plant Physiology. Springes-Verlag Berlin Heidelberg New York

Animal PhysiologyFIZZWI30 hrs lectures, 30 hrs lab coursesII year, spring semester6 ECTS

Excitable cell: neuron, striated muscle, smooth muscle. Input and output of information: transmissionthrough synapses, neurotransmiters, structure and function of receptors. Senses: smell, taste, touch,sound receptors, sense of balance, thermoreceptors, photoreceptors, nocyceptors. Processing ofinformation: CNS, ANS, endocrine system, hormones. Basic physiological phenomena: respiration,circulation. digestion. Homeostasis: salt and water balance. glucostasis, thermoregulation. Biologicalrhythms: rhythm of sleeping and waking, menstrual cycle. The effects of alcohol, drugs andenvironmental pollution on physiological phenomena.Lecturer: prof. dr. hab. Andrzej Dugaj (Institute of Zoology)References:Gill J. 1987. Zarys fizjologii porwnawczej zwierzt. PWN.WarszawaGanong W.F. 1994. Fizjologia. PZWL. WarszawaSchmidt-Nielsen K. 1992. Fizjologia zwierzt. PWN. Warszawa


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Advanced and Specialization Courses

EnzymologyENZY30 hrs lectures, 60 hrs lab coursesIII year, winter semester7 ECTS

Collision and transition state theories. Basic equations of enzyme kinetics (Michaelis-Menten, Briggs-Haldane). Competitive inhibitors and other types of enzyme inhibition. Types of chemical catalysis.Methods of determination of kinetic parameters and their meaning. The influence of pH, ionic strengthand temperature on enzyme activity. Catalytic mechanism of serine proteinases, carboxypeptidase Aand ribonuclease. Mechanisms of lowering of the transition state barrier (induced fit, transition statestabilization).Thermodynamics of protein-protein/ligand/substrate recognition. Chemical modificationsof enzymes. Conformational and chemical properties of amino acid side chains. Basic informationsabout spatial structure of proteins and methods of its determination. Relationship between structureand function of some enzymes. Energetics of proteins: hydrogen bonds, van der Waals andelectrostatic interactions, hydrophobic effect.Lecturer: prof. dr hab. Jacek OtlewskiReferences:

Witwicki J Ardelt W 1989 Elementy enzymologii. PWN. WarszawaFersht A 1985 Enzyme structure and mechanism. Freeman, San Francisco

Animal Cell and Tissue CulturesHODKOZ15 hrs lectures, 30 hrs lab coursesIII year, spring semester2 ECTS

The course gives the general - theoretical and practical knowledge of animal cell culture as analternative research models. The program consists: information on organization and equipment of cellculture laboratory, sterile work conditions, primary and secondary cell cultures techniques, methods oftissues disintegration, cultures on solid and fluid substratum, media composition, cell lines, cryo-

preservation. Hepatocyte as a biomedical model in vitrocytotoxicity assay. The effect of drugs used incancer therapy on cytoskeletal organization of the culture fibroblasts L1210 leukaemia lymphocytesand hepatocytes.Lecturer: prof. dr hab. Maria Malicka-BaszkiewiczReferences:Culture of Animal Cells. A manual of basic technique. R. I. Freshney 1994 Willey-Lis Inc.

Plant Cell and Tissue CulturesHODKOR15 hrs lectures, 30 hrs lab coursesIII year, spring semester2 ECTS

History and basics of in vitro culture. Techniques of clonal propagation. Dedifferentiation andtotipotency of cells. Models of plant regeneration: embryogenesis and organogenesis. Suspensionculture initiation, isolation, subculture, and selection of mutants. Somato-clonal variation, culturetechniques, methods of selection, genetic causes of somaclonal variation. Haploids production process of androgenesis and gynogenesis, the use of natural anomalies of plant fertilisation andembryo development. Protoplast fusion and its products: somatic hybrids. Methods of genes transfer vectorial and direct transformation of plants. Cryopresevation and storage of germplasm. Secondarymetabolism in plant tissue culture. Mycorrhiza and in vitro culture.Lecturer: prof. dr hab. Krystyna Kromer (Plant Tissue Culture Laboratory, Botanical Garden).Peferences:Zenktler M.; Hodowla komrek i tkanek rolinnych, PWN, Warszawa, 1984Biekowska-Mochtak E.; Zastosowanie kultur in vitro w uprawie i hodowli rolin. PWR i L, Warszawa,1984

Malepszy S., Niemirowicz-Szczytt K., Przybecki Z.; Biotechnologia w genetyce i hodowli rolin. PWN,Warszawa, 1989Kopcewicz J, Lewak S.; Podstawy fizjologii rolin. PWN, Warszawa, 1998


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Molecular Principles of Genomes EvolutionMOLEWGEN15 hrs lectures, 60 hrs lab coursesI year master, winter semester6 ECTS

Origin and structure of procaryotic, eucaryotic and organelle genomes. Physical techniques formapping of genomes. Sequencing of genomes. Mutations and recombinations as basic processes ofgenome evolution. Spontaneous and induced mutations. DNA repair. Homologous and localizedrecombinations. Transposomes and rethroelements. Stoichiometric variations in heteroplasmicgenomes. Localization of genomes in DNA sequences. Determination of the gene function. How newgenes are formed. Intracellular transfer of genes. How new genes are acquired from other species.The origin and types of introns. Non-coding DNA. Posttranscriptional (editing) and posttranslational(splicing) alternations of genetic information. Molecular phylogenetics.Lecturer: dr hab. prof. Hanna Jaska, dr hab. Ryszard RzepeckiReferences:Current scientific publications

Genetic Manipulations in Laboratory PracticeMANGEN15 hrs lectures, 15 hrs lab coursesI year master, spring semester3 ECTS

Expression of eucaryotic proteins in bacterial cells. The choice of the expression system (types ofexpression systems, properties of plasmids, choice of bacterial cells and plasmids for DNApropagation and subcloning). Standard expression procedures and their optimalization for given tasks.Non-typical applications and solving the problems related to. Exogenic protein expression in eucaryoticcells. Systems of the expression in D. melanogaster cells and their applications. The choice of thesystem related to the task of the experiment (plasmid, fluorescent or immunological markers,additional protein sequences). Baculovirus system. Transgenic organisms why and how they areformed. Transformation, transfection, cotransformation and cotransfection. Genetic manipulationsfor decrease of the expression of the given protein. RNAi technique. Homologic recombination.Transformation with the use of antisense RNA. Non-genetic methods for studying of protein functions.Permeabilized cells. Microinjections of RNA. In vitro nuclear assembly technique.Lecturer: dr hab. Ryszard RzepeckiReferences:Current scientific publications

GenomesGENOM15 hrs lectures, 105 hrs lab coursesI year master, winter semester7 ECTS

Organization of genetic material in bacteria. Plasmids. Biogenesis of mitochondria and chloroplasts.

Organization of mitochondrial and chloroplast genomes; evolutionar dymamics of these genomes.Replicon as the unit of replication. Mutagenesis, repairment and recombination of DNA. Structure andfunction of procaryotic and organelle genomes. Regulation of gene expression in procariota,mitochondria and chloroplasts. Nuclear control of organelle genomes. Nucleus ultrastructure and itsrelationship to particular functions of the nucleus. Nuclear matrix proteins and the modulation of theirinteractions with chromatin and/or DNA/RNA. Eucaryotic genomes the size, repeat and uniquesequences. Exons and introns. The number and array of genes. Pseudogenes. Nucleosomes,chromosomes and chromatin organization in cell cycle. Replicon. DNA replication DNA polimerases,PCNA, RFC, other proteinaceous factors. Phage T4 replication system. Restriction and DNAmodyfication system. Recombination. Transposomes. Initiation of transcription elements and types ofpromotor, DNA-dependent RNA polymerases, transcription factors, transcription and DNA repair.Regulation of transcription; induced factors, DNA-binding domains, steroid hormon binding domains,momeodomains, helix-loop-helix, leucine locks, methylation and demethylation. RNA processing andtransport. Nuclear splicing sites of splicing, snRNA, splicesome, group I and group II introns,alternative splicing, yeast tRNA splicing. Catalytic RNA autosplicing of group I introns, secondarystructure, ribozymes, protein-coding introns. RNA editing. DNA rearangement yeast active and nonactive loci, Ti plasmid, plant genome.


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Lecturer: dr hab. prof. Hanna Jaska, dr hab. Ryszard RzepeckiReferences:Benjamin Lewin Genes VI Oxford University Press, 1997.Current scientific publications

Structure and Function of Biological MembranesBIOMEM15 hrs lectures, 75 hrs lab coursesI year master, winter semester7 ECTSPeripheral and integral membrane proteins. Methods of biomembrane isolation. Methods of isolation,crystallization and reconstitution of membrane proteins. Application of chemical and enzymaticlabeling, antibodies and proteolytic enzymes in determination of membrane disposition of proteins.Cross-linking reagents. Examples of the detailed structure of some membrane proteins. Computeranalysis of primary structure and hydrophobic labeling in analysis of membrane disposition of proteins.Proteins covalently attached to lipids. Models and mechanisms of insertion of proteins into themembrane. Peripheral membrane proteins. Interaction of peripheral membrane proteins with intrinsicmembrane domain. Erythroid and nonerythroid spectrin. Pathologies connected with the geneticdefects of membrane proteins. Membrane transport. Passive and active transport, facilitated diffusion.Channels, pores and carrier. Membrane ATP-ases (Type P, F, and V). ATP-ases carrying organicanions and ATP-ases of ABC-type. Examples of proteins responsible for cell-to-cell or cell-toextracellular matrix adhesion.Lecturer: prof. dr hab. Aleksander SikorskiReferences:Genis, Biomembranes, 1988, SpringerAlberts, Bray, Lewis, Raff, Roberts & Watson, Molecular Biology of the Cell, 1994, Garland Publ.Lodish, Baltimore, Zipursky, Matsudaira & Darnell,Molecular Cell Biology, 1995, Sci. Am. Books

Structure and Function of ProteinsSTRUFUB15 hrs lectures, 75 hrs lab coursesI year master, winter semester7 ECTS

Functional survey of protein structures. Methods which facilitate investigation of structure-functionrelationship: structural analysis, kinetic and thermodynamic relationships, directed and randommutagenesis, protein libraries. protein-protein recognition. Proteins which recognize DNA and RNA;zinc fingers, leucine zippers, repressor proteins. proteins of immune system: immunoglobulins andMHC. Structure-specificity relationship of serine proteases. Growth factors. Minimization of proteins.Lecturer: prof. dr hab. Jacek Otlewski

Polyketide AntibioticsANTPOLI15 hrs lectures, 15 hrs lab coursesI year master, spring semester3 ECTS

Secondary metabolism definitions. Cellular localization of pathways. Products of the secondarymetabolism and their importance for humans. Polyketide and polyketide-protein antibiotics.Biotechnology of polyketide antibiotics. Antibacterial antibiotics. Antifungal antibiotics. Anticancerantibiotics.Lecturer: prof. dr hab. Arkadiusz KozubekReferences:Chmiel A., Grudziski S. Biotechnologia i chemia antybiotykw, PWN 1998Current scientific literature


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PhotobiologyFOTBIO15 hrs lecturesI year master, spring semester, lecture of choice2 ECTS

Light and color in the nature and scientific laboratory. Photophysical and photochemical interaction oflight with biological macromolecules. Plant photoreceptors: molecular basis of phytochrome systemaction - reception, transfer and control of information; role of chlorophylls, their precursors andderivatives in the capture, migration and transfer of energy. Bacterial and animal photoreceptors:structure, function and mechanism of action of bacteriorhodopsin and rhodopsin. Application ofmolecular photobiology: in medicine - photosesibilizers in diagnostics and treatment of cancer; inbiotechnology and preservation of nature - monitoring, production and biomass utilization; in bionics -immobilized photoreceptors as transmitters of energy and information.Lecturer: dr Barbara BerezaReference:Biofizyka dla biologw, 1987, red. W.Leyko, PWN, Warszawa

Biology of MitochondriaBIOMIT15 hrs lecturesI year master, spring semester2 ECTS

Recent data on mitochondrial structure. Genetic information and inheritance of mitochondrial genes(human, yeast, plant). Unique properties of replication, transcription and translation in mitochondria.Incorporation of nuclear and mitochorndrial-genome encoded proteins into the membranes.Degradation of proteins in mitochondria. Processing and ATP-dependent proteases. Coordination ofnuclear and mitochondrial gene expression. Cytoplasmic male sterelity molecular principles.Structure-function analysis of oxidative phosphorylation complexes. Mitochondrium as the source ofthe active oxygen species. Mitochondrial theory of aging. Mitochondrion and apoptosis.Lecturer: dr hab. prof. Hanna JaskaReferences:Brennicke, A., Kuck, U. (1993) Plant mitochondria. VCH-Weinheim

Liposome TechnologyLIPOTECH15 hrs lectures, 75 hrs lab coursesI year master, winter semester6 ECTS

Chemistry of lipids and liposomes. Structure of amphiphilic aggregates. Preparation of liposomes -thin-film hydration methods, injection methods, demulsification methods, other methods. Liposomeproperties. Liposome formation and characterization. Liposomes in basic sciences: biochemistry,biophysics, chemistry and theoretical sciences, applications in the studies of the evolution of life.Liposomes as drug delivery system in pharmacology and medicine. Liposomes in the treatment of

inflammations and infectious diseases. Liposomes as immunoadjuvants. Liposomes in anticancertherapy. Liposomes in cosmetics. Liposomes in genetic engineering. Liposomes in food industry andecology. Industrial manufacturing of liposomes.Lecturer: prof. dr hab. Arkadiusz KozubekReferences:G. Gregoriadis, 1993, Liposome Technology (Vol. I-III). CRC Press, Boca RatonD.D. Lasis, 1993, Liposomes: From Physics to Applications. Elsevier, AmsterdamD. D. Lasic, Y. Barenholz, 1995, Handbook of Nonmedical Application of Liposomes, CRC PressJanoff A. S. 1999, Liposomes. Rational Design. Marcel Dekker, New YorkBasu S. C., Basu M. 2002, Liposome, Methods and Protocols. Humana Press, New York


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Crystallographic Analysis of MacromoleculesKRYSMAK15 hrs lecturesI year master, spring semester, lecture of the choice2 ECTS

How can we "see" atoms? electron microscopy, tunneling microscopy, atomic forcemicroscopy. Crystal patterns, vector lattices and point lattices. Space groups, space group types,crystal systems. Crystal lattices, reciprocal lattice. Protein crystallization, heavy-atom derivatives.Crystal structure solution and least-squares refinement of the structure. Crystallography ofmacromolecules: peptides, nucleic acids, viruses, ribosomes. The databases: Protein Databank,Cambridge Structural Database. Presenting structures: coordinates, bond lengths, bond angles,torsion angles, thermal parameters, other geometric parameters. Integration of crystallographic resultswith data from other sources: NMR, spectroscopic, molecular dynamic.Lecturer: prof. dr hab. Tadeusz Lis (Institute of Chemistry)References:Voet D., Voet J.G. 1995 Biochemistry, John Wiley & Sons, New YorkCiunik Z. (Ed.) 1996 Instrukcje do wicze z krystalografii , cz 2, Wydawnictwo Uniw.Wrocawskiego

Molecular MarkersMARMOLE15 hrs lectures, 30 hrs lab coursesI year master, spring semester4 ECTS

Types of molecular markers. Markers related to simple polymorphism. Markers related to compositepolymorphism. Genetic and biochemical differences between organisms as molecular markers.Identification of molecular markers with molecular biology and biochemical techniques. Molecularprobes (DNA sequences, monoclonal antibodies). Diagnostic tests for genetic, cancer, infectiousdiseases. Molecular markers in taxononic and phylogenetic research. Markers for mitochondrial DNA.Lecturer: dr Magdalena WooszyskaReferences:Current scientific publications

Proteinases as Regulators of Biological ProcessesPROREG15 hrs lecturesII year master, winter semester2 ECTS

Classification, identification and specificity of proteinases. Multiple biological function of proteinases.Naturally occurring proteinase inhibitors and some selected topics concerning their possible function.Proteinases in blood coagulation and fibrinolysis as an example of cascade reactions. Kininogen andkininogenases. Proteinases in virus infection. Post-translational proteolytic processing and generationof biologically active peptides. Multicatalytic proteinases and ATP-dependent proteolysis. Proteolytic

enzymes in semisynthesis of proteins. The role of proteolytic enzymes in biotechnology.Lecturer: prof. dr hab. Tadeusz WiluszReferences:V.Turk and L.J.Vitale 1981 Proteinases and their Inhibitors: Structure, Function and Applied Aspects.Mladinska Knjiga, Pergamon Press, Ljubljana, OxfordH. Fritz, I. Schmidt and V. Turk 1990 Proteinase Inhibitors and Biological Control (2nd Int. Symp.)Biol. Chem. Hoppe-Seyler, Walter de Gruyter, Berlin, New York


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Biocins and Peptide AntibioticsBIOCANTYP15 hrs lecturesI year master, spring semester2 ECTS

Probiotic bacteria - myth or reality. Biocins - antibacterial peptides; structure and biological properties;lantibiotics - biosynthesis, industrial production and application. Deffensins - occurrance and biologicalproperties. Biologically active peptides from protein hydrolysates - hemocins, caseinomorphins.Antibacterial enzymes - cathepsin G, lysozymes; chemical and biological properties, modifications,

industrial and medical applications. -lactam antibiotic - cyclic amino acid derivatives; biosynthesis,chemical and biological properties, technology of manufacture, enzyme technology of 6-aminopenicyllanic acid and 7 amino cephalosporanic acid as well as their derivatives.Lecturer: prof. dr hab. Antoni PolanowskiReferences:Antibiotics IV. Biosynthesis (J.W. Corcoran Ed.) Springer-Verlag Berlin, Heidelberg,Current scientific publications

Mutagenesis Induced by MetalsMETAL

15 hrs lecturesI year master, spring semester, lecture of the choice2 ECTS

The aim of this lecture is to present the key role of metal ions in supporting life functions, as well astheir toxic and therapeutic properties. The effects of transition metals will be emphasized, becausethese are often neglected in standard biochemistry courses. The issues presented in detail will include,among others: - the role of Zn(II) in formation of biostructures (zinc fingers) - transport, metabolismand functions of copper in the body- metal ion-catalysed radical reactions - the mitochondrial theory ofaging-metal carcinogenesis (Cr, Ni) - the mechanism of action of platinum anticancer drugs.Lecturer: prof. dr hab. Henryk Kozowski (Institute of Chemistry)References:S. J. Lippard, J.M. Berg, Principles of Bioinorganic Chemistry

R. A. Goyer, C. D. Klaassen, M. P. Waalkes, Metal Toxicology

Experimental Techniques in Structural BiologyTECHBIOS15 hrs lecturesI year master, spring semester2 ECTS

Experimental methods for determination of macromolecular structures. Crystallography background,applicationof X-ray diffraction for studying of biomolecules. Two- and tri-dimensional crystals.Crystallization of cytosolic and membraneaceous proteins. Data acquisition methods. Solving thestructures. Nuclear magnetic resonance (NMR). Uni-, di and multi-dimmensional spectra. Enrichmentof the samples with radioisotopes. Heteronuclear spectra. Assigment of the signals and determination

of biopolymer structures. Spectroscopic methods of determination of secondary structures. Circulardichroism. Methods for automatic analysis of data. Infrared spectroscopy. Application for analysis ofmacromolecular structures. Fluorescence. Application of fluorescence for structural analysis ofbiopolymers. Electron crystallography. Application of spectroscopic techniques for determination of thestructure of carbohydrates, lipids and their aggregates. Comparison of experimental techniques withtheoretical methods of macromolecular structure prediction.Lecturer: dr Daniel KrowarschReferences:D. E. McFree, Practical Protein Crystallography. 1993, Academic Press.K. Wuthrich, NMR of Poteins and Nucleic Acids. 1986, John Wiley & Sons.G. D. Fasman, Circular Dichroizm and the Conformational Analysis of Biomolecules. 1996, PlenumPress.J. Twardowski, Biospektroskopia, t. I-V, 1990, PWN


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Fluorescence Techniques and Introduction to Image AnalysisTECHFLU15 hrs lectures, 45 hrs lab coursesI year maste, winter semester5 ECTS

Introduction to fluorescence. Fluorescent probes used in biological sciences. Application offluorescence for determination of lacal physicochemical parameters. Chosen applications offluorescence in the study of biological material. Fluorescence techniques in the studies of multi-component systems. Fluorescence imaging. Examples of probes. Fluorescence markers.Determination of the probe localization. Chosen aspects of biological applications of fluorescence.Computer assisted acquisition and analysis of the images.Lecturer: dr hab. Marek Langner (Technical University Wroclaw)References:Current scentific publications

BionanostructuresBIONANO15 hrs lectures + 15 hrs lecturesI year master, spring semester, II year master, winter semester, lecture of the choice

2 + 2 ECTS

Formation and biological function of supramolecular aggregates. Properties of macromoleculesimportant in formation of aggregates. Formation and properties of lipid aggregates. Protein structureand its meaning in the interactions with biological structures. Chosen methods used in studies ofsupramolecular aggregates. Technological and medical applications of aggregates. Biological matteras aggregation structure. Lipid aggregates. Proteins conformational structures. DNA as linearpolyion. Amphiphilicity and partition coefficient. Multimolecular aggregates. Macromolecular aggregatesas carriers of drugs and genetic material.Lecturer: dr hab. Marek Langner (Technical University Wroclaw)References:Current scientific publications

Posttranslational Steps in Protein BiosynthesisPOMOBIAL15 hrs lecturesI year master, winter semester2 ECTS

Chloroplasts structure, six different location for proteins in chloroplast, their proteincomposition. Chloroplast proteins coded for by chloroplasts DNA, Chloroplast proteins coded for bynuclear DNA. The chloroplast genome, structure and function. Structure and function of thechloroplastic protein import apparatus of the envelope. Translocation of protein across chloroplastenvelope: transit peptides, cytosolic factor, energetics of import, stromal processing peptidase,insertion of prosthetic groups, assembly of active complexes. Targeting of protein into or across thethylakoid membrane - a multitude mechanisms. Methods of studies of protein transport into

chloroplasts; preparation of precursor protein: in vitrotranscription and translation of cloned precursorgene or overexpression in E.coli. Protein import by isolated chloroplasts, protein import by isolatedthylakoids. Mitochondrial proteim import. Protein targeting to the endoplasmic reticulum membranes.Import of protein into nucleus. Secretion of protein by bacteria. Similarity of the protein transport inbacteria and chloroplasts: SecA dependence, membrane potential dependence, spontaneoustransport.Lecturer: dr hab. prof. Andrzej SzczepaniakReferences:Current scientific publications


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GlycoproteinsGLIKOP15 hrs lecturesI year master, spring semester2 ECTS

Structure of glycoproteins. Glycoside bonds in glycoproteins. Biosynthesis of N-glycosidicglycoproteins. Biosynthesis of O-glycosidic glycoproteins. Glycosyltransferases. Inhibitors ofglycosylation. Regulation of glycosylation. The role of oligosaccharide moieties in glycoproteins.Proteoglycans. Mucins. Bacterial glycoproteins. Lectins. Structural analysis of glycoproteins. Syntheticglycoconjugates. Glycosylation of recombinant proteins. Medical and pharmaceutical applications ofpolysaccharides and glycoconjugates.Lecturer: dr hab. prof. Wiesaw WtorekReferences:Current scientific publications

Gene BiologyBIOLGEN15 hrs lecturesII year master, winter semester2 ECTS

Fundamentals of gene structure and control. Control of plant gene expression. Transgenic plants.Vectors, gene transfer systems and plant regeneration techniques.Controlling transgene expression.Inactivation of gene expression in plants. Antisense strategies for genetic manipulations in plants.Parameters affecting the activity of antisense RNA. Co-suppression and co-expression of native andintroduced genes, flavonoid genes in Petunia and HMG-CoA reductase in Arabidopsis. Planttransposones and retrotransposones, occurrence, gene activity, amplification, evolution. The role ofbrassinosteroids in plant development. Plant senescence and stress responses. ABA and desiccationresponsive genes. Wound-induced gene expression. The ethylene signal transduction pathway.Manipulating plant metabolism. Plants as bioreactors.Lecturer: prof. dr hab. Jan SzopaReferences:Alberts B., Bray D., Lewis J., Raff M., Roberts K., Watson J.D., Molecular Biology of the Cell 1994,Garland Publ.; DNA cloning vol. I-III, ed. by D.M. Glover, 1987 IRL Press

Methods of Theoretical Analysis and Modeling of ProteinsMETAMOB15 hrs lectures, 15 hrs lab coursesI year master, winter semester2 ECTS

Aminoacid sequence and secondary structure classical methods of prediction of secondary andhigher structures (Chou-Fasman, GOR, Lima). General rules of formation of regular and irregularstructures. Determination of degree of significance of homology in analyzed proteins and nucleotidesequences (review of methods). Algorithms used for comparison of sequences in biological systems.

Variability of proteins and Markovs model of aminoacid substitution. Genetic semihomology algorithm.Statistical and non-statistical analysis of protein sequences - UM, GCM, MDM, PAM, BLOSUM,FASTA, BLAST, SEMIHOM. Multiple alignment - ClustalX, MultAlin, SEMIHOM. Graphicalinterpretation Dot matrix of sequences - Dotplot, DotLet, SEMIHOM. Description and application ofchosen computer programs for structure prediction and comparison of proteins and nucleic acids(Predict7, HCA-Plot, Rasmol, WebLab Viewer, Protein Adviser, SEMIHOM, ProtSA, Antheprot, Macaw,ClustalX). Protein data bases and web servers (ExPASy, SWISS-PROT, NCBI, EMBL, PDB,GenBank)Lecturer: dr hab. Jacek Leluk


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Chosen Aspects of Gene TherapyTERGEN15 hrs lectures, 30 hrs lab coursesII year master, winter semester6 ECTS

Recombinant DNA techniques and their applications mutagenesis in vitro. RLFP technique in genemapping and diagnostics of genetic diseases. Genetics and rethrogenetic. Alteration of gene activity(over-expression and knockout). Localized cloning. Recombinant DNA technology in detection ofmutated alleles. Clone selection by functional complementation. Manipulations in genes (procaryotic,yeast, plant, animal organisms). Gene replacement and transgenic organisms. Problems, advantagesand possible drawbacks. Ethical problems. Methods for introduction of the exogenous genes (DNA)into the cell and tissue. Viral methods: adenoviruses, viruses associated with adenovirus (AAV), HSVvirus. Plasmid vectors. Physical methods: microinjections, infusion, DNA-calcium phosphateprecipitates, DNA-lipid complexes, DNA-polylysine complexes, genetic gun. Review of plasmids,viruses, rethroviruses and rethrotransposones used in gene therapy. Cassification. Life cycles,integration with host genome, propagation etc. Design of rethroviral vectors. Applications in researchand medicine. Gene therapy in the traetment of cancer. Problems, limitations and side effects.Lecturer: dr hab. Ryszard RzepeckiReferences:Current scientific publications

PCR Method Theory and Practical ApplicationsPCR15 hrs lectures, 45 hrs lab coursesI year master, winter semester5 ECTS

History of discovery of the PCR reaction. Background of PCR. Optimization of typical PCR process.Hot-start PCR. Equipment. Qualitative and quantitative PCR. PCR in mutagenesis. PCR in medicaldiagnosis, forensic medicine and in studies of the relationship between individuals. RT-PCR. Reversedtranscriptases: specificity, thermostability and other properties. Qualitative and quantitative RT-PCR.Competitive RT-PCR. Amplification of 5 i 3 ends of mRNA RACE technique.

Lecturer: dr Teresa OlczakReferences:Current scientific publications

Nonliposomal Drug CarriersNIELINOS15 hrs lectures, 30 hrs lab coursesI year master, spring semester4 ECTS

How drugs are degraded and removed from organism. How to direct drug to the right place inorganism. Physical and chemical barriers. Micro- and nano- emulsions as drug carriers. Polylacticnanospheres: preparation and applications. Polymeric carriers. Monoclonal antibodies as selective

carriers in cancer therapy. Biochips, nanotubes, dendrimers and fullerenes in transport andmicrodosing of drugs. Science-Fiction in pharmacology.Lecturer: dr Jerzy GubernatorReferences:Current scientific publications

Mechanisms of Transport in BacteriaMETRABA15 hrs lecturesII year master, winter semester2 ECTS

Diffusion and facilitated diffusion, porins. PEP-PTS system. Aquaporin. Transport dependent on

plasmid proteins. Resistance of bacteria upon chemical factors dependent on mechanisms oftransport. ATP-dependent transport (structure, mechanism, energetics). Uniport, symport and antiportenergetics. Model systems for studying transport in bacteria.Lecturer: dr Jarosaw Krliczewski


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BioenergeticsBIOENER15 hrs lecturesI year master, winter semester2 ECTS

Biophysics of complex systems: elements of nonequilibrium thermodynamics in biology. Oscillationsand chemical waves in multienzymatic reactions. Simulation of multistep dynamic processes.Acquisition, transmission and analysis of information in biological structures. Spatial organization ofbiopolymers and techniques used for its study. Dynamic properties of macromolecules. Transitions ofelectrons in biopolymers. Background, molecular organization and dynamics of biological membranes.Red-ox processes, mechanisms of transport of electrons and protons, migration of energy inbiostructures. Bioenergetics of mitochondria and chloroplasts. Transformation of electrochemicalgradient of ions to ATP. Oscillations in living organisms.Lecturer: dr hab. prof. Andrzej SzczepaniakReferences:Biofizyka dla biologw, red. M.Bryszewskiej,W. Leyko, 1995, PWN, WarszawaNicholls DG, Ferguson SJ, 1995 Bioenergetyka 2, PWN, WarszawaBiophysics, W.Hoppe, W.Lohmann, H.Markl, H.Ziegler, Springer Verlag 1983

Analytical Methods in Protein and Glycoconjugate ChemistryGLIKOKON15 hrs lectures, 45 hrs lab coursesII year master, winter semester2 ECTS

Peptide maps. Modification of polypeptide amonoacids. Chemical and enzymatic proteinfragmentation. Determination of aminoacid composition and sequence in polypeptides. HPLC, FPLCand low pressure chromatography. Quantitative analysis of sugars in glycoproteins. Isolation of glycanscovalently bound to protein. Analysis of glycan structure.Lecturer: dr Mariusz OlczakReferences:Current scientific publications

Intracellular and Extracellular Mechanisms of RegulationZEWEMER15 hrs lecturesI year master, spring semester, lecture of choice2 ECTS

Cellular signaling interactions of ligands with receptors. Great number of receptors is localized inbiomembranes. Main strategies of cell-cell communication. Transduction of signals via G-proteins.Receptors with enzymatic activities guanyl cyclases, tyrosine kinases, tyrosine phosphatases.

Domains: SH2, SH3, plextrin. Protein cascades related to Ras proteins and MAP kinases. Elements ofprotein cascades related to oncogenesis, apoptosis and morphogenesis. The role of variousmembrane structures (rafts, caveoles). Adaptation of the target cells. The logic of cellular signaling analogies to computer neuronal networks.Lecturer: prof. dr hab. Aleksander F. SikorskiReferences:Current scientific publications

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