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

General courses

English

I year winter semester 30 hrs (3 ECTS), passing test

I year spring semester 30 hrs (3 ECTS), passing test

II

year winter semester 30 hrs (3 ECTS), passing test

II

year spring semester 30 hrs (3 ECTS), egzam, level D,

Seminars in English

III

year winter semester 30 hrs (3 ECTS), passing test

III

year spring semester 30 hrs (3 ECTS), passing test

I year master winter semester 30 hrs (3 ECTS), passing test

I 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 the international scientific laboratories, based on chosen original research papers; increasing the knowledge of the specialized scientific dictionary and gaining the knowledge of presenting of the work and discussing it in English.

Sport activities

I year winter semester 30 hrs (0 ECTS), passing test

I year spring semester 30 hrs (0 ECTS), passing test

Humanistic Courses

Philosophy

II year master spring semester 15 hrs lectures, 2 ECTS

Economy

II year master spring semester 15 hrs lectures, 2 ECTS

Bioethics

II year master spring semester 15 hrs lectures, 2 ECTS

Law Protection of Intellectual Properties

II year master spring semester 15 hrs lectures, 2 ECTS

Economics of Production

II year master spring semester 15 hrs lectures, 2 ECTS

Economy in Company

II year master spring semester 15 hrs lectures, 2 ECTS

Informatics

INF 15 hrs lectures,30 hrs lab courses

II year winter semester

4 ECTS

Informatics and computers. Expression of a problem, searching the methods to solve it, constructing the algorithm and its realisation. Elementary comprehension of informatics. Computer - how does it work? Data storage and processing. Computer programs, operating system, translators, executable user programs. Elements of logic and computer arithmetic. Computer languages and compilers. Block schemes of algorithms. Examples of algorithms and their analysis. Recurent algorithms. Structuring of the 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

Bioinformatics

BIOINF

15 hrs lectures

I

year master spring semester

2

ECTS

Analysis and processing of information. The structure of the data base and its use. Access and use of available 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 nucleic acid structures. Molecular dynamics and quantum mechanics. Computer assisted analysis of the protein-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

Mathematics

MAT

15 hrs lectures, 30 hrs lab courses

I year winter semester

5 ECTS

Functions of one variable. Maximum and minimum functions of two variables. Integrals of functions of one variable. Elements of ordinary differential equations. Elements of linear algebra. Lecturer: prof. dr hab. Marek Bożejko (Institute of Mathematics) References:

F. Leja, Rachunek różniczkowy i całkowy, PWN, Warszawa 1997 I. Gelfand, Algebra liniowa, PWN, Warszawa 1977.

Statistics in Analysis and Planning of the Experiment STAT

15 hrs lectures, 45 hrs lab courses

I year winter semester

5 ECTS

Probability calculations and statistics. Methods used for processing of empirical data. Statistical methods to determine the "best" equation which fits a set of observations. Comparing sets of empirical data; Student’s t-test, significance of the differences. Relationships between variables, correlations, regression. Deterministic and probabilistic models of chosen processes present in the nature. Modeling of the natural processes.

Physical Methods in Biology MEFIB

30 hrs lectures, 60 hrs lab courses

I year winter semester

5 ECTS

Discussion of measuring error, theory of incidental error. Mean values, index dispersion. Interrelation between variable, correlation factor, linear regression. Accuracy and repeatability of methods. Physical basis and application in biology of absorption and emission spectroscopies, flame photometry refractometry, 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, physical basis and application in fractionation of biological materials using centrifugation, ultracentrifugation and centrifugation in gradient density. Lecturer: dr hab. prof. Andrzej Szczepaniak References:

Biofizyka dla biologów, red. M.Bryszewskiej,W. Leyko, 1995, PWN, Warszawa Bioenergetyka 2, Nicholls DG, Ferguson SJ, 1995 PWN, Warszawa

Biophysics

BIOFIZ

30 hrs lectures, 60 hrs lab courses

II year winter semester + II year spring semester

3 + 5 ECTS

Methods for the studies of biopolymers. Spectroscopic analysis of proteins and nucleic acids. The first law and the second law of thermodynamics, free energy and free enthalpy. Chemical work, electrical work and chemical potential. Thermodynamics of active transport. Redox reaction in biology, direction of redox reactions, concentration dependence of the oxidation-reduction potential. Factors affecting the redox potential. Biophysics of lipids, liquid crystal structure, phase transition, monolayers, liposomes. Biological membranes, structure and function, integral and peripheral membrane proteins. Transport across the membrane, diffusion, natural and induced permeability (ionophores, uncouplers). Proteins mediated transport, symport, uniport, antyport. Symport of sugars and amino acids, periplasmic transport 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 are inconsistent with the chemiosmotic theory. Mitochondrial respiratory chain, complexes I, II and III. Cytochrome oxidase, proton translocation. Light reaction in photosynthetic bacteria, connection with respiratory chain, bacterial photosynthetic reaction center. Photosynthetic electron transport chain in higher plants, photosystem I, photosystem II, oxygen evolution. Complex b 6 f, the Q cycle in mitochondria and chloroplast. Photosynthetic antenna, light energy transfer. Bacteriorhodopsin, structure and function. ATP-ase, structure and function, DG of ATP hydrolysis. Physical and chemical properties of DNA, parameters for description of DNA structure. Lecturer: dr hab. prof. Andrzej Szczepaniak References:

Biofizyka dla biologów, red. M.Bryszewskiej,W. Leyko, 1995, PWN, Warszawa Nicholls DG, Ferguson SJ, 1995 Bioenergetyka 2, PWN, Warszawa

General and Analytical Chemistry CHEM

30 hrs lectures, 30 hrs lab courses

I year winter semester

6 ECTS

Electron configurations of atoms and the periodic table of elements. Chemical bonding: ionic lattices and the Born-Haber cycle; the covalent s, p and d bond - molecular orbital theory, bonding and antibonding 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 chemical equilibrium. Activation energy and catalysis. Acid-base equilibria: pH, hydrolysis, buffer solutions. Solubility equilibria: the solubility product. Problems of chemical qualitative analysis. Redox reactions and standard electrode potentials. The coordination compounds and their applications in chemical analysis. 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, Warszawa Chang R. 1991 Chemistry. McGraw-Hill, Inc., New York

Organic Chemistry CHO

45 hrs lectures, 45 hrs lab courses

I year spring semester

10 ECTS

The structural theory (chemical bonds, molecular and atomic orbitals, orbital hybridization, polar covalent bond, inductive effects, homolysis and heterolysis of covalent bond, delocalized bonds and resonance theory, acids and bases in organic chemistry). Molecular structure and physical properties of organic compounds. Stereochemistry (chiral molecules, configuration, conformation, stereoisomers, stereospecific reactions). Structure, nomenclature, synthesis and chemical properties of monofunctional organic compounds (alkanes, alkenes, alkynes, arenes, haloalkanes, organometalic compounds, 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 and proteins, 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 York Mastalerz P. 1996 Podręcznik chemii organicznej. Wydawnictwo Chemiczne. Wrocław

Biophysical Chemistry CHFIZ

30 hrs lectures, 30 hrs lab courses

I year spring semester

6 ECTS

Thermodynamics: properties of gases, work, heat, laws of thermodynamics, state functions, thermo- chemistry, chemical equilibria. Electrochemistry: solutions of electrolytes, conductivity, electrochemical cells, electrodes, kinetics of electrode processes. Phase equilibria: phase transitions of pure substances and simple mixtures, „phase” rule, two and three components systems. Chemical kinetics:

rates of chemical reactions, kinetics of complex reactions, molecular reaction dynamics. Intermolecular interactions. Introduction to molecular spectroscopy: interaction of the electromagnetic radiation with the molecule, selection rules, methods of optical and resonance spectroscopy. Lecturer: prof. dr hab. Jacek Otlewski References:

L. Sobczyk, A. Kisza, 1985 Chemia fizyczna dla przyrodników, PWN Warszawa; Z. Kęcki, 1975 Podstawy spektroskopii molekularnej, PWN Warszawa; L. Sobczyk, A. Kisza, K. Gatner, A. Koll, 1982 Eksperymentalna chemia fizyczna, PWN Warszawa.

Bioprocess Engineering BIOPRO

15 hrs lectures

II year master, winter semester

2 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. inż. Andrzej Noworyta (Institute of Chemistry) References:

Aiba S., Humphrey

Bailey J.E., Ollis D.F. Biochemical Engineering Fundamentals. 2 ed. McGraw-Hill Book Co. New York: 1986.

Inżynieria biochemiczna. Wyd. 2. uzup. WNT Warszawa: 1977.

Protein Engineering INZBK

15 hrs lectures, 30 hrs lab courses

I year master, spring semester

4 ECTS

Protein engineering and methods used in this field. Protein structure: solvent accessible area, packing density of protein core, secondary structure of proteins: a-helix b-sheet and b-turn. The role of water in determining protein structure (surface water and integral water). Additive effects in protein chemistry. Protein - protein recognition: protein proteinase inhibitor-serine proteinase as a model system (binding of different amino acid side chains in S1 pocket of proteinases), structure of the human growth hormone-growth hormone receptor: alanine scanning, effects of single amino acid substitutions. Antibody-antigen interaction: structure and thermodynamics. Structural stability of proteins: effects of single amino acid substitutions on structure and stability of T4 lysozyme. protein folding problem:

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

Perutz M 1992 Protein Structure, Freeman, New York

Environmental Protection OSRO

30 hrs lectures

III

year, winter semester

3

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 and biological factors in polluting of the environment. Environment and diseases. The role of microorganisms 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 studies References: - as suggested by the lecturer

Methods in Environmental Biotechnology BIOTESRO

15 hrs lectures, 30 hrs lab courses

III

year, spring semester

3

ECTS

Circulation of the matter in the nature. Main human-related factors involved in the degradation of the environment. Pollution of water and classification of the water sources. Biotechnological processes used 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

Biology

BIOL

30 hrs lectures, 30 hrs lab courses

I year, winter semester

4 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. The development of multicellular organisms -principles of morphogenetic processes in plants. Sources of biodiversity. 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 and fruits (coevolution with insects).

Animal world organization - basis of systematics (criteria of homology, population, taxon, category, genotype, phenotype). Characteristic of Chordata. Ewolution of Vertebrates and philogenetic relations 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 its

derivatives, the skeleton, the alimentary canal and its derivatives, the circulatory system, the urogenital system and nervous system. Histology of organs. Biology and ecology of vertebrates. Lecturers: dr hab. Danuta Kwiatkowska, dr Aurelia Pawłowska-Indyk (Institute of Botany and Institute of Zoology) References:

Hejnowicz Z. Anatomia i histogeneza roœlin 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.

Grodziński 1979 Zoologia przedstrunowce i strunowce

N.

Bobriński, B. Matwiejew, A. Bannikow 1972 Zoologia strunowce

H.

Szarski 1987 Anatomia porównawcza kręgowców

K.

Ostrowski 1988 Histologia

K.

Sembrat 1981 Histologia porównawcza zwierząt

Hejnowicz Z. Anatomia i histogeneza roślin 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.

Microbiology

MIKROB

30 hrs lectures, 30 hrs lab courses

II year, spring semester

6 ECTS

Size, shape and structure of cells of microorganisms belonging to three domains: Eucaryota, Bacteria and Archaea. Genome organization and means of genetic information transfer in these groups. Metabolism – vast metabolic plasticity, diversity of ecological niches and nutritional types among procaryotic microorganisms. Interactions between microorganisms, aerobic and anaerobic trophic chains in ecosystems. C,N, S, P cycles in nature. Microorganisms in biotechnology and large scale production. Chosen aspects of microbial pathogens and microbial diagnostics. Relationship between microorganisms and human and aninal organisms (intestinal flora). Applications of genetic engineering in 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, Życie bakterii. PWN. Warszawa Trends in Biotechnology Annual Review of Microbiology

Structure and Function of Proteins and Shugars STRUBIAC

30 hrs lectures, 60 hrs lab courses

I year, spring semester

9 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. Wiesław Wątorek References:

L.

Stryer, Biochemia, PWN 1997,

R.

H. Garrett, C. M. Grisham, Biochemistry, Saunders College Publ. 1999, 2000

Structure and Function of Lipidic Compounds STRULIP

15 hrs lectures, 15 hrs lab courses

I year, spring semester

3 ECTS

Definitions of lipids. Chemical structure of lipidic compounds and their classification. Vitamins soluble in fats. Steroids and steroid hormons. Prostaglandins, thromboxanes and leucotrienes. Polyketide compounds. Amphiphiles. Self-assembly of lipids into the aggregates. Bilayer as one form of aggregates. Biological membranes, natural and model. Liposomes and black lipid membranes. Lecturer: prof. dr hab. Arkadiusz Kozubek References:

R. H. Garrett, C. M. Grisham, Biochemistry, Saunders College Publ. 1999, 2000

Introduction to Nucleic Acid Biochemistry NUCLA

15 hrs lectures, 15 hrs lab courses

I year, spring semester

3 ECTS

Nucleotides and nucleic acids: structural features, conformational variants of DNA, denaturation and renaturation, superhelical structures of DNA, types of RNA, posttranscriptional modifications. Lecturer: dr hab. Ryszard Rzepecki References:

D.Voet/J. Voet, Biochemistry, J. Whiley 1995 rok

L.

Stryer, Biochemia, PWN 1997 rok

R.

H. Garrett, C. M. Grisham, Biochemistry, Saunders College Publ. 1999, 2000

Metabolism of Proteins and Shugars MECUB

30 hrs lectures, 60 hrs lab courses

II

year, winter semester

6

ECTS

Metabolism – general definitions. Glycolysis. Tricarboxylic acids cycle. Transport of electrons and oxidative 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. Wiesław Wątorek References:

L.

Stryer, Biochemia, PWN 1997,

R.

H. Garrett, C. M. Grisham, Biochemistry, Saunders College Publ. 1999, 2000

Metabolism of Lipidic Compounds MELIP

15 hrs lectures, 30 hrs lab courses

II

year, winter semester

5

ECTS

Transport of small and macro molecules across biological membranes. Import of proteins by organelles. Katabolism of triglycerides, phospholipids, fatty acids and steroids. Lipases and phospholipases. 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 in signal transduction. Lecturer: prof. dr hab. Arkadiusz Kozubek References:

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

Metabolism of Nucleic Acids MEKWANU

15 hrs lectures, 30 hrs lab courses

II year, winter semester

5 ECTS

Rules of DNA replication. Structure and types of the replication systems. Bacterial, organelle and eucariotic DNA polymerases. Proteins initiating replication. Regulation of the replication initiation velocity. 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 gene expression. Bacterial, organelle and eucariotic RNA polymerases. Structure of promotors. Formation of

the 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 RNA from nucleus to cytosol. Degradation of RNA. Lecturer: dr hab. prof. Hanna Jańska References:

L.

Stryer, Biochemia, PWN 1997,

R.

H. Garrett, C. M. Grisham, Biochemistry, Saunders College Publ. 1999, 2000

Biochemical Technologies BIOTECH

30 hrs lectures, 60 hrs lab courses

III

year, winter semester

8

ECTS

Microorganisms in biotechnological processes: biology, selection, cultivation, strain improvement, maintenance and storage. Plant and animal cell culture and their technological application in agriculture and industry. Enzyme production - enzymes of plant and animal origin; microbial production of enzymes. Bio-reactors: batch operation, continuous reactors containing freely suspended bio-mass or immobilized bio-mass in suspension, surface and immersing surface reactors, fluidized bed reactors. Flow behavior of fermentation fluids and gas-liquid mass transfer. Downstream processing:

cell separation, flocculation and flotation, filtration, centrifugation, cell disruption, extraction, membrane filtration, ion-exchange and adsorption processes, precipitation reactions, purification, drying. The use of 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 Polanowski References:

Fundamentals of biotechnology (1987). (ed. P. Praeve i in.) VCH Weiheim, FRG. Chmiel A. 1998. Biotechnologia. Podstawy mikrobiologiczne i biochemiczne. PWN Warszawa Biotechnologia zwierząt (1997). (Praca zbiorowa pod red. L. Zwierzchowski, K. Jaszczak i J.A. Modlińskiego) PWN Warszawa. Wybrane zagadnienia biotechnologii roślin (1996). (red. K. Wypijewski) Wyd. Naukowe UAM

Biochemical Preparations BIOPREP

15 hrs lectures, 30 hrs lab courses

III

year, winter semester

4

ECTS

Selecting the material and establishing of the optimal parameters of the extraction. Clarifying and condensing 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, high performance 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 Wilusz References:

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 York

G.Piljac i V. Piljac, 1986, Genetic Engineering. Liquid Chromatography. TIZ Cakovec.

Techniques in Molecular Biology TEBIOM

15 hrs lectures, 30 hrs lab courses

II

year spring semester

3

ECTS

Isolation and purification of total, nuclear, mitochondrial and chloroplast DNA and RNA. Restriction endonucleases and their use. Cloning vectors (plasmid vectors, bactriophage-derived vectors, cosmid vectors, yeast cloning vectors, vectors for higher eukaryota). Cloning and subcloning. Introduction of genes 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. In organello translation. Lecturer: dr hab. prof. Hanna Jańska References:

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 Cell MOK

30 hrs lectures, 60 hrs lab courses

III year, spring semmester

7 ECTS

Procaryotic and Eucaryotic cells. How the cells are studied. Preparation of the specimens for light and electron microscope. Application of antibodies, in situ hybridization. Fractionation of cells. Biological membranes. Principles of membrane transport. Exo- and endocytosis. The compartmentalization of higher cells. Cytosol. Membrane skeleton. Microfilaments, intermediate filaments, microtubules. Cell nucleus, nuclear pores, nuclear matrix, transport of macromolecules into and out of the nucleus. Mitochondria and chloroplasts, structure and transport of proteins. Pe- roxisomes. Smooth and rough endoplasmic reticulum; functions, Membrane biosynthesis. Golgi apparatus and its role in carbohydrate components biosynthesis. Processing of the proteins during the formation of secretory vesicles. Lysosomes. Cell junctions. Extracellular matrix. Cell adhesion. Cell signaling. 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 cancer cells. Lecturer: prof. dr hab. Aleksander F. Sikorski References:

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

Genetics

GENET

30 hrs lectures, 30 hrs lab courses

II

year, spring semester

6

ECTS

Classical genetics, including Mendel’s laws and exclusions; Gene mapping. Molecular genetics (structure, expression, regulation, variability of genes and mutagenesis in bacteria, yeast, plant and animal cell). Background of the genetic engineering. Human genetics (genetic diseases and their treatment) and chosen aspects of immunogenetic. Cancers and mechanisms of their generation. Basic principles of population genetics, Hardy-Wieberg’s law and factors affecting the balance, including molecular evolution. Lecturer: prof. dr hab. Stanisław Ułaszewski (Institute of Microbiology) References:

Klug W. S., Cummings M. R. Concepts of Genetics Lasota Z. (red), Bilogia molekularna. Informacja genetyczna. PWN 1987, Węgleński P. (red), Genetyka molekularna. PWN 1995

Genetic Biochemistry BIOCHGEN

30 hrs lectures, 60 hrs lab courses

III

year, spring semester

7

ECTS

Fundamentals of nucleic acid biochemistry. Two types of DNA libraries.The cell nucleus, nuclear envelope, nuclear matrix, chromatin and chromosome organization. A nuclear DNA attachment and gene activity.Eukaryotic cell cycle. Methods commonly used to measure the lengths of the phases of the cellcycle. Control of the cell cycle in Go, G1, S, G2 and M phases. The correlated changes in the levels of MPF and cyclin during cell cycle. Regulation of kinases cascade. Control of DNA synthesis genes by the cell-cycle genes. STARTing the plant cell cycle.Cell cycle control in higher plants.Regulation of cell cycle-dependent gene expression. Transcriptional and posttranscriptional regulation 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 Szopa References:

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 Microbiology MIPRZE

30 hrs lectures, 30 hrs lab courses

III

year, spring semester

6

ECTS

Biological and biochemical characteristics of chosen groups of microorganisms used in industrial processes. Biological aspects of production technology: food products (vine, beer, bread, butter, cheese, yogurt); organic compounds (organic solvents, anibiotics, vitamins). Microorganisms in biotransformation of chemical compounds and as bio-indicators. Protection against microbial corrossion. Lecturer: dr Marcin Łukaszewicz (Institute of Microbiology) References:

Chmiel A. Biotechnologia. 1991. PWN. Warszawa Szewczyk K.W. Technologia biochemiczna. 1997. WPW. Warszawa. Bamforth C. Tap into the art and science of brewing. 1998. Plenum Press New York Reviews from: Trends in Biotechnology, Current Opinion in Biotechnology, Microbiological Reviews, Biotechnology Progress.

Immunology

IMMUNO

30 hrs lectures, 30 hrs lab courses

III

year, winter semester

5

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, immunological specificity immunological memory and toleration MHC antigens immunity connected with alimentary tract 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.

Virology

WIR

30 hrs lectures

III year, spring semester

2 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 the

development of autoimmunological diseases. Immunodeficiency in viral infections. Diagnostics of viral

infections.

Lecturer: dr hab. Egbert Piasecki (Institute of Immunology and Experimental Therapy PAS) References:

Januszkiewicz J., 1992. Zarys kliniki chorób zakaźnych. PZWL, Warszawa. Kańtoch M., Blaskovic D. 1991. Wirusologia lekarska. PZWL, Warszawa suggested by the lecturer original scientific papers

Amphiphiles and Lipids ALIP

15 hrs lectures

II

year, spring semester

2

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 aqueous solutions – aggregation. Micelle, shapes, aggregation number, CMC – methods for determination.

Types of aggregates. Solubilization = comicellization. Detergents – specific amphiphiles; application in biochemistry 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 Kozubek References:

D. M. Small, The Physical Chemistry of Lipids, Plenum Press, 1986

Suggested original scientific articles

Biochemistry of Tissues and Organs BIONAT

15 hrs lecures

II

year, spring semester

2

ECTS

The lecture will be focused on molecular basis of functioning of chosen human tissues and organs and some problems related to pathological processes in these tissues and organs. The following topics will be 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 of collagen. Pathologies of collagen. Biochemistry of vision. Muscle contraction. Biochemistry of actin and miosin, 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 cancer cell. Chemical factors inducing cancerogenesis in animal cells. Lecturer: prof. dr hab. Maria Malicka Błaszkiewicz References:

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.

Plant Physiology

FIZROS

30 hrs lectures, 30 hrs lab courses

II

year, winter semester

6

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 in biomembrane systems, solute transport mechanisms in plasma membranes). Water relationships in plant (water availability in soil, pathways of water transport across the cortex of root, transpiration as the main motion in water uptake and long-distance transport, the role of root pressure in active uptake of water). Mineral nutrition of plants (nitrogen sources for plants, nitrogen-fixation system, biochemistry of nitrogen fixation, assimilation of NO 3 - and NH 4 + -incorporation into amino acids, sulfate assimilation, functions of mineral nutrients in plant metabolism). Photosynthesis (photosynthetic active pigment system of chloroplast, photosynthetic electron and proton transport, structure of PSI and PSII, Q-cycle, PSII and water photolysis, mechanism of photophosphorylation, biochemical reactions of photosynthesis in C 3 , C 4 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 cycle and 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 aspects of growth and development, synthesis and degradation of plant hormones, mechanism of hormone action, photomorphogenesis, mode of phytochrome action in photomorphogenesis, flower formation and photo- and thermoperiodism). Plant movements (types of movements, molecular basis of phototropism and gravitropism, mechanism of turgor movements). Stress physiology (constitutive and adaptive resistance to water stress, osmoregulators and osmoprotectors in salt stress, resistance to heat and cold stress, biogenic stress and role of jasmonate in induction of disease resistance). Lecturer: dr hab. prof. Grażyna Kłobus (Institute of Botany) References:

Zurzycki J., Michniewicz M. 1986 Fizjologia Roślin. PWRiL Taiz L., Zeiger E 1991 Plant Physiology. Springes-Verlag Berlin Heidelberg New York

Animal Physiology FIZZWI

30 hrs lectures, 30 hrs lab courses

II

year, spring semester

6

ECTS

Excitable cell: neuron, striated muscle, smooth muscle. Input and output of information: transmission through synapses, neurotransmiters, structure and function of receptors. Senses: smell, taste, touch, sound receptors, sense of balance, thermoreceptors, photoreceptors, nocyceptors. Processing of information: CNS, ANS, endocrine system, hormones. Basic physiological phenomena: respiration, circulation. digestion. Homeostasis: salt and water balance. glucostasis, thermoregulation. Biological rhythms: rhythm of sleeping and waking, menstrual cycle. The effects of alcohol, drugs and environmental pollution on physiological phenomena. Lecturer: prof. dr. hab. Andrzej Dżugaj (Institute of Zoology) References:

Gill J. 1987. Zarys fizjologii porównawczej zwierząt. PWN.Warszawa Ganong W.F. 1994. Fizjologia. PZWL. Warszawa Schmidt-Nielsen K. 1992. Fizjologia zwierząt. PWN. Warszawa

Advanced and Specialization Courses

Enzymology

ENZY

30 hrs lectures, 60 hrs lab courses

III

year, winter semester

7

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 strength and temperature on enzyme activity. Catalytic mechanism of serine proteinases, carboxypeptidase A and ribonuclease. Mechanisms of lowering of the transition state barrier (induced fit, transition state stabilization).Thermodynamics of protein-protein/ligand/substrate recognition. Chemical modifications of enzymes. Conformational and chemical properties of amino acid side chains. Basic informations about spatial structure of proteins and methods of its determination. Relationship between structure and function of some enzymes. Energetics of proteins: hydrogen bonds, van der Waals and electrostatic interactions, hydrophobic effect. Lecturer: prof. dr hab. Jacek Otlewski References:

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

Animal Cell and Tissue Cultures HODKOZ

15 hrs lectures, 30 hrs lab courses

III

year, spring semester

2

ECTS

The course gives the general - theoretical and practical knowledge of animal cell culture as an alternative research models. The program consists: information on organization and equipment of cell culture laboratory, sterile work conditions, primary and secondary cell cultures techniques, methods of tissues disintegration, cultures on solid and fluid substratum, media composition, cell lines, cryo- preservation. Hepatocyte as a biomedical model in vitro cytotoxicity assay. The effect of drugs used in cancer therapy on cytoskeletal organization of the culture fibroblasts L1210 leukaemia lymphocytes and hepatocytes. Lecturer: prof. dr hab. Maria Malicka-Błaszkiewicz References:

Culture of Animal Cells. A manual of basic technique. R. I. Freshney 1994 Willey-Lis Inc.

Plant Cell and Tissue Cultures HODKOR

15 hrs lectures, 30 hrs lab courses

III

year, spring semester

2

ECTS

History and basics of in vitro culture. Techniques of clonal propagation. Dedifferentiation and totipotency of cells. Models of plant regeneration: embryogenesis and organogenesis. Suspension culture – initiation, isolation, subculture, and selection of mutants. Somato-clonal variation, culture techniques, methods of selection, genetic causes of somaclonal variation. Haploids production – process of androgenesis and gynogenesis, the use of natural anomalies of plant fertilisation and embryo development. Protoplast fusion and its products: somatic hybrids. Methods of genes transfer – vectorial and direct transformation of plants. Cryopresevation and storage of germplasm. Secondary metabolism 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 komórek i tkanek roślinnych, PWN, Warszawa, 1984 Bieńkowska-Mochtak E.; Zastosowanie kultur in vitro w uprawie i hodowli roślin. PWR i L, Warszawa,

1984

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

Molecular Principles of Genome’s Evolution MOLEWGEN

15 hrs lectures, 60 hrs lab courses

I year master, winter semester

6 ECTS

Origin and structure of procaryotic, eucaryotic and organelle genomes. Physical techniques for mapping of genomes. Sequencing of genomes. Mutations and recombinations as basic processes of genome evolution. Spontaneous and induced mutations. DNA repair. Homologous and localized recombinations. Transposomes and rethroelements. Stoichiometric variations in heteroplasmic genomes. Localization of genomes in DNA sequences. Determination of the gene function. How new genes 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 Jańska, dr hab. Ryszard Rzepecki References:

Current scientific publications

Genetic Manipulations in Laboratory Practice MANGEN

15 hrs lectures, 15 hrs lab courses

I year master, spring semester

3 ECTS

Expression of eucaryotic proteins in bacterial cells. The choice of the expression system (types of expression systems, properties of plasmids, choice of bacterial cells and plasmids for DNA propagation and subcloning). Standard expression procedures and their optimalization for given tasks. Non-typical applications and solving the problems related to. Exogenic protein expression in eucaryotic cells. Systems of the expression in D. melanogaster cells and their applications. The choice of the system related to the task of the experiment (plasmid, fluorescent or immunological markers, additional protein sequences). Baculovirus system. Transgenic organisms – why and how they are formed. Transformation, transfection, „cotransformation” and „cotransfection”. Genetic manipulations for 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 Rzepecki References:

Current scientific publications

Genomes

GENOM

15 hrs lectures, 105 hrs lab courses

I year master, winter semester

7 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 and function of procaryotic and organelle genomes. Regulation of gene expression in procariota, mitochondria and chloroplasts. Nuclear control of organelle genomes. Nucleus – ultrastructure and its relationship to particular functions of the nucleus. Nuclear matrix proteins and the modulation of their interactions with chromatin and/or DNA/RNA. Eucaryotic genomes – the size, repeat and unique sequences. 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 DNA modyfication system. Recombination. Transposomes. Initiation of transcription – elements and types of promotor, 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 and transport. 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, secondary structure, ribozymes, protein-coding introns. RNA editing. DNA rearangement – yeast active and non active loci, Ti plasmid, plant genome.

Lecturer: dr hab. prof. Hanna Jańska, dr hab. Ryszard Rzepecki References:

Benjamin Lewin „Genes VI” Oxford University Press, 1997. Current scientific publications

Structure and Function of Biological Membranes BIOMEM

15 hrs lectures, 75 hrs lab courses

I year master, winter semester

7 ECTS

Peripheral and integral membrane proteins. Methods of biomembrane isolation. Methods of isolation, crystallization and reconstitution of membrane proteins. Application of chemical and enzymatic labeling, antibodies and proteolytic enzymes in determination of membrane disposition of proteins. Cross-linking reagents. Examples of the detailed structure of some membrane proteins. Computer analysis 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 the membrane. Peripheral membrane proteins. Interaction of peripheral membrane proteins with intrinsic membrane domain. Erythroid and nonerythroid spectrin. Pathologies connected with the genetic defects 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 organic anions and ATP-ases of ABC-type. Examples of proteins responsible for cell-to-cell or cell-to extracellular matrix adhesion. Lecturer: prof. dr hab. Aleksander Sikorski References:

Genis, Biomembranes, 1988, Springer 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

Structure and Function of Proteins STRUFUB

15 hrs lectures, 75 hrs lab courses

I year master, winter semester

7 ECTS

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

Polyketide Antibiotics ANTPOLI

15 hrs lectures, 15 hrs lab courses

I year master, spring semester

3 ECTS

Secondary metabolism – definitions. Cellular localization of pathways. Products of the secondary metabolism and their importance for humans. Polyketide and polyketide-protein antibiotics. Biotechnology of polyketide antibiotics. Antibacterial antibiotics. Antifungal antibiotics. Anticancer antibiotics. Lecturer: prof. dr hab. Arkadiusz Kozubek References:

Chmiel A., Grudziński S. Biotechnologia i chemia antybiotyków, PWN 1998 Current scientific literature

Photobiology

FOTBIO

15 hrs lectures

I

year master, spring semester, lecture of choice

2

ECTS

Light and color in the nature and scientific laboratory. Photophysical and photochemical interaction of light with biological macromolecules. Plant photoreceptors: molecular basis of phytochrome system action - reception, transfer and control of information; role of chlorophylls, their precursors and derivatives in the capture, migration and transfer of energy. Bacterial and animal photoreceptors:

structure, function and mechanism of action of bacteriorhodopsin and rhodopsin. Application of molecular photobiology: in medicine - photosesibilizers in diagnostics and treatment of cancer; in biotechnology and preservation of nature - monitoring, production and biomass utilization; in bionics - immobilized photoreceptors as transmitters of energy and information. Lecturer: dr Barbara Bereza Reference:

Biofizyka dla biologów, 1987, red. W.Leyko, PWN, Warszawa

Biology of Mitochondria BIOMIT

15 hrs lectures

I

year master, spring semester

2

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 of nuclear and mitochondrial gene expression. Cytoplasmic male sterelity – molecular principles. Structure-function analysis of oxidative phosphorylation complexes. Mitochondrium as the source of the active oxygen species. Mitochondrial theory of aging. Mitochondrion and apoptosis. Lecturer: dr hab. prof. Hanna Jańska References:

Brennicke, A., Kuck, U. (1993) Plant mitochondria. VCH-Weinheim

Liposome Technology LIPOTECH

15 hrs lectures, 75 hrs lab courses

I year master, winter semester

6 ECTS

Chemistry of lipids and liposomes. Structure of amphiphilic aggregates. Preparation of liposomes - thin-film hydration methods, injection methods, demulsification methods, other methods. Liposome properties. 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 anticancer therapy. Liposomes in cosmetics. Liposomes in genetic engineering. Liposomes in food industry and ecology. Industrial manufacturing of liposomes. Lecturer: prof. dr hab. Arkadiusz Kozubek References:

G. Gregoriadis, 1993, Liposome Technology (Vol. I-III). CRC Press, Boca Raton

D.D. Lasis, 1993, Liposomes: From Physics to Applications. Elsevier, Amsterdam

D. D. Lasic, Y. Barenholz, 1995, Handbook of Nonmedical Application of Liposomes, CRC Press

Janoff A. S. 1999, Liposomes. Rational Design. Marcel Dekker, New York Basu S. C., Basu M. 2002, Liposome, Methods and Protocols. Humana Press, New York

Crystallographic Analysis of Macromolecules KRYSMAK

15 hrs lectures

I

year master, spring semester, lecture of the choice

2

ECTS

How can we "see" atoms? electron microscopy, tunneling microscopy, atomic force microscopy. 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 of macromolecules: 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 results with 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 York Ciunik Z. (Ed.) 1996 Instrukcje do ćwiczeń z krystalografii , część 2, Wydawnictwo Uniw. Wrocławskiego

Molecular Markers MARMOLE

15 hrs lectures, 30 hrs lab courses

I year master, spring semester

4 ECTS

Types of molecular markers. Markers related to simple polymorphism. Markers related to composite polymorphism. Genetic and biochemical differences between organisms as molecular markers. Identification of molecular markers with molecular biology and biochemical techniques. Molecular probes (DNA sequences, monoclonal antibodies). Diagnostic tests for genetic, cancer, infectious diseases. Molecular markers in taxononic and phylogenetic research. Markers for mitochondrial DNA. Lecturer: dr Magdalena Wołoszyńska References:

Current scientific publications

Proteinases as Regulators of Biological Processes PROREG

15 hrs lectures

II year master, winter semester

2 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 and kininogenases. Proteinases in virus infection. Post-translational proteolytic processing and generation of 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 Wilusz References:

V.Turk and L.J.Vitale 1981 Proteinases and their Inhibitors: Structure, Function and Applied Aspects. Mladinska Knjiga, Pergamon Press, Ljubljana, Oxford H. 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

Biocins and Peptide Antibiotics BIOCANTYP

15 hrs lectures

I

year master, spring semester

2

ECTS

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

Antibiotics IV. Biosynthesis (J.W. Corcoran Ed.) Springer-Verlag Berlin, Heidelberg, Current scientific publications

Mutagenesis Induced by Metals METAL

15 hrs lectures

I

year master, spring semester, lecture of the choice

2

ECTS

The aim of this lecture is to present the key role of metal ions in supporting life functions, as well as their toxic and therapeutic properties. The effects of transition metals will be emphasized, because these 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, metabolism and functions of copper in the body- metal ion-catalysed radical reactions - the mitochondrial theory of aging-metal carcinogenesis (Cr, Ni) - the mechanism of action of platinum anticancer drugs. Lecturer: prof. dr hab. Henryk Kozłowski (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 Biology TECHBIOS

15 hrs lectures

I

year master, spring semester

2

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 the structures. Nuclear magnetic resonance (NMR). Uni-, di and multi-dimmensional spectra. Enrichment of the samples with radioisotopes. Heteronuclear spectra. Assigment of the signals and determination of biopolymer structures. Spectroscopic methods of determination of secondary structures. Circular dichroism. Methods for automatic analysis of data. Infrared spectroscopy. Application for analysis of macromolecular structures. Fluorescence. Application of fluorescence for structural analysis of

biopolymers. Electron crystallography. Application of spectroscopic techniques for determination of the structure of carbohydrates, lipids and their aggregates. Comparison of experimental techniques with theoretical methods of macromolecular structure prediction. Lecturer: dr Daniel Krowarsch References:

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, Plenum

Press.

J. Twardowski, Biospektroskopia, t. I-V, 1990, PWN

Fluorescence Techniques and Introduction to Image Analysis TECHFLU

15 hrs lectures, 45 hrs lab courses

I year maste, winter semester

5 ECTS

Introduction to fluorescence. Fluorescent probes used in biological sciences. Application of fluorescence for determination of lacal physicochemical parameters. Chosen applications of fluorescence 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

Bionanostructures

BIONANO

15 hrs lectures + 15 hrs lectures

I

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 macromolecules important in formation of aggregates. Formation and properties of lipid aggregates. Protein structure and its meaning in the interactions with biological structures. Chosen methods used in studies of supramolecular aggregates. Technological and medical applications of aggregates. Biological matter as aggregation structure. Lipid aggregates. Proteins – conformational structures. DNA as linear polyion. Amphiphilicity and partition coefficient. Multimolecular aggregates. Macromolecular aggregates as carriers of drugs and genetic material. Lecturer: dr hab. Marek Langner (Technical University Wroclaw) References:

Current scientific publications

Posttranslational Steps in Protein Biosynthesis POMOBIAL

15 hrs lectures

I

year master, winter semester

2

ECTS

Chloroplasts structure, six different location for proteins in chloroplast, their protein composition. Chloroplast proteins coded for by chloroplasts DNA, Chloroplast proteins coded for by nuclear DNA. The chloroplast genome, structure and function. Structure and function of the chloroplastic protein import apparatus of the envelope. Translocation of protein across chloroplast envelope: transit peptides, cytosolic factor, energetics of import, stromal processing peptidase, insertion of prosthetic groups, assembly of active complexes. Targeting of protein into or across the thylakoid membrane - a multitude mechanisms. Methods of studies of protein transport into chloroplasts; preparation of precursor protein: in vitro transcription and translation of cloned precursor gene or overexpression in E.coli. Protein import by isolated chloroplasts, protein import by isolated thylakoids. 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 in bacteria and chloroplasts: SecA dependence, membrane potential dependence, spontaneous transport. Lecturer: dr hab. prof. Andrzej Szczepaniak References:

Current scientific publications

Glycoproteins

GLIKOP

15 hrs lectures

I

year master, spring semester

2

ECTS

Structure of glycoproteins. Glycoside bonds in glycoproteins. Biosynthesis of N-glycosidic glycoproteins. Biosynthesis of O-glycosidic glycoproteins. Glycosyltransferases. Inhibitors of glycosylation. Regulation of glycosylation. The role of oligosaccharide moieties in glycoproteins. Proteoglycans. Mucins. Bacterial glycoproteins. Lectins. Structural analysis of glycoproteins. Synthetic glycoconjugates. Glycosylation of recombinant proteins. Medical and pharmaceutical applications of polysaccharides and glycoconjugates. Lecturer: dr hab. prof. Wiesław Wątorek References:

Current scientific publications

Gene Biology

BIOLGEN

15 hrs lectures

II year master, winter semester

2 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 and introduced genes, flavonoid genes in Petunia and HMG-CoA reductase in Arabidopsis. Plant transposones and retrotransposones, occurrence, gene activity, amplification, evolution. The role of brassinosteroids in plant development. Plant senescence and stress responses. ABA and desiccation responsive genes. Wound-induced gene expression. The ethylene signal transduction pathway. Manipulating plant metabolism. Plants as bioreactors. Lecturer: prof. dr hab. Jan Szopa References:

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 Proteins METAMOB

15 hrs lectures, 15 hrs lab courses

I

year master, winter semester

2

ECTS

Aminoacid sequence and secondary structure – classical methods of prediction of secondary and higher structures (Chou-Fasman, GOR, Lima). General rules of formation of regular and irregular structures. Determination of degree of significance of homology in analyzed proteins and nucleotide sequences (review of methods). Algorithms used for comparison of sequences in biological systems. Variability of proteins and Markov’s 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. Graphical interpretation Dot matrix of sequences - Dotplot, DotLet, SEMIHOM. Description and application of chosen 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

Chosen Aspects of Gene Therapy TERGEN

15 hrs lectures, 30 hrs lab courses

II

year master, winter semester

6

ECTS

Recombinant DNA techniques and their applications – mutagenesis in vitro. RLFP technique in gene mapping and diagnostics of genetic diseases. Genetics and rethrogenetic. Alteration of gene activity (over-expression and knockout). Localized cloning. Recombinant DNA technology in detection of mutated alleles. Clone selection by functional complementation. Manipulations in genes (procaryotic, yeast, plant, animal organisms). Gene replacement and transgenic organisms. Problems, advantages and 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), HSV virus. Plasmid vectors. Physical methods: microinjections, infusion, DNA-calcium phosphate precipitates, 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 research and medicine. Gene therapy in the traetment of cancer. Problems, limitations and side effects. Lecturer: dr hab. Ryszard Rzepecki References:

Current scientific publications

PCR Method – Theory and Practical Applications PCR

15 hrs lectures, 45 hrs lab courses

I year master, winter semester

5 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 medical diagnosis, forensic medicine and in studies of the relationship between individuals. RT-PCR. Reversed transcriptases: 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 Olczak References:

Current scientific publications

Nonliposomal Drug Carriers NIELINOS

15 hrs lectures, 30 hrs lab courses

I year master, spring semester

4 ECTS

How drugs are degraded and removed from organism. How to direct drug to the right place in organism. Physical and chemical barriers. Micro- and nano- emulsions as drug carriers. Polylactic nanospheres: preparation and applications. Polymeric carriers. Monoclonal antibodies as selective carriers in cancer therapy. Biochips, nanotubes, dendrimers and fullerenes in transport and microdosing of drugs. Science-Fiction in pharmacology. Lecturer: dr Jerzy Gubernator References:

Current scientific publications

Mechanisms of Transport in Bacteria METRABA

15 hrs lectures

II

year master, winter semester

2

ECTS

Diffusion and facilitated diffusion, porins. PEP-PTS system. Aquaporin. Transport dependent on plasmid proteins. Resistance of bacteria upon chemical factors dependent on mechanisms of transport. ATP-dependent transport (structure, mechanism, energetics). Uniport, symport and antiport energetics. Model systems for studying transport in bacteria. Lecturer: dr Jarosław Króliczewski

References:

Current scientific publications

Bioenergetics

BIOENER

15 hrs lectures

I

year master, winter semester

2

ECTS

Biophysics of complex systems: elements of nonequilibrium thermodynamics in biology. Oscillations and chemical waves in multienzymatic reactions. Simulation of multistep dynamic processes. Acquisition, transmission and analysis of information in biological structures. Spatial organization of biopolymers and techniques used for its study. Dynamic properties of macromolecules. Transitions of electrons in biopolymers. Background, molecular organization and dynamics of biological membranes. Red-ox processes, mechanisms of transport of electrons and protons, migration of energy in biostructures. Bioenergetics of mitochondria and chloroplasts. Transformation of electrochemical gradient of ions to ATP. Oscillations in living organisms. Lecturer: dr hab. prof. Andrzej Szczepaniak References:

Biofizyka dla biologów, red. M.Bryszewskiej,W. Leyko, 1995, PWN, Warszawa Nicholls DG, Ferguson SJ, 1995 Bioenergetyka 2, PWN, Warszawa Biophysics, W.Hoppe, W.Lohmann, H.Markl, H.Ziegler, Springer Verlag 1983

Analytical Methods in Protein and Glycoconjugate Chemistry GLIKOKON

15 hrs lectures, 45 hrs lab courses

II year master, winter semester

2 ECTS

Peptide maps. Modification of polypeptide amonoacids. Chemical and enzymatic protein fragmentation. Determination of aminoacid composition and sequence in polypeptides. HPLC, FPLC and low pressure chromatography. Quantitative analysis of sugars in glycoproteins. Isolation of glycans covalently bound to protein. Analysis of glycan structure. Lecturer: dr Mariusz Olczak References:

Current scientific publications

Intracellular and Extracellular Mechanisms of Regulation ZEWEMER

15 hrs lectures

I

year master, spring semester, lecture of choice

2

ECTS

Cellular signaling – interactions of ligands with receptors. Great number of receptors is localized in biomembranes. 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 of protein cascades related to oncogenesis, apoptosis and morphogenesis. The role of various membrane structures (rafts, caveoles). Adaptation of the target cells. The logic of cellular signaling – analogies to computer neuronal networks. Lecturer: prof. dr hab. Aleksander F. Sikorski References:

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