Objectives Content Learning outcomes Plant Biology · lipids, nucleotides and nucleic acids. Learning the nomenclature and techniques used in protein, lipids and carbohydrates biochemistry

Objectives Content Learning outcomes Plant Biology

To acquaint student with basic knowledge of the plant cell and tissues, and with plant body structure and function.

Structures and compartments specific to plant cell; selected issues on plant cell evolution; plant structure (organs, tissues), primary and secondary plant architecture; characteristics of the ecological plant groups, chosen aspects of the plant developmental biology.

Student: · knows the structure of the plant body and the

plant cell organization, identifies the plant cell organelles and understands their functions.

· recognizes the structure and function of the main plant tissues and organs.

· knows the main types of microscopes and selected techniques used in the plant cell/tissues studies.

· uses light microscopes; performs basic histochemical reactions and identifies observed structures.

· follows the basic laboratory protocols and safety rules during the classes; the student is active and well organized and is able to cooperate in team work.

Animal Biology

To acquaint student with basic knowledge of the structure and function of animal cell and tissues.

Animal cells: nucleus, cytoplasmic organelles, cell divisions. Animal tissues: epithelial, connective, muscle and nervous.

Student: · knows selected techniques used in the animal

cell/tissues studies. Student uses light microscopes and identifies observed structures.

· follows the basic laboratory protocols and safety rules during the classes; the student is active and well organized.

· knows the histological structure of animal cell and tissues, characterizes the cells types and extracellular components, explains the correlations of the cell and tissues structure and function.

· uses the theoretical knowledge to analyse histological sections. Is skillful in microscopic observations and able to identify animal tissues.

· is willing for microscopic observations, is able to cooperate in team work.

General and Inorganic Chemistry

· passing the knowledge necessary to understand the natural processes and phenomena,

· shaping the understanding of mechanisms that stand behind various chemical reactions, differentiation of various reaction types,

· introduction to the nomenclature of inorganic compounds,

· passing on the basic theoretical concepts of coordination chemistry, and developing the ability of using them in predicting the structure and reactivity of metal complexes,

· introduction to independent laboratory work and critical interpretation of results,

· introduction to the basic concepts and rules of analytical chemistry,

· introduction to the basics of laboratory practice.

Lectures: Basics of quantum mechanics, the wave function; energy levels of atoms and molecules. Explanation of the periodic table of the elements based on quantum numbers. Behavior of elements within periods and groups. Chemical bonding – covalent, ionic, metal and hydrogen bonds – conditions of forming, stability. Relationships between chemical bonding and macroscopic, thermodynamic properties. Symmetry of molecules. Molecular interactions and their relationship to gas phase, liquid phase and solid state properties. Chemical equations. Basic types of chemical reactions – acid-base reactions, reduction-oxidation reactions, organic chemistry reactions (addition, substitution and elimination). Chain reactions. Stoichiometry. Basic chemical calculations. Solutions and solvents. Basic concepts of chemical thermodynamics, reaction heat, enthalpy, entropy, Gibbs free

Student: · comprehend the basic chemical laws and

concepts that apply to the microscopic scale, and should be able to illustrate them by appropriate examples,

· is able to connect the physical properties to molecular structure,

· has the necessary knowledge to comprehend the common natural phenomena,

· is able to apply chemical calculations in every-day laboratory practice, know how to properly handle experimental data, and be able to list examples of situations where these skills are commonly used,

· knows the physicochemical properties of selected compounds and know the basic rules of handling chemicals, and laboratory hygiene and safety.

· is able to define and explain basic laws and concepts of chemistry,

· is able to apply the rules that govern handling chemicals and laboratory safety,

· is able to use basic laboratory equipment and perform basic laboratory activities,

· is able to identify the various factors that can influence the outcome of conducted research, and should be able to find the main sources of

energy. Chemical equilibrium, reversible and irreversible reactions, examples from geochemistry, biochemistry, industrial processes and common-day applications. Basic concepts of chemical kinetics. Catalysts and catalysis. Reactions of radicals. Basics of organic chemistry – vital types of organic molecules and their characteristic reactions. The carbon cycle. Photosynthesis as a chain of consecutive photochemical and redox reactions of organic compounds; energetics of photosynthesis. Examples of element cycles in nature – geochemical processes. Modern chemical analysis: spectroscopy (IR, UV-Vis, NMR, EPR), electrochemistry, chromatography – theoretical background and applications. Laboratory: General rules and safety regulations for work in the chemical laboratory. Concentration of hydrogen ions and pH indicators. Buffer solutions. Qualitative analysis of inorganic compounds. Classical quantitative analysis: acid-base titration: standardizing a sodium hydroxide solution and determining the concentration of chloric acid.

experimental error, · knows to solve problems encountered during

research, based on various resources. · is aware of his overall knowledge and

understand the need of its constant improvement,

· is able to work in a team environment, and be responsible for the tasks and duties placed upon him,

· is able to use literature sources in order to find the necessary information,

· is able to take responsibility for the safety of himself and others around him.

Mathematics Knowledge and understanding are fundamental to studying mathematics and form the base from which to explore concepts and develop problem-solving skills. Through knowledge and understanding students develop mathematical reasoning to make deductions and solve problems. At the end of the course, students should: · know and be able to use selected concepts and

theorems of calculus, algebra and differential equations,

· use appropriate mathematical concepts and skills to solve problems in both familiar and unfamiliar situations including those in real-life contexts,

· select and apply general rules correctly to solve problems including those in real-life contexts.

Preliminaries: Algebraic equations, Graphs of functions. Vectors, matrices and complex numbers. Differential equations in one variable. Introduction to system of two differential equations. Equilibrium types in systems of two differential equations. Linear approximations of non-linear 2D systems.

Student · understands the importance of mathematical

methods required for description and interpretation of biological phenomena and processes, as well as biological experiments.

· knows and is able to use main mathematical methods required in biological sciences.

Computer Sciences The main objective of this course is to introduce students to the advanced features of Microsoft Excel 2000, such as analysis toolpack package including basic statistics, hypothesis testing, one-way Anova. In the second part the basic features of Linux operating system (such as grep, sed, awk, bash) are presented. Students will also learn how to write basic bash and Perl script and use these tools in practise, especially in case of large data sets.

Introduction to MS Excel, Linux operating system, Perl language

Student: · knows computational methods known in the

field of statistics, as well as computer tools allowing for data analysis and interpretation of the results.

· uses basic statistical methods and computer technology to describe biological phenomena and analysis of experimental data.

· understands the need for continuing education throughout the whole life, including deepening knowledge in computer science.

Physicochemical Methods in Biology After completion of this course students should develop basic knowledge about the major physicochemical methods of analysis. They should

Introductory Problems: The chemical and physical basis of the

Student: · has an introduction to the basics of

be able to determine what technique should be used to solve different analytical problems with a particular emphasis placed on the subjects related to pharmacology and biology.

measurements. The Beer-Lambert relation and its analytical applications. Classification of physicochemical methods of analysis. Atomic absorption and emission spectroscopy for trace metal analysis. Molecular spectroscopy: Basics of the UV-Vis absorption and emission spectrometry, its application in the qualitative and quantitative analysis. Infrared (IR) and Raman (R) spectroscopy as tools for structural analysis. Analytical applications of nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR). Application of mass spectrometry to the natural products analysis. Fundamentals and classification of electrochemical methods; potentiometry coulometry, conductometry and voltammetry. Separation techniques: gas and liquid chromatography, gel and capillary electrophoresis and their application for identification and separation of the biology and medicine relevant samples. Principles of polarimetry and refractometry.

physicochemical methods of analysis, · is able to apply the knowledge of the

appropriate principles to different analytical problems.

· understands the type of information that can be obtained from the measurement and limitation and/or requirements of the method.

Structure and Function of Biomacromolecules

Knowledge of the structure and functions of proteins, carbohydrates, lipids and nucleotides. Experimental skills in the analysis of proteins, carbohydrates and lipids

Molecular bases of life. Water in biological systems. Amino acids and proteins. Protein structures. Biological functions of proteins. Mechanisms of enzyme action, regulation of enzymes activity. The structure and function of lipids. Biological membranes . The structure and function of carbohydrates. The role of nucleotides, structure of nucleic acids. Vitamins. Quantitative and qualitative analysis of proteins, carbohydrates and lipids. Protein preparation technology, Glycoprotein analysis

Acquiring the advanced knowledge about structure and function of proteins, carbohydrates, lipids, nucleotides and nucleic acids. Learning the nomenclature and techniques used in protein, lipids and carbohydrates biochemistry. Developing the ability of using the professional literature dealing with structure and functions of proteins, carbohydrates, lipids, nucleotides and nucleic acids, developing the independent learning skills. The knowledge of basic biochemical methods and experimental techniques.

Organic Chemistry

To present and properly describe fundamental aspects of organic chemistry theoretically (lecture) and practically (laboratory). In addition the teaching labs focus on bringing a practical knowledge of basic organic reactions leading to formation of target molecules on a way of traditional synthetic approach, and show a correlation between theoretical predictions and a real product. The quality/purity of the obtained compounds verified with spectroscopic methodology (NMR).

Lecture: IUPAC system of the organic compounds naming; structure and properties (chemical and physicochemical) of the organic compounds; synthetic methodology; appearance in nature; applications in medicine, laboratory and industry. The structure of organic molecules. Chemical bonds in organic compounds. Structure and reactivity. Acids and bases in organic chemistry. Polar and nonpolar organic compounds. Alkanes – construction and reactivity. Free radical halogenations. Cycloalkanes.

Student: · has a fundamental knowledge about organic

molecules. · knows and understands a terminology and

nomenclature of organic compounds. · familiar with fundamentals of the analysis of

organic compounds. · characterizes basic types of organic reactions

and understands their mechanisms. · determines basic properties and reactivity of

organic compounds. · knows and understands the safety procedures

necessary in the lab work and applies disposal rules.

· an analysis of a basic synthetic approaches and

Stereoisomerism. Properties and reactivity of alkane halogens. Nucleophilic substitution – SN1 and SN2 mechanisms. Elimination reactions. Alcohols – properties and synthetic strategies. Ethers, crown ethers and epoxides. The nuclear magnetic resonance as a tool for determining organic molecules structure. Alkenes. The oscillation spectroscopy in organic chemistry. Alkynes. The electron spectroscopy in the UV-Vis for organic compounds. Benzen and aromaticity – electrophilic substitution (substituents influence on regioselectivity). Carbonyl group – aldehydes and ketones. Enols – reactivity of an enolate ion. Aldol condensation (a,b-unsaturated aldehydes and ketones). Carboxylic acids. Mass spectrometry in organic chemistry. Amines and their derivatives. Benzene derivatives (aromatic amines, phenoles , alkilbenzenes etc.) and their reactivity. Heterocyclic compounds – furan, thiophene, pyrrole, pyridine, porphyrin). Strategy in organic synthesis – basic principles. Aminoacids, peptides, proteins and nucleic acids (biopolymers). Organometallic compounds – synthesis, structure,

results of spectroscopic analysis of organic molecules.

· synthesizes chemical compounds with a usage of proper glassware.

· writes reports from a research and adopts correct tools to do so.

· describes and discuss chemical problems with a vocabulary characteristic for a scientific approach.

· assesses results of an experiment and verifies them with a literature data.

Social Competence: · a self-reliant in extending the chemical

knowledge. · responsibility for the work that has been

done especially for and interpretation of results with an extra accent at the scientific reliability.

· responsibility for a safety in lab-work.

properties and applications. Polymers – synthetic methodology, structure, properties and applications. Resins – phenol, epoxide and polyester. Biodegradable polymers. Laboratory: Reaction with bromine, oxidation reactions with KMnO4, Lucas test, iodoform test, Fehling test, Tollens’ test, reactions of amines and amino acids with HNO2, hydrolysis of carboxylic acid derivatives; synthesis, purification and 1H NMR of aspirin; separation of organic compounds mixture; n-butyl acetate synthesis; synthesis and isolation of meso-tetraphenylporphyrin (chromatography); isolation of limonene.

Metabolism of Proteins, Carbohydrates, Nucleotides and Lipids

Knowledge of metabolic pathways (biosynthesis and degradation) of proteins, carbohydrates and lipids occurring in live organisms

Metabolism – the general definition. Glycolysis. Tricarboxylic Acid Cycle. Electron transport and oxidative phosphorylation. Gluconeogenesis, glycogen and starch metabolism, pentose-phosphate pathway. Fatty acid oxidation and biosynthesis. Biosynthesis of triacyloglicerols. Metabolism of glycerophospholipids, sphingolipids, isoprenoid compounds and eiconosoids. Metabolism of amino acids. Metabolism of nitrogen bases and nucleotides. Integration of metabolic pathways. Biosynthesis and degradation of proteins.

Student: · has knowledge of protein, carbohydrate

nucleotides and lipids metabolism, knowledge of terminology, techniques and methodology used in protein, carbohydrate nucleotides and lipids biochemistry.

· has ability to use scientific literature on the taught subjects,

· has ability to study independently the subjects presented during the lecture.

· is familiar and follows the basic principles of safety procedures in the laboratory.

· understands the need for continuing education · knows how to work as a team to solve

problems and perform scientific experiments.

Metabolism of Nucleic Acids

The aim of the course is to gain basic knowledge at a molecular level from genes to proteins. The principles about DNA replication, recombination, repair as well as RNA transcription, posttranscriptional modifications and protein synthesis will be explained. The course will also cover the characteristic features of nuclear and organellar genetic code as well as regulation of gene expression at different levels.

Replication of DNA (general description of replication machinery, replication in bacteria and eukaryotic organisms, control of replication, differences between replication in prokaryotes and eukaryotes; replication of mitochondrial DNA and phage lambda. DNA mutations and repair (DNA modifications, type and causes of mutations, basic mechanisms of DNS repair). Recombination of DNA (classical model of homologous recombination, RecBCD pathway, transposition). Transcription (structure of gene and transcript in prokaryotes and eukaryotes, promoters, bacterial and eukaryotic RNA polymerases, regulation of transcription); maturation and degradation of RNA. Protein synthesis, genetic code, composition of prokaryotic and eukaryotic ribosomes, general mechanism of translation, differences between translation in prokaryotes and eukaryotes. Organization and variability of organellar genomes.

Student: · can make a qualitative and quantitative

description of the basic biological phenomena and processes connected with nucleic acids.

· has extensive knowledge in the field of biochemistry; knows the structure, function and metabolism of nucleic acids; can integrate the knowledge gained at the level of the whole cell metabolism.

· knows the basic concepts, terms, techniques used in biochemistry of nucleic acids; is versed in the development of the above-mentioned fields.

· reads and understands the scientific literature in the field of biochemistry, biotechnology, molecular biology of nucleic acids in English learns a given subject by himself.

Biophysical Chemistry The main objective of the curse is to know principles of physical and biophysical chemistry, basic rules of thermodynamics, chemical kinetics, chemical equilibria (acid-base, association, dissociation and complex equilibria). The objective is also to know physical and chemical principles of the methods used in laboratory, where knowledge regarding biophysical chemistry is required (calorimetry, electronic spectroscopy,

Principles of physical chemistry (basic rules and constants). Thermodynamics (I-III thermodynamic laws, enthalpy, entropy, Gibbs energy). Chemical equilibria with special attantion to acid-base equilibria of peptides and proteins. ITC and DSC calorimetries – principles of operations and application in thermodynamic

Student: · knows principles of biophysical chemistry and

their application in thermodynamic characterization and analysis of macromolecules

· determines and calculates association/dissociation constants and kinetic constants with the use of known physicochemical methods.

fluorimetry, spectropolarimetry, mass spectrometry and nuclear magnetic resonance).

characterization of proteins. Methods used for the determination of association/dissociation constants in biophysical chemistry. Chemical kinetics with enzymology. Circular dichroism – principles of operations and application in conformational studies of proteins. Mass spectrometry - principles of operations and application in macromolecules analysis. Principles of electrochemistry. Fluorimetry and its application in biophysical studies and cell imaging (with the use of fluorescent proteins and fluorescent chemical probes).

Genetics

Lecture: acquaintance with terminology used in genetics – from Mendelian genetics to molecular genetics. To introduce students into the field of contemporary genetics: structure of genomes, chromosomes and genes, mechanisms and control of expression genetic information, and mechanisms of evolution of genetic pool. Laboratory: acquaintance with terminology used in genetics by performing experiments on model organisms (e. g. fruit fly, yeast). Planning, realization and analysis of genetic crosses. Inference about gene location based on analysis of gene linkage. Practical genetic exercises. Analysis of mutagens’ effects on genetic material. The basic assessment of genetic pool in population.

Lecture: The principles of inheritance and the chromosomal basis of Mendelism, extensions of Mendelism. Linkage, crossing over, and chromosome mapping. Double helix structure, DNA replication, replication associated mutational pressure, DNA repair, DNA asymmetry and its consequences for functional structure of chromosomes and evolution. Structure of prokaryotic and eukaryotic genes and chromosomes. Mechanisms of transcription and translation. Regulation of gene expression. The genetics of bacteria and their viruses. DNA recombination mechanisms. Sex chromosomes and sex determination. The genetic basis of cancer.


description of the basic biological phenomena and processes.

· knows and understands the importance of mathematical and statistical methods required for the description, interpretation of phenomena and processes, as well as biological experiments.

· is familiar with the basic principles of health, safety and ergonomics procedures in the laboratory; knows procedures of work with genetically modified organisms.

· can take advantage of the online resources and the literature to obtain information on genetics.

· carries out simple experiments or research expertise under the guidance of a tutor in the

Laboratory: This course practically shows: the principles of inheritance of genetic information according to Mendel's laws and their violations. Chromosomal theory of inheritance. Mitotic and meiotic cell division from genetic point of view. The structure of chromosomes. Genetics of Drosophila melanogaster – practical application of genetics laws in genetic crosses. Sex-linked inheritance, sex-limited inheritance and sex-influenced inheritance. Genetics of Saccharomyces cerevisiae – complementation test and meiotic mapping. Cytoplasmic inheritance. Sources of genetic variation. Types of mutations. Characteristics of tests used in detection of mutagenic factors. Basic knowledge of population genetics - Hardy-Weinberg law and the measurement of frequency of alleles in population.

field of genetics can describe the results and present them in the form of a report.

· uses basic statistical methods and computer technology to describe biological phenomena and analysis of experimental data.

· makes the synthesis of information from various sources and is capable of correct conclusions based on them.

· uses proper scientific language and terminology in discussions of genetical problems.

· understands the need for careful planning of tasks and scientific experiments.

Microbiology

Gaining basic knowledge about the structure, metabolism, habitats and pathogenesis of prokaryotic microorganisms. Learning the basic methods of culturing bacteria and studying their physiological characteristics.

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Size, shape and structure of cells of microorganisms belonging to three domains: Eucarya, Bacteria and Archaea. Genome organisation and means of genetic information transfer in these groups. Metabolism - vast metabolic plasticity, diversity of ecological niches and nutritional types among procaryotic microorganisms. Microorganisms in biotechnology, applications of genetic engeneering in modern biotechnology. Interactions between microorganisms, aerobic and anaerobic trophic chains in ecosystems. C, N, S, P cycles in nature.


description of the basic microbiological phenomena and processes.

· is able to link theoretical knowledge of microbiology, microbial biochemistry and biotechnology, with its practical application in industry, health care and environmental protection.

· is familiar with the basic principles of health, safety and ergonomics procedures in the laboratory; knows procedures of work with genetically modified microorganisms.

· applies basic physical, chemical and

biochemical techniques necessary for the study of microbiological processes.

· uses basic statistical methods and computer technology to describe microbiological phenomena and analysis of experimental data.

· knows how to work as a team, works together to solve problems and performing scientific experiments.

· knows and follows the rules of safety and health at work.

Animal Physiology

Understanding, on the molecular level, of the basic mechanisms of the detection and processing of exo- and endogenous stimuli by animal organisms. Understanding of physiological processes – on the cellular and organismal level – necessary to maintain homeostasis of animal organism.

The mechanisms of excitability. Synaptic transmission. G-protein coupled receptors and signaling networks. Central and peripheral nervous system. Endocrine system. Muscle contraction and neural regulation of the locomotor system. Mechano- and thermoreceptors, nociceptors. Mechanism of visual stimuli perception and processing. Chemoreceptors: olfaction and gustation. Respiration and gas exchange. Circulatory system. Ion and volume homeostasis. Gluco- and thermostasis. Biological rhythms. The mechanism of addiction and psychoactive drug action.

Student: · has an advanced knowledge on biochemistry;

is familiar with structure, function and metabolism of: proteins, carbohydrates, lipids and nucleic acids; can integrate the knowledge on the level of whole-cell metabolism.

· reads and understands a scientific literature from biochemistry, biotechnology, molecular biology and microbiology in English,

· can synthesize the data coming from various sources and is able to correctly deduce on these bases,

· gives oral presentations on scientific issues, both in English and Polish, based on the bibliographic sources and is able to discuss about it

· sees the necessity to constantly update scientific knowledge; shows interest in advances in biotechnology

Plant Physiology

Acquiring knowledge on the physiological processes, they regulation and integration in plants.

Metabolic compartimentation of plant cell, membrane transport; solute uptake and transport in plant; energy transformation in cell membranes, electron and proton transport in tylakoid membranes, PSI and PSII structure, Q cycle, cyclic and non-cyclic electron transport; dark phase reactions in C3, C4 and CAM; molecular interactions between light and dark phase of photosynthesis; molecular physiology of acquisition, transport and assimilation of N, S and P; regulatory molecules, signal perception and transduction; hormonal regulation of the plant growth and development; photomorphogenesis and mechanism of phytochrom action.

Student: · knows the mechanism of water and nutrients

uptake and transport; · understands the light energy transformation in

chloroplasts; · describes main reactions of CO2 assimilation in

C3, C4 and CAM plants as well as uptake and assimilation of sulfur, phosphate and different nitrogen forms;

· explains the dependency of physiological processes on environmental changes;

· characterizes the plant growth and understands regulatory function of fitohormones and abiotic factors;

· is competent to characterize main metabolic processes in plants, understands regulation and interactions between them;

· is skilled to perform simple biological experiments; collects and interprets scientific data and draws proper conclusions.

· is creative and permanently updates biological knowledge; is open for discussions; effectively participates in a team work.

Techniques in Molecular Biology

The aim of this course is to explain the principles of the basic techniques of molecular biology.

Isolation, purification, as well as qualitative and quantitative determination of nucleic acids. Enzymes for DNA manipulation (polymerases, nucleases, restriction enzymes, ligases). Gene cloning (types of vectors and methods of introducing foreign DNA into cells). PCR and qRT-PCR methods.

Student: · knows the basic concepts, terms and research

methodology used in molecular biology. · acquire knowledge of the basic techniques and

research tools used in molecular biology. · is familiar with the basic principles of health

and safety and ergonomics procedures in the laboratory, know procedures of work with

Nucleic acids hybridization (hybridization probes, Northern Blot, Southern Blot, dot blot); genomic and cDNA libraries. DNA sequencing (standard methods of sequencing, next-generation sequencing). Basic information about global transcriptomics, proteomics and metabolomics approaches, as well as methods for validation of interactions between molecules. The course includes also presentations of short tutorial videos as well as solving of tasks concerning techniques of molecular biology.

genetically modified organisms. · applies basic molecular biology techniques

necessary for studying biological processes. · has skills to grow cell cultures and genetic

modification of microorganisms. · describes the results and presents them in the

form of a report. · understands the need for continuing education

throughout the whole life, including broadening knowledge about new techniques.

· knows how to work as a part of team, work together to solve problems and perform scientific experiments


· recognize and addresses the ethical problems associated with biotechnology.

· knows and follows the rules of health and safety at work.

Biophysics

The knowledge of structure and function of protein complexes carrying bioenergetics reactions.

Structure of biopolymers. First and second law of thermodynamics, entropy and Gibbs free energy. Electrical and chemical work, electrochemical potential. Thermodynamics linked active transport. Oxidation-reduction reactions in biology. Biophysics of lipids, phase transition, monolayer and liposomes. Biological membranes, structure and function, peripheral and integral membrane proteins. Transport across biological membrane, diffusion, natural permeability, ionophore mediated.

Student · is able to isolate the chloroplasts, thylakoid

membranes and is able properly select measuring techniques using spectrophotometer or Clark oxygenic electrode to study photosynthetic electron transport reactions.

· knows methods to determination of structure and function macromolecules and concepts of the thermodynamics.

· understands principle of bioenergetic reactions in eukaryotes and prokaryotes.

· is able to analyse quantitatively and qualitatively describe transport electron

Protein mediated transport, uniport, symport, antiport. Transport of sugars and amino acids, periplasmic transport system, transport of macromolecules. The chemiosmotic theory, the tenets of the chemiosmotic hypothesis. The chemisomotic proton circuit, the measurement of protonmotive forces, seprate estimation of membrane potential and proton gradient. Mitochondrial respiratory chains, complex I (NADH-UQ oxidoreductase), complex II , complex III (UQ-cyt c oxidoreductase), complex IV (ytochrome c oxidase). The light reaction of photosynthesis in bacteria. Structure of photosyntheticreaction centers. The photosynthetic electron transport in plant, oxygen evolution. The photosynthetic antenna pigment-protein complexes, light energy transfer. Gibbs energy content of reaction as a function of its displacement fron equilibrium. The ATP synthase, structure and function. Stereochemistry of ATP hydrolysis. Techniques of chloroplast and tylakoid preparation. Experimental methods in photosynthetic electron transfer chain study.

processes in thylakoid membranes and is able to perform reasoning based on acquired data and to interpret them.

· to learn the structure of complexes involved in bioenergetics reactions.




Cell Culture Techniques

Students are to gain basic knowledge about culturing animal cells. They are to get elementary skills how to culture animal cells and how to obtain simple primary cell cultures from animal tissues. General ken concerning fluorescence/confocal microscopy and its applications will be passed to the students.

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Attending the module will give the students an opportunity to get familiar with speciality of working in the laboratory where animal cells are cultured. During the lectures following topics are mentioned and discussed: organization of animal cell culture laboratory; preservation of sterile conditions during working with animal cells; primary cell cultures vs. cell lines; modern applications employing animal cell cultures in researches aiming to solve scientific problems raised in biology, pharmacology, biotechnology and medicine. During the practical course students will learn how to culture human tumour cell lines, how to establish simple primary cell cultures from chicken tissues, how to examine cell viability, how to count cells and passage them. Students will gain also skills how to prepare slides with fixed and stained cells and how to analyze cells morphology and distribution of selected actin cytoskeleton proteins within a cell with the help of inverted light microscope and confocal microscope, respectively. Some biochemical tests like estimating actin polymerization state in tested cells are also done.

Student · knows the basic concepts, terms, techniques

used In cell cultures; is versed in the development of the above-mentioned field.

· acquires knowledge of the basic techniques and research tools used in cell culture technologies.

· is familiar with the basic principles of health, safety and ergonomics procedures in the laboratory; knows procedures of work with genetically modified organisms.

· has the skills to conduct cell cultures. · uses proper scientific language and

terminology in discussions of problem with cell culture specialists.

· understands the need for continuing education throughout the whole life.



· understands the need for continuing education throughout the whole life.



Bioinformatics

The main objective of this course is to teach students about theoretical and practical aspects of different bioinformatics and genomics studies such as: searching biological databases, recognition of coding sequences, genome analyses, making sequence alignment, searching databases for homologous sequences, motifs and patterns searching, analyses of amino acid sequences and protein structure prediction, phylogenetic analyses.

Subject and levels of genomics and bioinformatics analyses. Types of biological databases. Problems in the databases. Computational methods in recognition of protein coding sequences in Prokaryota and Eukaryota. Structure and organization of genomes, genome analyses, comparative genomics. Computational analyses of RNA sequences. Alignment of pair of sequences and multiple sequence alignment. Searching databases for similar sequences (FASTA and BLAST algorithms). Motifs and patterns in sequences. Computational analyses of protein sequences, analysis of basic physicochemical properties, recognition of transmembrane regions, motifs and domains in proteins, determination of secondary structure. Databases of structures, methods predicting tertiary structure, structural classification of proteins. Phylogenetics and molecular evolution, construction and evaluation of phylogenetic trees, phylogenomics. System biology.

Student: · is able to search appropriate databases and

apply suitable bioinformatics software to specific problems and tasks related to analyses of biological data on the nucleotide and amino acid as well as genomic levels.

· can perform basic phylogenetic analyses.

Molecular Organization of the Cell

Major subject of teaching is the function of cellular organelles and compartments on the molecular level. In particular, membrane, vesicular traffic, structure and function of major organelles, cytoskeleton and cell adhesion structures and molecules. Important issue is to facilitate understanding regulation of the cell cycle and its aberrations. Experimental course will permit student to get acquainted with the cell fractionation and analysis techniques. Basic knowledge concerning microscopy is also provided. The aim of the course is to learn the cellular structure and processes on the molecular level. Methods of detection of different cellular compartments will be acquired, in particular, membranes, cytoskeleton, major organelles and signaling molecules. Up-to-date biochemistry methods as well as imaging techniques will be presented.

Procaryota and Eucaryota. Chosen methods used in the studies of the cell. Chosen microscopy techniques and techniques of microscopic sample preparation, electron microscopy techniques and sample preparation. Application of antibodies. Cell cultures. Compartmentation of eucaryotic cells. Biological membranes, lipid bilayer. Membranne proteins. Membranę asymmetry, Basics of the membranę transport phenomena. ABC-transporters. Exo- and endocytosis. Cytosol. Cytoskeleton: microfilaments, intermediiate filaments and microtubules. Organization and functions of cytoskeleton. Cell-cell and cell extracellular matrix junctions/adhesions. Extracellular matrix. Nucleus –nuclear envelope structure, nuclear pores, nuclear traffic. Nuclear matrix. Peroxisimes. Endoplasmic (rough and smooth) reticulum. Membrane biosynthesis. Golgi complex and its role in glycoprotein and glycolipid carbohydrate chains processing. Formation of secretory vesicles/granules. Lysosomes role and heterogeneity. Signal transduction to and within the cell.

Student: · is acquainted with knowledge concerning

molecular cell biology, at ultrastructural and molecular level.

· understands modern methods and techniques used in this field.

Growth and division of the cell. Eucaryotic cell cycle and its regulation. Molecular mechanisms of the cell cycle regulation; check points. Cyclins and cyclin-dependent kinases, growth factors and their receptor kinases. Reciprocal interactions of cells during development. TGF-β signaling. Stem cells. Programmed cell death and its regulation pathways. Basic concept of cancer. Protooncogens and tumor suppressor genes.

Biotechnology

The main objectives of this course are to introduce students to the modern biotechnology and preparation methods of selected bioproducts.

Microorganisms in biotechnology, biology, selection, improvement, kinetics of microbial growth. Bioreactor design, bioprocess control and optimization. Downstream processing, disintegration methods, bioproducts purification and formulation. Insect and mammalian cell culture. Enzyme biotechnology, enzymes from plants, animals and microorganisms. Recombined proteins: overexpression, purification, refolding, principles of protein design. Recombinant proteins of high value, therapeutic proteins. Biotransformations and bioproducts: amino acids, organic acids, microbial polysaccharides and lipids,

Students: · are able to make a qualitative and quantitative

description of selected bioprocesses, know the basic concepts, terms and methods used in biotechnology,

· get knowledge of the basic techniques and tools used in biotechnology,

· read and understand the scientific literature in the field of biotechnology,

· are able to take advantage of the scientific books, papers and online resources to obtain information on biotechnology,

· use proper language and scientific terminology in discussions with experts in the field of biotechnology,

· understand the need for continuing education throughout the live,

antibiotics and biodegradable plastics. The business of biotechnology. Basic information about bionanotechnology.

· recognize and address the ethical problems associated with the field of biotechnology.

Within the practice students have the ability to select conditions for the expression of proteins in a bacterial system, knowledge of recombined protein preparation by affinity chromatography, followed by biophysical characterisation of. Moreover, by conducting a series of experiments, students know how to design experiments, perform data analysis and interpret the results.

Preparative Biochemistry

Student will learn protein purification techniques and be able to plan protein purification strategy. The goal of the course is to purify basic pancreatic tripsin inhibitor from bovine lungs (BPTI) and finally asses quality of purified sample.

Choice of tissue (plant/animal) material and setup of extraction conditions. Clarification and condensation of extracted material. Basic techniques applied during protein and peptides purification (precipitation, fractionation, ion-exchange chromatography, hydrophobic chromatography, gel filtration, affinity chromatography, immuno-precipitation. HPLC and FPLC techniques; reverse phase chromatography (RP). Purification of recombinant protein. Scaling up of purification process.

Student: · acquires knowledge of the basic techniques

and research tools used in biochemistry, molecular biology and biotechnology.

· applies basic physical, chemical and biochemical techniques necessary for the study of biological processes.

· carries out simple experiments or research expertise under the guidance of a tutor in the field of biotechnology; can describe the results and present them in the form of a report.

· performs basic physical and chemical measurements inside and outside the laboratory.



Industrial Microbiology

· Obtaining knowledge of the basics of industrial microbiology.

· The acquisition extended knowledge of selected topics in the field of industrial microbiology and biotechnology especially in the areas of the greatest economic importance such as dairy, brewing, brewing, wine production, yeast, antibiotics, biopolymers and related issues such as GMP, GLP, HACCP, safety and hygiene, cleaning and disinfection, scale-up, technology and equipment.

· Obtaining the ability to apply a variety of experimental methods needed to work in the biotechnology research and industry.

· Mastering of linguistic tools and skils in the collection, compilation and critical presentation of information obtained in the course of work.

· Prepare the student for independent or collaborative analytical work and research, discussion of results, formulation of opinions and writing reports.

Biological and biochemical characteristics of selected groups of microorganisms used in industrial processes. Biotechnological aspects of the production technology: food (wine, beer, bread, butter, cheese, yogurt), organic compounds (organic solvents, antibiotics, vitamins). The use of microorganisms for biotransformation of chemical compounds and as bioindicators. Microbial corrosion. The basic technological solutions. Scaling-up biotechnological processes. Bioreactors. Issues associated with magnification scale. Introduction to organizational and legal issues related to the production (GMP, GLP, HACCP, ISO, PKN).

Student: · knows and understands the importance of

mathematical and statistical methods needed to describe, interpret phenomena and processes and planning experience,

· has a basic knowledge of industrial microbiology,

· has an extensive knowledge of the processes and the most important technologies used the main fields of industrial microbiology,

· is familiar with the basic concepts, terms and methods used in the research of industrial microbiology,

· is able to link theoretical knowledge of biochemistry, biotechnology, molecular biology and microbiology with its practical use in industry, health and the environment,

· knows the basic rules of health and safety in work and standardization in the industry,

· read and understand the scientific literature in the field of industrial microbiology in English,

· can take advantage of the online resources available and the literature to obtain information on industrial microbiology,

· carry out simple experiments or research expertise under the guidance of a tutor in industrial microbiology,

· uses basic statistical methods and information technology to describe the experimental data,

· makes the synthesis of information from various sources and the correct inference from them,

· use appropriate language and scientific

terminology · understands the need for continuing self-

education including deepening expertise in industrial microbiology,

· know how to work as a team, working together to solve problems

· understands the need for careful planning tasks, scientific experiments, production planning and ergonomics,

· is able to think and act in an entrepreneurial manner.

Bioprocess Engineering

Acquisition of the skills of using various experimental techniques required for employment in the bioprocess engineering.

Lecture: Microorganisms of industrial importance; the isolation, preservation and improvement of industrially important microorganisms; the development of inocula for industrial fermentations; media for industrial bioprocesses; sterilization; classification of microbial growth techniques and kinetics, the recovery and purification of fermentation products; fermenters - structure, functions, division; examples of industrial production of biomass and secondary and primary metabolism products; economics of bioprocess engineering; mass and energy balance of the microbial growth in industrial processes. Laboratory: · Unit processes of bioprocess engineering

associated with the separation and purification: extraction, sublimation, filtration, crystallization of small organic compounds and protein molecules. The control and selection of appropriate conditions for an increase in the efficiency of unit processes.


description of the basic biological phenomena and processes using in bioprocess engineering.

· is able to link theoretical knowledge of biochemistry, biotechnology, molecular biology and microbiology with its practical application in industrial realization of biotechnology.

· can analyze data and draw conclusions in the field of bioprocess engineering with the use of qualitative and quantitative analysis methods and a thorough knowledge of the biochemistry, biotechnology, molecular biology and microbiology.

· can identify the methods and technologies used in bioprocess engineering.

· can describe selected topics in the area of bioprocess engineering using specialist language.


· Balance and kinetic aspects of industrial bioprocesses: the element composition of microbial with industrial use, concept of C-mole, mass and energy balance of the microbial growth in industrial processes, kinetics of thermal sterilization.

· Principles of the working of bioreactors and criteria for selection of a type of bioreactors.

Enzymology

Objectives of education are: basic knowledge of enzyme kinetics, the parameters of the enzymatic reaction, mechanisms of action of enzymes and inhibitors, dependence on the temperature and pH of the enzymatic activity, knowledge of the structure of enzymes and amino acids that build active sites of enzymes.

Lecture: Course is devoted to the structure, mechanisms of action and enzyme kinetics. Topics covered: equations of enzyme kinetics (Michaelis-Menten, Briggs-Haldane); the basic parameters of the enzymatic reaction (kcat, Km, kcat / Km); the kinetics of the first row, pseudo-first-row, second row; chemical catalysis (acid-base catalysis, electrostatic, involving metal ions, electrophilic); theories explaining the acceleration of the enzymatic reaction (a transition-state theory, collision theory); mechanisms and types of inhibition (competitive, acompetitive, noncompetitive, irreversible); effect of pH and temperature on enzymatic reactions (Arrhenius equation, the dependence of kinetic parameters on pH); the mechanism of action of serine proteases (acyl-enzyme detection, the reaction catalyzed by chymotrypsin); allosteric enzymes (enzymes with subunits, MWC model, KNF model, phosphofructokinase); the structure of enzymes. Laboratory: Elements of enzymes kinetics necessary for understanding of the mechanism of action and a quantitative description of the enzymatic activity.


description of the basic enzymatic phenomena and processes;

· knows and understands the importance of mathematical and statistical methods required for the description, interpretation of enzymatic phenomena and processes;

· knows the basic concepts, terms and techniques used in enzymology; acquires knowledge of the basic techniques and research tools used in enzymology;

· is able to link theoretical knowledge of enzymology with its practical application in industry, health care and environmental protection;

· reads and understands the scientific literature in the field of enzymology in English;

· uses basic statistical methods and computer technology to describe enzymatic reactions and analysis of experimental data;

· uses proper scientific language and terminology in discussions of problem with specialists in enzymology;

· learns on himself on given subject;

Topics covered: determination of kinetic parameters of the synthetic substrate hydrolysis catalyzed by trypsin, determination of the concentration of active trypsin inhibitor (BPTI) by titration with trypsin inhibitor; measurement of association constant of chymotrypsin-BPTI complex by the measuring of residual enzyme activity; specific, chemical modifications of amino acid residues in the active center of trypsin and chymotrypsin by PMSF and TLCK, and its effect on enzyme activity.

· understands the need for continuing education throughout the whole life, as well as need for careful planning of tasks and scientific experiments.

Immunology

After completion of this course student should understand basic regulatory mechanisms in human immune system, should know mechanisms of action of immunomodulating drugs, methods of production and use of antibodies. After completion of laboratory lessons student should be able to analyze quantitatively and qualitatively immune cells from human peripheral blood and to study such functions of immune cells as phagocytosis and production of reactive oxygen species. Student should be able to project and perform ELISA tests.

Structure and function of the immune system. Innate and acquired immunity. Immunoglobulins, their types and function. Immune tolerance, MHC system and its functions. Immunology of reproduction, immune tolerance towards fetus, immune causes of infertility. Immunity of newborns. Grafts and immunosuppression. Primary and acquired immunodeficiences. Autoimmunity, causes, symptoms and treatment. Allergies, diagnostics and treatment. Vaccination. Tumor immunology. Inflammation and anti-inflammatory drugs. Immune techniques in diagnostics and in research. Antibodies, polyclonal and monoclonal, modifications of antibodies and their use.

Student: · is able to analyze quantitatively and

qualitatively describe immune processes in human body,

· is able to perform reasoning based on acquired data and should be able to interpret them.

· knows current tools and methods used in immunology.

· performs basic physical and chemical measurements inside and outside the laboratory

· has gained continuous interest in advances of immunology.


Economics

The aim of Economics lecture is: · Development of the basic knowledge of

economics theories and analyses through learning of: demand, supply, market, consumer choice, GDP, inflation, unemployment, economic growth and government policies;

· Acquisition of knowledge of basic economic indicators;

· Preparation of the student to conduct: an independent or collaborative research practice;

The presented material will enable the students to understand better the evolutionary mechanisms of economic development, market mechanisms in capital economy.

Economics and the economy. Tools of economic analysis. Demand, supply and the market. Elasticities of demand and supply. Consumer choice and demand decisions. Costs and supply. Perfect competition and pure monopoly. Market structure and imperfect competition/The labour market. Welfare economics. Government spending and revenue. Natural monopoly: public or private? Fiscal policy and foreign trade. Money and banking. Monetary and fiscal policy. Aggregate supply, prices and adjustment to shocks. Inflation, expectations and credibility. Unemployment. Economic growth. International trade. Poverty, development and globalisation.

Student: · knows computational methods known in the

field of statistics, as well as computer tools allowing for data analysis and interpretation of the results

· makes the synthesis of information from various sources and is capable of correct conclusions based on them

· knows how to orally present in English treatises from selected scientific issues and make discussions

· learns on himself on given subject · knows how to work as a team, works together

to solve problems and perform scientific experiments


Documents

Objectives Content Learning outcomes Plant Biology · lipids, nucleotides and nucleic acids. Learning the nomenclature and techniques used in protein, lipids and carbohydrates biochemistry