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Final state exams

N-BCT Biochemical and Cellular Technologies

  • The Master’s final state examination in the Biochemical and Cellular Technologies programme includes Thesis defense and two subjects: (1) Advanced biochemistry and its methods and (2) Cellular technologies.
  • The students will be required to demonstrate a deep understanding of the fields, utilizing the knowledge obtained in the compulsory courses.

Final state exam subject areas

Advanced biochemistry and its methods

Biochemistry

  1. Amino acids, peptide bond, peptides, proteins. Composition, structure and function of proteins, primary, secondary, tertiary, quaternary structure.
  2. Saccharides, glycosides, oligosaccharides, polysaccharides (starch, glycogen, chitin), heteropolysaccharides.
  3. Lipids, acylglycerols, phospholipids, sphingolipids, steroids.
  4. Nucleic acids, nucleosides, nucleotides, DNA, RNA. Composition, structure and function of nucleic acids. Base pairing, double helix. Genetic information, gene, genetic code. Reading frames. Nucleic acid sequences and methods for their determination.
  5. Thermodynamics in biochemistry, high-energy molecules, reaction kinetics, enzymes, their active site, prosthetic groups, coenzymes, mechanism of enzyme catalysis.
  6. Coenzymes and vitamins, nicotinamide and NAD, flavins, ATP, AMP, cAMP, biotin, thiamin, coenzyme A, lipoic acid, folic acid, pyridoxal phosphate, vitamin B12, metalloporphyrins, iron-sulfur proteins, vitamin C, lipophilic vitamins.
  7. Michaelis-Menten equation, Km, turnover number, enzyme activity.
  8. Anabolism, catabolism, their regulation, anaerobic glycolysis.
  9. Gluconeogenesis, synthesis of PEP, glycogenolysis, synthesis of glycogen, Cori cycle.

Bioinformatics

  1. Molecular phylogeny. Phylogeny data. Trees and methods of their building-up.
  2. Gene and promotor prediction. Prokaryotes. Eukaryotes. Prediction based on sequence homology, ab initio Tools and programs for gene prediction.
  3. Tools for nucleic acid analysis. Palindromes. Restrictases and restrictase on-line databases. PCR. Primer design.
  4. RNA properties and tools for their prediction. RNA structure prediction. RNA bioinformatics.
  5. Prediction of protein properties. Prediction of protein basic properties and localization. Prediction of posttranslational modifications. Prediction of interacting partners.
  6. 2D, 3D, and 4D protein structure prediction. Coordinates. Formats. Visualization tools.
  7. Saccharides and lipids. Structure, importance and function. Bioinformatical potential of saccharides. Glycoproteins and their encoding in genome. Nomenclature and graphical representation. Databases and tools for glyco- and lipido-bioinformatics.
  8. Small molecules. Importance, function, databases.

Biotechnology

  1. Microbial pharmaceutical biotechnology: Introduction to pharmaceutical production. Selection of production systems. Optimization of fermentation. Separation and purification of intracellular and extracellular products. Drying of fermentation products and final processing. Finalization of obtained products. Biotransformation.
  2. Animal cell biotechnology: Introduction to animal cells and their characteristics. Potency and differentiation, Hayflick limit, immortalized cell lines, cultivation and differentiation. Use of animal cells for pharmaceutical production. Use of stem cells in drug screening and production. Animal cells and cell therapy. Special applications and future perspectives (3D cultivation, organoids, 3D bioprinting, in vitro tissue and organ substitutes).
  3. Plant and photosynthetic biotechnology: Introduction to plant cell physiology. Methods for the development of GMO crops, their applications, and risks. Plant-based production of biotechnologically significant compounds. Evolution of photosynthesis and endosymbiosis. Structure of pigments and energy conversion mechanisms. Carbon dioxide fixation and genetic improvement of photosynthesis. Photosynthetic microorganisms and cultivation methods. Optimization of production and control of cultivation processes.

Nanobiotechnology

  1. Carbon nanotubes, semiconductor nanoparticles – quantum dots. Metal-based nanostructures – nanowires and bioelectronics. Gold nanoparticles (nanorods, nanocages, nanoshells). Magnetic nanoparticles. Photon-upconversion nanoparticles. Polymer nanostructures (dendrimers). Protein-based nanostructures – nanomotors from microbes and mammalian cells (myosin). Nanomachines based on nucleic acids.
  2. Experimental techniques. Scanning probe microscopies (STM, AFM, SNOM, SECM). Physical principles, basic and advanced measuring modes. Imaging of bioobjects – from atoms and molecules to cells and tissues. Combined techniques with inverted optical and fluorescence microscopes. Raman imaging. Biointeractions at the molecular level.
  3. Self-assembling techniques. Separation, characterization and modification of nanoparticles. From natural to artificial structures. Nanolithography and nanomanipulations. Nanoparticles for biological labeling and cellular imaging. Nanobiosensors and nanobioanalytical systems. Microfluidics, cell sorting and lab-on-a-chip. Biochips and sensing arrays, nanodeposition of biomolecules.
  4. Medical applications. Cytotoxicity of nanoparticles. Nanostructures in drug discovery, delivery, and controlled release. Nanostructures in cancer research. Nanotechnology for tissue engineering and regenerative therapy.

Immunochemical techniques

  1. Immune system. General introduction to the immune system, innate and adaptive immune system, lymphoid organs, B cells, clonal selection, generation of antibody diversity, affinity maturation, complement system, immunoglobulin superfamily and function of antibody classes IgG, IgM, IgD, IgA, IgE, antibody binding, affinity vs. avidity, antigen determinants, raising an immune response in laboratory animals, generation of monoclonal antibodies.
  2. Antibodies as immunological tools. Handling of antibodies, antibodies as immunochemical reagents, antibody affinity, antibody engineering, monoclonal antibodies, antibody alternatives: recombinant, humanized, cameloid, heavy chain antibodies, phage display, aptamers (SELEX), molecularly imprinted polymers (MIPs).
  3. Definition and key developments of immunoassays, applications of immunoassays (diagnostic, environmental, food safety), labeling and signal amplification strategies (enzymes, fluorophores, NPs, radionuclides, immune PCR, chemiluminescence), matrix interference (medical, environmental samples) and non-specific binding, analytical parameters (sensitivity, limit of detection), competitive and non-competitive assays, heterogeneous and homogeneous immunoassays, RIA, ELISA, nanoparticle-based assays, fluorescence polarization, fluorescence resonance energy transfer (FRET), lateral flow assays, biosensors, microarrays, suspension arrays (magnetic beads), multiplexing, single-molecule immunoassays.
  4. Immunoaffinity techniques. Immune agglutination/precipitation, immune diffusion, immunoblotting, co-immunoprecipitation, analysis of protein-protein interactions, affinity chromatography.
Cellular technologies

Cell biology

  1. Cellular and noncellular forms of life: history and technical limits of cellular analyses by microscopy, light and electron microscopy, organization of living system, noncellular forms of life, cellular forms of life – types of prokaryotic and eukaryotic cells, basic chemistry of a cell (chemical elements in living systems, atomic bonds in molecules, main types of organic molecules), principles of functional organization of a cell.
  2. Storage and expression of genetic information: definitions of a gene and genetic information, main functions of genetic material, chemistry of genetic material, structure of DNA and RNA, replication of DNA, principles of gene expression, prokaryotic and eukaryotic transcription, modification of primary transcript, RNA splicing, translation and genetic code.
  3. Biomembranes and internal cell organization: structure and function of biomembranes, transport function of biomembranes, plasmatic membrane, osmotic phenomena, biomembranes of prokaryotic cells, compartmentalization of eukaryotic cells, organelles of eukaryotic cells – composition and function, membrane fusion, principles of vesicular transport, endocytosis and exocytosis.
  4. Cytoskeleton: components and basic functions, methods of visualization, microtubules, actin filaments, intermediate filaments, nuclear and cortical skeleton, cytoskeleton of prokaryotes.
  5. Intracellular transport: cell compartmentalization, protein folding and chaperons/chaperonins, protein sorting, protein import to membrane organelles, transport of molecules to nucleus, secretion and endocytic pathways, transport vesicles, endoplasmic reticulum and Golgi apparatus in intracellular transport.
  6. Cell cycle: phases and kinetics of a cell cycle, molecular principles of cell cycling, cell cycle regulators, types of cyclins, cell cycle checkpoints, p53 and Rb proteins in cell cycle regulation, models and methodical approaches to cell cycle research.
  7. Cell division: types of cell division, binary division in prokaryotes, changes of chromatin during eukaryotic cell division, composition of eukaryotic chromosomes, mitosis and meiosis, roles and phases of mitosis and meiosis, cytokinesis in plant and animal cells.
  8. Extracellular matrix- and cell-cell interactions: the cell wall of prokaryotes, the cell wall of plants and fungi, extracellular matrix (ECM) of animal cells, ECM composition and function, ECM-cell interactions, cell-cell interactions (adhesion belts, desmosomes, plasmodesmata, tight junctions, gap junctions).
  9. Cell pathology: physiological and pathological life conditions, cell response to stress, types of stress factors, physical stress factors (temperatures shifts, visible light, UV light, ionizing radiation), chemical stress factors (nonspecific toxins, specific inhibitors), biological stress factors – intracellular parasitism, types of cell death, physiological cell death (autophagy, apoptosis), catastrophic cell death – necrosis.
  10. Cell evolution: hypotheses on origin of organic compounds and biopolymers, Miller test, ribozymes and RNA world, primitive proteosynthesis, encapsulation, origin of first cells, evolutionary relations among cells, origin and development of eukaryotic cell, endosymbiotic theory.

Gene technologies

  1. Chemical structure of nucleic acids, transcription and its regulation by prokaryotes (sigma factor, LAC operon, activators and repressors) and eukaryotes (enhancers of transcription, epigenetics), translation and its regulation by prokaryotes and eukaryotes.
  2. Model organisms used in biotechnology – bacteria ( coli), yeast (Pichia, Saccharomyces) and fungi (Penicillium), Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, house mouse, animal cell cultures, Arabidopsis thaliana, viruses (bacteriophages, retroviruses). DNA replication in eukaryotes and prokaryotes, repair processes, in vitro DNA synthesis (PCR, reverse transcription).
  3. Basic technologies of recombinant DNA – enzymes, vectors, transformation methods, construction of gene libraries. Genome editing techniques, CRISPR.
  4. Recombinant proteins – protein expression in bacteria (cloning strategies, codon usage, reduction of toxic effects due to overproduction, increased stability and secretion, glycosylation), protein expression in eukaryotic cells (yeast, insect cells, mammalian cells), advantages and disadvantages of individual expression systems.
  5. Genomics and gene expression – gene mapping techniques, non-coding parts of the genome, bioinformatics tools, pharmacogenetics, DNA microarrays, RNA-seq techniques, metagenomics, epigenetics.
  6. RNA-based technologies – RNA division, importance of non-coding RNAs, antisense RNAs and gene silencing, ribozymes.
  7. Transgenic plants – tissue cultures, plant genetic engineering, functional genomics, biotechnological applications. Transgenic animals – production techniques, methods of transgene expression control, application of RNA technologies, examples of transgenic animals.
  8. Gene therapy – congenital defects in higher organisms, identification of defective genes, general principle of gene therapy, gene therapy using retroviruses and adenoviruses, aggressive gene therapy, use of RNA in therapy, targeted gene editing.

Immunology

  1. Immunes system, cells and organs of the immune system.
  2. Phagocytes, inflammation, complement.
  3. Antigens, major histocompatibility complex, antigen presentation.
  4. Origin and development of T- and B-lymphocytes.
  5. Antibodies, their structure, characteristics and functions.
  6. Cell communication in immune system.
  7. Infectious diseases, immunity against viruses, bacteria, fungi, and parasites.
  8. Autoimmunity, primary and secondary immunodeficiencies.
  9. Allergy and hypersensitivity.
  10. Immunomodulation, vaccination.
  11. Transplantation and cancer immunology.

DNA diagnostics

  1. Nucleic acid extraction, isolation, and purification, quantitation methods, agarose and polyacrylamide gel electrophoresis.
  2. PCR, principles of PCR, factors influencing PCR performance, isothermal amplification.
  3. DNA polymorphisms and restriction analysis: types of DNA polymorphisms, restriction enzymes and RFLP analysis.
  4. Real-Time PCR: quantitative PCR principles, fluorescence-based detection methods (SYBR Green, TaqMan probes), clinical applications in virology, oncology, pharmacogenomics.
  5. DNA microarrays, and sequencing (Sanger, NGS, third-generation technologies).
  6. Molecular diagnosis of genetic diseases, human identification, paternity testing, forensic applications.
  7. DNA diagnostics of infectious diseases: molecular detection of bacteria, fungi, and viruses, sample collection and preparation, quality assurance.

Cell signaling

  1. Signaling mechanisms: irritability, intercellular signaling, reception of external signals, signaling components, processing of multiple signals, signaling networks.
  2. First messengers: hormones (amino acid derivatives, peptides, proteins, nucleotides, fatty acid derivatives, steroids, retinoids, and small inorganic molecules), neurotransmitters, growth factors, differentiation factors, cytokines, inflammatory mediators, vasoactive agents, hydrophobic messengers, adhesion molecules.
  3. Receptors and ion channels: transmembrane receptors (G-protein coupled receptors, receptors with protein kinase activity, receptors coupled to protein kinases, and ligand-gated ion channels), intracellular receptors, ligand binding, agonists and antagonists.
  4. Second messengers and protein kinases: cytosolic messengers (Ca2+, cAMP, cGMP, and IP3), membrane-bound messengers (DAG and PIP3), protein kinases (PKA, PKG, and PKCs).
  5. Gene expression regulation: constitutive and regulatory transcription factors (developmental, ligand-activated, and signal-activated), MAPKs.
  6. Regulation of cell reproduction, proliferation, and differentiation: cell cycle phases, cyclins, CDKs, CKIs, ErbB receptors, RAS-MAP, STAT, TGF-beta receptors, WNT.
  7. Signaling in the immune system: innate immunity, Toll-like receptors, inflammation signaling (TNF, chemokines, and integrins), adaptive immunity, TCR, interleukins, interferon signaling.
  8. Nutrient signaling: signaling pathways of insulin, glucagon, adrenalin, aldosterone, and cortisol.
  9. Sensory signaling: visual system (rhodopsin and G-protein-coupled transduction mechanism), sense of smell and taste (metabotropic receptors and ion channels), sound perception.
  10. Muscle signaling: adrenoreceptors, cholinergic receptors, muscle contraction (striated muscle and smooth muscle).
  11. Malfunction in signaling: tumorigenesis (mutations, oncogenes, tumor suppressors, p53, apoptosis, caspases).

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