Molecular Biology 1400-215BM
DNA structure. DNA replication in eukaryotic organisms. Details of Okazaki fragment structure and role in DNA replication and issues regarding its termination. The role and structure of telomere. DNA damage types and their repair mechanisms. Non-homologous end joining and homologous recombination.
Tools in molecular biology and DNA sequencing. Chemical synthesis of oligonucleotides and their application in PCR. Enzymes utilised in molecular biology laboratory procedures. Methods for genome sequencing: Sanger’s method and next generation sequencing. The history of human genome sequencing. DNA data storage.
Genome structure, its elements and evolution. The first sequenced genomes and their characteristics. Hypotheses regarding the evolutionary origin of genes. Key structural elements of genes. Genome organisation. Transposable elements, their structures and mechanisms of transposition.
Examples of different regulatory mechanisms of gene expression in prokaryotic organisms at the level of initiation and termination of transcription (e.g. Lac operon, arabinose operon, tryptophan operon. attenuation). Expression of prokaryotic genes: regulatory mechanisms. Regulation at the following levels (i) post-transriptional level with the participation of proteins and regulatory RNA (including riboregulation, riboswitches), (ii) translation and (iii) post-translational level. Operon, regulon, modulon. Global regulation at the cellular (including a two-component regulatory system) and the entire population level (including quorum sensing). DNA replication in bacteria.
Eukaryotic replication, recombination and DNA repair. Chromatin. Structure of genetic material of eukaryotes: histones, nucleosomes, higher order structures of chromatin. RNA: transcription and processing. Regulation of eukaryotic transcription: RNA polymerases, transcription factors, chromatin remodeling, histone modifications. Interference RNA: microRNA and RNAi.DNA methylation and epigenetic mechanisms.
Eukaryotic translation. Amino acids and polypeptide chain. Primary, secondary, tertiary and quarternary protein structure. Protein folding. Chaperones, chaperonins. Posttranslational modifications of proteins.
Restriction endonucleases and enzymes used to modify DNA. DNA recombination and cloning. Methods applied to introduce DNA to bacterial cells. Competent cells and bacterial transformation. Plasmid vectors. Antibiotics applied in molecular biology. Isolation of plasmid DNA, DNA electrophoresis, estimation of its purity and quality. Application of Escherichia coli lac operon in DNA cloning. Methods applied to the selection of recombinant DNA, alfa-complementation. Catabolic repression.
Purification of the recombinant enzymatic protein expressed in E. coli cells by the means of immobilized-metal affinity chromatography (IMAC). Evaluation of the quality of protein preparations, what includes: i) evaluation of catalytic activity in the protein preparation, ii) analysis of protein purity by SDS polyacrylamide gel electrophoresis (SDS PAGE) (various gel staining techniques, Coomassie Brilliant Blue staining, silver staining and staining with fluorescent dye, will be compared), iii) immunological identification of the protein by Western blotting (secondary antibodies conjugated with alkaline phosphatase or horseradish peroxidase will be used and various detection methods, including enhanced chemiluminescence, will be applied).DNA isolation from plant cells.
Transgenic plants as examples of genetically modified organisms - generation, application and analysis. Transformation of tobacco plants - leaf infiltration with the Agrobacterium tumefaciens bacterial culture carrying the genetic construct with the marker gene.
Reporter genes, like green fluorescent protein (GFP), luciferase, glucouronidase (GUS), etc, often used to indicate of whether a certain gene has been taken up by or expressed in the plant . The methods of testing protein interactions, such as yeast two-hybrid system, FRET (Föster Resonance Energy Transfer) will also be discussed and presented.
Databases of scientific publications (PubMed) and sequences of DNA and proteins. Analysis of SC5316 gene (alcohol dehydrogenase 2) to plan the cloning of the gene into pCAMBIA plasmid, what includes: i) searching the DNA sequence in database (BLAST), ii) selection of restriction enzymes, iii) PCR primers design. Gene function prediction on the basis of protein domain analysis and basic phylogenetic analysis.
Molecular biology methods used in analyses of Arabidopsis mutants and transgenic lines. Plant genetics - forward and reverse genetics approaches for Arabidopssi thaliana model; mutagenesis and forward genetic screen of Arabidopsis mutants; mapping of point and insertional mutations, PCR analysis of polymorphic sequences in two Arabidopsis ecotypes.
Type of course
Having completed the course and the lab the student:
1. He has basic knowledge in the field of molecular biology. Know and understand the molecular basis of the functioning of prokaryotic and eukaryotic cells (K_W01 Bt1).
2.He can identify the most important scientific discoveries in the history of molecular biology (K_W02 Bt1).
3. Demonstrates knowledge of basic techniques and tools in the study of natural phenomena in the field of molecular biology (K_W04 Bt1).
4. Knows the basics of the planning and construction of genetic modifications in biological material (K_W04 Bt1).
5. Knows the basics of information technology and use of tools for obtaining information from databases (K_W08 Bt1).
1. Uses basic techniques appropriate for molecular biology (K_U01 Bt1).
2. Is able to use basic databases of scientific papers as well as DNA and protein sequences (K_U03 Bt1).
3. Performs basic research experiments in molecular biology under the supervision (K_U04 Bt1).
4. Demonstrates the ability of correct reasoning on the basis of experimental data (K_U06 Bt1).
1. Demonstrates responsibility for the own safety and the safety of others (K_K03 Bt1).
2. Demonstrates responsibility for the entrusted equipment in the laboratory of molecular biology (K_K03 Bt1).
3. It has the ability to effectively perform experimental work in a team (K_K04 Bt1).
In order to complete the laboratory student is obliged to: (i) attend at least 85% of classes; (ii) work during the laboratory classes in a way that allows positively assess the knowledge, skills and social competence, which were obtained in the course of the classes (described in the syllabus as a subject educational outcomes); (iii) pass the final test.
Detailed conditions: (i) attendance and active participations in the classes; (ii) passing the written test, including both open and close-ended questions. Duration of the test: 90 minutes. To pass the test, one should get more than half of the points.
In order to complete the whole course student is obliged to pass the final exam, for which one is admitted on the basis of assessment of laboratory classes. The final exam consists of four parts concerning: (i) genomics, (ii) the molecular biology of prokaryotes, (iii) the molecular biology of eukaryotes, (iv) the basic knowledge of proteins. To pass the exam, student must get a positive grade for each component of the exam. The final grade is the average of the ratings of the individual parts. Form of the exam: written (multiple choice test, multiple response test, open-ended questions). Duration of the exam: 120 minutes.
Biologia molekularna bakterii. J. Baj, Z. Markiewicz. Wyd. PWN.
Mikrobiologia. J. Baj. Wyd. PWN. 2018
Biochemia. J.M. Berg, J.L. Tymoczko, L. Stryer. Wyd. PWN.
Biologia molekularna. Krótkie wykłady. P.C. Turner, A.G. McLennan, A.D. Bates, M.R.H. White
Ćwiczenia z biochemii. L. Kłyszejko - Stefanowicz
Genetyka molekularna. P. Węgleński. Wyd. PWN.
Genomy. T.A. Brown
Introduction to Protein Structure. C. Branden, J. Tooze, Garland Publ.
Genes IX. B.Lewin
Brock Biology of Microorganisms. M.T. Madigan, J.M. Martinko
Materials provided by the teaching team.
Information on level of this course, year of study and semester when the course unit is delivered, types and amount of class hours - can be found in course structure diagrams of apropriate study programmes. This course is related to the following study programmes:
Additional information (registration calendar, class conductors, localization and schedules of classes), might be available in the USOSweb system: