University of Warsaw - Central Authentication SystemYou are not logged in | log in
course directory - help

Molecular Biology

General data

Course ID: 1400-215BM Erasmus code / ISCED: 13.104 / (0511) Biology
Course title: Molecular Biology Name in Polish: Biologia molekularna
Organizational unit: Faculty of Biology
Course groups: Requisite courses for second-year students of Biology
Requisite subjects for second-year students of Biotechnology
ECTS credit allocation (and other scores): 8.00 OR 6.00 (depends on study program)
view allocation of credits
Language: Polish
Type of course:

obligatory courses

Prerequisites:

Biochemistry D 1400-113BCH
Genetics and Genetic Engineering 1400-114GEN

Prerequisites (description):

Students are obliged to complete the 1st year of the first level studies (Bachelor's) before starting the subject

Mode:

Classroom

Short description:

Discussion of selected genomes and methods of their sequencing. Genome evolution. DNA microarrays. Mechanisms for the regulation of prokaryotic gene expression at the level of transcription initiation and post-transcriptional. Global regulation of gene expression in bacteria (regulons, quorum sensing). DNA replication. Chromatin. Eukaryotic recombination and DNA repair. Regulation of eukaryotic transcription. RNA interference. Epigenetic mechanisms. Eukaryotic translation. Amino acids and polypeptide chain. Protein folding. Posttranslational modifications of proteins.

Laboratory classes are divided into three blocks run by employees of the Institute of Biochemistry, the Institute of Experimental Biology and Plant Biotechnology, and the Institute of Microbiology.There are four meetings within each part. Classes cover methods of DNA cloning and manipulation, recombinant proteins isolation, methods of plant molecular biology and basics of DNA sequence analysis and databases.

Full description:

Lecture.

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 and recombination 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.

Laboratory.

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), and BiFC (Bimolecular fluorescence complementation) will also be discussed and presented. The transient transformation of plants will be performed and the introduced gene expression will be analysed by observing the green fluorescence protein under the fluorescence microscope. The DNA constructs used during the experiment contain genes encoding GFP translational fusions with proteins from various parts of the cell. This will allow the localization of these proteins to be analyzed. Observations of plants expressing the glucuronidase gene under the control of various tissue-specific promoters will be carried out.

The course will discuss the real-time PCR technique, principles of operation, including specific and non-specific detection of nucleic acids, and issues related to experiment planning, such as the selection of reference genes and the design of oligonucleotides. Variants of the method and possible applications will be presented.

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.

Bibliography:

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.

Learning outcomes:

Having completed the course and the lab the student:

KNOWLEDGE:

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).

ABILITIES:

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).

SOCIAL AWARENESS:

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).

Assessment methods and assessment criteria:

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 participation in the classes; (ii) fulfillment of tasks assigned for self preparation (iii) 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. Form of the exam: written (single-choice test, multiple choice test, open-ended questions, essay questions). The condition for passing it is to obtain 60% of the possible points.

Practical placement:

No.

Classes in period "Winter semester 2020/21" (past)

Time span: 2020-10-01 - 2021-01-31
Choosen plan division:


magnify
see course schedule
Type of class: Class, 60 hours more information
Lecture, 30 hours more information
Coordinators: Agnieszka Girstun, Monika Radlińska
Group instructors: Monika Adamczyk-Popławska, Rafał Archacki, Agnieszka Girstun, Piotr Golec, Takao Ishikawa, Roksana Iwanicka-Nowicka, Marta Koblowska, Helena Kossowska, Piotr Kowalec, Piotr Kozłowski, Agnieszka Kwiatek, Monika Radlińska, Joanna Trzcińska-Danielewicz
Students list: (inaccessible to you)
Examination: Course - Examination
Class - Grading
Lecture - Examination

Classes in period "Winter semester 2021/22" (in progress)

Time span: 2021-10-01 - 2022-02-20
Choosen plan division:


magnify
see course schedule
Type of class: Class, 60 hours more information
Lecture, 30 hours more information
Coordinators: Agnieszka Girstun, Monika Radlińska
Group instructors: Monika Adamczyk-Popławska, Rafał Archacki, Agnieszka Girstun, Piotr Golec, Takao Ishikawa, Roksana Iwanicka-Nowicka, Marta Koblowska, Helena Kossowska, Piotr Kowalec, Piotr Kozłowski, Agnieszka Kwiatek, Monika Radlińska, Joanna Trzcińska-Danielewicz
Students list: (inaccessible to you)
Examination: Course - Examination
Class - Grading
Lecture - Examination
Course descriptions are protected by copyright.
Copyright by University of Warsaw.