Designed for 3rd-year BSc and 1st-year MSc students in life sciences with abackground in organic chemistryThe course will start the week of October 6. The date and time - Doodle
This course introduces the fundamentals of chemical biology through the lens of organic chemistry, based on Introduction to Bioorganic Chemistry and Chemical Biology by Van Vranken & Weiss. Students will explore how chemical principles and synthetic tools are used to understand and manipulate biological molecules and processes. Topics include the structure and reactivity of nucleic acids, proteins, carbohydrates, lipids, and natural products, as well as modern tools such as chemical probes, bioorthogonal reactions, and imaging agents. Emphasis is placed on applications relevant to cell signaling, enzyme function, and gene expression. Designed for 3rd-year BSc and 1st-year MSc students in life sciences with a background in organic chemistry, the course combines lectures, problem-solving, and analysis of real-world case studies to develop a molecular-level understanding of biological systems.
The Chemical Biology course will begin the week of October 6. The exact date and time will be determined based on an additional Doodle selection.
Last update: Šebková Nataša, RNDr., Ph.D. (22.09.2025)
Tento kurz představuje základy chemické biologie z pohledu organické chemie a vychází z knihy Introduction to Bioorganic Chemistry and Chemical Biology autorů Van Vranken a Weiss. Studenti se seznámí s tím, jak jsou chemické principy a syntetické nástroje využívány k pochopení a ovlivňování biologických molekul a procesů. Témata zahrnují strukturu a reaktivitu nukleových kyselin, proteinů, sacharidů, lipidů a přírodních látek, stejně jako moderní nástroje, jako jsou chemické eseje, bioortogonální reakce a zobrazovací činidla. Důraz je kladen na aplikace relevantní pro buněčnou signalizaci, funkci enzymů a genovou expresi. Kurz je určen pro studenty 3. ročníku bakalářského a 1. ročníku magisterského studia v oblasti biologických věd se znalostmi organické chemie. Kombinuje přednášky, řešení problémů a analýzu případových studií z praxe s cílem rozvíjet porozumění biologickým systémům na molekulární úrovni.
Kurz bude zahájen v týdnu od 6. října. Přesné datum a čas konání bude stanovený na základě dodatečného Doodle výběru.
Last update: Šebková Nataša, RNDr., Ph.D. (22.09.2025)
Literature -
Main source: Introduction to Bioorganic Chemistry and Chemical Biology (David Van
Vranken and Gregory Weiss)
Last update: Šebková Nataša, RNDr., Ph.D. (15.05.2025)
Main source: Introduction to Bioorganic Chemistry and Chemical Biology (David Van Vranken and Gregory Weiss)
Last update: Šebková Nataša, RNDr., Ph.D. (26.06.2025)
Requirements to the exam -
Credit: Presentation of a published article in the field of Chem Biol.;
Written exam on the knowledge acquired during the study.
Last update: Šebková Nataša, RNDr., Ph.D. (26.06.2025)
Zápočet: Prezentace publikovaného článku z oboru Chem Biol.;
Písemná zkouška ze znalostí získaných v průběhu studia.
Last update: Šebková Nataša, RNDr., Ph.D. (26.06.2025)
Syllabus
1. The Fundamentals of Chemical Biology (The central dogma of molecular
biology, Genes and genomes, siRNA, monoclonal antibodies, immortal cancer
cell lines …) (HC)
2. The Chemical Origins of Biology (arrow-pushing in organic chemistry, prebiotic
chemistry, nonbonding reactions…) (HC)
3. Tools of Chemical Biology (biorthogonal reactions, chromophores, cell
imaging…) (MV)
4. DNA (Chemical and physical properties of DNA, forms of helixes, DNA
superstructures, chemical and biological synthesis of DNA, DNA analysis, DNA
as target for cytotoxic drugs…) (HC)
5. RNA (Chemical and physical properties of RNA, chemical and biological
synthesis of RNA, types of RNA, mRNA processing in eukaryotic cells,
degradation of RNA, ribosomal translation, RNA modifications and their role…)
(HC)
6. Peptide and Protein Structure (Genetic code and Amino acids, chemical and
biological synthesis of peptides/proteins, protein secondary and tertiary structure,
posttranslational modifications…) (MV)
7. Students Journal Club (Introduction of selected manuscript from Chemical
Biology field)
8. Protein Function (Receptor-Ligand Interaction, Organic Cofactors, Engineering
of new proteins, Introduction of modified amino acids…) (MV)
9. Glycobiology (Structure and nomenclature, the chemistry and enzymology of
the glycosidic bond, polysaccharides, glycoproteins, glycolipids, glucose
homeostasis…) (MV)
10. Chemical Control of Signal Transduction (Universality of chemical signaling,
nuclear and cell-surface receptors, receptor tyrosine kinases, Ion channels…)
(HC+MV)
11. Students Project Introduction (Student should identify the knowledge gap in
chemical biology field and propose potential project, which would solve this
problem) alternatively exam
Last update: Šebková Nataša, RNDr., Ph.D. (15.05.2025)
Learning outcomes
Chemical Biology – Learning outcomes (Bloom’s taxonomy)
After successfully completing the course, the student will be able to:
Define and explain key concepts in chemical biology (central dogma, genome, siRNA, monoclonal antibodies, cell lines) and describe their roles in modern life sciences. (Remember – Understand)
Explain chemical principles relevant to the origins of biology (prebiotic chemistry, noncovalent interactions) and interpret their significance for the emergence of biomolecules. (Understand – Analyze)
Apply core organic chemistry principles (reaction mechanisms / “arrow pushing”) to reactions relevant to biomolecules and chemical biology. (Apply)
Distinguish and compare major chemical biology tools (chemical probes, chromophores, imaging agents, tagging strategies) and select an appropriate tool for a given biological question. (Understand – Apply)
Describe and explain the principles of bioorthogonal and click reactions and evaluate their suitability for biological systems (selectivity, kinetics, toxicity, orthogonality). (Understand – Evaluate)
Characterize the chemical and physical properties of DNA (helix forms, superstructures) and explain how these properties influence biological function and DNA analysis. (Understand – Analyze)
Compare chemical and biological synthesis of DNA and RNA and evaluate their advantages and limitations for research and applications (e.g., modifications, purity, scalability). (Analyze – Evaluate)
Explain peptide/protein structure (secondary and tertiary structure) and analyze how post-translational modifications affect protein stability, localization, and function. (Understand – Analyze)
Analyze mechanisms of RNA processing and degradation in eukaryotic cells and interpret their impact on gene expression and translation. (Analyze)
Explain and apply concepts of receptor–ligand interactions, organic cofactors, and enzyme function to specific examples in cell signaling and regulation. (Apply – Analyze)
Describe core principles of glycobiology (glycosidic bond chemistry, nomenclature, polysaccharides, glycoproteins/glycolipids) and evaluate the roles of glycans in cellular processes and glucose homeostasis. (Understand – Evaluate)
Critically evaluate a selected chemical biology research paper (Journal Club): identify the hypothesis, assess experimental design and data, draw justified conclusions, and propose meaningful follow-up experiments. (Analyze – Evaluate – Create)
Last update: Macíčková Cahová Hana, Ing., Ph.D. (03.02.2026)
Entry requirements -
Passed exam in organic chemistry and biochemistry.
Last update: Šebková Nataša, RNDr., Ph.D. (26.06.2025)
Splněná zkouška z organické chemie a biochemie
Last update: Šebková Nataša, RNDr., Ph.D. (26.06.2025)
