Methods in Chemical Biology
A.Y. 2024/2025
Learning objectives
The aim of this course is to illustrate the modern methodologies applied at the chemistry/biology interface to observe, probe or interfere with relevant biological processes. The application of such methodologies to pre-clinical drug discovery will also be discussed.
The course will allow the students to: adapt to the ever-evolving chemistry field, especially in synergy with physics and biology; individually study and critically evaluate frontier research from primary literature; understand how to interfere with complex biological processes via small molecular probes or biorthogonal chemistry; improve their written and oral communication skills by means of individual or group presentation of selected case studies.
The course will allow the students to: adapt to the ever-evolving chemistry field, especially in synergy with physics and biology; individually study and critically evaluate frontier research from primary literature; understand how to interfere with complex biological processes via small molecular probes or biorthogonal chemistry; improve their written and oral communication skills by means of individual or group presentation of selected case studies.
Expected learning outcomes
At the end of the course, successful students will be able to explain how chemical and biophysical methods are used to study the regulation and function of biomolecules and to discuss the use of chemical biology in biomedical research and pre-clinical drug discovery.
In particular, they will be able: 1) to describe the chemical basis of replication, transcription, translation, post-translational modifications (PTMs) and how each of these central processes can be expanded to include new chemical matter; 2) to critically read and evaluate the literature and effectively communicate research in a peer setting; 3) to describe the substance and importance of chemical biology.
In particular, they will be able: 1) to describe the chemical basis of replication, transcription, translation, post-translational modifications (PTMs) and how each of these central processes can be expanded to include new chemical matter; 2) to critically read and evaluate the literature and effectively communicate research in a peer setting; 3) to describe the substance and importance of chemical biology.
Lesson period: First semester
Assessment methods: Esame
Assessment result: voto verbalizzato in trentesimi
Single course
This course can be attended as a single course.
Course syllabus and organization
Single session
Responsible
Lesson period
First semester
Course syllabus
1. What is chemical biology? Introduction to the course; the central dogma of molecular biology; genes and genomes; hydrogen bond and nonbonding interactions
2. DNA. Forms, structure, superstructures; chemical synthesis and DNA sequencing; operons, plasmids and recombinant DNA technology; site-directed mutagenesis.
3. RNA. Gene transcription; transcriptional control; unnatural amino acids incorporation, codon expansion.
4. Protein structure and function. Coding RNA translation; protein folding and unfolding, chaperones, protein-protein and protein-ligand interactions. Structure-function relationship; directed evolution.
5. Non-coding RNAs
6. Post-translational modifications.
7. Biorthogonal chemistry. NCL, SPAAC, etc
8. Glycobiology. The sugar code; carbohydrate binding proteins; self and non-self; cell adhesion; glycan arrays; glyco-conjugates and glycomimetics
9. Imaging. Fluorescent proteins, fluorophores, fluorogenic probes.
10. Signal transduction. Cell receptors, allosteric regulation, quorum sensing
11. Therapeutic biomolecules. Antibodies, Antibody-drug conjugates (ADCs), aptamers.
12. Paper discussion
2. DNA. Forms, structure, superstructures; chemical synthesis and DNA sequencing; operons, plasmids and recombinant DNA technology; site-directed mutagenesis.
3. RNA. Gene transcription; transcriptional control; unnatural amino acids incorporation, codon expansion.
4. Protein structure and function. Coding RNA translation; protein folding and unfolding, chaperones, protein-protein and protein-ligand interactions. Structure-function relationship; directed evolution.
5. Non-coding RNAs
6. Post-translational modifications.
7. Biorthogonal chemistry. NCL, SPAAC, etc
8. Glycobiology. The sugar code; carbohydrate binding proteins; self and non-self; cell adhesion; glycan arrays; glyco-conjugates and glycomimetics
9. Imaging. Fluorescent proteins, fluorophores, fluorogenic probes.
10. Signal transduction. Cell receptors, allosteric regulation, quorum sensing
11. Therapeutic biomolecules. Antibodies, Antibody-drug conjugates (ADCs), aptamers.
12. Paper discussion
Prerequisites for admission
Consolidated knowledge about structure and function of biological macromolecules and metabolic processes. Basic knowledge of protein-ligand interactions and enzyme kinetics. This content can be found, for example, in the course Biological Chemistry in the Bachelor degree programs in Chemistry and Industrial Chemistry (UNIMI).
Teaching methods
The course is delivered mainly by classroom lectures, possibly integrated by seminars on specific course topics.
Teaching Resources
Introduction to Bioorganic Chemistry and Chemical Biology, 1st Edition
by David Van Vranken (Author), Gregory A. Weiss (Author)
Ed. Garland Science
Advanced Chemical Biology: Chemical Dissection and Reprogramming of Biological Systems
Matthew R. Pratt, Howard C. Hang, Jennifer A. Prescher
Ed. Wiley
Chemical Biology and Drug Discovery
Marco F. Schmidt
Ed. Springer
Some course material will consist of advanced topics from published journal articles. Students can acquire these references online through the university library.
by David Van Vranken (Author), Gregory A. Weiss (Author)
Ed. Garland Science
Advanced Chemical Biology: Chemical Dissection and Reprogramming of Biological Systems
Matthew R. Pratt, Howard C. Hang, Jennifer A. Prescher
Ed. Wiley
Chemical Biology and Drug Discovery
Marco F. Schmidt
Ed. Springer
Some course material will consist of advanced topics from published journal articles. Students can acquire these references online through the university library.
Assessment methods and Criteria
The knowledge acquired by the students will be verified through a final literature presentation and a written test. Each part will count for 50% of the final pass mark (scale from 18 to 30 cum laude).
Final literature presentation: the students will be asked to create individually or in small groups (depending on the total number of students) a PowerPoint (20 minutes + 5 minutes of discussion) critically presenting and discussing one (or more) paper(s) dealing with one (or more) topic(s) of the course. This work will be presented in class (or in a separate session for non-attending students) and evaluated as a whole (including the topic/paper choice, the clarity and content of the presentation and the ability to understand and discuss the topic(s)).
Written test: 5 open questions on the course content (2 hours).
The final mark will be an average of the final literature presentation and the written test marks.
Final literature presentation: the students will be asked to create individually or in small groups (depending on the total number of students) a PowerPoint (20 minutes + 5 minutes of discussion) critically presenting and discussing one (or more) paper(s) dealing with one (or more) topic(s) of the course. This work will be presented in class (or in a separate session for non-attending students) and evaluated as a whole (including the topic/paper choice, the clarity and content of the presentation and the ability to understand and discuss the topic(s)).
Written test: 5 open questions on the course content (2 hours).
The final mark will be an average of the final literature presentation and the written test marks.
CHIM/06 - ORGANIC CHEMISTRY - University credits: 6
Lessons: 48 hours
Professor:
Sattin Sara
Shifts:
Turno
Professor:
Sattin SaraEducational website(s)
Professor(s)
Reception:
by appointment
Chemistry Department, via Golgi, 19, Building 5, 3rd floor, corpo (unit) B, Room 3058B