Biomolecular Chemistry
Code: 43435 ECTS Credits: 6| Degree | Type | Year | Semester |
|---|---|---|---|
| 4314939 Advanced Nanoscience and Nanotechnology | OT | 0 | 1 |
Contact
- Name:
- Adela Vallribera Masso
- Email:
- adelina.vallribera@uab.cat
Teaching groups languages
You can check it through this link. To consult the language you will need to enter the CODE of the subject. Please note that this information is provisional until 30 November 2023.
Teachers
- Ramon Alibes Arques
- Joan Suades Ortuņo
- Adela Vallribera Masso
- Jean-Didier Marechal
- Xavier Ceto Alseda
- Oscar Palacios Bonilla
Prerequisites
The students involved in this module should have background in chemistry (Analytical Chemistry, Physical Chemistry, Inorganic Chemistry and Organic Chemistry), as well as knowledge in Mathematics, Physics and Biology. Students should also have skills in management of common office applications, possess the English knowledge necessary for understanding lectures, scientific texts, documents, seminars and conferences. Graduates in Chemistry, Chemical Engineering, Materials Science, Nanoscience, Environmental Sciences, Biotechnology, Biochemistry have enough background to take part of this module.
Advanced level of English (level B1) of the Common European Framework Reference for Languages of the European Council is required.
Objectives and Contextualisation
The role of bioanalytical, bioorganic and bioinorganic chemistry in genomics, proteomics, metabolomics and medicine.
- Applying basic concepts of chemistry in biological systems in the field of human health, environmental control, food safety and biotechnology industry.
- Integrating bio recognition and biological reactions in chemical methodology.
- Handling the most common techniques in chemistry to analyze, separate, identify and synthesize compounds in a biological context.
- Applying this knowledge to solve daily problems.
Competences
- Analyse the benefits of nanotechnology products, within one's specialisation, and understand their origins at a basic level
- Communicate and justify conclusions clearly and unambiguously to both specialised and non-specialised audiences.
- Continue the learning process, to a large extent autonomously
- Identify and distinguish the synthesis/manufacture techniques for nanomaterials and nanodevices typically adopted in one's specialisation.
- Identify the characterisation and analysis techniques typically adopted in nanotechnology and know the principles behind these, within one's specialisation.
- Seek out information in the scientific literature using appropriate channels, and use this information to formulate and contextualise a research topic.
- Show expertise in using scientific terminology and explaining research results in the context of scientific production, in order to understand and interact effectively with other professionals.
- Solve problems in new or little-known situations within broader (or multidisciplinary) contexts related to the field of study.
- Use acquired knowledge as a basis for originality in the application of ideas, often in a research context.
Learning Outcomes
- Apply general methods for analysing and characterising biomolecules.
- Communicate and justify conclusions clearly and unambiguously to both specialised and non-specialised audiences.
- Continue the learning process, to a large extent autonomously
- Design synthesis strategies and recognise the properties of natural products.
- Differentiate between ligand-receptor interactions and relate these to specific biorecognition processes.
- Identify the contribution of biomolecular chemistry to medical and biomedical applications.
- Recognise the structure of biomolecules and mimetics and relate this to their biological function.
- Seek out information in the scientific literature using appropriate channels, and use this information to formulate and contextualise a research topic.
- Show expertise in using scientific terminology and explaining research results in the context of scientific production, in order to understand and interact effectively with other professionals.
- Solve problems in new or little-known situations within broader (or multidisciplinary) contexts related to the field of study.
- Use acquired knowledge as a basis for originality in the application of ideas, often in a research context.
- Use modified biomolecules in bioanalysis.
Content
Topics
- Structure, function and biorecognition of natural and recombinant biomolecules such as enzymes, antibodies, DNA, cellular receptors, DNA/RNA, metal-containing biomolecules. Biomimetics.
- Molecules for medical diagnosis and therapy
- Structure and function of medicinal natural products. Groundwork in natural product chemistry and phytochemistry.
- Computational Techniques in Biomolecular Chemistry. Relationship between chemical, biological and conformational space.
- Biomolecule production. Monoclonal and polyclonal antibodies. Recombinant proteins. Separation of biomolecules and labelling with nanotags. Bioanalysis. Immunoassays, PCR, biological catalysed methods.
- Integration of nanomaterials in rapid diagnostic test (lateral flow, biosensors, agglutination test, immunoassays) for diagnostics of emerging infection diseases.
Biomolecules & Biomimetics. Structure, function and biorecognition
Contents:Proteins: enzymes, affinity proteins, antibodies, diabodies, affibodies, avimers, cellular receptors. Biorecognition and function: enzyme/substrate; antigen/antibody; receptor/ligand interaction. Cell signaling. DNA/RNA structure and function. Amplification. Molecular beacons. Aptamers.Molecular imprinted polymers and plastic antibodies.
Metal-containing biomolecules: structure, function, and mimetics.
Content: The biochemistry of metal ions. Uptake, transport and storage of metal ions in biology. Electron transfer, respiration, and photosynthesis. Oxygen metabolism. Other metaloproteins of interest. Metal ion receptors and signaling. Metals in medicine.
Computational Techniques in BiomolecularChemistry
Content: Specificities of computation at the interface chemistry-biology. Relationship between chemical, biological and conformational space. Protein-ligand dockings. Molecular Dynamics. Multiscale. Advantages, limitations. Reactivity in biochemical systems. Examples.
Chemistry and biomedicine: molecules for medical diagnosis and imaging
Content: General aspects of imaging techniques. SPECT radiopharmaceuticals based on Tc-99m (nuclear and chemical properties, kit reactions and some examples of relevant technetium radiopharmaceuticals). Other SPECT radiopharmaceuticals. PET radiopharmaceuticals, 18F-Fluorodeoxyglucose and C-11 radiotracers. Therapeutic radiopharmaceuticals. Magnetic resonance imaging contrast agents.
Natural products: biosynthesis and properties
Content: Natural products in drug discovery and therapeutic medicine: historical overview. Carbohydrates, the sweet molecules of life. The acetate pathway: fatty acids and polyketides. The mevalonate pathway: terpenoids and steroids. The shikimate pathway: aromatic aminoacids and phenyl propanoids. Alkaloids, secrets of life.
Biomolecule production, separation, modification and determination
Contents:Isolation and production of biomolecules. The immune system: production of polyclonal and monoclonal antibodies. Separation strategies. Labelling with nanotags and immobilization of biomolecules on nanostructured materials. Bioanalysis: immunochemical methods, DNA assays, PCR, biological catalysed methods, other biological catalysts: DNAzymes, biosensing. Chips and arrays.
Nanomaterials in biosciences
Contents: Biorecognition with biologically-modified quantum dots, carbon nanotubes, metal and magnetic nanoparticle: medical diagnosis, nanomedicine and bioanalysis.
Methodology
Lectures
Problem-solving lectures
Cooperative activities
Seminars Preparation and oral presentation of papers
Tutorials
Annotation: Within the schedule set by the centre or degree programme, 15 minutes of one class will be reserved for students to evaluate their lecturers and their courses or modules through questionnaires.
Activities
| Title | Hours | ECTS | Learning Outcomes |
|---|---|---|---|
| Type: Directed | |||
| Lectures | 30 | 1.2 | 8, 5, 6, 10, 3, 7, 11 |
| Problems | 8 | 0.32 | 9, 10, 11, 12 |
| Type: Supervised | |||
| Tutorials | 5 | 0.2 | 8, 2, 3 |
| Type: Autonomous | |||
| Autonomous learning and studying | 49 | 1.96 | 1, 8, 5, 4, 6, 10, 3, 7, 12 |
| Preparation of oral presentation and papers | 40 | 1.6 | 1, 8, 5, 9, 6, 10, 2, 3, 7, 11, 12 |
Assessment
The evaluation of this module will take into account the attendance and participation in class as well as the work and assessments presented by the students. All subjects are compulsory attendance. The different topics presented by each of the professors will be separately evaluated, by different assesments including writing exams, theoretical and practical tests, oral presentations, research papers discussion, in-class brief questions, written works, etc.
- Every professor decides the number and typology of evaluation activities: oral presentations, written exams, delivery of discussed articles, tests.
- The final mark of the module will be the sum of the marks of every professor multiplied by the percentage of his classes in the total teaching of the module.
- To pass a module, it is mandatory a mark over 5 in a 75% of all the activities in order to average with other marks of the professor and/or the module.
- There will be a period in January to repeat written exams with marks under 5. In the case of exams under 3,5, it will be mandatory to the student. In the case of exams between 3,5 and 5 it would be optional.
- The marks of other evaluations activities (i. e. oral presentations) will average with the rest of the marks of the professor/module independently of the value. There will be not option of repeating these evaluation activities.
VERY IMPORTANT: Partial or total plagiarising will immediately result in a FAIL (0) for the plagiarised exercise and the WHOLE subject. PLAGIARISING consists of copying text from unacknowledged sources -whether this is part of a sentence or a whole text - with the intention of passing it off as the student's own production. It includes cutting and pasting from internet sources, presented unmodified in the student's own text. Plagiarising is a SERIOUS OFFENCE. Students must respect authors' intellectual property, always identifying the sources they may use; they must also be responsible for the originality and authenticity of their own texts.
In the event of a student committing any irregularity that may lead to a significant variation in the grade awarded to an assessment activity, the student will be given a zero for this activity, regardless of any disciplinary process that may take place. In the event of several irregularities in assessment activities of the same subject, the student will be given a zero as the final grade for this subject.
Assessment Activities
| Title | Weighting | Hours | ECTS | Learning Outcomes |
|---|---|---|---|---|
| Oral defense of projects | 40% | 6 | 0.24 | 1, 8, 5, 4, 9, 6, 10, 2, 3, 7, 11, 12 |
| Reports and problems | 30% | 4 | 0.16 | 1, 8, 5, 4, 9, 6, 10, 2, 3, 7, 11, 12 |
| Writing Assessments | 30% | 8 | 0.32 | 1, 8, 5, 4, 9, 6, 10, 2, 3, 7, 11, 12 |
Bibliography
Medicinal natural products. A biosynthetic approach, P.M. Dewick, Jonh Wiley & Sons, 2002
Química Bioinorgánica, J. S. Casas, V. Moreno, A. Sánchez, J. L. Sánchez, J. Sordo, Editorial Síntesis, Colección Biblioteca de Químicas, 2002
Bioanalytical Chemistry, S. Mikkelsen, E. Corton, Wiley, 2004
Molecular Modelling Principles and Applications - Second Edition -Andrew R. Leach - Ed: Prentice Hall 2001
Further bibliography
Natural Products: their chemistry and biological significance, J. Mann, R.S. Davidson, J. B. Hobbs, D.V. Banthorpe, J. B. Harborne Prentice Hall, 1994
Natural Products Chemistry: A mechanistic and biosynthetic approach to secondary metabolism, K.B.G. Torsell, John Wiley & Sons, 1983
Inorganic Chemistry in Biology,P. C. Wilkins, R. G. Wilkins, Oxford Chemistry Primers, n. 46, Oxford University Press, 1997
Principles of Bioinorganic Chemistry, S. J. Lippard, J.M. Berg, University Science Books, 1994
Principles and Practice of Bioanalysis, R. F.Venn, (Editor), Taylor & Francis, 2000.
Bioanalytical Chemistry, A. Manz, N. Pamme, D. Iossifidis, Imperial College Press, 2004.
Principles of Chemical and Biological Sensors, D. Diamond (Editor), Wiley, 1998.
Biosensors, Elizabeth A. H. Hall, Open Univ Press, 1991
Software
Not necessary