Important notice
The course guide is provisional.
The PDF version of the course guide may take a few days to become available in the DDD.
Function of Biomolecules in Health and Illness
Code: 45557Credits: 9
| Degree programme | Type | Course |
|---|---|---|
| Advanced Biotechnology | OP | 1 |
Contact lecturer
- Name :
- Susanna Navarro Cantero
- Email :
- susanna.navarro.cantero@uab.cat
Group languages
You can consult this information at the end of the document.
Prerequisites
The requirements for the Master's degree. The classes will be mostly in Catalan, but they will also be taught in Spanish depending on the faculty. Classes could be conducted in English if requested by the students with sufficient advance notice, and if there is consensus within the student group and with the professor.
Objectives
Upon completion of the module, the student will be able to:
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Plan experiments for the identification, expression, purification, and functional characterization of biomolecules.
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Analyze the structure and function of proteins using bioinformatics techniques.
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Relate structural and functional changes in biomolecules to pathologies.
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Select and apply methodologies for the design of enzyme inhibitors.
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Identify and characterize enzyme inhibitors as drugs.
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Utilize enzymatic technology for biomedical and biotechnological applications.
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Recognize biomolecules associated with human pathologies and use them as therapeutic targets.
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Associate specific diseases with the accumulation of misfolded proteins.
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Understand the molecular basis of diseases caused by dynamic mutations and epigenetic changes.
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Assess the functional role of membrane lipids and their involvement in specific pathologies.
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Familiarize themselves with the main techniques and facilities in a reference clinical biochemistry laboratory.
Competencies
Advanced Biotechnology
Apply techniques for modifying living organisms or parts thereof to improve pharmaceutical and biotechnological processes and products, or to develop new products. (Specialization in Molecular and Therapeutic Biotechnology)
Ability to synthesize, analyze alternatives, and engage in critical debate.
Integrate the content of metabolic pathways in living organisms under normal, pathological, or exogenously modified conditions (Specialization in Molecular and Therapeutic Biotechnology).
Apply acquired knowledge and problem-solving skills in new or unfamiliar environments within broader (or multidisciplinary) contexts related to their field of study.
Effectively communicate their conclusions, as well as the knowledge and ultimate reasons underlying them, to specialized and non-specialized audiences in a clear and unambiguous manner.
Possess learning skills that enable them to continue studying, largely through self-directed and autonomous work.
Possess knowledge that provides the foundation or opportunity for originality in the development or application of ideas, often in a research context. Utilize and responsibly manage bibliographic information and computer resources related to biotechnology.
Biochemistry, Molecular Biology, and Biomedicine
Analyze research results to obtain new biotechnological or biomedical products and transfer them to society.
Analyze and accurately interpret the molecular mechanisms operating in living organisms and identify their applications.
Apply techniques for modifying living organisms or parts thereof to improve pharmaceutical and biotechnological processes and products, or to develop new products.
Develop critical reasoning within the field of study and in relation to the scientific or business environment. Identify and utilize bioinformatic tools to solve problems related to biochemistry, molecular biology, and biomedicine.
Integrate content in biochemistry, molecular biology, biotechnology, and biomedicine from a molecular perspective.
Apply acquired knowledge and problem-solving skills in new or unfamiliar environments within broader (or multidisciplinary) contexts related to their field of study.
Effectively communicate their conclusions, as well as the knowledge and ultimate reasons underlying them, to specialized and non-specialized audiences in a clear and unambiguous manner.
Possess learning skills that enable them to continue studying, largely through self-directed and autonomous work.
Possess knowledge that provides the foundation or opportunity for originality in the development or application of ideas, often in a research context.
Utilize and manage bibliographic information and computer resources related to biochemistry, molecular biology, or biomedicine. Utilize scientific terminology to argue research results and effectively communicate them orally and in writing.
Learning outcomes
- CA08 (Transfer knowledge of advanced processes and methodologies to the study of biomolecules relevant to biomedicine in order to obtain new biotechnological or biomedical products for transfer to society, taking into account potential sources of sex/gender-based inequalities.) Transfer knowledge of advanced processes and methodologies to the study of biomolecules relevant to biomedicine in order to obtain new biotechnological or biomedical products for transfer to society, taking into account potential sources of sex/gender-based inequalities.
- CA09 (Work both individually and as a team to address current problems and challenges of society in the fields of biochemistry, molecular biology and biomedicine while demonstrating ethical responsibility and respect for fundamental rights and duties, diversity and democratic values, in accordance with the Sustainable Development Goals.) Work both individually and as a team to address current problems and challenges of society in the fields of biochemistry, molecular biology and biomedicine while demonstrating ethical responsibility and respect for fundamental rights and duties, diversity and democratic values, in accordance with the Sustainable Development Goals.
- KA09 (Identify the molecular mechanisms of key biological functions and those related to the onset of diseases.) Identify the molecular mechanisms of key biological functions and those related to the onset of diseases.
- KA10 (Identify biomolecules whose function/dysfunction intervenes in human pathologies.) Identify biomolecules whose function/dysfunction intervenes in human pathologies.
- KA11 (Provide advanced methodologies for the functional study of biomolecules, both in normal and pathological conditions.) Provide advanced methodologies for the functional study of biomolecules, both in normal and pathological conditions.
- SA07 (Relate the molecular mechanisms of relevant functions responsible for diseases.) Relate the molecular mechanisms of relevant functions responsible for diseases.
- SA08 (Use methodologies, including bioinformatics, to analyse enzyme active sites and drug design.) Use methodologies, including bioinformatics, to analyse enzyme active sites and drug design.
- SA09 (Propose the molecular mechanisms of relevant functions in biomedicine.) Propose the molecular mechanisms of relevant functions in biomedicine.
Contents
Block 1: Identification, acquisition, and purification of biomolecules. Functional characterization.
Practical concepts for protein purification.
Methods for identifying substrates or potential inhibitors, and detecting enzymatic activity.
Practical considerations for enzymatic assays. Applied aspects of enzyme kinetics.
Identification of functional regions of enzymes using bioinformatics tools. Practical session in the computer lab.
Structural and functional analysis of enzyme inhibitors that act as drugs. Practical session in the computer lab.
Drug repositioning: Identification and development of new uses for existing drugs.
Block 2: Enzymes associated with human pathologies. Diagnostic and therapeutic applications.
Enzymes of retinoid metabolism. Associated pathologies.
Urea cycle disorders. Biochemical and computational approaches to evaluate the cause of the pathology.
Enzymes that modify chromatin and their role in human pathologies.
Enzyme replacement therapy. Enzyme activators. Pharmacoperones or pharmacological chaperones. Therapeutic applications.
Enzymes and nanomedicine. Enzyme encapsulation. Controlled drug release. Role of infectious proteins in degenerative diseases.
Strategies for treating lysosomal diseases: enzyme, cell, and gene therapy. Proteases and protease inhibitors. Biomedical applications and strong binding kinetics.
Yeast as a model organism. Three applications in biomolecule characterization: protein-lipid interactions, protein-protein interactions, and genetic interactions.
Block 3: Conformational diseases.
Proteostasis and conformational diseases.
Prions and related diseases.
Therapies in development for conformational diseases: Introduction to conformational diseases. Light chain amyloidosis. Alzheimer’s disease.
Block 4: Membrane lipids in Biomedicine.
Role of lipids in various functions and dysfunctions of biomembranes: dynamics of lipid microdomains (lipid rafts, etc.); endocytosis and exocytosis; oxidative stress; apoptosis. Study techniques.
Block 5: Visits to the Clinical Laboratories Service at the Consorci Corporatiu Sanitari Parc Taulí (Sabadell).
Visit to the genetics, biochemistry, immunology, microbiology, and hematology laboratories.
Block 6: In silico strategies for pharmacological identification.
Identification of pharmacophores against a specific protein involved in antibiotic resistance.
In silico screening through molecular docking.
Molecular dynamics and affinity energy calculations between molecules.
Learning activities and methodology
| Title | Hours | ECTS | Learning outcomes |
|---|---|---|---|
| Theory classes | 38 | 1.52 | CA08, KA09, KA10, SA07, SA09 |
| Visit to clinical laboratories | 4 | 0.16 | KA10, SA08, SA09 |
| Independent work of the student | 77 | 3.08 | CA09, KA09, SA07, SA08 |
| Practical activities in the computer classroom | 8 | 0.32 | CA08, CA09, KA10, SA08 |
| Oral presentation | 5 | 0.2 | CA08, KA11, SA08 |
| Preparation and presentation of an individual work | 10 | 0.4 | CA09, KA10, SA09 |
The module consists of theoretical classes, computer lab practical classes, a visit to a reference Clinical Biochemistry laboratory, and a seminar presentation by the student. The organization and teaching methodology for these educational activities are described below.
Theory classes:
The content of the theory program will be primarily delivered by professors in the form of lectures with audiovisual support. The presentations used by the professor in class will be made available beforehand on the Virtual Campus of the subject. It is recommended that students have access to this material as a support for their classes. It is advised that students regularly consult the recommended books listed in the Bibliography section of this teaching guide to consolidate and clarify, if necessary, the content explained in class. It is also advisable for students to use the links provided in the presentations of different topics, which contain videos and animations related to the processes explained in class.
Computer lab practical classes:
Students will be directly called to the classroom for the development of the session. The work will be individual, and it will be important for the student to have prior knowledge of the software to be used.
Visit to a reference Clinical Biochemistry laboratory:
The session will take place at the Clinical Analysis Laboratory of the Parc Taulí Hospital in Sabadell, where the student will receive explanations about the functioning of all the facilities and the methodologies used by healthcare professionals. After the visit, a multiple-choice knowledge test will be conducted.
Seminar presentation:
Each student will be required to give a seminar presentation.
The student will prepare a seminar on a topic agreed upon with a tutor professor and will present it publicly in class using audiovisual means.
Preparation tutorials for the seminar:
There will be a group tutorial session led by the module coordinator to distribute the seminar topics and propose the general organization of the material to be presented. Students may also have individual tutorials with professors directly involved in the chosen topic to guide them in the preparation of the material.
Note: 15 minutes of a class, within the schedule established by the institution/program, will be reserved for students to complete evaluation surveys of the faculty's performance and evaluation of the subject/module.
Assessment
Continuous assessment activities
| Title | Weight | Hours | ECTS | Learning outcomes |
|---|---|---|---|---|
| Continuous assessment | 30% | 30 | 1.2 | CA09, KA09, KA10, SA07, SA08, SA09 |
| Presentation of a seminar | 20% | 5 | 0.2 | CA08, KA09, KA10, SA07, SA09 |
| Theory exams | 40% | 10 | 0.4 | CA08, KA09, KA10, SA07, SA09 |
| Attendance and active class participation | 10% | 38 | 1.52 | CA09, KA11, SA08, SA09 |
- Attendance and active participation in class:
In addition to attendance, the degree of participation, discussion, and resolution of questions that the professor may pose in class will be assessed in the different teaching areas of the subject. A record of this activity will be sent to the module coordinator by the professor after each class. This evaluation will account for 10% of the final grade.
- Preparation and oral presentation of a seminar:
Presentation of a seminar publicly in class, with subsequent discussion. This part will account for 20% of the final grade for the students who present it.
- Written tests:
The presentation of written assignments or tests requested by the professors of each part of the subject will be assessed. Additionally, the general understanding of the seminar sessions will be evaluated through written questions. This part will account for 10% of the test grade.
This part will account for 40% of the final grade.
- Continuous assessment:
The continuous assessment includes activities proposed during the theory sessions, practicals in the computer lab, and field practicals.
Classroom practicals.
Field practicals:
A visit to the Clinical Analysis Service of the Consorci Hospital Parc Taulí (Sabadell) will be conducted.
A multiple-choice test will be administered to evaluate the understanding of the visit.
This part will account for 30% of the final grade.
Assessment:
The calculation of the final assessment will be done with the following formula:
Final grade = T0.40 + Ac0.30 + Sm0.20 + As0.10
T - theory
Ac - continuous assessment
As - attendance and active participation
Sm - seminar
It will be considered \"not assessable\" when the assessment activities (final test, exit test) do not allow obtaining a minimum overall grade of 5.0.
Attendance to practical sessions and field practicals is mandatory. Students will receive a \"Not Assessable\" grade when their absence exceeds 20% of the scheduled sessions.
- Important: If plagiarism is detected in any of the submitted work, it may result in the student failing the entire module.
This subject/module does not provide for a single assessment system.
Bibliography
- Abbenante, G., Fairlie, D.P. \"Protease Inhibitors in the Clinic\". Medicinal Chemistry, 2005, 1, 71-104
- LA Bagatolli, JH Ipsen, AC Simonsen, OG Mouritsen An outlook on organization of lipids in membranes: Searching for a realistic connection with the organization of biological membranes Progress in Lipid Research
49 (2010) 378-389
- Bommarius, A.S., Riebel, B.R. \"Biocatalysis - Fundamentals and Applications\". 2004. Wiley-VCH. Weinheim.
- Bieth, J.G. \"Theoretical and Practical Aspects of Proteinase Inhibition Kinetics\". Methods in Enzymology.
1995, Vol 248, pp. 59-84. Academic Press. NY.
- Carey, P.R. (ed.) \"Protein engineering and design\". 1996. Academic Press. New York.
- O Ces & X Mulet Physical coupling between lipids and proteins: a paradigm for cellular control Signal
Transduction 6 (2006) 112 - 132
- Chaplin, M.F., Bucke, C. \"Enzyme Technology\". 1990. Cambridge University Press.
- Copeland, R.A. \"Enzymes. A practical introduction to structure, mechanism and data analysis\". 2000. Wiley-VCH. New York.
- Copeland, R.A. \"Evaluation of enzyme inhibitors in drug discovery\" 2005. Wiley. Hoboken. New Jersey
- Cornish-Bowden, A. \"Fundamentals of enzyme kinetics\". 3rd ed. 2004. Portland Press. London.
- Chávez, M. et al: Selección de temas: Purificación de Enzimas. Inmovilización de Enzimas. Fundamentos de
Cinética de Reacciones Enzimáticas. Cinética de Inhibición de Unión fuerte. En Enzimología Biotecnológica.
2007. Editora ELFOS. La Habana.
- De Leenheer, A.P., Lambert, W.E., Nelis, H.J. (Editors) \"Modern chromatographic analysis of vitamins\" 2nd edition. 1992. Chromatographic Science Series vol 60. Marcel Dekker Inc, New York.
- Deulofeu, R., Olmedilla, B. (Editors) \"Vitaminas, Vol 2, Liposolubles\" 2006. Sociedad Española de Química
Clínica.
- Engel, P.C. (ed.) \"Enzymology Labfax\". 1996. Academic Press, San Diego, CA.
- Eisental, R., Danson, M.J. \"Enzyme Assays\". 2002. 2ª ed. Oxford Univ. Press. Oxford
- H. Feldmann, editor \"Yeast: Molecular and Cell Biology\", (2012) Wiley-Blackwell
- Fersht, A., \"Structure and Mechanism in Protein Science\". 1999. W.H. Freeman. New York.
- KS. George & S Wu Lipid raft: A floating island of death or survival. Toxicology and Applied Pharmacology
259 (2012) 311-319
- Glusker, J.P., Lewis, M., Rossi, M. \"Crystal Structure Analysis for Chemists and Biologists\". 1994. VCH Publishers
- Janson, J-C., Ryden L. \"Protein Purification, Principles, High Resolution Methods and Applications\". 1998. R.K. Wiley & Sons , Inc, NY
- Grunwald, P. \"Biocatalysis. Biochemical Fundamentals and Applications\". 2009. Imperial college Press, London.
- Knight C.G. \"Active Site Titration of Peptidases\". Methods in Enzymology. 1995. Vol 248, pp. 85-100. Academic Press. NY.
- McGrath, B.M., Walsh, G. (Editors) \"Directory of Therapeutic Enzymes\". 2005. CRC, Taylor & Francis.
- McPherson, A. (2003) \"Introduction to macromolecular crystallography\" John Wiley & Sons, Inc., New Jersey
- Núñez de Castro, I. \"Enzimología\". 2001, Pirámide, Madrid.
- Pandey, A., Webb, C., Soccol, C.R., Larroche, C. \"Enzyme Technology\". 2006. Springer-Verlag
- Price, N.C., Stevens, L. \"Fundamentals of Enzymology\". 1999. 3ª edició. Oxford University Press. Oxford.
- M. Ramírez-Alvarado, J.W. Kelly, C. M. Dobson (2010) Protein Misfolding diseases: current and emerging principles and therapies. Ed. Wiley
- Reymond, J.-L. \"Enzyme assays: High-throughput screening, genetic selection and fingerprinting\". 2006, Wiley-VCH.
- Rhodes G. \"Crystallography made crystal clear\" 2006. 3rd ed. Elsevier Academic Press.
- Tietz, N. W. \"Textbook of Clinical Chemistry\". 1999. 3rd ed. WB Saunders.
- G. van Meer, DR Voelker & GW Feigenson Membrane lipids: where they are and how they behave Nature
Reviews (Molecular Cell Biology) 9 (2008) 112-124
Software
Pymol vs 2.5
Autodock Vina
Gromacs
VMD (Visual Molecular Dynamics)
https://www.uniprot.org/ (online database)
https://www.rcsb.org/ (online database)
https://www.ebi.ac.uk/Tools/msa/clustalo/ (online tool)
Course groups and languages
The information provided is provisional until November 30. After this date, you will be able to consult the language of each group through this link. To access the information, you will need to enter the course CODE