1. General information
Course:
MOLECULAR SYSTEMS BIOLOGY AND BIOINFORMATICS
Code:
13327
Type:
CORE COURSE
ECTS credits:
6
Degree:
341 - UNDERGRADUATE DEGREE PROGRAMME IN BIOCHEMISTRY
Academic year:
2023-24
Center:
501 - FACULTY OF ENVIRONMENTAL SCIENCES AND BIOCHEMISTRY
Group(s):
40
Year:
3
Duration:
C2
Main language:
Spanish
Second language:
English
Use of additional languages:
English Friendly:
Y
Web site:
Bilingual:
N
Lecturer:
ELENA BONZÓN KULICHENKO
- Group(s):
40
Building/Office
Department
Phone number
Email
Office hours
ICAM, despacho 0.30
QUÍMICA INORG., ORG., Y BIOQ.
926051477
Elena.Bonzon@uclm.es
By appointment by email
Lecturer:
BOIKO YUDA COHEN COHEN
- Group(s):
40
Building/Office
Department
Phone number
Email
Office hours
QUÍMICA FÍSICA
Boiko.Cohen@uclm.es
Lecturer:
CAROLINA ESCOBAR LUCAS
- Group(s):
40
Building/Office
Department
Phone number
Email
Office hours
Sabatini/029
CIENCIAS AMBIENTALES
5434
carolina.escobar@uclm.es
Wednesdays and Thursdays from 12:00 to 15:00. Please write first an email to carolina.escobar@uclm.es to confirm the tutoring a few days in advance. LOCATION: BUILDING SABATINI, OFFICE 029
Lecturer:
Mª DE LA MONTAÑA MENA MARUGAN
- Group(s):
40
Building/Office
Department
Phone number
Email
Office hours
Sabatini/029
CIENCIAS AMBIENTALES
5434
montana.mena@uclm.es
Tuesdays and Wednesdays from 11 to 15 h.
Previous appointment by e-mail is required.
2. Pre-Requisites
Not established
3. Justification in the curriculum, relation to other subjects and to the profession
It is a compulsory subject that belongs to the subject of "Instrumental Methodologies" in the module of "Biochemical Methods and Molecular Systems Biology".
Recent advances in high-throughput technologies in molecular biology provide vast amounts of data on various model organisms, which are handled with bioinformatics techniques. Systems Molecular Biology addresses the analysis of these comprehensive collections of data and their integration into global networks (omics) to provide new interpretations and formulate hypotheses about biological systems. Therefore, the subject provides the tools for the analysis, integration and interpretation of global molecular data and the construction of interpretative models of biological processes and systems.
The subject requires the knowledge previously provided by the various subjects related to molecular biology and functional biology of organisms, Genetic Engineering and biostatistics and Biochemical Methodology and instrumentation.The competences that will be developed in the subject are of obligatory application in the two itineraries of specialization (Biotechnological and Biosanitary) and will be very useful in the development of the Final Degree Projects in all the topics related to Molecular Biology.
In professional terms, Molecular Systems Biology and Bioinformatics provides an integrative vision of biomolecular sciences and methodological tools indispensable for a biochemist in any sector of research, teaching, production or services, since omics will be increasingly used for innovation in the sectors of agri-food, health, Environment and industry.
4. Degree competences achieved in this course
| Course competences | |
|---|---|
| Code | Description |
| E01 | Express themselves correctly in basic biological, physical, chemical, mathematical and computer terms. |
| E04 | To know the principles and applications of the methods and instrumentation used in bioanalytical determinations. |
| E12 | Have the numerical and computational skills to apply mathematical procedures for data analysis. |
| E13 | Correct handling of different computer tools |
| E17 | To know the fundamentals and applications ofomic technologies: genomics, transcriptomics, proteomics, metabolomics, etc; and to know how to use the basic computer tools and the most common databases related to these technologies. |
| G01 | To possess and understand the knowledge in the area of Biochemistry and Molecular Biology at a level that, based on advanced textbooks, also includes cutting-edge aspects of relevance in the discipline |
| G02 | To know how to apply the knowledge of Biochemistry and Molecular Biology to professional practice and to possess the necessary intellectual skills and abilities for this practice, including the capacity for: information management, analysis and synthesis, problem solving, organization and planning and generation of new ideas. |
| G03 | Be able to collect and interpret relevant data, information and results, draw conclusions and issue reasoned reports on relevant social, scientific or ethical issues in connection with advances in Biochemistry and Molecular Biology. |
| G06 | Acquire skills in the handling of computer programs including access to bibliographic, structural or any other type of databases useful in Biochemistry and Molecular Biology. |
| T01 | Proficiency in a second foreign language, preferably English, at level B1 of the Common European Framework of Reference for Languages |
| T02 | User-level knowledge of Information and Communication Technologies (ICT). |
| T03 | A correct oral and written communication |
| T05 | Organizational and planning skills |
| T06 | Capacity for design, analysis and synthesis |
| T08 | Ability to work as a team and, where appropriate, exercise leadership functions, encouraging entrepreneurship |
| T10 | Ability to self-learn and to obtain and manage bibliographic information, including Internet resources |
5. Objectives or Learning Outcomes
| Course learning outcomes | |
|---|---|
| Description | |
| Develop the capacity to integrate the high volume and diversity of molecular information obtained with "omics" technologies, apply systemic approaches to their analysis and interpret the underlying complex biological processes. | |
| Be able to analyse, interpret and draw conclusions from experimental data. | |
| To know and exercise the main bioinformatics tools for the management, analysis, prediction and modeling of biological data derived from structural and functional "omic" studies. | |
| Understand correctly the functioning of the basic instrumentation used in biochemical research | |
| To know and understand the conceptual basis of high performance technologies for the determination of the genome sequence, the study of global gene expression, the characterization of the proteome, its post-translational modifications and the analysis of metabolic pathways. | |
| Acquire the necessary skills to use relevant techniques in biochemistry. | |
| Additional outcomes | |
| Not established. |
6. Units / Contents
-
Unit 1: -Genomics I: Genome sequencing and bioinformatic tools for data analysis and interpretation. Applications of genomics.
-
Unit 1.1: -Genome sequencing and Genome Projects. Applications in Biotechnology and Biomedicine.
-
Unit 1.2: -Databases and bioinformatics analysis of biological sequences
-
Unit 1.3: -Laboratory practice in Genomics I
-
-
Unit 2: Genomics II: Functional Genomics and Applications
-
Unit 2.1: Transcriptomics: DNA microarrays. Analysis and interpretation of global gene expression profiles
-
Unit 2.2: Functional genomics from the transcriptome using microarrays
-
Unit 2.3: Applications of transcriptomics using microarrays
-
-
Unit 3: Proteomics
-
Unit 3.1: Introduction to Proteomics. Concept of Proteomics. First and Second Generation Proteomics
-
Unit 3.2: Molecular structure and chemical properties of amino acid moieties of peptides. Isoelectric Point of Proteins. Calculation of the isoelectric point. Some reactions of interest in proteomics
-
Unit 3.3: Interpretation of mass spectra. Resolution. Precision. Isotopic envelope. Calculation of the isotopic envelope. Spectra deconvolution
-
Unit 3.4: Ionization methods and analyzers most used in proteomics. MALDI. Electrospray. TOF. Quadrupole. Ion trap. Linear trap. FT. Orbitrap. Features and differences
-
Unit 3.5: Molecular mechanism of peptide fragmentation. Fragmentation series. Interpretation of MS/MS spectra of peptides
-
Unit 3.6: Tandem mass spectrometry (MS/MS) and peptide fragmentation. Liquid chromatography-MS. Peptide separation by reverse phase HPLC. Miniaturization. Micro and nanospray. Nanomate. Triple quadrupole. Quadrupole-TOF. Fragmentation in linear ion trap. TOF-TOF. Linear-orbitrap trap. Quadrupole-orbitrap. Multiple fragmentation. Scan modes. Parent scan. Neutral loss scan
-
Unit 3.7: High-throughput peptide identification. Quality of peptide-spectrum match. Error rate control
-
Unit 3.8: Identification of post-translational modifications (PTMs). PTM enrichment techniques. Open searches
-
Unit 3.9: Quantitative proteomics using second generation techniques. Stable isotopic dilution. Metabolic methods: SILAC. Isobaric methods: iTRAQ, TMT. Targeted proteomics
-
Unit 3.10: Applications of proteomics. Analysis of interactomes. Differential expression and systems biology. Biomarkers
-
Unit 3.11: Laboratory practice in Proteomics.
-
-
Unit 4: Metabolomics and lipidomics
-
Unit 4.1: Introduction to metabolomics
-
Unit 4.2: Metabolomic approaches
-
Unit 4.3: Study design and sample collection
-
Unit 4.4: Analysis techniques used in metabolomics
-
Unit 4.5: Modeling and data analysis in metabolomics
-
Unit 4.6: Metabolomic Applications in Biomedicine: Biomarkers
-
Unit 4.7: Lipidomics. Obtaining and separating lipids. Identification and quantification of cellular lipids
-
Unit 4.8: Laboratory practice in Metabolomics
-
7. Activities, Units/Modules and Methodology
| Training Activity | Methodology | Related Competences (only degrees before RD 822/2021) | ECTS | Hours | As | Com | Description | |
| Class Attendance (theory) [ON-SITE] | Lectures | E01 E04 E17 T01 T03 | 1.4 | 35 | N | N | Master classes in which the theoretical contents will be developed. Master classes will be available to the student in Moodle. | |
| Computer room practice [ON-SITE] | Guided or supervised work | E01 E12 E13 E17 G06 T01 T02 T10 | 0.72 | 18 | Y | Y | Practical sessions will be carried out directed by the teachers of the subject, corresponding to the different thematic blocks (4.5 h of Genomics, 4.5h of Proteomics and 9 of Metabolomics). The realization of the practices is mandatory and not recoverable. Only those students who have completed the practices can be evaluated. | |
| Writing of reports or projects [OFF-SITE] | Combination of methods | E12 E13 E17 G02 G03 G06 T01 T02 T06 | 0.4 | 10 | Y | N | Autonomous resolution of problems and seminars related to metabolomics / lipidomics. This activity is not recoverable. | |
| Other on-site activities [ON-SITE] | Assessment tests | E01 E13 E17 G02 G03 G06 T01 T02 T06 | 0.04 | 1 | Y | Y | A written test of the contents of genomics and proteomics practices will be carried out. Only those students who have completed the practices can be evaluated. The evaluation will be recoverable, either in the extraordinary or special call for completion. | |
| Problem solving and/or case studies [ON-SITE] | Problem solving and exercises | E01 E13 E17 G02 G03 G06 T01 T02 T06 | 0.12 | 3 | Y | N | Problems related to proteomics issues will be solved. This activity is not evaluable. | |
| Study and Exam Preparation [OFF-SITE] | Self-study | E12 E13 E17 G01 G02 G06 T02 T05 | 3.2 | 80 | N | N | Self-instruction | |
| Final test [ON-SITE] | Assessment tests | E01 E17 G06 T03 T10 | 0.12 | 3 | Y | Y | The final test will consist of a global examination of the three thematic blocks of the subject: genomics, proteomics and metabolomics / lipidomics. The evaluation will be recoverable in the extraordinary or special call. | |
| Total: | 6 | 150 | ||||||
| Total credits of in-class work: 2.4 | Total class time hours: 60 | |||||||
| Total credits of out of class work: 3.6 | Total hours of out of class work: 90 | |||||||
As: Assessable training activity Com: Training activity of compulsory overcoming (It will be essential to overcome both continuous and non-continuous assessment).
8. Evaluation criteria and Grading System
| Evaluation System | Continuous assessment | Non-continuous evaluation * | Description |
| Test | 16.00% | 16.00% | A written test of the contents of genomics (8%) and proteomics (6%) practices will be carried out. Only those students who have completed the practices can be evaluated. The evaluation of the same will be recoverable, either in the extraordinary or special call for completion. A minimum grade of 4 out of 10 is required to calculate the weighted average with the rest of the activities. |
| Other methods of assessment | 6.00% | 0.00% | The answer to questions raised by the professors of proteomics and metabolomics / lipidomics about problem solving or scientific publications proposed in the seminars corresponding to these thematic blocks will be evaluated. This activity is not recoverable. |
| Final test | 70.00% | 76.00% | The final test will consist of a global examination of the three thematic blocks that make up the subject: genomics, proteomics and metabolomics / lipidomics. A minimum grade of 4 out of 10 is required to calculate the weighted average with the rest of the activities. It will be necessary to obtain a final grade of at least 5 (out of 10) to pass the subject. |
| Practical exam | 8.00% | 8.00% | Resolution of an on-line case study during metabolomics and lipidomics practices. This activity is not recoverable. |
| Total: | 100.00% | 100.00% |
According to art. 4 of the UCLM Student Evaluation Regulations, it must be provided to students who cannot regularly attend face-to-face training activities the passing of the subject, having the right (art. 12.2) to be globally graded, in 2 annual calls per subject , an ordinary and an extraordinary one (evaluating 100% of the competences).
Evaluation criteria for the final exam:
-
Continuous assessment:The modality assigned by default to the student will be the continuous evaluation. Any student may request the change to the non-continuous evaluation modality (before the end of the class period) by sending an email to all the teachers of the subject, provided that they have not completed 50% of the evaluable activities.
Attendance at internships is mandatory and will be an essential requirement to pass the subject. A minimum grade of 4 out of 10 will be required in the final exam and in the practice test (genomics and proteomics) to calculate the weighted average of these grades and count the rest of the activities. The final grade of the subject will be calculated taking into account the percentages of the previous table. To pass the subject, the overall grade must be equal to or greater than 5 out of 10. -
Non-continuous evaluation:Attendance to laboratory practices is mandatory and will be an essential requirement to pass the subject. A minimum grade of 4 out of 10 in the final exam and in the practice test (genomics and proteomics) will be required to calculate the weighted average of these grades and count the metabolomics/lipidomics case study. The final grade of the subject will be calculated taking into account the percentages of the previous table. A final grade of 5 out of 10 will be required to pass the subject.
Specifications for the resit/retake exam:
For the extraordinary call, the qualifications of the non-recoverable activities carried out throughout the course will be taken into account. A 4 out of 10 will be required to keep the grade of the ordinary call in the final exam or in the practice test. In addition, a minimum grade of 4 out of 10 is required in the global exam of the three thematic blocks and in the practice test (genomics and proteomics) to calculate the weighted average of these grades and count the rest of the activities. The final grade of the subject will be calculated taking into account the percentages of the previous table. A final grade of 5 out of 10 will be required to pass the subject.
Specifications for the second resit / retake exam:
In this call there will only be a final test that will represent 100% of the grade, in which each thematic block will represent a third of the final grade. Attendance to laboratory practices is mandatory and will be an essential requirement to pass the subject. The subject will be passed with a 5 out of 10.
9. Assignments, course calendar and important dates
| Not related to the syllabus/contents | |
|---|---|
| Hours | hours |
10. Bibliography and Sources
