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Molecular methods

Code: MBE06     Acronym: MMO

Classification Keyword
CNAEF Medicine

Instance: 2021/2022 - 1S (of 13-09-2021 to 06-02-2022) Ícone do Moodle

Active? Yes
Responsible unit: Departamento de Biomedicina
Course/CS Responsible: Metabolism - Biopathology and Experimental

Cycles of Study/Courses

Acronym No. of Students Study Plan Curricular Years Credits UCN Credits ECTS Contact hours Total Time
MBE 6 Plano Oficial 1 - 9 66 243

Teaching Staff - Responsibilities

Teacher Responsibility
Carlos Manuel Gomes Reguenga
Celso Albuquerque Reis

Teaching language

Suitable for English-speaking students


The unit provides theoretical-practical knowledge on the molecular organization and functioning of the cell and the methodologies available to study cell components. The student will have a hands on learning process of the different experimental approaches, their fundaments, applications, practical requirements, advantages and limitations. Students are expected to plan the best approach to solve a particular scientific question. These competencies will help the student with the design and execution of the master thesis’s research project, will allow him to understand the work performed by others and to gain critical assessment of scientific data.

At the end of this unit, students are expected to discuss and interpret the latest scientific and technical developments in omics, namely proteomics, glycoproteomics, glycomics and metabolomics, a central and emerging research field in systems biology applied to health sciences. Several studies showed that integrated analysis results in better understanding this biology of systems and the different human diseases. The main challenge for this approach is the integration of the heterogeneity and complexity of data. Students will gain experience in some computer tools and statistics applied to this complex data analysis.

Learning outcomes and competences

This curricular unit is organized in two modules that complement each other allowing students to come into contact with the theoretical and practical fundaments concerning the cell functioning and the methodology currently available for the molecular study of the cell components. This knowledge is important to understand the molecular and cellular abnormalities in pathological conditions associated to metabolism.


In module 1, termed “Molecular Biology”, coordinated by Carlos Reguenga, the different levels of molecular organization of the cell will be explained, namely mechanisms associated to DNA, RNA and proteins, and organelle dynamics. Molecular Biology methods will be addressed with focus on nucleic acid and protein analysis, as well as techniques for gene manipulation and silencing. Their advantages and disadvantages will be discussed, as well as the principles that should govern the choice of the most appropriate experimental approach to achieve the objectives in study. This knowledge will give the student the possibility to analyze and plan, with solid foundation, its own experiments during the preparation of the experimental part of the master's thesis or in a future scientific career. This module also contains practical laboratory classes and tutorial sessions, which are pedagogic modalities important to understand and consolidate the acquired knowledge. To this end, this unit takes advantage of a teaching staff with expertise in the field of Cell and Molecular Biology.


Module 2, termed “omics” and coordinated by Pedro Oliveira, will cover the main applications of proteomics, glycoproteomics, glycomics and metabolomics in system biology but also the available methodological approaches that can be used. General knowledge of all subjects contributes to objectives 1 and 2. In-depth study of each subject discussed in the theoretical classes contributes to the learning outcome 3. The learning outcomes 4, 5 and 6, depends on the frequency and on the subjects discussed in the theoretical-practical classes.

Working method



Module 1- Molecular Biology

Structural overview of the cell (compartments, cytoskeleton and intracellular trafficking)

Genome organization and regulation of gene expression

DNA Replication; Repair & Recombination

Transcription and regulation

Translation & protein degradation

Methods for nucleic acid analysis

Methods for protein analysis

Molecular cloning of recombinant DNA

Gene silencing (microRNA, interfering RNA and genome editing by CRISPR-Cas9)

Model organisms and genetic engineering



Module 2- omics

Omics in basic and clinical research

Basic concepts, novel and practical applications examples

Metabolomics:     Definition and validation;   Basic principles and applications;     Technical aspects

Metabolomics data analysis and integrative discussion of data

Bioinformatics tools and statistical treatments

Building integrative maps of metabolomics data

Protein analysis by mass spectrometry




Immunodetection of proteins in normal and disease conditions

Mandatory literature

Lodish, Berk, Kaiser, Krieger, Scott, Bretscher, Ploegh, Matsudaira; Molecular Cell Biology , Freeman and company, 2012
Griffiths, W. J. ; Metabolomics, metabonomics and metabolite profiling, Elsevier

Teaching methods and learning activities

Module 1: Molecular Biology

The course plan comprises 10 lectures (19h) and laboratory classes (24h), hands on learning in the research environment, in small size groups with access to all the equipment. At the end of the practical classes, the students must write two reports, in which all the experimental results are presented and discussed. To increase critical thinking of the students, additional classes (4h) will be prepared as Journal Club. A written exam, consisting in 25 multiple-choices questions and 2 assays, will also be performed to evaluate the understanding of the theoretical concepts and the capability to design a suitable experimental protocol to approach scientific problems.

The final grade at the module is calculated from the mark of the written test (50%) Journal club (30%) and lab. report (20%).


Module 2: Omics

The contents will be covered in theoretical (6h) and theoretical-practical (13h) classes. The student will be evaluated by the presentation of a scientific article on the subject of the module



Evaluation Type

Distributed evaluation without final exam

Assessment Components

Designation Weight (%)
Apresentação/discussão de um trabalho científico 30,00
Teste 50,00
Trabalho escrito 20,00
Total: 100,00

Amount of time allocated to each course unit

Designation Time (hours)
Apresentação/discussão de um trabalho científico 4,00
Estudo autónomo 177,00
Frequência das aulas 25,00
Trabalho laboratorial 37,00
Total: 243,00

Eligibility for exams

To attend 75% of the classes

Calculation formula of final grade

The  mark of module 1 (Molecular Biology) is calculated from the score of the written test (50%) Journal club (30%) and lab. report (20%).

The mark of module 2 (omics) is the result of the evaluation of the presentation and discussion of a research paper.

The final grade is the weighted average of the marks obtained in module 1 (accounting for 67%) and module 2 (accounting for 33%) of the curricular unit.

Classification improvement

The student can only repeat the written exam of module 1 in the ongoing year. All the other evaluations can be improved by attending the course in the subsequent year.
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