Molecular and Cellular Biology

General characterization

Prerequisites

No prerequisites.

Bibliography

Molecular Cell Biology

Lodish H, Berk A, Kaiser CA, Krieger M, Bretscher A, Ploegh H, Amon A, Scott MP

7th Ed. WH Freeman & Company, NY, 2012

 

. Molecular Biology of the Cell

Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P

5th Ed. Garland Science, NY, 2007

 

. The World of the Cell

Hardin J, Bertoni GP, Kleinsmith LJ, ,

8th Ed. Benjamin Cummings Publ. Co., 2010

 

. The Cell. A molecular Approach

Cooper GM, Hausman RE

5th Ed. Sinauer Associates Inc., 2009

 

. Principles of Cell Biology 3rd Edition

.Biologia Celular e Molecular 

Ed. Carlos Azevedo e Cláudio Sunkel. Ed Lidel

 

. Scientific papers

Teaching method

The pedagogical strategy is based on the principle of separating theoretical and theoretical-practical classes, teaching one theoretical class (1.5h) and one theoretical-practical class (2h) per week.

The semester is divided into two blocks, taught by different professors, the first on Cell Biology and the second on Molecular Biology. Theoretical classes are expository in nature, encouraging student participation during classes.

Theoretical-practical classes are dedicated to problem solving and exercises on the contents explored in the theoretical classes. Learning is complemented by solving questionnaires independently, after each theoretical-practical class and by carrying out group work in each block.

Evaluation method

A) BMC Rules of Conduct 2023-2024

1. Students may only change TP shifts in exceptional and duly justified cases. The exchange requires prior authorization from teachers.
2. Communication between teachers and students and the provision of materials for T and TP classes will be done via Moodle.
3. The rules for assessment and attendance of the subject are registered in CLIP.

EVALUATION METHODOLOGY

The Molecular and Cellular Biology discipline is divided into 2 modules: Molecular Biology module (BM) and Cellular Biology module (BC). Since each module is taught by a different teacher, the particular functioning of T and TP classes may differ. However, the general rules of conduct and evaluation in the discipline are transversal.

A) Attendance in the subject:
1. To obtain attendance to the subject, it is mandatory to attend and submit a number of work elements corresponding to 2/3 of the number of classes taught in each module (BC and BM).
2. To control attendance, attendance at TP classes is recorded by signature on an attendance sheet.
3. Students present in the TP class must submit, individually, elements of work to be carried out during the TP classes in Moodle. This element must clearly indicate the student''s name and number.
In each TP class, exercise sheets or other work elements on Molecular/Cellular Biology subjects will be available. In these classes, students will be divided into pre-formed groups of ~5 students/group. During the TP classes, students must carry out the work elements in accordance with the instructions provided in each class. Until the end of the TP class, each student must upload the element indicated by the teacher. If there is no network, the teacher may indicate another deadline for submitting the work.
4. Only students present in TP classes will be able to submit work on Moodle. There will be a dedicated place to upload documents to Moodle every week. Work placed in the wrong TP class will not be considered.
5. Students who have not signed the attendance sheet and/or have not uploaded their work in the appropriate location will be considered absent (absent).
6. Delays of more than 20 minutes prevent the student from being admitted to the TP class, with the corresponding absence, and from doing/delivering the work element corresponding to that day. Unexcused absences have the same effect.
7. Certificates and other valid justifications for absences will only be accepted if delivered in the week''s class immediately after the day of absence.
8. Student workers, and other exceptional cases, who do not attend theoretical-practical classes must carry out an assessment (to be agreed with the teacher) to obtain attendance to the subject.

B) Assessment in the discipline
B.1) Assessment Rules
The final classification of the subject (scale from 0 to 20 values) results from the sum of the scores from 2 components of the assessment:
i) Assessment of the theoretical/theoretical-practical component (70% = 14 points). A written test, for individual assessment of knowledge of theoretical and theoretical-practical class content for each module (BM and BC). The final grade for this component results from the arithmetic average of the grade from the 2 tests, rounded to the nearest tenth. Approval requires obtaining at least 7.0 val/14 val (50%) in the average score of the 2 tests.
The test date is announced at the beginning of classes and marked in the CLIP, and there are no alternative date(s), nor repetition of any of the tests.
Alternatively, students can pass the subject by taking a final exam (Appeal Period) – scheduled in CLIP. The appeal exam will cover the material given in the 2 modules, BM and BC, with a quotation of 50% of the exam grade for each module. Approval requires obtaining at least 7.0 val/14 val (50%) in the overall grade of the appeal exam.
ii) Continuous assessment (theoretical-practical) (30% = 6 points).
The grade for this component results from the preparation of group work during the semester, on a topic proposed by the teachers. The work has a final classification of 6 val.
There is no minimum grade or obligation to do these works. The specific rules for the work will be announced at the beginning of the semester.

B.2) Conditions for obtaining Approval
Have frequency, have a classification equal to or greater than 7.0/14 val in the assessment of the theoretical/theoretical-practical component (by tests or appeal exam); have a final grade resulting from the sum of the 2 evaluation components equal to or greater than 9.5 values.

Exame de Recurso
Individual assessment of knowledge of theoretical and theoretical-practical class content. Written exam lasting a maximum of 2 hours. It is aimed at students who fail (final grade lower than 9.5 points), but who attend the subject, or for students who wish to improve the theoretical/theoretical-practical assessment component.
The appeal exam, whether for approval or improvement, will have to be completed completely, ie, the BM module and the BC module. There is no possibility of making partial improvements to any of these modules.

Subject matter

T classes – Molecular Biology

A. Nucleic acids
- Structure and composition of nucleic acids
- DNA as the genetic material
- DNA base pairing and supercoiling
- DNA topologic forms
- Gene organization in chromosomes
- Genomes of model organisms and organels
- Plasmids, definition and functions

B. DNA replication
- Basic mechanism and enzymology
- Semi- discontinuous replication
- Bacterial and eukaryotic DNA polymerases
- Priming, elongation and termination process
- DNA damage and repair

C. Transcription process
C.1. Gene structure and transcription in bacteria
- E. coli RNA polymerase.
- Iniciation, sigma factors, elongation and termination.
C.2. Eukaryotic transcription
- RNA polymerases
- Promoters and enhancers
- General transcription factors
- Chromatin structure and regulation
- RNA Processing: exons and introns, splicing, capping, polyadenylation

D. Translation process
- Ribosome structure and function
- Initiation, elongation and termination
- Genetic code
- Results from DNA modifications

TP classes – Molecular Biology

Class 1. DNA extraction methods
- Phenolic extraction
- Plasmid extraction

Class 2. DNA analysis - part I
- Agarose gel electrophoresis
- Restriction mapping

Class 3. DNA analysis - part II
- UV-vis spectroscopy

Class 4. PCR – DNA amplification – part I
- amplification conditions
- polymerases

Class 5. PCR – DNA amplification – part II
- primer design

Class 6. Molecular cloning
- Molecular cloning in E. coli
- DNA transformation

 

T classes – Cell Biology

1. The eukaryotic cell

. The cell theory

. Major structural differences between eukaryotic cells and prokaryotic cells

. The eukaryotic cell as a fundamental tissue unit and as a boundary unit of the various organelles

. The main eukaryotic cell organelles

2. Cell Membrane and Biological Transport

. Structure and composition of cell membranes: Fluid Mosaic Model

. Different types of active and passive transport

. Ion channels and membrane transporters

. Important gradients in physiological processes

. Integration and interplay of transport activity in a cell

. Distribution of transporters and cell function

3. Characterization of eukaryotic cell organelles

3.1. Endomembranous system:

. Subcellular location, relative size, structure and function of smooth and rough endoplasmic reticulum and Golgi apparatus

. The role of the rough endoplasmic reticulum in protein synthesis

. Transport and sorting of proteins through the endoplasmic reticulum and the different cisterns of the Golgi apparatus

. Classic protein secretion pathway

3.2. Lysosomes:

. Structural and functional characterization of lysosomes

. Transport via the Golgi trans network and lysosome formation

. Lysosome maturation

. Lysosomal acid hydrolases

. Lysosomes involved in nutrition and cell defense processes: characterization of different types of autophagy (macroautophagy, microautophagy and chaperone-mediated autophagy)

. The importance of autophagy in physiological and pathological processes

3.3. Peroxisomes:

. Structural and functional characterization of peroxisomes

. Peroxisome formation

. Importance of peroxisomes in metabolic pathways

. Changes in peroxisomal activity and relationship to pathologies

3.4. Mitochondria:

. Structural and functional characterization of mitochondria

. Mitochondrial genome

. Regulation of the active mitochondrial population (fission, fusion and mitophagy)

. Pathological changes related to loss of mitochondrial homeostasis

. The central role of mitochondria in metabolism and cell death by apoptosis.

4. Intracellular Signaling and Signal Transduction Mechanisms

. Communication by extracellular signals and types of extracellular signals.

. Main intracellular signaling pathways and signal transduction: Signaling by intracellular receptors (receptors of cholesterol-derived ligands) and signaling by cell surface receptors (receptors linked to the activity of G proteins).

. Methods of identification, characterization and modulation of some signal transduction pathways through the presentation of practical cases.

5. Cytoskeleton:

. Structural and functional characterization of the cytoskeleton

. Microtubules, microfilaments (actin filaments) and intermediate filaments. Intracellular transport dependent on motor proteins (kinesins and dyneins)

. Participation of cytoskeleton elements in cell homeostasis

 

TP classes – Cell Biology

Solving exercises and problems, and searching for current scientific literature, individually or in groups, on the subject of the previous theoretical class:

. Eukaryotic cell and cell membrane

. Endoplasmic reticulum and Golgi apparatus

. Lysosomes and peroxisomes

. Mitochondria

. Cell signaling pathways

. Cytoskeleton

 

Programs

Programs where the course is taught: