Module: Life Science Academic year: 2017-2018 Year: 2017 Term: Second Degree / Course: First Code: 51206 Number of credits: 6 Total number of hours committed: Complete Teaching language: English Lecturer: Berta Alsina is the subject coordinator. Other professors participating in the theoretical classes are Bàrbara Negre, José Ayté and Elena Hidalgo. Berta Alsina, Bàrbara Negre, Laura Taberner and Margarita Cabrera will also contribute to the teaching of seminars and practical classes.
Timetable: Complete
2. Presentation of the course
DIRECTIONS: You must write a brief introduction that gives students a general idea of the subject, that helps to situate and contextualise the subject within the course as a whole, that identifies key aspects and that introduces the approach presented.
Some key points that must be taken into consideration in the presentation of the subject are: • Contextualisation (what is the context of the subject? ) • Type and focus of the subject (introduction, specialisation, what does it contribute to the competence profile to be gained…) • Key aspects of the subject (focusing on comprehension, application…) • General recommendations (areas that the teacher sees appropriate to introduce)
MCB is a mandatory subject of the Curriculum of the Bioinformatics grade. It will
be given in the 2nd trimester of the 1st year and will include 6 credits ECTS, 3 of them of theory and 3 practical/seminars. Objectives
Molecular Biology combined with Cellular Biology means to study the molecular processes occurring and ruling the cell’s physiology. The teaching project of this subject pretends, among other goals, to:
1. Introduce the student into the world of Molecular Biology, to understand the transfer of genetic information from nucleic acid till protein synthesis and cell function.
2. Help the student to know the general structure, organization and function of eukaryotic cells. We aim to transmit the student how morphology, structure and function are connected.
3. Teach to student the bases of basic research in molecular and cellular biology, and help them reaching the correct conclusions from their experimental results.
This is an introductory course and basic information on molecular and cellular
mechanisms will be given to provide students with basis to comprehend specialized courses of bioinformatics curricula.
3. Competences to be worked in the course
General competences Specific competences
CB1, CB2, CB4, CG1 CE1, CE2, CE4, CE7
I. General competences
CB1. That the students have demonstrated to have acquired the knowledge and understanding in a field of study that starts from the basis of general secondary education, and is typically at a level that although it is supported by advanced textbooks, includes some aspects that involve knowledge of the forefront of their field of study.
CB2. That the students know how to apply their knowledge to their work or vocation in a professional manner and have competencies typically demonstrated through devising and defending arguments and solving problems within their field of study.
CB4. That the students can convey information, ideas, problems and solutions to both specialist and non-specialist audiences.
CG1. That the students will acquire an intra- and interdisciplinary training in both computational and scientific subjects with a solid basic training in biology.
II. Specific competences
CE1. To acquire biological knowledge from the cellular to the organismal level, with an interdisciplinary vision and special emphasis on biomedical applications.
CE2. To manage and exploit all kinds of biological and biomedical information to transform it into knowledge. CE4. To acquire technical knowledge of how to perform experiments in the laboratory in the areas of molecular and cell biology
CE7. To demonstrate knowledge, skills and appropriate practices in the area of the biology of organisms and biosystems.
Learning outcomes
RA1.1. Validate appropriate knowledge and skills in the area of biological sciences.
RA1.3 Understand the stages of gene expression: phenomena of cell division and death in unicellular and multicellular organisms, regulation and use of RNA as a functional molecule.
RA1.4. Identify the main metabolic pathways and the process of transmission of extracellular signals.
RA2.1. Visualize, manipulate and extract biological data.
RA2.2 Improve understanding of disease onset and progression.
RA4.1. Process, manage and interpret basic omics data (genomics, proteomics, transcriptomics).
4. Contents
DIRECTIONS: The core themes around which the subject is organised must be determined. The primary reason for specifying core themes is to identify the basic organisation for the subject. Therefore, it is not necessary to adjust the blocks of content to themes.
• Basic description of contents outlined for the curriculum
This course covers the basic principles of cell structure and function, in both prokaryotic and eukaryotic cells. Subjects include the cytoskeleton, the plasma membrane and extracellular matrix, cell communication and organization of tissues. The course also explores molecular mechanisms and replication, transcription and translation, as well as regulation and control.
• Provide more detail and expand upon the description of contents
A) TRANSFER OF GENETIC INFORMATION (15 hours)
Session 1. DNA: base of the genetic information (1.5 h)
Heredity material: DNA. Transfer of genetic information in bacteria. Types of genetic elements. Genetic information and evolution.
Session 2. DNA replication (I) (2 h)
DNA replication as a semiconservative process. General aspects of replication using Escherichia coli as a model system. Replication of eukaryotic chromosomes; telomeres, telomerase. Replication of RNA genomes such as HIV; reverse transcriptase. Replication fidelity. Session 3. DNA replication (II): control of the cell cycle in eukaryotes (1,5 h) Control of DNA replication in eukaryotic cells. Phases and control of the cell cycle. Molecular bases of cancer. Cell cycle modeling.
Session 4. DNA Recombination, damage and repair (2 h)
Molecular bases of genetic variation: recombination and mutation. DNA damage, and DNA repair.
Session 5. Transcription in prokaryotes (1 h)
DNA as template of RNA: the transcription process. Basic mechanisms of transcription in bacteria. Regulation of transcription: induction and repression.
Session 6. Transcription in eukaryotes (2.5 h)
The eukaryotic genome: size, structure, especial elements, repetitive sequences. Nucleosomes and chromatin. Basic mechanisms of transcription. Regulation of transcription and chromatin remodeling. mRNA processing: 3’, 5’ or capping, splicing.
Session 7. mRNA translation and post-transcriptional regulation of gene expression
(2.5 h) The genetic code: translation of nucleotide triplets to amino acids. Components of the translation machinery: mRNA, tRNA, ribosomes. Control of translation. Mechanisms of post-transcriptional control of gene expression: siRNA, microRNAs.
Session 8. Processing, degradation and intracellular transport of proteins (2 h)
Final steps in protein synthesis: folding, cleavage, covalent modification. Regulation of protein degradation in eukaryotes: the lysosomal and ubiquitin-based systems. Intracellular targeting of proteins.
B) BASICS OF EUKARYOTE CELL: FROM STUCTURE TO ORGANIZATION (15
hours)
Session 9: Gene Regulation (1 hour)
Gene regulatory elements. Transcription factors. Linking chromatin structure and transcription. Chromatin modifications and organization. Imprinting
Session 10. The plasma membrane and cell adhesion components (1h) The plasma membrane as mediator of the inside and outside cellular milieu. Composition and functions. Cell to cell contacts. Adherent Junctions, Occluding Junctions, Desmosomes, Communication Unions.
Session 11. The transport through plasma membranes and extracellular
matrix (2h) Principles of membrane transport. Transporters and active transport. Passive diffusion. Pumps, channels and transporters. The extracellular matrix components. Collagens: structure and distribution. Elastin, proteoglicans and glucoproteins. Hyaluran. Functional integration. The basal lamina: morphology, structure and function.
Session 12. The cytoskeleton and cell shape changes (2 h)
General organization of cytoskeleton. The microtubules, associated proteins and dynamics. Microtubules Organizing Centers (MTOC). Centrosome. Actin microfilaments: organization, dynamics and associated proteins. Intermediate filaments: classification and organization, differences with microfilaments and microtubules. Cilia and flagella. Cellular motility and cell shape rearrangements. Session 13: Development and basics of organization of tissues (2h) From zygote to embryo. General organization of animal tissues. Basic properties of epithelial, connective, nervous and muscular tissues. Cell polarity. Epithelial- mesechymal transition (EMT). Basics of development of nervous and immune systems.
Session 14: Cellular Communication between animal cells (2 h)
Basic principles of cell signaling. Characterization of signaling components: signaling molecules, receptors, second messengers, effectors, signaling complexes. Integration and amplification of signals. Basic classification and characterization of membrane receptors. Intracellular/nuclear receptors.
Session 15: Examples of classical signaling pathways (2h)
Session 16: Pluripotency and differentiated cells (2h)
General concepts of pluripotency and differentiation. Stem cells. Symmetric and Asymmetric divisions. Cancer stem cells. Balance between proliferation and differentiation in tissues. Regeneration and reprogramming.
Session 17: Cell death and cellular aging (1h)
Cell death pathways. Caspases, Necrosis versus apoptosis. Autophagy. Balance between aging and cancer. Cellular senescence.
SEMINARS (8 hours)
Seminar 1. Conclusions from Molecular Biology practical laboratory work (with
computers) (1.5 h) Seminar 2. Conclusions from Cellular Biology practical laboratory work (with computers) (1.5 h)
Seminars 3 to 5. Advanced techniques in Molecular and Cellular Biology
Seminar 3. Basic principles in the generation of transgenic and knock-out animals. The CRISP-Cas9 system (2 h) Seminar 4. Study of protein structure and proteomes by modelling and mass spectrometry (1,5 h) Seminar 5. Basic uses of flow cytometry in cell biology (1,5 h)
PRACTICAL LABORATORY WORK (24 hours)
The practical work will last 6 days (3 for molecular biology, 3 for cellular biology), with a total of 24 hours.
Molecular Biology practical work. Basic techniques – generation and
sequencing of DNA (12)
The student will learn some basic techniques in molecular biology, such as transformation of bacteria, purification of plasmid DNA and sequencing and analysis of this DNA, as well as PCR amplification of some template DNAs.
Cellular Biology practical work. Basic Techniques in cell culture and
analysis of cell processes (10,5) The student will learn basic techniques in cell biology such as practical manipulation and culture of mammalian cells. Cell transfection and beta-galactosidase activity analysis. Fluorescent labeling of cellular components and visualization.
5. Assessment
A series of exams are used to measure the success in meeting the course learning objectives. In order to successfully complete this course, the student must pass at least with 50 % on the final mandatory examination. All exams are compulsory.
The course assessment will be performed as follows: from 10 points, 7 points will correspond to the evaluation of the theoretical contents (5 points theoretical final exam, 1 point mid-term theoretical exam on Molecular Biology, 1 point mid-term theoretical exam on Cell Biology), 3 points to the evaluation of practical and seminar contents.
5 points, Evaluation of theoretical final exam will consist in:
a) Multiple Choice: 70% b) Short Questions: 30%
1 point, Evaluation of molecular biology part mid-term theoretical exam will consist in: True/False type of exam: 100% Grades given after 15 days maximum
1 point, Evaluation of cell biology part mid-term theoretical exam will consist in: True/False type of exam: 100% Grades given after 15 days maximum
3 points, Evaluation of practical and seminars contents will consist in:
Exam of short questions of practicals and seminars: 1.8 points Handling of practical questionnaire (one handled the last day of the molecular Biology lab week, the last day of the Cellular Biology lab week): 1.2 points
FINAL MARKS THEORY
Mid term - MB (week 4) Mid term – CB (week 8) Final exam - multiple choice (24) (w 12) Final exam – short questions (6) (w 12)
PRACTICAL / SEMINARS Practical guide – MB (w 10) Practical guide – CB (w 10) Final exam – MB practical work (w 10) Final exam – CB practical work (w 10) Final exam – seminars (w 10)
The laboratory practices are mandatory. The assessment will be individual.
Copy in any exam or plagiarism in the essay implies failing the course. A specific exam will be provided to the student only when particular impossibility to attend to the exam (death of close relative, student medical problem). Information of Make-up Exams
Only the students that after the evaluation have not passed the course can go retake the final theoretical exam in July. The grades obtained at the new exam will substitute the grades of the previous failed exam during the trimester and will be used to calculate the final grade according to the percentages reported above.
Assessmen Time Type of Assessment agent Type Grouping Weig
t elements period assessme of ht nt activit (%) y Com Op Lectur Self- Co- Indi Grou p t er assess asse v p ss (#) Theoretical Week x Berta synthe x 10% Mid- Term 8 Alsina sis- Exam based Exam of Week x Bàrbar applica x 18% Practicals 10 a tion- and Negre based seminars Theoretical x All synthe x 50% Final Exam sis- based Theoretical Week x Elena synthe x 10% Mid- Term 5 Hidalg sis- Exam o/Jose based Ayté Handling of Weeks x Bàrbar applica grou 12% practical 3 and a tion- p questionnai 7 Negre based res
6. Bibliography and teaching resources
Text books:
TYMOCZKO, BERG, STRYER. Bioquímica, Curso básico. 2ª edición. Ed. Reverté.
2013
BERG, J. M.; TYMOCZKO, J. L.; STRYER, L AND GATTO, G. J. Biochemistry. 7th ed. Londres, UK, WH FREEMAN. ISBN. 9781429276351. 2011.
Total or partial copy and/or plagiarism will imply a failure in the subject with a final grade of zero points and no access to the make-up exam. According to the academic regulations specified in the Disciplinary rules for students of Universitat Pompeu Fabra, other additional sanctions may apply depending on the seriousness of the offence.
