TEACHING PLAN FOR

Molecular and Cell

Biology

1. Basic description

Name of the course: Molecular and Cell Biology

Module: Life Science
Academic year: 2016-2017
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

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 integrate clinical and omics data for a greater understanding of biological
phenomena.

CE7. To demonstrate knowledge, skills and appropriate practices in the area of the
biology of organisms and biosystems.

Learning outcomes

RA1.1, RA1.3, RA1.4

RA2.1, RA2.2
RA4.1

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

• 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
endoplasmic reticulum, lysosomes, chromosome, nucleus and cytoplasmic
organelles. 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; telomers, telomerase. Replication of RNA genomes such as
HIV; reverse transcriptase. Replication fidelity.

Session 3. DNA replication (II): control of the cell cycle in eukaryots (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 prokaryots (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 eukaryots (2.5 h)

The eukaryotic genome: size, structure, especial elements, repetitive
sequences. Nucleosomes and chromatin. Basic mechanisms of transcription.
Regulation of transcription and chromatine compactness. 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, ncRNAs, asRNA.

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 eukaryots: the lysosomal and ubiquitin-
based systems. Intracellular targeting of proteins.

B) BASICS OF EUKARYOTE CELL: FROM STUCTURE TO ORGANIZATION

(15 hours)

Session 9. The plasma membrane and extracellular matrix (2h)

The plasma membrane as mediator of the inside and outside cellular milieu.
Composition and functions. Cell to cell contacts and cell extracellular matrix.
Adherent Junctions, Occluding Junctions, Desmosomes, Communication
Unions.
Extracellular matrix components. Collagens: structure and distribution. Elastin,
proteoglicans and glucoproteins. Hyaluran. Functional integration. The basal
lamina: morphology, structure and function.

Session 10. The extracellular matrix (1h)

Extracellular matrix components. Collagens: structure and distribution. Elastin,
proteoglicans and glucoproteins. Hyaluran. Functional integration. The basal
lamina: morphology, structure and function.

Session 11. 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 cellular shape
rearrangements.

Session 12: Cell death and cellular aging (2h)

Cell death pathways. Caspases, Telomeres. Balance between aging and
cancer.

Session 13: Cytology (2h)

General organization of animal tissues. Basic properties of epithelial,
connective, nervous and muscular tissues. Cell polarity. Epithelial-mesechymal
transition (EMT)
Session 14: Pluripotency and differentiated cells (2h)
General concepts of pluripotency and differentiation. Stem cells. Symmetric and
Asymmetric divisions. Balance between proliferation and differentiation in
tissues. Regeneration and reprogramming.

Session 15: Cellular Communication between animal cells (3 h)

Basic principles of cell signaling. Characterization of signaling components:
signallng molecules, receptors, second messengers, effectors, signaling
complexes. Integration and amplification of signals. Basic classification and
characterization of membrane receptors. Intracellular/nuclear receptors.

Session 16: Cell Signaling and Gene Regulation (1 hour)

Basic signaling pathways. Signaling disruption in disease. Cancer

SEMINARS (12 hours)

Seminar 1. Introduction to the Molecular Biology practical laboratory work (1.5

h)
Seminar 2. Introduction to the Cellular Biology practical laboratory work (1.5 h)
Seminar 3. Conclusions from Molecular Biology practical laboratory work (with
computers) (2 h)
Seminar 4. Conclusions from Cellular Biology practical laboratory work (with
computers) (2 h)

Seminars 5 to 8. Advanced techniques in Molecular and Cellular Biology

Seminar 5. Basic principles in the generation of transgenic and knock-out
animals. The CRISP-Cas9 system (1 h)
Seminar 6. Ultrasequencing and chromatin immuno-precipitation techniques (2
h)
Seminar 7. Study of protein structure and proteomes by modelling and mass
spectrometry (1 h)
Seminar 8. Basic uses of flow cytometry in cell biology (1 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

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
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 labelling of cellular components and
visualization. Proliferation interference.

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, 1 point essay), 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 mid-term theoretical exam will consist in:

True/False type of exam:100%
Grades given after 15 days maximum

1 point, Evaluation of written essay of a topic of the course provided by the

teachers
Grades given after 15 days maximum

3 points, Evaluation of practical and seminars contents will consist in:

Short questions: 80%
Assistance and participation: 20%

The laboratory practices and seminars are mandatory. The assessment will be
individual. Assistance and participation to practical and seminars will be part of
the grade.

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).

Recuperation Information

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.

Assessment Time period Type of Assessment agent Type of Grouping Weight

elements assessment activity (%)
Comp Opt Lecturer Self- Co- Indiv Group
assess asses (#)
s
Written essay x Berta synthesis- x 10%
Alsina based
Evaluation of x Bàrbara applicatio x 30%
Practicals Negre n-based
and seminars
Theoretical 20-27 x All synthesis- x 50%
Final Exam March based
Theoretical x Elena synthesis- x 10%
Mid- Term Hidalgo/J based
Exam ose Ayté

Working competences and assessment of learning outcomes:

Learning
outcomes

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.

LODISH, KAISER, BRETSCHER, AMON, BERK, KRIEGER, PLOEGH,

SCOTT. Molecular Cell Biology, seventh Edition. 2013.

MATHEWS, C. K.; VAN HOLDE, K. E.; AHERN, K.G. Biochemistry. 3ª ed. San
Francisco: Benjamin/Cummings, 2002.

GARRETT, R. H.; GRISHAM, C. M. Biochemistry. Saunders. Orlando (Fla.):

Brooks/Cole, 2005.

VOET, D.; VOET, J. G.; PRATT, C. W. Fundamentos de bioquímica. 2ª ed.

Editorial Médica Panamericana, 2007.

LEWIN, B. Genes IX. Nova York: Oxford University Press, Inc., 2007.

ALBERTS, B.; JOHNSON, A.; LEWIS, J.; RAFF, M.; ROBERTS, K.; WALTER,
P. Molecular Biology of the Cell. Garland Science, 5ª ed., 2008.
COOPER, G.M. i HAUSMAN, R.E. The Cell. A molecular approach.
Washington D.C. and Sunderland, 2007.

GARTNER, L. P.; HIATT, J. L. Histología. Texto y Atlas. Mèxic: McGraw-Hill

Interamericana, 2007.

Other books:

MATHEWS, C. K.; VAN HOLDE, K. E. Bioquímica. Madrid: McGraw-

Hill/Interamericana de España, S.A.U., 1998.

ZUBAY, G.; WM, C. Biochemistry. Dubuque (Ia.): Brown Publishers, 1998.

LEWIN, B. Genes VI. Nova York: Oxford University Press, Inc., 1997.

FRAYN, K. N. Regulación del metabolismo. Barcelona: Ediciones Omega, S.A.,

1998.

CHAMPE, P. C.; HARVEY, R. A. Biochemistry. Filadèlfia: Lippincott Company,

1994.

MADIGAN, M. T.; MARTINKO, J. M.; PARKER, J. Brock Biology of

Microorganisms. Nova Jersey: Prentice-Hall, Inc., 1997.

7. Methodology

Theoretical classes, seminars and practicals: Face-to-face

Essay: Independent
8. Scheduling activities

PAD BMC 2016-17 (6 ECTS)- 66 classroom hours

Each student will receive 66 hours of class:

30 h theoretical
12 h seminars (2 group, 20 alumni/group)
24 h practical lessons (2 groups, 18-20 alumni/group, 1 teacher/group)

1) Scheduling activities under the curriculum, from:

• In the classroom: 1) Lecture classes, 2) Seminars, 3) Face-to-face tutorials, 4) “Regulated” practical
classes (lab…)
• Outside the classroom: 5) Group work, 6) Individual work (reports, exercises…), 7) Internships
(outside companies), 8) Independent study

Week Activity in the classroom Activity outside the classroom

Grouping/type of activity Grouping/type of activity
Week 1 • Theoretical classes -3 hours 8-Study hours 3 hours
(Sessions 1 and 2)

Week 2 • Theoretical classes -3 hours 8-Study hours 3 hours

(Sessions 2 ,3, 4)
Week 3 • Theoretical classes- 3 hours 8-Study hours 5 hours
(Sessions,4, 5 and 6)
• Seminars 1 and 3 – 3.5 hours
• Practical Classes BM- 12 hours
Week 4 • Theoretical classes- 3 hours 8-Study hours 3 hours
(Sessions 6, and 7)
Week 5 • Theoretical classes- 3 hours 8-Study hours 5 hours
(Session 7 and 8)
• Seminars 5 and 6 - 3 hours
Week 6 • Theoretical classes- 3 hours 8-Study hours 5 hours
(Session 9 and 10)
• Mid-term exam (until session 6)-
1 hour
Week 7 • Theoretical classes-3 hours 8-Study hours 5 hours
(Sessions 11 and 12)
• Seminars 2, and 4- 3.5 hours
• Practical classes BC-12 hours
Week 8 Theoretical classes- 3 hours 8-Study hours 5 hours
(Sessions 12, and 13) 6-Essay- 2 hours work
Seminars 7 and 8- 2 hours
Week 9 • Theoretical classes-3 hours 8-Study hours 3 hours
(Session 14)
• Exam Practicals and Seminars
Week 10 Theoretical classes-3 hours 8-Study hours 3 hours
(Session 15)

Week final exams

La còpia i/o plagi total o parcial als treballs i/o exàmens comportarà suspendre
l'assignatura amb una qualificació de zero sense dret a recuperació, sense
perjudici de l'aplicació de les altres sancions previstes al Reglament de Règim
disciplinari dels estudiants de la Universitat Pompeu Fabra en funció de la
gravetat de la infracció.

La copia y/o plagio total o parcial en los Trabajos y/o exámenes comportará
suspender la asignatura con una calificación de cero sin derecho a
recuperación, sin perjuicio de la aplicación de las otras sanciones previstas en
el Reglamento de Régimen disciplinario de los estudiantes de la Universitat
Pompeu Fabra en función de la gravedad de la infracción.

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.