Mestrado Universitario en Bioloxía Molecular , Celular e Xenética
Descriptors
Cycle
Period
Year
Type
Credits
Official Master's Degree
2nd four-month period
First
Optional
3
Language
Spanish
English
Teaching method
Face-to-face
Prerequisites
Department
Bioloxía
Coordinador
Becerra Fernandez, Manuel
E-mail
manuel.becerra@udc.es
Lecturers
Becerra Fernandez, Manuel
Cerdan Villanueva, Maria Esperanza
Lamas Maceiras, Mónica
Vizoso Vázquez, Ángel José
E-mail
manuel.becerra@udc.es
esper.cerdan@udc.es
monica.lamas@udc.es
a.vizoso@udc.es
Web
General description
Dentro do Máster en Bioloxía Molecular, Celular e Xenética, esta asignatura, ten como obxectivos coñecer e manexar os fundamentos teóricos e as aproximacións experimentais ao análise das propiedades físcias e químicsa das macromoléculas biolóxicas, en especial as proteínas, co fin de relacionar as suas estruturas coa su función e actividade biolóxica. Estudiaranse os conceptos necesarios para a descrición das estruturas, os métodos computacionais e experimentais utilizados para o seu estudio e os fundamentos teóricos que os xustifican.
Study programme competencies
Code
Study programme competences
A3
Skills of understanding the functioning of cells through the structural organization, biochemistry, gene expression and genetic variability.
A9
Skills of understanding the structure and dynamics of proteins to individual and proteomic level, as well as the techniques that are necessary to analyze them and to study their interactions with other biomolecules.
B2
Skills of decision making for the problem solving: that are able to apply theoretical knowledges and practical acquired in the formulation of biological problems and the looking for solutions.
B3
Skills of management of the information: that are able to gather and to understand relevant information and results, obtaining conclusions and to prepare reasoned reports on scientific and biotechnological questions
B4
Organization and work planning skills: that are able to manage the use of the time as well as available resources and to organize the work in the laboratory.
C3
Using ICT in working contexts and lifelong learning.
C8
Valuing the importance of research, innovation and technological development for the socioeconomic and cultural progress of society.
Learning aims
Learning outcomes
Study programme competences
Ability to understand concepts and theories related to the dynamics of proteins in cells
AR3 AR9
BR2
CC3 CC8
Familiarization with the bibliographic and information sources where you can get updated information
AR3 AR9
BR2
CC3 CC8
Know the systems for the determination of structures by x-ray diffraction
AR9
BR2
CC3 CC8
Learn different computer programs for the representation of proteins and their use
AR3 AR9
BR2
CC3 CC8
Learn the techniques to determine interactions between proteins and proteins with other biomolecules and ligands
AR3 AR9
BR4
CC8
Ability to interpret critically the data of a structure of a protein in a publication
AR3 AR9
BR3
CC3
Contents
Topic
Sub-topic
Structural classification of proteins.
Structural domains of proteins. Classification of proteins according to its three-dimensional structure. Alpha proteins. Alpha/beta protein. Protein beta. Structural classes of proteins. CATH classification. SCOP classification. DALI classification. SMART classification.
Criteria for the choice of a method of purification and preliminary characterization.
Chromatographic techniques: gel filtration, ion exchange, affinity and hydrophobic interaction. Purification strategies. Preliminary characterization of the protein conformation: State of aggregation, compactness. Secondary structure and tertiary structure indicators. Quantification of proteins.
Experimental determination of the structure of proteins using diffraction X.
Crystallization techniques. Tools and strategies for diffraction data. Interpretation of the XRD. Obtaining and refinement of the molecular model. Parameters for calculating the convergence of the model. Modelling.
Interactions between biomolecules.
Interactions of proteins for the formation of complexes with proteins and other ligands. Experimental methods used to determine these interactions and their structure. The double hybrid method. The split-ubiquitin method. Pull-down. GST-Pull-down. FRET. EMSA trials. CHIP test. Other methodologies.
Planning
Methodologies / tests
Competencies
Ordinary class hours
Student’s personal work hours
Total hours
Guest lecture / keynote speech
A9
14
28
42
Laboratory practice
A9 B3 B2 B4 C8
4
6
10
ICT practicals
A3 C3
2
3
5
Mixed objective/subjective test
A9
1
15.5
16.5
Personalized attention
1.5
0
1.5
(*)The information in the planning table is for guidance only and does not take into account the heterogeneity of the students.
Methodologies
Methodologies
Description
Guest lecture / keynote speech
Oral presentation complemented with the use of audiovisual media in order to pass on knowledge and facilitate learning.
Laboratory practice
Methodology that enables students to learn effectively, through practical activities (demonstrations, simulations, etc.) the theory of a field of knowledge, through the use of communications and information technologies.
ICT practicals
ICT allow display of protein structure models and design interaction experiments.
Mixed objective/subjective test
Combination of multiple choice questions and short of relationship questions
Personalized attention
Methodologies
Laboratory practice
ICT practicals
Description
The personalized attention that is described in relation to these methodologies are conceived as moments of face-to-face student work with the teacher by involving a compulsory student participation.
Students with part-time dedication or waiver of presence should contact the teachers of the subject in the early going to establish a schedule of activities to acquire and evaluate in a complementary way the competences.
Assessment
Methodologies
Competencies
Description
Qualification
Laboratory practice
A9 B3 B2 B4 C8
Regular attendance and active participation at the laboratory practices will be evaluated.
15
Mixed objective/subjective test
A9
Test relating to knowledge and skills
75
ICT practicals
A3 C3
Attendance and active participation will be valued
10
Assessment comments
To get honours preference will be given to the students evaluated at the
first opportunity in June.
Sources of information
Basic
Banaszak,
L. J. (2000). Foundations of structural biology. Academic Press.
Berg, J.
M., Tymoczko, J. L., Stryer. L. (2003). BIOQUÍMICA. 5ª Edición. Reverté.
Branden,
C. & Tooze, J. (1998). INTRODUCTION TO PROTEIN STRUCTURE. 2nd edition
Garland Publishing, Inc, New York.
Cerdán Villanueva, M.
E. (2005). Curso avanzado de proteínas y ácidos nucleicos. Universidade da Coruña.
Creighton,
T. E. (1993). PROTEINS: STRUCTURES AND MOLECULAR PROPERTIES, 2nd edition. W.H.
Freeman & Company, New York.
Gómez-Moreno,
C. & Sancho, J. (Coords). (2003). ESTRUCTURA DE PROTEÍNAS. Ariel Ciencia, Barcelona.
Lesk, A.
M. (2000). INTRODUCTION TO PROTEIN ARCHITECTURE. THE STRUCTURAL BIOLOGY OF
PROTEINS. OxfordUniversity Press, Oxford.
Nelson, D. L., Cox, M.
M. (2000). LEHNINGER PRINCIPLES OF BIOCHEMISTRY.
Worth Publishers.
Rodes,
G. (2000). Crystallography. Made Crystal Clear. Academic Press.
Complementary
§
Carter, Jr., C.V. y Sweet, R. M. (1997). Macromolecular Crystallography,
parts A and B. Methods in Enzymology, vols. 276 y 277. Academic Press. NY.
§
Casari, G., Sander, C., Valencia, A. (1995). A method to predict functional
residues in proteins. Nature Struct. Biol., 2: 171178.
§
Clore, G. M. y Gonenborg, A. M. (1998).
New methods of structure
refinement for macromolecular structure determination by NMR. Proc. Natl. Acad.
Sci., 95, 58915898.
§
Del Sol Mesa, A., Pazos, F., Valencia,
A. (2003). Automatic
methods for predicting functionally important residues. J. Mol. Biol., 326:
12891302.
§
Ducruix, A., Giegé, R. (1999). Crystallisation of Nucleic Acids and
Proteins. A Practical Approach, edn 2. OxfordUniversity Press. Oxford.
§
Eyrich, V. A., MartiRenom, M. A.,
Przybylski, D., Madhusudhan, M.S., Fiser, A., Pazos, F., Valencia, A., Sali, A.
y Rost, B. (2001). EVA:
continuos automatic evaluation of protein structure prediction servers.
Bioinformatics, 17: 12421243.
§
Ferentz, A.E. y Wagner, G. (2000). NMR spectroscopy: a multifaceted
approach to macromolecular structure. Quarter Rev. Biophys. 33, 2965.
§
Fersht, A. R. (1999). Structure and Mechanism in Protein Science, Freeman
and Co., NY.
§
Frank, J. (1996). Three dimensional electron microscopy of macromolecular
assemblies. Academic Press, San Diego.
§
Harris,
E. L. V. y Angel, S. (eds.) (1999): Protein purification methods. A practical
approach. IRL Press. Oxford.
§
James, T. L., Dötsch, V. y Smith, U. (2001). Nuclear Magnetic Resonante of Biological
Macromolecules. Part A and B. Methods Enzymol., 338, Academic Press, San Diego.
§
Juan, D.,
Graña, O., Pazos, F., Fariselli, P., Casadio, R., Valencia, A. (2003). A neural network approach to evaluate
Fold recognition results. Proteins Mar 1,(4): 50, 600608.
§
Kleanthous,
C. (ed.) (2000). ProteinProtein Recognition. OxfordUniversity Press, Oxford.
§
Mayo, K. H. y Daragan, U. A. (2003). Protein dynamics using NMR relaxation. World
Scientific, Nueva Jersey.
§
McEwen, B. F. y Marcko, M. (2001). The emergente of electrón tomography as an important
tool for investigating cellular ultrastructure. J. Histochem. Cytochem. Vol 49,
553563.
§
Mc
Pherson, A. (2002). Introduction to Macromolecular Crystallography. John Wiley
and Sons. Inc., NY.
§
Naomi,
E. C. (2004). Turning Protein crystallisation from an art into a science.
Current Opinion in Structural Biology, 14: 577583.
§
Sinha,
N. y SmithGill, S. J. (2002). Protein structure to function via dynamics.
Protein Peptid Letters, 9: 367377.
§
Van
Heel, M. (2000). Single particle electrón cryomicroscopy: towards atomic
resolution. Q. Rev. Byophis. Vol. 33, 307369.
§
Igor Stagljar
and Stanley Fields (2002). Analysis of membrane protein
interactions using yeast-based technologies
• REVIEW . Trends in Biochemical Sciences, 27: 559-563.
§
Sandor Vajda and Carlos J. Camacho (2004). Protein–protein docking: is the glass half-full or
half-empty? Trends in Biotechnology, 22:
110-116.
§
Dobrin
Nedelkov and Randall W. Nelson (2003). Surface plasmon resonance mass
spectrometry: recent progress and outlooks • REVIEW Trends in Biotechnology, 21: 301-305.
§
Takashi
Ito, Tomoko Chiba and Mikio Yoshida (2001). Exploring the protein interactome
using comprehensive two-hybrid projects • REVIEW . Trends in Biotechnology, 19
(Supplement 1): 23-27.
§
Valerio
Orlando (2000). Mapping chromosomal proteins in vivo by
formaldehyde-crosslinked-chromatin immunoprecipitation • REVIEW . Trends in Biochemical Sciences,
25: 99-104.
§
Dobrin
Nedelkov and Randall W. Nelson (2003) Surface plasmon resonance mass
spectrometry: recent progress and outlooks • REVIEW . Trends in Biotechnology,
21: 301-305.
§ PhilippeI. H.
Bastiaens and Rainer Pepperkok (2000). Observing proteins in
their natural habitat: the living cell
• REVIEW . Trends in Biochemical Sciences, 25: 631-637
Subjects that it is recommended to have taken before
Molecular Techniques/610441002
Advanced Cellular Biology/610441003
Subjects that are recommended to be taken simultaneously
Recombinant proteins and protein Engineering /610441012
Proteomics/610441013
Bioinformatics and Biomolecular models /610441020
Subjects that continue the syllabus
Project/610441022
Other comments
(*)The teaching guide is the document in which the URV publishes the information about all its courses. It is a public document and cannot be modified. Only in exceptional cases can it be revised by the competent agent or duly revised so that it is in line with current legislation.