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Código: 18213 Centro: Facultad de Ciencias Titulación: Grado en Bioquímica Nivel: Grado Tipo: Obligatoria Nº de créditos: 6
ASIGNATURA / COURSE TITLE
ESTRUCTURA DE MACROMOLÉCULAS / STRUCTURE OF MACROMOLECULES
1.1. Código / Course number
1.2. Materia / Content area
Bioquímica y Biología Molecular / Biochemistry and Molecular Biology
1.3. Tipo / Course type
Formación obligatoria / Compulsory subject
1.4. Nivel / Course level
Grado / Bachelor
1.5. Curso / Year
2º / 2nd
1.6. Semestre / Semester
1º / 1st
1.7. Número de créditos / Credit allotment
6 ECTS / 6 ECTS
1.8. Requisitos previos / Prerequisites
Se requiere un conocimiento previo básico de Química, Termodinámica y Bioquímica. Se requiere además un conocimiento muy básico sobre estructura de proteínas y ácidos nucleicos, que debería haberse adquirido como parte de la asignatura Fundamentos de Bioquímica durante el primer curso del Grado en Bioquímica. Es muy conveniente tener un buen nivel de inglés.
Código: 18213 Centro: Facultad de Ciencias Titulación: Grado en Bioquímica Nivel: Grado Tipo: Obligatoria Nº de créditos: 6
A previous, basic knowledge on Chemistry, Thermodynamics and Biochemistry is required. A vary basic knowledge on protein and nucleic acid structure is also required, that should have been acquired as a part of the course Basic Principles of Biochemistry during the 1 st^ year of the Bachelor Degree in Biochemistry. A good level of English is very convenient.
1.9. Requisitos mínimos de asistencia a las sesiones
presenciales / Minimum attendance requirement
La asistencia es muy recomendable / Attendance is highly advisable. La asistencia a los seminarios, clases de problemas y casos prácticos es obligatoria / Attendance to seminars, problem-based and practical sessions is mandatory.
1.10. Datos del equipo docente / Faculty data
Mauricio García Mateu (coordinador) Departamento: Bioquímica y Biología Molecular Facultad: Ciencias Teléfono: 91 1964575 E-mail: [email protected] URL: http://www.cbm.uam.es/mkfactory.esdomain/webs/CBMSO/plt_LineasInvesti gacion.aspx?IdObjeto=
Horario de atención al alumnado: Por favor contactar previamente por E-mail. Los profesores de universidad tienen que dedicar sus horas de trabajo también a actividades de investigación en el laboratorio que no siempre pueden ser planificadas con antelación, y pueden no estar disponibles en ciertos días/horas.
Office hours: please make an appointment by E-mail. University lecturers and professors have to devote their work hours also to research activities in the laboratory that cannot be always planned in advance, and may not be available at certain dates/hours.
1.11. Objetivos del curso / Course objectives
El objetivo principal del curso se expresa en la competencia específica (CE) que se asignó a la asignatura en la Memoria de Verificación del Grado en Bioquímica (CE4):
Código: 18213 Centro: Facultad de Ciencias Titulación: Grado en Bioquímica Nivel: Grado Tipo: Obligatoria Nº de créditos: 6
i) The student will learn the techniques and approaches used to determine the structure of proteins, nucleic acids and their complexes. ii) the student will know the structural elements of proteins and nucleic acids. iii) the student will understand the thermodynamic principles that underly protein and nucleic acid structure and folding, and molecular recognition in macromolecular complexes. iv) the student will understand the relationship between the physico-chemical structure of proteins and nucleic acids and the biological function of these macromolecules and their complexes. v) the student will understand the basis of the molecular evolution of proteins. vi) the student will be capable to solve technical and scientific questions and problems related with protein and nucleic acid structure, as the foundation of the biological functioning of these biomacromolecules and their complexes. vii) The student will learn to search, obtain and interpret the information contained in structural databases, and to use computer graphics tools for the study of biomacromolecular structures. viii) The student will acquire the ability to state and solve questions and problems, and to critically interpret results and conclusions in Structural Biology, using the Scientific Method.
This course assumes in addition the corresponding part of each General Competence and each Transversal Competence assigned to the Bachelor Degree in Biochemistry in the Verification Report.
1.12. Contenidos del programa / Course contents
PROGRAMA
PARTE A- ASPECTOS GENERALES
TEMA 1. MACROMOLECULAS BIOLOGICAS.
El dogma central de la Biología Molecular. Ácidos nucleicos y proteínas. Reconocimiento molecular. Monómeros y polímeros. Biomacromoléculas. Complejos supramacromoleculares. Funciones de las biomacromoléculas. Relaciones estructura-función.
TEMA 2. DETERMINACION DE LA ESTRUCTURA ESPACIAL DE BIOMACROMOLECULAS Y COMPLEJOS SUPRAMACROMOLECULARES. Microscopía electrónica. Microscopía de fuerzas atómicas. Cristalografía de rayos X. Espectroscopía de Resonancia Magnética Nuclear (NMR). Bancos de
Código: 18213 Centro: Facultad de Ciencias Titulación: Grado en Bioquímica Nivel: Grado Tipo: Obligatoria Nº de créditos: 6
datos de estructuras. Gráficos moleculares. Modelado molecular. Otras técnicas estructurales.
PARTE B- ESTRUCTURA DE PROTEINAS
TEMA 3. ESTRUCTURA PRIMARIA DE PROTEINAS. Aminoácidos proteinogénicos. Características estructurales y propiedades. El enlace peptídico. Síntesis química de péptidos, biosíntesis de proteínas y determinación de la estructura primaria de proteínas mediante secuenciación de péptidos (se referirá al alumno a las asignaturas donde se explican con detalle estas técnicas). Modificaciones covalentes post-traduccionales de proteínas: procesamiento proteolítico, puentes disulfuro, modificaciones de cadenas laterales.
TEMA 4. ESTRUCTURA SECUNDARIA DE PROTEINAS. Mesomería y conformación del enlace peptídico. Conformaciones permitidas del esqueleto polipeptídico: Representación de Ramachandran. Tipos de estructura secundaria. Hélice alfa y otras estructuras helicoidales. Cadenas y láminas beta. Giros. Bucles. Determinación de estructura secundaria en proteínas.
TEMA 5. ESTRUCTURA TERCIARIA Y CUATERNARIA DE PROTEINAS. Proteínas globulares. Estructura espacial. Dominios estructurales. Núcleo hidrofóbico y empaquetamiento. Superficie expuesta al solvente. Sitios de unión de ligandos. Centros activos. Motivos estructurales (estructuras supersecundarias). Proteínas multidominio. Proteínas oligoméricas. Simetría. Diferencias con las proteínas monoméricas. Complejos macromoleculares proteicos. Flexibilidad y dinámica de proteínas. Proteínas de membrana. Proteínas fibrosas. Otros tipos estructurales.
TEMA 6. TIPOS ESTRUCTURALES Y EVOLUCION DE PROTEINAS. Clasificación de proteínas: clases y familias estructurales. Evolución de proteínas.
TEMA 7. ESTABILIDAD Y PLEGAMIENTO DE PROTEINAS. Estados nativo y desnaturalizado. Estabilidad termodinámica de proteínas. Plegamiento de proteínas. Estados de transición e intermediarios de plegamiento. El modelo del “embudo de plegamiento”. Plegamiento en la célula: chaperonas moleculares. Plegamiento de proteínas y enfermedad.
TEMA 8. PREDICCION DE LA ESTRUCTURA DE PROTEINAS. Predicción de estructura secundaria: Aproximaciones probabilísticas y quimico-físicas. Predicción de estructura terciaria por homología. Predicción de estructura terciaria de novo.
Código: 18213 Centro: Facultad de Ciencias Titulación: Grado en Bioquímica Nivel: Grado Tipo: Obligatoria Nº de créditos: 6
THEME 2. DETERMINATION OF THE THREE-DIMENSIONAL STRUCTURE OF
BIOMACROMOLECULES AND SUPRAMOLECULAR COMPLEXES.
Electron microscopy. Atomic force microscopy. X-ray Crystalography. Nuclear magnetic resonance (NMR) spectroscopy. Structural data banks. Molecular graphics. Molecular modeling. Other structural techniques.
PART B- PROTEIN STRUCTURE
THEME 3. PRIMARY STRUCTURE OF PROTEINS. Protein-forming amino acids. Structural features and properties. The peptide bond. Chemical synthesis of peptides, protein biosynthesis, and determination of the primary structure of proteins by peptide sequencing (the student will be referred to the courses where these techniques are described in detail). Covalent post-translational modifications of proteins: proteolytic processing, disulfide bonds, modification of side chains.
THEME 4. SECONDARY STRUCTURE OF PROTEINS. Mesomery and peptide bond conformation. Allowed conformations for the polypeptide backbone: Ramachandran plot. Types of secondary structure. Alfa helix and other helical structures. Beta- s. Turns. Loops. Determination of secondary structure in proteins.
THEME 5. TERTIARY AND QUATERNARY STRUCTURE OF PROTEINS. Globular proteins. Three-dimensional structure. Structural domains. Hydrophobic core and packing. Solvent-exposed surface. Ligand binding sites. Active centers. Structural motifs (supersecondary structures). Multidomain proteins. Oligomeric proteins. Symmetry. Differences with monomeric proteins. Macromolecular (protein) complexes. Protein flexibility and dynamics. Membrane proteins. Fibrous proteins. Other structural types.
THEME 6. STRUCTURAL CLASSIFICATION AND EVOLUTION OF PROTEINS. Protein classification: structural classes and families. Protein evolution.
THEME 7. PROTEIN STABILITY AND FOLDING. Native and denatured states. Thermodynamic stability of proteins. Protein folding. Transition states and folding intermediates. The folding funnel model. Folding in the cell: molecular chaperones. Folding and disease.
THEME 8. PREDICTION OF PROTEIN STRUCTURE. Secondary structure prediction: probabilistic and physicochemical approaches. Prediction of tertiary structure by homology. De novo tertiary structure prediction.
PART C- NUCLEIC ACID STRUCTURE
Código: 18213 Centro: Facultad de Ciencias Titulación: Grado en Bioquímica Nivel: Grado Tipo: Obligatoria Nº de créditos: 6
THEME 9. PRIMARY STRUCTURE OF NUCLEIC ACIDS
Bases derived from purine or pirimidine: Tautomery and mesomery; conformation. Pentoses: conformations. Nucleosides. Nucleotides. Nomenclature. Properties of bases, nucleosides, nucleotides. Phosphoester bonds. Biological relevance of the DNA primary structure: genetic information. Chemical synthesis of oligonucleotides, nucleic acid biosynthesis, and determination of the primary structure of nucleic acids by DNA sequencing (the student will be referred to the courses where these techniques are described in detail).
THEME 10. SECONDARY STRUCTURE OF DNA. Determination of the secondary structure of DNA. Watson-Crick model of the double helix. DNA structural parameters. Irregular vs. monotomous DNA. DNA detailed conformation and sequence dependence. DNA deformability and curvature. DNA polymorphism: DNA B, DNA A, DNA Z, DNA H, DNA G. Other DNA structures. Biological roles of structural irregularities and polymorphism of DNA.
THEME 11. TERTIARY AND QUATERNARY STRUCTURE OF DNA. Flexible vs. rigid DNA. DNA looping. DNA supercoiling and topology. Supercoiling analysis. Proteins that modify DNA supercoiling: topoisomerases. Biological role of supercoiling. Quaternary structure of DNA. Nucleosomes and chromatin.
THEME 12. SECONDARY, TERTIARY AND QUATERNARY STRUCTURES OF RNAs. Secondary and tertiary structures of tRNA and other small RNAs. RNA secondary structure prediction. Secondary and tertiary structures of rRNAs and other RNAs. Quaternary structure of RNAs. The ribosome.
1.13. Referencias de consulta / Course bibliography
A- MATERIAL DOCENTE:
Al principio del curso se subirán a la página Moodle de la asignatura una colección de documentos pdf que contendrán:
1-Colecciones de cuestiones conceptuales y problemas numéricos para resolver por el alumno de forma no presencial, y contrastar en clases prácticas en Aula y/o tutorías.
Código: 18213 Centro: Facultad de Ciencias Titulación: Grado en Bioquímica Nivel: Grado Tipo: Obligatoria Nº de créditos: 6
otros aspectos que no forman parte del programa). Muy apropiado para estudiar aspectos fundamentales de la estructura de proteínas. Recomendado. 6-Whitford. PROTEINS. STRUCTURE AND FUNCTION. Wiley, 2005. Muy básico, demasiado en algunos temas, pero muy apropiado para estudiar aspectos fundamentales de la estructura de proteínas. (Cubre además otros aspectos que no forman parte del programa). Recomendado. 7-Gómez-Moreno, Sancho (coordinadores). ESTRUCTURA DE PROTEÍNAS. Ed. Ariel, 2003. Excelente, actualizado y muy completo. Incluye direcciones en Internet y prácticas de visualización de estructuras por ordenador. Muy recomendado. 8-Creighton, PROTEINS. STRUCTURE AND MOLECULAR PROPERTIES, 2ºed. Freeman, 1993. Excelente (aunque en bastantes aspectos se ha quedado anticuado. Se espera una nueva edición). Útil para complementar las refs. 5- 7 en algunos aspectos. 9- Liljas y otros, TEXTBOOK OF STRUCTURAL BIOLOGY, World Scientific, 2009. En gran medida trata sobre relaciones estructura-función en muchas proteínas importantes. Nivel avanzado. Muy actualizado. 10-Branden , Tooze, INTRODUCTION TO PROTEIN STRUCTURE, 2ºed. Garland,
- Excelente para entender la arquitectura de proteínas, pero no trata otros aspectos importantes. Nivel intermedio. 11-Lesk, INTRODUCTION TO PROTEIN ARCHITECTURE. THE STRUCTURAL BIOLOGY OF PROTEINS. Oxford University Press, 2001. Centrado sobre todo en la arquitectura de proteínas. Muchas ilustraciones, en estéreo. Nivel intermedio. 12-Kyte, STRUCTURE IN PROTEIN CHEMISTRY, 2ª ed. Garland, 2007. Completo pero tratamiento irregular en diversos aspectos. Nivel avanzado. 13-Sinden , DNA STRUCTURE AND FUNCTION. Academic Press, 1994. Muy completo para estructura de DNA (aunque ciertos aspectos pueden requerir la consulta de otros libros). Recomendado. 14- Blomfield, Crothers, Tinoco, NUCLEIC ACIDS: STRUCTURE, PROPERTIES AND FUNCTION. University Science Books, 2000. Libro bastante completo y actualizado. Nivel avanzado.
D-LIBROS PARA CONSULTA ESPECIALIZADA:
Estos libros se recomiendan sólo para aquellos estudiantes interesados en profundizar en algún tema particular. En general son de nivel intermedio o avanzado.
15-Cantor, Schimmel, BIOPHYSICAL CHEMISTRY. Freeman, 1980. Libro clásico sobre fundamentos quimico-físicos de la Bioquímica. Muy anticuado en algunos aspectos, pero no en muchos conceptos básicos. Avanzado.
Código: 18213 Centro: Facultad de Ciencias Titulación: Grado en Bioquímica Nivel: Grado Tipo: Obligatoria Nº de créditos: 6
16-Van Holde, Johnson, Ho, PRINCIPLES OF PHYSICAL BIOCHEMISTRY. Prentice Hall, 1998. Para entender en profundidad los fundamentos quimico- físicos de la estructura de biomacromoléculas. Avanzado. 17-Rhodes , CRYSTALLOGRAPHY MADE CRYSTAL CLEAR, 2ª ed. Academic Press,
- Un libro que permite entender claramente los fundamentos y técnica de la cristalografía de rayos X. Nivel intermedio. 18-Blow, OUTLINE OF CRYSTALLOGRAPHY FOR BIOLOGISTS. Oxford University Press, 2002. Similar a la referencia 17. Nivel intermedio. 19-Lesk, PROTEIN ARCHITECTURE. IRL Presss, Oxford University Press, 1991. Para arquitectura de proteínas exclusivamente. Un poco anticuado. Avanzado. 20-Creighton, PROTEIN FOLDING. Freeman, 1992. Para aspectos de plegamiento de proteínas. Algo anticuado pero útil. Avanzado. 21-Fersht, STRUCTURE AND MECHANISM IN PROTEIN SCIENCE. Freeman, 1999. Para diferentes aspectos de la estabilidad y plegamiento de proteínas, de reconocimiento proteína-ligando y de catálisis enzimática. Avanzado. 22-Ellis, THE CHAPERONES. Academic Press, 1996. Para profundizar en chaperonas moleculares. Algo anticuado en algunos aspectos. Avanzado. 23- Lesk, INTRODUCTION TO BIOINFORMATICS. Oxford University Press. 2002. Buena introducción a las bases de datos y bioinformática. 24-Saenger , PRINCIPLES OF NUCLEIC ACID STRUCTURE. Springer-Verlag, 1984. Adecuado para algunos aspectos de estructura 1ª, 2ª y 3ª de DNA y RNA. Anticuado en muchos aspectos, especialmente en interacciones ácido nucleico-proteína. Avanzado. 25-Shabarova, Bodganov, ADVANCED ORGANIC CHEMISTRY OF NUCLEIC ACIDS. VCH, 1994. Para propiedades químicas de nucleótidos y estructura primaria de ácidos nucleicos. Avanzado. 26-Calladine, Drew, UNDERSTANDING DNA, 2ºed. Academic Press, 1997. Muy bueno para ciertos aspectos de estructura secundaria y terciaria de DNA. Nivel intermedio. 27-Neidle, DNA STRUCTURE AND RECOGNITION. IRL Press, 1994. Breve resumen de diversos aspectos de estructura secundaria de DNA e interacción con ligandos. 28-Bates , Maxwell, DNA TOPOLOGY. IRL Press. Oxford University Press, 1993. Muy bueno para estructura terciaria de DNA. Avanzado. 29-Travers , DNA-PROTEIN INTERACTIONS. Chapman and Hall, 1993. Aspectos de estructura 2ª y 3ª de DNA, y sobre todo, interacciones DNA-proteína. Avanzado. 30-Steitz , STRUCTURAL STUDIES OF PROTEIN-NUCLEIC ACID INTERACTION. Cambridge University Press, 1993. Similar al anterior, pero enfocado más a las proteínas. Avanzado. 31-Nagai , Mattaj (eds.), RNA-PROTEIN INTERACTIONS. IRL Press. Oxford University Press, 1994. Para estructura secundaria y terciaria de RNA e interacciones RNA-proteína. Avanzado.
Código: 18213 Centro: Facultad de Ciencias Titulación: Grado en Bioquímica Nivel: Grado Tipo: Obligatoria Nº de créditos: 6
Lista de recursos educativos en Internet que contemplan la estructura de proteínas.
http://www.ncbi.nlm.nih.gov National Center for Biotechnology Information (NCBI). Base de datos anotada sobre secuencias de ácidos nucleicos (GenBank). En coordinación con el European Bioinformatics Institute. Análisis de secuencias y estructuras y diversos enlaces
http://www.ebi.ac.uk European Bioinformatics Institute (EBI). Base de datos anotada sobre secuencias de ácidos nucleicos (EMBL Data Library). En coordinación con el National Center for Biotechnology Information. Análisis de secuencias y estructuras y diversos enlaces.
http://www.expasy.ch Swiss Institute of Bioinformatics. Base de datos anotada sobre secuencias de proteínas (SWISS-PROT). En colaboración con la EMBL Data Library. Análisis de secuencias y estructuras y diversos enlaces.
A- TEACHING MATERIAL:
Several pdf documents will be uploaded to the Moodle webpage at the beginning of this course. These documents will include:
1-Two collections of conceptual questions and numerical problems to be solved by the student as part of his/her out-of-classroom learning activities, and discussed during practical sessions in the classroom. 2-References to Protein Data Bank atomic coordinate files of proteins and nucleic acids, for computer visualization and manipulation by the student of macromolecular structures, either during practical sessions in the classroom or during out-the-classroom learning activities. 3-Figures that reproduce most of the PowerPoint slides that will be presented in the classroom. In this way there will be no need to copy or draw generally complex schemes and molecular structures. This should allow to focus the student attention on what is being said, commented on, or discussed in the classroom.
Each student should print a complete photocopy set of those documents and bring the appropriate ones to the classroom, or alternatively bring his/her own computer containing those files for direct visualization. This material will be used during lectures and other teaching activities along this course.
Código: 18213 Centro: Facultad de Ciencias Titulación: Grado en Bioquímica Nivel: Grado Tipo: Obligatoria Nº de créditos: 6
B-GENERAL BIOCHEMISTRY BOOKS:
It would be essential for the student to revise and remember, at the beginning of this course, the basic principles of protein and nucleic acid structure. Those principles were taught as a part of the Basic Principles of Biochemistry course during the First Year of the Biochemistry Degree. In order to do that, the student should read and understand the appropriate chapters in one of the many General Biochemistry books available. There is no need to use a very recent edition. Some options, among many:
1-Mathews, Van Holde, Ahern, BIOCHEMISTRY, 3ºed Benjamin/ Cummings,
- Arguably some of the best basic chapters on protein and nucleic acid structure. Highly recommended. 2-Berg, Tymoczko, Stryer , BIOCHEMISTRY, 7ºed. Freeman, 2010. 3- Voet, Voet , BIOCHEMISTRY, 4ºed. Wiley 2010. 4-Zubay , BIOCHEMISTRY, 4ºed. WCB 1998.
C-BOOKS ON PROTEIN OR NUCLEIC ACID STRUCTURE:
No book covers the entire contents of this course. However, the following references are especially recommended: refs. 5 and 6 (basic aspects) and 7 and 8 (more advanced topics) for protein structure; and ref.13 for DNA structure.
5-Petsko, Ringe. PROTEIN STRUCTURE AND FUNCTION. NSP, 2004. Basic coverage of different aspects of protein structure (in addition to other topics that are not included in the program of this course. Most adequate to study fundamental aspects of protein structure. Recommended. 6-Whitford. PROTEINS. STRUCTURE AND FUNCTION. Wiley, 2005. Very basic, too basic for some topics, but fine to study fundamental aspects of protein structure (it includes also further topics that are not covered in this course). Recommended. 7-Gómez-Moreno, Sancho (coordinators). ESTRUCTURA DE PROTEÍNAS. Ed. Ariel, 2003. Excellent, updated and complete. It includes Internet addresses and laboratory experiments on computer graphics to visualize macromolecular structure. Highly recommended. 8-Creighton, PROTEINS. STRUCTURE AND MOLECULAR PROPERTIES, 2ºed. Freeman, 1993. Excellent (though for a number of topics it is now rather outdated. A new edition is expected soon). Useful to complement some aspects as treated in refs. 5-7. 9- Liljas et al., TEXTBOOK OF STRUCTURAL BIOLOGY, World Scientific, 2009. A book that focuses on structure-function relationships in many important proteins. Up-to-date. Advanced level.
Código: 18213 Centro: Facultad de Ciencias Titulación: Grado en Bioquímica Nivel: Grado Tipo: Obligatoria Nº de créditos: 6
24-Saenger , PRINCIPLES OF NUCLEIC ACID STRUCTURE. Springer-Verlag, 1984. Useful for some aspects of DNA and RNA structure. Outdated in many aspects, especially regarding nucleic acid-protein interactions. Advanced level. 25-Shabarova, Bodganov, ADVANCED ORGANIC CHEMISTRY OF NUCLEIC ACIDS. VCH, 1994. For acquiring a deep knowledge on the chemical properties of nucleotides and the primary (chemical) structure of nucleic acids. Advanced level. 26-Calladine, Drew, UNDERSTANDING DNA, 2ºed. Academic Press, 1997. Very good for understanding certain difficult-to-grasp aspects of DNA structure. Intermediate level. 27-Neidle, DNA STRUCTURE AND RECOGNITION. IRL Press, 1994. A brief summary of DNA structure and recognition. 28-Bates , Maxwell, DNA TOPOLOGY. IRL Press. Oxford University Press, 1993. Very good for understanding DNA topoligy and supercoiling. Advanced level. 29-Travers , DNA-PROTEIN INTERACTIONS. Chapman and Hall, 1993. DNA structure and DNA-protein interactions. Advanced level. 30-Steitz , STRUCTURAL STUDIES OF PROTEIN-NUCLEIC ACID INTERACTION. Cambridge University Press, 1993. Similar to ref. 29, but focused more on the protein side. Advanced level. 31-Nagai , Mattaj (eds.), RNA-PROTEIN INTERACTIONS. IRL Press. Oxford University Press, 1994. Focuses on RNA structure and RNA-protein interactions. Advanced level.
For more advanced and/or specific references (including review articles), please search the bibliography data bases, or talk to the supervisor. There are no problem books adequate for this course. Some of the books listed above contain some questions and problems. Collections of related problems will be provided by the supervisor (see above).
E- SOME INTERNET ADDRESSES:
http://www.rcsb.org/pdb Access to Protein Data Bank (PDB). It contains coordinate files for all proteins and nucleic acids whose structure has been solved, and other relevant information. The coordinate files are needed for visualization and manipulation of the structural models using a computer.
http://oca.ebi.ac.uk/oca-bin/ocamain Access to PDB from the European Bioinformatics Institute. May be easier to use than the original site.
http://www.umass.edu/microbio/rasmol/index2.htm Access to RasMol program webpage. RasMol is freeware, can be downloaded in PC or Mac versions together with an instruction manual, and used to visualize
Código: 18213 Centro: Facultad de Ciencias Titulación: Grado en Bioquímica Nivel: Grado Tipo: Obligatoria Nº de créditos: 6
protein and nucleic acid structures. To do the latter, the coordinate files of the molecules of interest must be downloaded from the PDB (previous addresses). There are other molecular graphics programs, including Protein Explorer (a RasMol-based version), or Pymol.
http://www.usm.maine.edu/~rhodes/RasTut A RasMol tutorial.
http://www.cryst.bbk.ac.uk/PPS2/ On-line course on protein structure.
http://www.rcsb.org/pdb/education.html List of education resources in Intenet about protein structure.
http://www.ncbi.nlm.nih.gov National Center for Biotechnology Information (NCBI). Nucleic acid sequence database (GenBank). In coordination with the European Bioinformatics Institute. Sequence and structure analysis and various links.
http://www.ebi.ac.uk European Bioinformatics Institute (EBI). Nucleic acid sequence database (GenBank). In coordination with the National Center for Biotechnology Information. Sequence and structure analysis and various links.
http://www.expasy.ch Swiss Institute of Bioinformatics. Annotated protein sequence database (SWISS-PROT). In collaboration with EMBL Data Library. Sequence and structure analysis and various links.
2. Métodos docentes / Teaching methodology
1. Clases teóricas interactivas. Se explicarán lógicamente los conceptos, utilizando material gráfico proyectado y la pizarra. Se recurrirá de modo frecuente a ejemplos y aplicaciones, intercambiando preguntas y respuestas entre el profesor y los alumnos. Para ilustrar los diferentes conceptos se irán presentando de modo interactivo en el ordenador, usando un programa de gráficos moleculares, las estructuras tridimensionales de diversas proteínas y ácidos nucleicos. Se suministrará al principio del curso abundante bibliografía (adjunta). Aunque se requerirá inevitablemente el aprendizaje de memoria de algunas informaciones básicas, el uso de la memoria se reducirá al mínimo. En lugar
Código: 18213 Centro: Facultad de Ciencias Titulación: Grado en Bioquímica Nivel: Grado Tipo: Obligatoria Nº de créditos: 6
1- Interactive lectures. Concepts will be logically explained, with the frequent help of many examples and applications, and by exchanging questions and answers between the lecturer and the students. To illustrate the different concepts, many structures of proteins and nucleic acids will be inspected during the lectures by using a computer, a molecular graphics program and a projector. Abundant references (see above) will be provided at the beginning of the course, Memorization of a few important pieces of information will be inevitably required, but this will be reduced to the minimum. Instead, learning most of the contents will require a deep understanding of different important concepts.
2- Presentation and discussion by the students of some current research topics. Case studies will be provided by the supervisor along the course. Each case should be solved by a reduced group of students. The group will meet out of classroom hours to collect information on the assigned case (in books, journal articles, Internet…) and develop a possible solution. It will be previously decided if a group would have to either give a short oral presentation or prepare a brief written report. Oral presentations will be given and discussed during practical sessions in the classroom.
3- Problem-based learning. An extensive collection of problems and questions that illustrate most of the important concepts will be provided at the beginning of the course. These problems will be of a similar format than those included in the final examination test. The students will have to try and solve those problems out of classroom hours. During some practical sessions in the classroom some of those questions and problems will be jointly solved.
4- Hands-on computer graphics of protein, nucleic acid and supramolecular complex structures. Some selected Protein Data Bank accession numbers will be provided. The students should download the selected PDB files for the exploration and manipulation of protein or nucleic acid structures using RasMol, a molecular visualization program.
5- Tutorials for individual students or reduced groups. In addition to the above in-classroom teaching activities, tutorials will be available upon request for individual students or reduced groups. The place, date and time will be appointed by the students in agreement with their supervisor, without interfering with any other programmed activity. These
Código: 18213 Centro: Facultad de Ciencias Titulación: Grado en Bioquímica Nivel: Grado Tipo: Obligatoria Nº de créditos: 6
tutorials could be used, for example, to discuss some aspects of the assigned case study before it is presented, or the way to solve specific problems, or to clarify the conceptual doubts that may have arisen during lectures.
3. Tiempo de trabajo del estudiante / Student
workload
4. Métodos de evaluación y porcentaje en la
calificación final / Evaluation procedures and
weight of components in the final grade
La presencia del estudiante en todas las clases es necesaria para poder obtener la máxima calificación, ya que la evaluación estará basada en parte en aspectos que requieren la participación activa del alumno en clase
Nº de horas / Nº hours
Porcentaje/ Percent
Presencial/ In- classroom activities
Clases teóricas / Lectures 34 h
37%
Presentación de casos de estudio por los alumnos/ Presentation of case studies by students 8 h Sesiones prácticas. Incluyen: i) resolución de problemas; ii) uso del ordenador y programas de gráficos moleculares para explorar estructuras de macromoléculas/ Practical sessions. They include: i) problem solving; ii) use of a computer and a molecular graphics program to explore macromolecular structure
11 h
Realización del examen final / Final examination 3 h
No presencial/ Out-of- classroom activities
Resolución de un caso de estudio y preparación del correspondiente breve trabajo oral o escrito / Work on a case study and its presentation in the classroom or in written form
14 h
Resolución de cuestiones y problemas / Work on^ 63% solving questions and problems 25 h Estudio y comprensión de conceptos / Study and understanding concepts 55 h Carga total de horas de trabajo / Total workload (hours) 150 h
