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SUBJECTS

AMPLIACION DE FUNDAMENTOS QUIMICOS DE LA INGENIERIA. BIOQUIMICA (ITA Hortofruticultura y Jardinería)

QUIMICA II (ITA Industrias Agrarias y Alimentarias)

ESTRUCTURA Y DINAMICA DE LAS MEMBRANAS BIOLOGICAS. BIOQUIMICA

BIOQUIMICA AMBIENTAL

LABORATORIO INTEGRADO I

LABORATORIO INTEGRADO II

 

 

 

 

 

 

 AMPLIACION DE FUNDAMENTOS QUIMICOS DE LA INGENIERIA and QUIMICA II. BIOQUIMICA

  Outline

1. Introduction to Biochemistry. Molecular composition of the living cell.
2. Properties of the water molecule
3. Amino acids
4. Peptides
5. Enzymes, coenzymes and vitamins
7. Lipids: structure and properties
8. Biological membranes
9. Carbohydrates: structure and properties
10. Nucleic acids
11. Expression of cellular genetic information

  Content

UNIT 1: Bases of biochemistry. Molecular composition of living organisms.

Introduction.

What is biochemistry?

Biochemistry as an interdisciplinary science.

Biochemistry as a chemical science.

Biochemistry as a biological science.

UNIT 2: The water. Acid-base properties.

Physical properties and hydrogen bonds in water.

Structure of liquid water.

Other properties of hydrogend bonds.

Water solvent properties.

Hydrophobic interactions.

Solute effects on water properties.

Water ionization.

Water ionic product.: pH scale.

UNIT 3: Amino acids(I, II & III).

Description.

Frequent and rare amino acids in proteins.

Non-protein amino acids.

Acid-base properties in amino acids.

Amino acid stereochemistry.

Amino acid chemical reactions.

UNIT 4: Peptides.

Peptide structure.

Acid-base properties in peptides.

Optical and chemical properties in peptides.

Separation and analysis of peptides.

UNIT 5: Proteins (I, II, III & IV).

Tridimensional conformation of proteins.

Secondary structure: folding regular forms in polypeptide chains.

Structure description: helices, beta sheets, turns, random structures.

Ramachandram representations.

Fibrous proteins: keratin, collagen, elastin.

Globular proteins. Structure-function relation.

Factors involved in determining secondary and tertiary structures.

Quaternary structure of proteins.

UNIT 6: Enzyme structure and mechanism. Coenzymes and vitamins.

Enzyme substrate specificity.

Identification of essential functional groups in catalysis.

Factors involved in determining catalytic efficiency of enzymes.

Regulating enzymes.

Allosteric enzymes.

Covalent modulation of regulating enzymes.

Conceptual relations between coenzyme and vitamin.

Oxide-reduction coenzymes: niacin nucleotides, flavin nucleotides, lipoic acid, quinones, cytochromes.

Phosphate transport system: ADP.

Amino group transport system. Pyridoxal phosphate.

Acetyl transporters. Conzyme-A.

Monocarbonated fragment transporters. tetra hydro pholate and derivates. Cobalamin. Biotin.

UNIT 7: Lipid structure and properties (I, II).

Lipid molecular structure and behaviour.

Fatty acids.

triacylglycerols: fats.

Soaps and detergents.

Waxes.

Lipid components of biological membranes.

Glycerophospholipids.

Sphingolipids and  glycosphingolipids.

Cholesterol.

Terpenes and derivates.

UNIT 8: Biological membranes.

Membrane structure and properties.

Fluid mosaic model.

Membrane movement.

Membrane asymmetry.

Characteristics of membrane proteins.

Red blood cell membrane as an example of membrane structure.

UNIT 9: Carbohydrates: structure and properties.

Monosaccharide families.

Monosaccharide stereoisomery.

Mutarrotation and anomaric forms of D-glucose.

Effects of acids and bases on monosaccharides.

Monosaccharide most important derivates.

Disaccharides and trisaccharides.

Identification and analysis of monosaccharides and oligosaccharides.

Structural and storage polysaccharides.

UNIT 10: Nucleic acids (I & II).

Chemical nature of nucleic acids.

DNA and RNA.

Nucleotide properties.

Stability and formation of phosphodiester bond.

Primary structure of nucleic acids.

Secondary and tertiary structure of nucleic acids.

Double helix.

Semiconservative nature of DNA replication.

Supercoiling.

Denaturalization of nucleic acids.

UNIT 11: Genetic information expression.

Genetic material replication.

DNA transcription.

RNA translation into proteins.

Objectives

Biochemistry: the main teaching objective is the description of the most important macromolecules which form biological systems, supplying conceptual and theoretical bases for the biophysical processes they intervene. Concepts are complemented with the description of the molecular structure and the biochemical properties of the macromolecules involved, not only proteins and lipids, but also carbohydrates and nucleic acids.

The objectives aimed at in theory classes are: (i) summarise the biochemical units which are subject of study, which are specified in the subject syllabus; (ii) show the student the most relevant aspects of each unit and relate them with the biological function; (iii) clarify physical, chemical and biochemical concepts needed for the understanding of the subject.

 

Practical Sessions

Practice 1: PROTEINS REACTIONS IN DISSOLUTION. ISOLATING MILK CASEIN.
Practice 2: IDENTIFICATION AND VALUATION OF LIPIDS.
COMPUTER PRACTICES: biological molecules visualization.
BIOCHEMISTRY PROBLEMS.

 

Practice global objectives

It aims at familiarising the student with the basic elements in a biochemistry lab: volumetric material (graded material for measurement), performance material and basic instruments such as granataries and centrifuges, etc.
Complementarily, the student is taught to analYse and interpret the results obtained in which the study of proteins, lipids and carbohydrates as important molecules are involved. Finally, and related with computer assisted activities, the student should learn software management: load molecules files, rotate, move and approach molecules, visualise proteins with quaternary structure, etc., and answer in the outline and with the help of the computer all the questions proposed.

 

Teaching Methodology

Theoretical lessons are in-room, in the form of teacher lecturing. The use of slides and transparencies is a constant, and hard copies of what is shown in class are distributed among the students. Students are recommended to consult complementary/additional bibliography to expand class notes.

In practical sessions, students are given an outline of the practical activities in the form of a note-book, where all the stages involved are detailed. As the student must be in the classroom for these sessions, he is able to ask and solve any doubt he could have in the course of the activity.

 

Evaluation

PRACTICAL ACTIVITIES
a) Regarding biochemistry, students will deal with lab and computer-similation practical activities.
b) Date and place of practical activities performance, and group composition, will be announced at the beginning of the term. Group changes will not be allowed unless justified cause, which will be told to the teachers in due time.
c) The student will attend practical clases punctually, wearing a white coat, calculating machine, and note-book.
d) To pass the whole subject the student must pass the practical part compusorily. For this, the content of the note-book, the answers to the questionnaires for lab and computer activities and student attitude will be evaluated.
e) Passing the practical part of the subject is maintained during one academic year.

EXAMS
a) To be able to attend the exams the student will have to present ID card, driving licence, passport or UMH card.
b) There will be one ordinary final exam in June and one extraoedinary final exam in September. It will be composed og multiple choice questions (4 options and one true answer). Each 4 wrong answers will invalidate one right answer. Blank answers are not taken into account. NB: As exam correction is dome using a laser scanner, student will come to exam with a convenient pencil (Nº 2).
c) As the subject is divided into two parts: 1) Instrumental analysis; 2) Biochemistry, to pass the subject (considering what appears in PRACTICAL ACTIVITIES section) the student will have:
i) to pass both parts (mark 5 or above) in the final exam.
ii) Arithmetic mean of both parts, bearing in mind that the minimum mark to compensate should be 4 or above. The subject will not be passes if one of the two marks is below 4, no matter if the mean is 5 or above.
d) If the student fails one of the part with a mark below 4 (cannot compensate), the mark of the part which has been passed (5 or avobe) will be kept exclusively for the extraordinary exams of September and December.

SUBJECT EQUIVALENCES
For complete subject equivalence the Centro de Gestión de Campus (CEGECA) instructions should be followed.

ADAPTATIONS
a) Students who had passed the subjects of Análisis Instrumental or Química II in academic years before 1998-1999 in the Degree of Ingeniería Técnica Agrícola, division of Hortofruticultura, Agropecuaria, Industrias or Agrónomos, will adapt automatically that part of the subject.
b) Students who had adapted part of the subject will only take the exam of the complementary part of the subject to pass it globally, in ordinary or extraordinary exam. In these cases, the final mark will be calculated with the arithmetic mean of the mark obtained in the exam and the mark appearing in the academic file of the student.
c) The realization of the practical activities corresponding to the adapted parts will depend on the teacher criteria, by means of direct contact with the teacher.

 

Comments

It is highly recommended to attend theory classes as they are not only a mere description of information, but also a way of emphasizing the most relevant and conceptual aspects for which further explanation is needed. The use of bibliography is also recommended to have a complete view of the subject (class notes are insufficient).

 

Bibliography

1.-Mathews and van Holde. Bioquímica. Ed. McGraw Hill.
2.-Stryer. Bioquímica. Ed. Reverté.
3.-Lehninger-Nelson-Cox. Principios de Bioquímica. Ed. Omega.
4.-Lehninger. Bioquímica. Ed. Omega.
5.-Voet-Voet. Bioquímica. Ed. Panamericana
6.-Macarulla y Goñi. Biomoléculas. Ed. Reverté.
7.-Lehninger. Bioquímica Estructural. Ed. Tebar Flores.
8.-Goodwin-Mercer. Plant Biochemistry. Pergamon Press.

 

 

 

ESTRUTURA Y DINAMICA DE LAS MEMBRANAS BIOLOGICAS. BIOQUIMICA

  Outline

1. Structure and Composition of Biological Membranes
2. Structure and Properties of Lipids
3. Characterization and Structural Principles of Membrane Proteins
4. Dynamics of Biomembranes and Lipid-Protein Interactions
5. Signal Transduction in Biomembranes
6. Prokaryotic and Eukaryotic signalling
7. Biomedicine and Biotechnology

  Content

UNIT 1. Structure and composition of biomembranes. introduction to biomembranes.

Membrane morphology.

Prokaryotic and eukaryotic membranes.

The fluid mosaic model.

Biomembrane study methods.

Lipidic component.

Protein component.

Biological membrane isolation.

UNIT 2. Structure and properties of lipids. Calssification of lipids.

Lipid purification and characterization.

Lipid-water mixture: structure and properties.

Biomembrane model systems.

Lipidic phases: typology and characteristics.

UNIT 3. Characterization and structural principles of membrane proteins.

Typology and characteristics of membrane proteins.

Purification strategies/techniques.

Functional reconstruction of membranes proteins.

Physico-chemical properties of membrane proteins.

Membrane protein study methods.

Tridimensional structure and membrane protein models.

Pores, channels and transporters.

Minimalistic or modular aproximation to membrane proteins.

Membrane protein peptide models.

UNIT 4. Biomembrane dynamics and lipid-protein interactions.

Biomembrane components movility.

Lipid bilayer fluidity.

Alteration/perturbation of physico-chemical properties in biomembranes by small molecules.

Lipid-protein interactions: characterization and measurement.

Analysis of ligand adsorption to lipid bilayers.

UNIT 5. Signal transduction in biomembranes.

General principles in cell signalling.

Membrane receptors: families and modus operandi.

Cell amplification and adaptation/desensibilization.

Intracell signalling: second messengers.

UNIT 6. Eukaryotic and prokaryotic signalling.

Visual signalling. Olfactory and gustative signalling.

Thermal signalling. Mechanic signalling.

Signalling strategies in plants.

Bacteria chimiotaxis. Chimiotactic receptors.

UNIT 7. Biomedicine and Biotechnology.

Liposome applications. Medication/drug transport.

Biosensor design.

Objectives

This subject intends to inform the student about the nature, structure and functions of biological membranes from a molecular pint of view. The subject describes the most relevant cellular events biomembranes carry out, focusing not only on bacteria but also on vegetal and animal cells.

The first set of objectives aims at gaining the structural knowledge, setting, and biological activity of the most important biomolecules which form biomembranes, with special emphasis in the study of lipids and proteins. In a second part, the study of biomolecule dynamics will be carried out, together with its particular relevance in lipid-protein interactions. Regarding the third group of objectives, the student will be able to know molecular bases in the prokaryotic and eukaryotic cell communication, and signal transduction. Finally, some notions on biomedicine and biotechnology will be introduced, including practical applications and biosensors design.

 

Practical Sessions

Included in Integrated Lab II

 

Teaching Methodology

Theoretical lessons are in-room, in the form of teacher lecturing. The use of slides and transparencies is a constant, and hard copies of what is shown in class are distributed among the students. Students are recommended to consult complementary/additional bibliography to expand class notes.

 

Evaluation

Written exam composed of questions-problems

Comments

It is highly recommended to attend theory classes as they are not only a mere description of information, but also a way of emphasizing the most relevant and conceptual aspects for which further explanation is needed. The use of bibliography is also recommended to have a complete view of the subject (class notes are insufficient).

 

Bibliography

- Gennis, R.B. (1989) Biomembranes. Molecular Structure and Function. Springer-Verlag. New York.
- Jones, M.N. and Chapman, D. (1995) Micelles, Monolayers and Biomembranes. Wiley-Liss. New York.
- Düzgünes, N. (1993) Membrane Fusion Techniques. Academic Press. San Diego. California.
- Graham, J.M. and Higgins, J.A. (1997) Membrane Analysis. Introduction to Biotechniques. Bios Scientific Publishers.
- Hilderson, H.J. and Ralston, G.B. (1994) Physicochemical Methods in the study of biomembranes. In: Subcellular Biochemistry, Vol 23. Plenum Press. New York.
- Merz, K.M. Jr. and Roux, B. (1996) Biological Membranes. Springer-Verlag. New York.
- Op Den Kamp, J.A.F. (1996) Molecular Dynamics of Biomembranes. Springer-Verlag. New York.
- Pullman, A., Jortner, J. and Pullman, B. (1992) Membrane Proteins: Structures, Interactions and Models. Kluwer Academic Publishers. Dordrecht.
- Yeagle, P.L. (1993) The Membranes of Cells. Academic Press. San Diego.

 

 

 

 

BIOQUIMICA AMBIENTAL

  Outline

1. Composición Molecular de los seres vivos.
2. El agua.
3. Ácidos y bases.
4. Aminoácidos I y II.
5. Péptidos.
6. Proteínas I. II y III.
7. Equilibrio y Velocidad de Reacción.
8. Enzimas I y II.
9. Cinética Enzimática.
10. Inhibición Enzimática.
11. Regulación Enzimática I y II.
12. Lípidos: estructura y propiedades I y II.
13. Membranas Biológicas.
14. Transporte a través de Membrana.
15. Ácidos Nucleicos: Estructura y Propiedades I y II.
16. Replicación del Material Genético I y II.
17. Transcripción I y II.
18. Traducción I y II.
19. Código Genético: Mutaciones Moleculares.
20. Regulación de la Expresión Genética.
21. Ingeniería Genética I y II.
22. Metabolismo: Generalidades.
23. Oxidaciones Biológicas.
24. Bioenergética.
25. Transporte Electrónico Mitocondrial I y II.
26. Fosforilación Oxidativa I y II.
27. Fotosíntesis I y II.
28. Ciclo de los Ácidos Tricarboxílicos I y II.
29. Hidratos de Carbono: estructura y propiedades.
30. Glucolisis I y II.
31. Gluconeogénesis.
32. Ruta de las Pentosas Fosfato.
33. Metabolisismo del Glucógeno I y II.
34. Degradación de Triglicéridos y Ácidos Grasos I y II.
35. Biosíntesis de Triglicéridos. Ácidos Grasos y Lípidos Complejos I. II y III.
36. Destino del Nitrógeno.
37. Ciclo de la Urea.
38. Metabolismo de aminoácidos.
39. Relaciones Metabólicas entre Órganos y Tejidos I y II.

 

LABORATORIO INTEGRADO I

  Outline

 

PRÁCTICA 1.- Procesador de textos.
Práctica1a. Edición de un texto científico.
Práctica1b. Ilustración y maquetado de una página de un artículo científico.
PRÁCTICA 2.- Hoja de cálculo
Práctica 2a. Cálculo del coeficiente de partición superficial en un experimento de unión de un péptido derivatizado con una sonda fluorescente (NBD) a SUV¿s de PA.
Práctica 2b. Cálculo de la concentración de lípidos totales.
Práctica 2c. Cálculo de la concentración de una proteína.
Práctica 2d. Hoja de cálculo IV: cinética enzimática.
PRÁCTICA 3.- Representaciones gráficas
Práctica 3a. Representación x-y con Origin.
Práctica 3b. Representación x-y normalizada con Origin.
Práctica 3c. Representación de barras con Origin.
Práctica 3d. Representación x-y múltiple con SigmaPlot.
Práctica 3e. Representación barras apiladas con SigmaPlot.
PRÁCTICA 4.- Tratamiento de imágenes
Práctica 4a. Tratamiento de imágenes (bitmaps) con Paint Shop Pro.
Práctica 4b. Tratamiento de imágenes (vectores) con Canvas.
Práctica 4c. Presentación de imágenes con PowerPoint.
PRÁCTICA 5.- Gestión de bibliografía
Práctica 5a. Búsqueda en Internet (PUBMED).
Práctica 5b. Base de datos bibliográfica con Reference Manager.
PRÁCTICA 6.- Manejo de datos del laboratorio
Práctica 6a. Interconversión de ficheros.
Práctica 6b. Estimaciones de estructura secundaria en una proteína de membrana en base a ajustes de componentes de la banda amida I del espectro de infrarrojo.

Sesiones Prácticas de Laboratorio.
Sesión 1.- Introducción a las sesiones prácticas.
Sesión 2.- Preparación de disoluciones amortiguadoras.
Sesión 3.- Cromatografía de filtración en gel y electroforesis de proteínas.
Sesión 4.- Espectroscopía de absorción.
Sesión 5.- Determinación de vitamina C, calcio y glucosa en materiales de interés biológico.
Sesión 6.- Aislamiento de proteínas. Reacciones de las proteínas en disolución. Identificación y valoración de lípidos.
Sesión 7.- Enzimas y actividad enzimática.
Sesión 8.- Bioenergética y transporte.
Sesión 9.- Utilización de liposomas para la encapsulación de sustancias.
Sesión 10.- Estudio in vitro de la actividad respiratoria en mitocondrias aisladas de rata.
Sesión 11.- Biosíntesis de macromoléculas.
Sesión 12.- Aislamiento, caracterización y propiedades de una proteína: lectina (hemaglutinina) de lenteja.
Sesión 13.- Aislamiento del ADN de un bacteriófago. Transformación bacteriana.

Simulación bioquímica avanzada.

1. Procesos de purificación de enzimas.
2. Fraccionamiento subcelular.
3. Alineamiento de secuencias proteicas.
4. Generación del potencial de membrana.
5. Estudio del modelo de Hogkin/Huxley del potencial de acción.
6. Análisis de corrientes eléctricas macroscópicas de canales iónicos activados por voltaje.
7. Análisis de corrientes eléctricas de canal único dependiente de voltaje.

LABORATORIO INTEGRADO II

  Outline

Session 1: Heterologous expression of ion channels in xenopus oocytes
Session 2: Expression and purification of SNARE complex subunits
Session 3: Membrane fusion induced by viral proteins
Session 4: Immobilized enzymes