2010-11 Academic Year
Basic Sciences II (20333)
Qualification/course: Bachelor's Degree in Human Biology
Year: 1
Term: 2
Number of ECTS credits: 6
Number of study hours: 150
Course Language(s):Catalan
Teaching Staff: Jordi Segura (coordinator), Josep A. Pascual, Rosa Ventura, Josep Marcos, Ricardo Gutiérrez
1. Presentation of the course
Chemistry (Basic Sciences II) is an obligatory subject of the Human Biology syllabus, which is taught in the second term of the first year of the degree course.
2. Competences to be achieved
The following are the competences that are to be acquired during this course:
1. To learn about the fundamental aspects relating to atomic and molecular structure; the importance of isomers, with particular attention to stereochemistry; reactivity and chemical equilibrium.
2. To learn more about chemical nomenclature, especially in organic chemistry, and about the resolution of practical problems concerning laboratory work, stoichiometric calculations and the understanding of reactivity.
3. To obtain a global vision of organic chemistry in fundamental aspects and particularly in those aspects most related to molecules of biological interest.
4. To obtain an introduction into bioinorganic chemistry to complete the understanding of the chemical basis of processes of biological interest.
5. To learn about and practise basic chemical laboratory operations.
3. Contents
The topics that will be taught during the course include the following:
- Atomic and molecular structure
- Chemical reactivity
- Chemical equilibrium in biological systems
- Introduction to organic chemistry and stereochemistry
- Chemistry of carbon bonded to hydrogen
- Chemistry of carbon bonded to oxygen
- Chemistry of carbon bonded to nitrogen
- Chemistry of carbon bonded to other elements
- Bioinorganic chemistry
The lectures follow the following syllabus:
Topic 1. Atomic and molecular structure
The quantization of matter and energy. Atomic structure according to the Bohr-Sommerfeld model. The Schrödinger wave function and atomic orbitals. Periodic classification of the elements and their properties. Chemical bonding: Lewis theory. Ionic bonding. Covalent bonding, molecular orbitals and orbital hybridisation. Carbon atom bonds. Coordination chemistry: dative covalent bonding and the formation of complexes. Nomenclature. Weak bonds: dipolar interactions, Van der Waals bonds and hydrogen bonds.
Topic 2. Chemical reactivity
Principles of thermodynamics. Enthalpy, entropy and free energy. Equilibrium constants. Chemical kinetics. Order of reaction and reaction mechanisms. Factors that affect the speed of reaction. Catalysts.
Topic 3. Chemical equilibrium in biological systems
Law of mass action. Equilibrium constant. Equilibrium displacement. Properties of water as a solvent. Solubility equilibrium. Common ion effect. Complex formation. Redox equilibrium. Electrochemical series. Oxidation number. Semi-reactions. Electrode potential. Electric battery cell concept. Nernst Equation. Ionization of water. Concept of pH. Acid-base equilibrium. pH of salt solutions. Buffer solutions. Neutralization. Indicators.
Topic 4. Introduction to organic chemistry and stereochemistry
Organic compounds. Functional groups. Isomers and types of isomer. Structural isomers. Geometric isomers. Optical isomers: Chiral centre, racemic mixture, optical activity. Nomenclature of the optical isomers. Molecules with various chiral centres. Chemical and biological importance of optical isomers.
Topic 5. Bioorganic Chemistry (I)
Carbon bonded to hydrogen. Hydrocarbons and their classification: alkanes, alkenes and alkynes, nomenclature and isomers. Conformational analysis. Addition reactions. Conjugation of double bonds and aromaticity. Benzene and polycyclic aromatic systems. Reaction mechanisms and velocity. Transition state and reaction intermediaries. Carbocations, carbanions and radicals. Electrophilic substitution reactions. Relevant properties in their interaction with the biological environment.
Topic 6. Bioorganic Chemistry (II)
Carbon bonded to oxygen (i). Carbon-oxygen bond. Structure. Nomenclature. Alcohols, ethers, aldehydes and ketones. Chemical properties. Keto-enol tautomerism. Generalities about their reactivity.
Topic 7. Bioorganic Chemistry (III)
Carbon bonded to oxygen (ii). Carboxylic acids. Chemical properties. Formation and properties of salts, esters and amides, acyl halides and anhydrides.
Topic 8. Bioorganic Chemistry (IV)
Carbon bonded to nitrogen. Chemistry of the nitrogen atom. Functional groups with nitrogen. Nomenclature. Amines: molecular structure, physical and chemical properties and reactivity. Heterocyclic compounds with nitrogen. Aminoacids: stereochemistry, acid-base properties, properties of the side chains. Peptide bond. Determination of the primary structure of peptides.
Topic 9. Bioorganic Chemistry (V)
Carbon bonded to other elements. Chemistry of the C-S and S-S bonds. Disulphide bond: importance in protein structure. Alkyl halides: chemistry of halogen atoms, nomenclature, physical properties, reactivity, applications and biological importance.
Topic 10. Bioinorganic Chemistry (VI)
Abundance of the bioinorganic elements. Essentiality. Predominant elements: alkali and alkaline-earth metals. Iron, zinc and trace elements. Molybdenum and ultratrace elements.
The seminars are dedicated to the following specific topics:
Seminar 1. Chemical bonding
Seminar 2. Thermodynamics
Seminar 3. Stoichiometry
Seminar 4. Acid-base equilibrium
Seminar 5. Stereochemistry
Seminar 6. Organic chemical nomenclature
The practical sessions consist of computer work and work in the experimental laboratory. Students participate in three practical sessions with computer tools and four practical sessions in the laboratory. The three computer practical sessions last one hour each, while the laboratory practical sessions have a duration of four hours each.
The laboratory practical sessions combine basic laboratory operations and practical application of the chemical knowledge acquired, in accordance with the following list:
1. Introduction to laboratory work.
2. Test-tube reactions - speed of reaction - solution/dilution heat - acid-base reactions - redox reactions - complex formation reactions - precipitation reactions - separations: filtration and solution - recognition of cations and anions.
3. Titrations - potentiometry of a polyprotic acid - oxidation-reduction volumetry: hydrogen peroxide - complexometry: hardness of water.
4. Setting up experiments in the laboratory: distillation - setting up a still. Understanding its component parts - separation of two liquids with and without a fractionating column.
5. Organic synthesis: synthesis of aspirin - vacuum filtration - vacuum desiccation - purification by recrystallization - fusion point determination.
4. Assessment
The assessment will take into account all aspects relating to knowledge acquired and working practices shown in the context of the subject. 60% of the mark will correspond to the theoretical aspect of the subject, and 40% to the practical aspect.
The mark corresponding to the theoretical part will be obtained through multiple-choice questions, resolving of problems, and questions concerning the development of concepts.
For the practical part, the assessment will be based on the work carried out in the computer and experimental laboratories, and questions related to the practical sessions and the laboratory log book. The attendance at the laboratory practical sessions and the handing in of the corresponding laboratory log book prior to the final examination are both obligatory.
Midway through the term an assessment will take place of the themes studied so far, which will have an augmentative effect on the end-of-term mark for those students who attain the pass mark.
5. Bibliography and teaching resources
5.1. Basic bibliography
- Holum, John R. Fundamentos de química general, orgánica y bioquímica para ciencias de la salud. Mèxic, D. F.: Limusa-Wiley, 1999.
- PetrucciI, Ralph. Química general. Madrid: Prentice Hall, 2003.
5.2. Complementary bibliography
- Atkins, P. W. Química general. Barcelona: Ediciones Omega, 1992.
- Barán, Enrique J. Química bioinorgánica. Madrid: McGraw-Hill, 1994.
- Garrido Pertierra, Amando. Fundamentos de química biológica. Madrid: McGrawHill, 1991.
- Saña Vilaseca, Josep. Química per a les ciències de la naturalesa i de l'alimentació. Barcelona: Vicens Vives, 1993.
5.3. Teaching resources
Computer-assisted teaching:
- Smith, S. i d'altres. Comprehensive Chemistry. Wellesley (EUA): Falcon Software.[CD-ROM]. ext - Journal of Chemical Education. "Chemistry comes alive!".
Complementary reference books:
Year: Handbook of chemistry and physics: a ready-reference book of chemical and physical data. Editor en cap: David R. Lide. Boca Raton: CRC Press.
- The Merck Index. An encyclopedia fo chemicals, drugs and biologicals. Editor: Maryadele J. O'Neil. Whitehouse Station. Merck.
6. Methodology
The course consists of theoretical content and laboratory practical sessions. The theoretical content is taught through 25 hours of lectures and 15 hours of specific seminars. Lectures are intended for the whole class. The seminars represent an opportunity to enter into further detail and discuss specific aspects, and are held with half of the students in the class. They also include the solving of problems related to the relevant theory.
With regard to the practical sessions, 3 hours are of an interactive nature using computer tools and programs, while 17 hours are dedicated to experimental work at the laboratory. These practical activities are undertaken in groups made up of a quarter of the class students.
Students are required to dedicate 65 hours of individual study to solving questions relating to the content of the course.
7. Activities schedule