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2020/2021

Bioorganic Chemistry

Code: 102518 ECTS Credits: 6
Degree Type Year Semester
2502444 Chemistry OT 4 0
The proposed teaching and assessment methodology that appear in the guide may be subject to changes as a result of the restrictions to face-to-face class attendance imposed by the health authorities.

Contact

Name:
Adelina Vallribera Massó
Email:
Adelina.Vallribera@uab.cat

Use of Languages

Principal working language:
catalan (cat)
Some groups entirely in English:
No
Some groups entirely in Catalan:
Yes
Some groups entirely in Spanish:
No

Prerequisites

To attend this course it is necessary to have previously approved the subjects: "Estructura i reactivitat dels compostos orànics" "Mètodes de sintesi" i Laboratori de síntesi"

Objectives and Contextualisation

The general objective of the subject "Bioorganic Chemistry" is to provide the students with a general overview of natural products (structural, biosynthetic and ecological characterictics, and their applications as a source of biological active compounds.

Notions about the structural chemistry and biosynthesis of natural products will be provided as well as their function and utility as drugs or other interesting biological activities.

The training objectives of the subject can be summerized in:

1- To understand and know the structures of the importsnt natural products of the secondary metabolism and their biosynthesis

2- To know the biological and pharmacological activities of the most relevant natural secundary metabolites

3- To undertand the ecological and general importance of natural products

4. To be able to propose biosynthestic routes for secundary metabolites

 

Competences

  • "Interpret data obtained by means of experimental measures, including the use of IT tools; identify their meaning and relate the data with appropriate chemistry, physics or biology theories."
  • Adapt to new situations.
  • Apply knowledge of chemistry to problem solving of a quantitative or qualitative nature in familiar and professional fields.
  • Communicate orally and in writing in one’s own language.
  • Evaluate the health risks and environmental and socioeconomic impact associated to chemical substances and the chemistry industry.
  • Handle chemical products safely.
  • Handle standard instruments and material in analytic and synthetic chemical laboratories.
  • Learn autonomously.
  • Manage the organisation and planning of tasks.
  • Manage, analyse and synthesise information.
  • Obtain information, including by digital means.
  • Propose creative ideas and solutions.
  • Reason in a critical manner
  • Recognise and analyse chemical problems and propose suitable answers or studies to resolve them.
  • Resolve problems and make decisions.
  • Show an understanding of the basic concepts, principles, theories and facts of the different areas of chemistry.
  • Show initiative and an enterprising spirit.
  • Show sensitivity for environmental issues.
  • Use IT to treat and present information.
  • Use the English language properly in the field of chemistry.
  • Work in a team and show concern for interpersonal relations at work.

Learning Outcomes

  1. Adapt to new situations.
  2. Carry out basic synthesis, separation and purification procedures in an organic chemistry laboratory.
  3. Classify natural products in accordance with their biosynthesis.
  4. Communicate orally and in writing in one’s own language.
  5. Critically analyse synthetic pathways described in the bibliography.
  6. Describe and identify the main groups of natural products and the distinctive characteristics of each.
  7. Describe the processes and reactions that occur in biological systems.
  8. Describe the structures of the natural products of secondary metabolism.
  9. Describe the synthesis of natural products in living beings.
  10. Describe useful reactions in organic synthesis.
  11. Design reasonable biosynthetic pathways for natural products.
  12. Handle English language terms in relation to the synthesis of organic and bioorganic compounds.
  13. Identify the ecologic and pharmacologic importance of natural products.
  14. Identify the importance of natural products as a source of biologically active compounds.
  15. Identify the main structural traits of biomolecules in order to analyse or modify them.
  16. Identify the most relevant documentary sources on organic chemistry.
  17. Identify the risks involved in the handling of chemical compounds used in biological chemistry, and apply suitable protocols for the storage or elimination of the waste generated.
  18. Justify the results obtained in the laboratory for synthesis, separation, purification and characterisation processes of organic and bioorganic compounds on the basis of knowledge about their structure and properties.
  19. Learn autonomously.
  20. Manage the organisation and planning of tasks.
  21. Manage, analyse and synthesise information.
  22. Obtain information, including by digital means.
  23. Perform synthesis of organic and bioorganic compounds using protocols written in the English language.
  24. Properly handle glass and other common materials in an organic chemistry laboratory.
  25. Properly interpret data obtained in the laboratory after computerised treatment and on the basis of the acquired knowledge.
  26. Propose creative ideas and solutions.
  27. Reason in a critical manner
  28. Recognise strategies for the design of organic syntheses.
  29. Recognise the common chemical compounds found in the laboratory that require special safety measures.
  30. Recognise the three-dimensional view of molecules and organic reactions.
  31. Resolve problems and make decisions.
  32. Safely manipulate chemical reagents and organic compounds.
  33. Show initiative and an enterprising spirit.
  34. Show sensitivity for environmental issues.
  35. Use IT to treat and present information.
  36. Use basic instruments to characterise organic chemical compounds.
  37. Use spectroscopic techniques for the structural elucidation of organic and bioorganic compounds.
  38. Work experimentally with biological material (inert, aseptic and/or controlled atmospheres).
  39. Work in a team and show concern for interpersonal relations at work.

Content

PROGRAM

Biosynthetic routes

Primary and secondary metabolism. Main biosynthetic routes: shikimate, acetate, mevalonate. Methods used in the determination of biogenetic sequences.

Semiochemicals

Ecological chemistry. Classification of semiochemicals. Interactions plant-insect. Allelopathy. Phytoalexines. Pheromones

Fatty acids and poliketides

The acetate hypothesis. Saturated fatty acids. Unsaturated fatty acids. Aromatic poliketides. Macrolides.

Shikimic acid derivatives

Phenolic compounds. Aromatic amino acids (tryptophan, phenylalanine, tyrosine) and derivatives. Transamination and NIH shift. Cinamic acids and derivatives. Pharmacological applications: L-DOPA, salicine as a model of Aspirin. Lignanes and lignines. Flavonoids.

Terpenoids

Structural classification. Acetate-mevalonate pathway. Monoterpenes. Sesquiterpenes. Diterpenes. Steroids. Cholesterol.

Secondary metabolism amino acids

Prebiotic amino acid formation. Antibiotic b-lactamics. Penicillins and cephalosporines.

Alkaloids I

Alkaloids derived from ornithine, lysine and nicotinic acid.

Alkaloids II

Benzylisoquinoline type alkaloids. Opium alkaloids (thebaine, morphine, codeine), physiological effects and biosynthesis. The Curare and the strychnine. Quinine: the base remedy against malaria.

 

 

 

 

Methodology

In accordance with the objectives of the subject, the student will have to be involved in a series of activities to achieve the stablished knowledge and skills. These activities can be grouped into three different types:

Master class (classroom and virtual classes): During these classes the teacher will transmit the basic knowledge of the subject; knowledge that will be complemented with the individual work of the student consulting the bibliography that the professor will indicate. The master classes are conceived as a fundamental unidirectional method of transferring the teacher's knowledge to the student. During the classes student's participation will be encouraged through the dynamization of classes by the resolution of cases and questions in a regular way.

Problem classes (classroom and virtual classes): A dossier of exercises will be given. These exercises should be solved by the students along the course. A selected part of them will be solved by the problem's teacher so that the students can learn the appropriate methodology to find the solutions. In these sessions, the solutions proposed by the students will be also discussed, based on the autonomous work developed. During this process, student's participation will be important. Teacher will help to develop the critical sense and logical reasoning, in order to increase the ability of the students to solve problems.

Practical Classes: There will be laboratory sessions (4 sessions of 4 hours each) related to natural products, through which the students will also practice laboratory techniques referring to the manipulation of chemicals as well as the use of small equipment and instrumental techniques. The work will be supervised by a teacher that will evaluate the students considering their attention and performance in the laboratory as well as the reports and laboratory notebook. If a student is involved in an incident that may have serious consequences of security, he can be expelled from the laboratory and in consequently he will suspend the subject.

 

Activities

Title Hours ECTS Learning Outcomes
Type: Directed      
Practical classes 16 0.64 1, 4, 23, 2, 20, 17, 25, 18, 24, 32, 34, 29, 31, 39, 38, 36, 37
Theoretical classes 35 1.4 19, 3, 4, 9, 7, 6, 8, 11, 20, 21, 14, 13, 16, 15, 22, 31
Type: Supervised      
Tutorials 5 0.2 9, 11, 21, 25, 26, 27, 31
Type: Autonomous      
Learning anr problems resolution 87.2 3.49 5, 3, 4, 9, 7, 6, 8, 10, 11, 21, 14, 13, 16, 15, 22, 30, 28, 35

Assessment

The competences of this subject will be evaluated through two modules, which include the Written Tests Module and the Laboratory Module, which will be assigned a specific weight in the final grade.

It is necessary to obtain a minimum grade of 5 points in the global evaluation to pass de subject.

The non-presented: A student receives the grade of non-presented if he did not attend any written test and if he did not attend any of the laboratory practices

1. Written Tests Module:

It will consist of two compulsory partial exams. To pass by partials, you must have a minimum grade of 5.0 points in each, and the final grade will be the simple average of the marks of the two partials. For students who do not pass one of the partials or both, there will be a second-chance examination (written final examination). In this case the grade will be the weighted average of the written final test (90%) and of the marks obtained in the two partial tests (remaining 10%). It is necessary to obtain a minimum of 5 in the grade of the final test to pass the subject.

These exams will consist mainly of practical exercises to solve and some short theoretical questions

First partial exam:

Will collect approximately 40% of the subject matter.

Second partial exam:

The second written test will be carried out after finishing the theoretical classes and may include some of the concepts that have been already evaluated in the first partial exam as well as in the practical classes.

Second-chance examination:

It will be done after the two partials and will include all the course material. * To participate the students must have been previously evaluated in the partial exams.

*The students who did not pass the continuous evaluation, but have obtained a minimum of 7 points out of 10 in one of the partial exams, will be exempt of doing the corresponding part of the second-chance exam and will keep the same mark for averaging with the other marks of the evaluation.

 2. Laboratory Module:

The laboratory practices are obligatory. Reports will be delivered, and the skills of the student will be assessed.

 

Assessment Activities

Title Weighting Hours ECTS Learning Outcomes
Laboratory Module 15% 1.1 0.04 1, 19, 33, 23, 2, 20, 21, 17, 25, 18, 12, 24, 32, 34, 22, 26, 27, 29, 39, 38, 36, 35, 37
Written Test Module 85% 5.7 0.23 5, 3, 4, 9, 7, 6, 8, 10, 11, 14, 13, 16, 15, 27, 30, 28, 31

Bibliography

Medicinal natural Products. A biosynthetic approach. P. M. Dewick, John Wiley and Sons, 2002. Find Electronic Version in the Library UAB

Natural products: their chemistry and biological significance. J. Mann, R. S. Davidson; J. B. Hbbs, D. V. Banthorphe and J. B. Harbone. Pearson Education Limited, 1994. In the Science Library you can find the electronic version.