Biochemistry II
Code: 100876 ECTS Credits: 6| Degree | Type | Year | Semester |
|---|---|---|---|
| 2500252 Biochemistry | FB | 2 | 1 |
Contact
- Name:
- Josep Antoni Biosca Vaque
- Email:
- josep.biosca@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
Other comments on languages
The classes of theory and problems will be in Catalan, but most of the graphic material and the bibliography will be in English or Spanish.Prerequisites
There are no official prerequisites. However, it is assumed that the student has acquired the knowledge taught in previous courses of the first year of the degree of Biochemistry, in particular the contents of those of Organic Chemistry of Biochemical Processes, Microbiology, Histology, Cell Biology and in particular of Biochemistry I, such as those referring to principles of bioenergetics, enzymology, structure and function of carbohydrates, lipids, proteins and nucleic acids.
Objectives and Contextualisation
The subject Biochemistry II constitutes the second part of the subject "Biochemistry" of the Degree in Biochemistry. Biochemistry II covers the basic aspects of the metabolic pathways, the associated energy changes, their physiological significance, their interconnections and response to biological signals from a basic and general point of view, as corresponds to a second year subject. The general objective of the subject is to provide the students the basics of the metabolic aspects necessary for the follow-up of many subjects of the Degree in Biochemistry.
Specific objectives:
- Describe the general mechanisms through which living beings obtain and transform the energy of the environment.
- To know the main molecular mechanisms for the transduction of biological signals.
- Describe the transporters of metabolites through the membranes.
- Describe the central pathways of the metabolism of carbohydrates, lipids, amino acids and nucleotides.
- Know the components of the electronic transport chains, their coupling with oxidative phosphorylation or photophosphorylation, and how metabolic energy is obtained.
- Give an overview of the interconnections between the metabolic pathways, as well as the mechanisms that regulate them in a coordinated way and their alterations in various physiopathological situations.
- Know how to apply the acquired knowledge to solve qualitative and quantitative problems.
- Know how to handle the bibliography and apply the information resources for the search of information.
Competences
- Act with ethical responsibility and respect for fundamental rights and duties, diversity and democratic values.
- Collaborate with other work colleagues.
- Describe intercellular and intracellular communication systems that regulate the proliferation, differentiation, development and function of animal and plant tissues and organs.
- Describe metabolic routes, their interconnections and their physiological significance, and also understand the mechanisms that regulate their activity to satisfy physiological needs.
- Interpret experimental results and identify consistent and inconsistent elements.
- Introduce changes in the methods and processes of the field of knowledge to provide innovative responses to the needs and demands of society.
- Manage bibliographies and interpret the information in the main biological databases, and also know how to use basic ICT tools.
- Manage information and the organisation and planning of work.
- Read specialised texts both in English and one's own language.
- Take account of social, economic and environmental impacts when operating within one's own area of knowledge.
- Take sex- or gender-based inequalities into consideration when operating within one's own area of knowledge.
- Use ICT for communication, information searching, data processing and calculations.
Learning Outcomes
- Act with ethical responsibility and respect for fundamental rights and duties, diversity and democratic values.
- Collaborate with other work colleagues.
- Correctly use the terminology of biochemistry and its text and reference books.
- Describe correctly the structural and thermodynamic bases of cell bioenergetics and transport across membranes.
- Describe the metabolism of glucids, lipids, amino acids and nucleotides.
- Identify the components of the electronic transport chain, its coupling with oxidative phosphorylation and the generation of metabolic energy.
- Identify the principal metabolic pathways and their mechanisms of control and integration.
- Interpret experimental results and identify consistent and inconsistent elements.
- Introduce changes in the methods and processes of the field of knowledge to provide innovative responses to the needs and demands of society.
- Manage information and the organisation and planning of work.
- Read specialised texts both in English and one's own language.
- Take account of social, economic and environmental impacts when operating within one's own area of knowledge.
- Take sex- or gender-based inequalities into consideration when operating within one's own area of knowledge.
- Understand the molecular mechanisms responsible for signal transduction.
- Use ICT for communication, information searching, data processing and calculations.
Content
Theory.
Topic 1. Basic concepts of metabolism.
Energy needs of living things. Laws of Thermodynamics. Free energy in biological processes. Sources of energy and carbon in living things. Metabolism and metabolic pathways. Phases of metabolism. Concept of homeostasis. Free energy changes from chemical reactions. Coupled reactions. Role of ATP and other phosphorylated compounds in metabolism. Energy transfers in metabolism. Oxide-reductions in biochemical processes. Role of electron transporters in metabolism. Control and compartmentalization of metabolic pathways. Experimental methods for the study of metabolism.
Topic 2. Biosignaling.
Characteristics of signal transduction processes. Hormones, neurotransmitters, growth factors and other primary messengers. Membrane and intracellular receptors. Molecular mechanisms of signal transduction. Integration of cytoplasmic and nuclear effects.
Topic 3. Carbohydrate metabolism.
Glucose transporters. Glucose degradation: glycolysis. Fermentations. Gluconeogenesis. Cori Cycle. Regulation of glycolysis and gluconeogenesis. Phosphate pentose pathway.
Topic 4. Glycogen metabolism and coordination in the control of carbohydrate metabolism.
Metabolic pathways leading to the formation of acetyl coA. The pyruvate dehydrogenase complex. Citric acid cycle. Energy efficiency and regulation. Amphibolic nature of the cycle: connections with biosynthetic pathways. Anaplerotic reactions. Glyoxylate cycle.
Mitochondrial electronic transport chain. Origin and use of reduced substrates. Chemiosmotic coupling: ATP synthase and oxidative phosphorylation. Mitochondrial transport systems. Regulation of oxidative phosphorylation. Energy balance of oxidative metabolism (example of glucose). Protein uncouplers and thermogenesis. Photosynthesis: Electronic transport and photophosphorylation. Comparison between photosynthesis and oxidative phosphorylation. Regulation of photosynthesis. Photorespiration and C4 cycle.
Topic 7. Metabolism of lipids.
Use of triacylglycerols in animals. Lipoprotein metabolism. Description and regulation of the oxidation pathway of fatty acids. Ketogenesis. Fatty acid biosynthesis: Activation of acetyl-CoA and fatty acid synthase. Elongation of the carbon chain and formation of unsaturations in fatty acids. Biosynthesis of triacylglycerols and phospholipids. Metabolism of cholesterol and its derivatives.
Topic 8. Metabolism of nitrogen compounds: Metabolism of amino acids.
Nitrogen cycle. General characteristics of amino acid synthesis and degradation. Destiny of the carbon atoms of amino acids. Ammonia removal and urea cycle. Hemo metabolism.Synthesis of amines of biological interest.
Topic 9. Nitrogen compound metabolism: Nucleotide metabolism.
General characteristics of the metabolism of purine and pyrimidine nucleotides. Deoxyribonucleotide synthesis: Regulation of ribonucleotide reductase. Biomedical applications of glutamine and nucleotide analogues: AIDS, cancer.
Metabolic specialization of tissues. Metabolic characteristics of the liver, muscle and adipose tissue. Metabolic adaptations to various pathophysiological situations: changes associated with various nutritional states, exercise and the effects of stress. Metabolic disorders in diabetes and obesity. Biotransformation and detoxification of drugs.
The problems refer to some aspects of the Theory program. The characteristics of the various parts of the syllabus mean that problem statements can focus on certain aspects such as enzymatic reactions (oxidation-reduction, chemical group transfer, etc.) that are used in various stages of metabolism, its regulation in response to the activation of different signaling pathways and its importance in various pathophysiological conditions. Problem statements will be delivered through the Virtual Campus in advance of the class of problems to be addressed.
Delivery of works by the Virtual Campus:
Two works will be proposed through the Virtual Campus, which will have to be solved by the teams (of three / four people) of students formed at the beginning of thecourse. THe work must be submitted before a specific date, announced through the Virtual Campus.
Methodology
The subject of Biochemistry consists of theoretical classes, classes for resolution of practical cases and problems, submission of homework by the Virtual Campus and tutorials.
Theory classes:
The content of the theory programme will be imparted by the teacher in the form of lectures, both live and recorded. The presentations used in class by the teacher will be available to students in the Virtual Campus of the subject in advance at the beginning of each of the topics of the course. These expository sessions will constitute the most important part of the theory section. . Students are advised to consult regularly the books recommended in the bibliography section of this educational guide in order to consolidate and clarify, if necessary, the contents explained in class.
Problems classes:
It is intended that these classes serve to consolidate the contents previously worked in the theory classes and also to make the students familiarize with some of the experimental strategies used in biochemistry, with the interpretation of scientific data and the resolution of problems posed under real experimental situations.
For the problems classes the students will be divided into two groups (A and B) whose lists will be made public at the beginning of the year by the Degree Coordination. The student must consult which group they belong to and attend the classes corresponding to their group.
There will be 10 problems sessions for each group, which will be devoted to the resolution of practical cases and experimental problems related to the contents of the theory program. A dossier with the formulation of the problems will be delivered through the Virtual Campus and they will be resolved throughout the sessions. In a limited number of sessions distributed throughout the semester, the teacher will expose the experimental and calculation principles necessary to work on the problems, explainingthe guidelines for their resolution and, if necessary, by giving a complementary part of theory to facilitate their resolution. At the end of each session the teacher will indicate the problems that must be resolved by the next one. Students will work out problems out of the class hours, in work groups of three to four people which will be organized at the beginning of the semester and kept throughout the classes of problems. At the beginning of each session, each working group will bring the problems solved, which will be discussed and corrected with the participation of all students, so that each one of the problems will be solved by one of the different randomly selected work groups. Before starting the resolution of the problem, the chosen group will deliver the document with the resolution they propose (one delivery per group of three to four people). The teacher will ensure that all groups have the opportunityto publicly explain their problem-solving proposals throughout the semester. As indicated in the evaluation section, the public resolution of the problems will be taken into account in the final grade.
Submission of homework by the Virtual Campus:
Periodically (before each of the two partial tests of theory) a set of questions will be proposed through the Virtual Campus that students will have to solve before a specific date.
This activity aims to work on the competence of teamwork, by organizing students into working groups in which all members must actively participate in solving questions.
The methodology of this activity will be as follows:
• At the beginning of the course students will be organized in groups of three/four people, registering the groups through the Virtual Campus before the deadline indicated by the teacher.
• The groups will work on the issues indicated for this activity outside of class hours.
• The works will be delivered through the Virtual Campus. The grade obtained will be applicable to all members of the working group to which the student belongs.
The statements of the deliveries will be published through the Virtual Campus where the delivery dates will also be indicated.
Tutorials:
Individual tutorials will be carried out at the request of the students. In the event that the number of applications was extremely high, especially in the face of partial examinations, a classroom tutorial could be held before each partial of theory (two in total), that would be announced through the Virtual Campus in due time. The objective of these sessions will be to solve doubts, review basic concepts and guide on the sources of information to consult. These sessions will neither be used to expose new topics nor to advance in the theory program but they will be sessions of debate and discussion.
Annotation: Within the schedule set by the centre or degree programme, 15 minutes of one class will be reserved for students to evaluate their lecturers and their courses or modules through questionnaires.
Activities
| Title | Hours | ECTS | Learning Outcomes |
|---|---|---|---|
| Type: Directed | |||
| Problems classes | 10 | 0.4 | 15, 2, 14, 4, 5, 10, 6, 7, 8, 11, 3 |
| Theory classes | 35 | 1.4 | 1, 13, 12, 14, 4, 5, 6, 7, 8, 9, 11, 3 |
| Tutorials | 6 | 0.24 | 14, 4, 5, 6, 7, 8, 3 |
| Type: Supervised | |||
| Submission of homework by the Virtual Campus | 12 | 0.48 | 15, 14, 4, 5, 10, 6, 7, 8, 11, 3 |
| Type: Autonomous | |||
| Study - autonomous work | 72 | 2.88 |
Assessment
Evaluation.
This subject will be evaluated by continuous assessment. The objective of the continuous assessment is to encourage the students’ effort throughout the course, allowing them to evaluate their degree of follow-up and understanding of the subject.
Theory (70% of the overall grade)
Individual assessment through:
Two partial exams with test and short questions, which will be eliminatory if their qualification is equal to or greater than 4 (out of 10). The weight of each partial exam will be 35% of the overall grade.
A retrieval exam of theory with test and short questions corresponding to the first or second partials. To be eligible for the retake process, the student should have been previously evaluated in a set of activities equalling at least two thirds of the final score of the course or module. Thus, the student will be graded as "No Avaluable" if the weighting of all conducted evaluation activities is less than 67% of the final score.
Those students who have obtained a score lower than 4.0 (out of 10) in the previous examination of one or both of the partials will have to perform the examination of the corresponding partial (s) (first partial, second partial or both).
On the occasion of the retrieval exam of theory it will be possible to take the examination to improve the score of one or both partials. In this case, it is understood that the previous qualification is waived and the qualification obtained in the second test will be considered as the qualification of the partial.
The total weight of the theory evaluation will be 70% of the overall grade.
Evaluation through Virtual Campus: (10% of the overall grade)
Periodically (2 times during the course), a set of questions will be proposed that must be solved before a specific date. The works prepared in groups of 4 people will be delivered through the Virtual Campus. For the assessment, not only the correct resolution of the work but also its approach and presentation will be taken into account. All the group will receive the same rating. If deemed necessary, the teacher may request that an individual questionnaire be completed regarding the group's work. Although the results of this questionnaire will not initially have a specific weight in the qualification of the subject, in case of detecting negative assessments of a person by the other members of his group who show that he has not participated in the work, the grade obtained by the group will not be applied or may be reduced. The total weight of the evaluation by Virtual Campus will be 10% of the global mark (each delivery will be 5% of the global mark).
Problems (20% of the overall grade)
1-Individual assessment:
There will be an exam where problems related to those dealt with in problems classes will have to be resolved. This test will be carried out shortly after the problems classes are finished. The weight of this test will be 15% of the overall grade.
On the day of the retrieval exam of theory, those students who have not obtained a mark equal to or greater than 4.0 (out of 10) in the test of problems will have to retake the exam on the problems.
The weight of individual problem assessment will be 15% of the overall grade.
2- Team-work assessment:
In the course of the classes of problems it will be necessary to work in a team to resolve the problems,which will be exposed in class and evaluated. This activity will be done in groups of 3-4 students and the weight of the test will be 5% of the overall grade.
The total weight of the evaluation of problems will be 20% of the overall grade.
In all cases the acquisition of written communication skills will be taken into account in addition to the knowledge.
The three sections (Theory, Problems and Homework submitted by Virtual Campus) are inseparable, so that the student must participate, and be evaluated, in all three in order to pass the subject.
To pass the subject, it is necessary to obtain a final global grade equal to or greater than 5.0 (out of 10). In addition, the partial notes of theory and problems, must be equal to or greater than four.
Any student, who cannot attend an individual assessment test any justified reason (such as illness, death of a first-degree relative or accident) and brings in the corresponding official documentation to the teacher or theDegree Coordinator, willbe entitled to perform themissed test on another date.
Assessment Activities
| Title | Weighting | Hours | ECTS | Learning Outcomes |
|---|---|---|---|---|
| Evaluation of homework sent by the Virtual Campus | 10% | 6 | 0.24 | 15, 14, 4, 5, 10, 6, 7, 8, 11, 3 |
| Evaluation of problems | 20% | 3 | 0.12 | 2, 14, 4, 5, 6, 7, 8, 3 |
| Theory partial exams | 70% | 6 | 0.24 | 1, 13, 12, 14, 4, 5, 6, 7, 8, 9 |
Bibliography
Basic bibliography (alphabetical order)
Berg, J.M., Tymoczko, J.L., Gatto, G. J. i Stryer, L. "Biochemistry" (2019). 9ª ed. W.H. Freeman, New York. Edició traduïda: "Bioquímica" (2013). 7ª ed. Ed. Reverté. Traduït de la 7ª ed. anglesa de l'any 2012. Accés des de la UAB: http://www.ingebook.com.are.uab.cat/ib/NPcd/IB_Escritorio_Visualizar?cod_primaria=1000193&libro=7705
Mathews, C. K., van Holde, K. E., Appling, D., Anthony-Cahill, S. "Biochemistry" (2013), 4ª ed. Pearson Education. Upper Saddle River. Edició traduïda: “Bioquímica" (2013), 4ª ed. Pearson Educación. Accés des de UAB: http://www.ingebook.com.are.uab.cat/ib/NPcd/IB_BooksVis?cod_primaria=1000187&codigo_libro=3938
Nelson, D.L. and Cox, M.M. "Lehninger Principles of Biochemistry" (2017). 7ª ed. Freeman, New York. Nelson, D.L. i Cox, M.M. Edició traduïda: "Lehninger-Principios de Bioquímica" (2014) 6ª. ed. Ed. Omega. Traduït de la 6ª ed. anglesa de l'any 2013.
Voet D., Voet J.G. i Pratt C.W “Voet's Principles of Biochemistry” (2018). 5th Edition, Global Edition (2018). Edició traduïda: Voet D., Voet J.G. i Pratt C.W. “Fundamentos de Bioquímica. La vida a nivel molecular" (2016) 4ª ed. Ed. Médica Panamericana. Traduït de la 4ª ed. anglesa de l'any 2013. Accés des de la UAB: https://www-medicapanamericana-com.are.uab.cat/VisorEbookV2/Ebook/9786079356972#{%22Pagina%22:%22Portada%22,%22Vista%22:%22Indice%22,%22Busqueda%22:%22%22}
Material available on the Virtual Campus.
Presentations used by the teacher in theory classes.
A dossier with the formulation of the problems to work in problems classes.
Software
Software
Some of the software that will be used during the semester will be:
COPASI.
COPASI is a program to simulate and analyze metabolic networks and their dynamics.
PYMOL.
It is a program for molecular visualization.
CHEMBIODRAW.
Software that allows to draw biological structures and also, chemical structures.