Biochemistry
Code: 100938Credits: 9
| Degree programme | Type | Course |
|---|---|---|
| Biotechnology | FB | 1 |
Contact lecturer
- Name :
- Javier Garcia Pardo
- Email :
- javier.garcia.pardo@uab.cat
Teaching staff
- Guillem Prats Ejarque
- Enea Sancho Vaello
- Javier Garcia Pardo
Group languages
You can consult this information at the end of the document.
Prerequisites
There are not prerequisites to follow the course successfully. Nonetheless it would be desirable if students were familiar with basic knowledge of biology and chemistry.
Much of the literature is in the English language, which is also used in the figures projected in theory classes.
Objectives
Learning outcomes
- CM15 (Work collaboratively in teams to solve problems in the field of biochemistry.) Work collaboratively in teams to solve problems in the field of biochemistry.
- KM13 (Describe the principles of bioenergetics and enzymatic catalysis.) Describe the principles of bioenergetics and enzymatic catalysis.
- KM14 (Accurately describe the molecular bases of protein folding, trafficking, modification, and turnover.) Accurately describe the molecular bases of protein folding, trafficking, modification, and turnover.
- SM14 (Correctly interpret data and observations in the field of biochemistry.) Correctly interpret data and observations in the field of biochemistry.
- SM15 (Analyse three-dimensional structures of macromolecules.) Analyse three-dimensional structures of macromolecules.
Contents
Lesson 1. Molecular elements and physical environment of living organisms.
Concept of biochemistry. Chemical elements in living organisms. Biomolecules. Structural hierarchy in the molecular organization of cells. Non-covalent interactions in aqueous systems. Biological relevance of water. Water ionization, ionic equilibrium and buffer systems.
Lesson 2. Bioenergetics principles.
Production and use of metabolic energy. Universality of the principles of thermodynamics. Life as a system far from thermodynamic equilibrium: biochemical reactions and free energy. Basic processes in bioenergetics: Phosphate transfer and redox reactions. ATP and other phosphorylated compounds. Electron carriers.
Lesson 3. Proteins: primary structure and biological functions.
Protein types and functions. Amino acids structure and properties. Classification. Peptides and peptide bond. Composition and amino acid sequence of proteins. Protein sequence databases. Sequence alignments.
Lesson 4. 3D protein structure.
Levels of protein structure. Description of helix and beta-sheets. Tertiary structure. Fibrous proteins. Globular proteins. Quaternary structure. Protein folding: key factors; chaperones. Conformational diseases. Prions. Protein structure prediction. Protein structure databases.
Lesson 5. Function and evolution of proteins: oxygen-binding proteins.
Oxygen storage: Myoglobin. Oxygen transport: Hemoglobin. Cooperativity and allosteric regulation. Analysis of cooperativity. Hemoglobin variants: physiological adaptation and molecular pathology. Examples of protein evolution.
Lesson 6. Carbohydrates.
Types and functions. Monosaccharides, description and properties. Glycosidic bond. Oligosaccharides. Polysaccharides. Glycoproteins and glycolipids. Carbohydrates as information-carrying molecules.
Lesson 7. Lipids and biological membranes.
Lipid types and functions. Fatty acids. Storage and membrane lipids. Cholesterol and derivatives. Fat soluble vitamins. Eicosanoids. Lipoprotein structure and function. Biological membranes.
Lesson 8. Biological catalysts.
Nature and function. Enzyme classification and nomenclature. Catalytic effects in chemical reactions: general mechanisms. Description of enzymatic mechanisms. Initial velocity. Enzyme kinetics: the hypothesis of Michaelis-Menten. Enzyme cofactors. Two substrate reactions. Enzyme inhibition. Regulation of enzyme activity: allosteric changes, covalent modifications and changes in the enzyme concentration. Biomedical and biotechnological applications.
Lesson 9. Nucleic acids: Structure levels.
Nucleic acids: nature and function. Nucleotides. The primary structure of nucleic acids. Secondary structure: the model of Watson and Crick and alternative models. Tertiary structure: DNA supercoiling and transfer RNA. Protein-DNA complex: chromosome organization. DNA denaturation and renaturation.
Lesson 10. Introduction to metabolism.
Concept of metabolism and metabolic pathways. Metabolism stages. Bioenergetic considerations. Control and compartmentalization of metabolic pathways. Experimental approaches for metabolism study.
Lesson 11. Biosignaling.
Hormones, neurotransmitters and other primary messengers. Membrane and intracellular cell receptors. Molecular mechanisms for signal transduction: receptor enzymes, G protein-coupled receptors and ion channels. Second messengers. Integrated response of different signals both at cytoplasm and nucleus levels.
Lesson 12. Carbohydrate metabolism (1).
Glucose metabolism. Glycolysis. Fermentations. Feeder pathways for glycolysis. Gluconeogenesis. Coordinated regulation of glycolysis and gluconeogenesis. The pentose phosphate pathway.
Lesson 13. Carbohydrate metabolism (2).
Glycogen metabolism: synthesis, breakdown and coordinated regulation. Coordination in the metabolic control of glucose and glycogen: relevance of metabolic tissue specialization.
Lesson 14. Core routes in oxidative metabolism.
Acetyl-CoA production. Citric acid cycle. Energy balance and control. Anaplerotic reactions. Glyoxylate cycle.
Lesson 15. Electron transport and oxidative phosphorylation.
Mitochondrial electron transport chain. Origin and utilization of reduced substrates. Chemiosmotic coupling: ATP synthase and oxidative phosphorylation. Mitochondrial transport systems. Oxidative phosphorylation control. Energy balance of oxidative metabolism (using glucose as an example).
Lesson 16. Photosynthesis.
Basic processes in photosynthesis. Photosynthetic pigments. Energy absorption of light. Electron transport and photophosphorylation. CO2 assimilation and photosynthetic carbohydrate biosynthesis (Calvin cycle). Photosynthesis control. Photorespiration.
Lesson 17. Lipid metabolism.
Triacylglycerol metabolism in animals. Lipoproteins. Description and control of the fatty acid oxidation pathway. Ketogenesis. Description and control of fatty acid biosynthesis pathway. Triglyceride and phospholipid biosynthesis. Cholesterol metabolism.
Lesson 18. Nitrogen compounds metabolism.
Nitrogen cycle. Intracellular degradation of proteins. Basic mechanisms of amino acid degradation. Fate of the carbon skeleton. Ammonia excretion and the urea cycle. Amino acid biosynthesis. Nucleic acid and nucleotide degradation. Nucleotide recovery and de novo synthesis. Biomedical applications of nucleotide analogs.
Lesson 19. Metabolism Integration.
Coordination of metabolism between liver, skeletal and cardiac muscle, adipose tissue and brain. Major control hormones. Stress and metabolism adaptation.
Learning activities and methodology
| Title | Hours | ECTS | Learning outcomes |
|---|---|---|---|
| Learning exercises | 39 | 1.56 | CM15, KM13, KM14, SM14, SM15 |
| Individual work | 105 | 4.2 | KM13, KM14, SM14, SM15 |
| Tutor sessions | 0 | 0 | KM13, KM14, SM14, SM15 |
| Classes of problem resolution | 15 | 0.6 | CM15, KM13, KM14, SM14, SM15 |
| Theory classes | 55 | 2.2 | CM15, KM13, KM14, SM14, SM15 |
The Biochemistry course consists of theory classes, problem-solving sessions, and tutorials. The organization and teaching methodology that will be followed for each of these learning activities are described below.
Theory classes
The contents of the theoretical syllabus will be taught mainly by the lecturer in the form of lectures supported by audiovisual material. The presentations used by the lecturer during the classes will be made available in advance on the course Virtual Campus. Students are recommended to have this material available to follow the lectures.
Students are also advised to consult regularly the textbooks listed in the "Bibliography" section of this course guide in order to consolidate and, if necessary, clarify the concepts explained during the lectures. It is also recommended to use the links included in the presentations for the different topics, which contain videos and animations related to the processes explained in class.
Problem-solving sessions
During these sessions, the class will be divided into two groups (A and B). Students should check which group they belong to and attend the corresponding sessions.
These sessions are scheduled during the second semester and will be devoted to solving experimental problems related to the contents covered in the theory lectures. Their aim is to consolidate the concepts previously introduced in the lectures, as well as to facilitate students' understanding of the techniques used in biochemistry, the interpretation of scientific data, and the solution of problems based on real experimental situations.
The collection of problems to be worked on during these sessions will be available on the course Virtual Campus.
Tutorials
Individual tutorials will be held upon request by students. If the number of requests is high, particularly before the partial examinations, a group tutorial session may be organized before each partial exam. These sessions will be announced in due course through the Virtual Campus.
The purpose of these tutorials is to answer students' questions, review key concepts, and provide guidance on the information sources consulted.
Assessment
Continuous assessment activities
| Title | Weight | Hours | ECTS | Learning outcomes |
|---|---|---|---|---|
| Problem solving | 20 | 3 | 0.12 | CM15, KM13, KM14, SM14, SM15 |
| Partial exams | 80 | 8 | 0.32 | CM15, KM13, KM14, SM14, SM15 |
Assessment of this course will consist of three theory midterm examinations and one problem-solving examination.
Assessment
Individual assessment
Assessment will be based on:
-Three midterm examinations consisting of multiple-choice questions and short-answer questions. The first midterm examination accounts for 26% of the final grade. The second and third midterm examinations each account for 27% of the final grade. A minimum grade of 3.5 out of 10 must be obtained in each examination.
-One problem-solving examination, which will be held on the same day as the first theory midterm examination. This examination accounts for 20% of the overall course grade. A minimum grade of 3.5 out of 10 is required to pass this examination.
-To be eligible for the resit examination, students must have previously completed assessment activities corresponding to at least two-thirds (67%) of the total course grade.
-Students who have obtained grades higher than 3.5 out of 10 and wish to improve the grade obtained in any of the midterm or problem-solving examinations may retake the corresponding examination on the day scheduled for the resit examinations. However, students should note that sitting the resit examination implies renouncing the previously obtained grade, regardless of the result obtained in the resit.
Overall course assessment
To pass the course, students must obtain an overall grade of 5.0 out of 10 or higher, as well as a minimum grade of 3.5 out of 10 in each midterm examination and in the problem-solving examination.
If the grade obtained in any of these examinations is below 3.5 out of 10, the maximum final grade for the course will be 3.5 out of 10.
Students will receive the grade "Not Assessable" (No Avaluable) if the assessment activities completed account for less than 67% of the final course grade.
Single assessment
The single assessment consists of one comprehensive examination covering the entire theory syllabus, accounting for 80% of the final grade, and one problem-solving examination, accounting for the remaining 20% of the final grade. The grade obtained in these examinations constitutes 100% of the final course grade.
The single assessment examination will take place on the same date scheduled for the last continuous assessment examination (the third midterm examination).
The same resit system as that applied to continuous assessment will apply to the single assessment.
Use of Artificial Intelligence (AI) Technologies
In this course, the use of Artificial Intelligence (AI) technologies is not permitted at any stage. Any work that includes content generated by AI will be considered a breach of academic integrity and may result in a partial or total penalty in the grade for the activity, or more severe disciplinary measures in serious cases.
In the event of academic fraud:
Any deliberate behaviour aimed at altering the grade of an examination through copying or the use of tools not authorized by the teaching staff will result in a grade of 0 for the examination. This incident will be reported to the degree programme coordinator.
Bibliography
Basic References (listed alphabetically):
- Murray, R.K. et al. Harper's Illustrated Biochemistry (2015). 30th edition. Mc Graw Hill Education.
- Nelson, D.L. and Cox, M.M. Lehninger-Principles of Biochemistry (2021). 8th edition. Macmillan Learning.
- Jeremy Berg; Gregory Gatto Jr.; Justin Hines; John L. Tymoczko; Lubert Stryer Biochemistry (2023). 10th edition.
- Tymoczko, J.L., Berg, J.M. and Stryer L. Bioquímica. Curso básico (2014). Ed. Reverté. Traduït de la 2ª edició (2013). W.H. Freeman and Co.
- Tymocsko, J.L., Berg, J.M. and Stryer, L. Biochemistry: A Short Course (2016). 3rd edition. Macmillan Learning, W.H. Freeman and Co.
- Donald Voet, Judith G. Voet, Charlotte W. Pratt “Fundamentals of Biochemistry: Life at the Molecular Level,” 5th Edition. Wiley ed. ISBN: 978-1-118-91840-1
Web links: They can be found in the files available on the course Virtual Campus, where they are kept up to date.
Software
No specific software is required
Course groups and languages
The information provided is provisional until November 30. After this date, you will be able to consult the language of each group through this link. To access the information, you will need to enter the course CODE
| Type of teaching | Group | Language | Semester | Shift |
|---|---|---|---|---|
| (TE) Theory | 41 | Catalan | annual | morning-mixed |
| (PAUL) Classroom practices | 411 | English | annual | afternoon |
| (PAUL) Classroom practices | 412 | English | annual | afternoon |