INTEGRATED COURSE ON BIOCHEMISTRY AND BIOINFORMATICS
- Overview
- Assessment methods
- Learning objectives
- Contents
- Bibliography
- Delivery method
- Teaching methods
Knowledge of Molecular Biology, General Chemistry and Organic chemistry.
The examination is designed to assess the skills acquired by the student concerning:
1. knowledge and understanding of the basis of biological chemistry and ability to find correlations between the various aspects of the topic.
2. ability to understand the interconnections between different metabolic pathways, to understand the regulation of energy metabolism, biomolecules and biological information. Ability to extract information from a text book or research paper and to identify the critical aspects.
3. quantitative Knowledge of biochemical phenomena.
4. Understanding of bioinformatics (methods and practices)
In detail:
- Written examination: questions will be focused on "Organic Macromolecules" and " Exercises" about the pH and energy balance of reactions. Four questions concerning the structure of biological macromolecules (to which it is attributed half of the evaluation in quantitative terms), (b) Three exercises focused on energy balance and enzyme kinetics (to which are attributed to half of the evaluation in quantitative terms).
Marks are expressed on a scale of 30 (minimum marks: 18) (weight on the final vote: 30%).
- Passing the written test will allow the oral test to take place. In the oral exam, the student will be asked to use the knowledge about the sections "Metabolism", "Integration of Metabolism and Cellular Signaling" and "Informational Metabolism" of the program to demonstrate the knowledge of metabolic-related reactions and their interrelationships adjustment.
Marks are expressed on a scale of 30 (minimum marks: 18) (weight on the final vote: 30%) (weight on the final score: 50%).
- The knowledge learned in the Bioinformatics module will be evaluated by the production of an elaborate to evaluate the ability to apply the bioinformatic approach to solving biological problems. Marks are expressed on a scale of 30 (minimum marks: 18) (weight on the final vote: 20%).
The final vote will be the weighted average of the results of the individual trials.
The Subject is formed by 2 main parts:
Metabolism, e.g. the study of the stracture/function relationschips in biological molecules, biological pathways and their regulation. Molecular basis for some major pathologies and the ìir moleculr therapy
Bioinformatics, e.g. the study of computational resources for analysis of sequences and structural properties of biological molecules
In the metabolism part will be studied the main classes of biological molecules (sugars, proteins, lipids and nucleic acids). The metabolic pathways for their synthesis and catabolism. Aim: understand the molecular basis of life. Understanding the model biotechnological applications of organisms and molecules. Understanding the modern approaches to biochemical research.
LEARNING OUTCOMES
• Cognitive skills
- Basic elements of Biological Chemistry and metabolism of nutritional elements;
- comprehension of molecular basis of physiological and pathological processes;
- knowledge of main biological databases and bioinformatic tools
• Practical and subject specific skills
- Application of biochemical knowledge for the comprehension of function of organism and environment;
- Ability to understand the interconnections between metabolic pathways and macromolecule metabolism;
- Ability to exploit bioinformatic tools (data banks, servers, software).
- Ability to understand the alteration of pathologic dysfunctions and potential biotechnological applications;
- Ability to understand and discuss bioinformatic analysis
• Communication skills
- Ability to write a concise report;
- Ability to communicate the results of a research in written and oral mode;
- Ability to convert numerical data into plots;
- Ability to read and comment a scientific text.
The water and pH- Chemical composition of the body: Introduction to the course. Macro-and trace elements.
- Water and aqueous solutions: physical-chemical properties of the water. Solubility of inorganic and organic compounds in the water. Acid-base balance.
Biological molecules
- Amino Acids: Structure, chemical properties and isoelectric point. The peptide bond.
- Proteins: Levels of structural organization of proteins and interactions stabilizers. The denaturation of proteins. Classification of proteins. Outline of the main techniques for the analysis of protein structure.
- Carbohydrates: Main aldoses and ketoses. Chirality and stereoisomerism. Cyclic and open forms. Glyosidic bond. Major oligosaccharides. Polysaccharides (glycogen, starch, cellulose and other components of dietary fiber).
- Lipids: Fatty acids: structure, classification, physical and chemical properties. Triglycerides. Glycerophospholipids and sphingolipids. structure and function of cholesterol, bile acids and steroid hormones. Biological membranes and membrane transport: mechanisms of facilitated transport. Pumps and ion channels.
- Nucleotides and Nucleic Acids: Biochemical functions of nucleotides. Structure of nucleic acids.
- Enzymes: Catalysis. Nomenclature and classification of enzymes. Substrate specificity. Examples of catalytic mechanisms: chymotrypsin. Enzyme kinetics and units of measurement of enzyme activity. Enzyme assay. Enzyme cofactors.
- Introduction to metabolism: - Energy Balances related to the metabolism of carbohydrates, proteins and lipids. Production, interconversion and consumption of energy in cells. ATP as a universal carrier of metabolic energy. Oxygen, the biological oxidations. The pyridine nucleotides as carriers of reducing power. Anabolism and catabolism. Compartmentalization of metabolic pathways.
- Metabolism of carbohydrates: glycolysis and production of pyruvate (regulation). The alcoholic and lactic fermentation. Glycogenolysis (regulation). Gluconeogenesis. The pentose phosphate metabolism. Glycogen synthesis (stages, meaning and regulation). Second messengers: cAMP. Photosynthesis. Tricarboxylic acid cycle (regulation and energy balance). The oxidative phosphorylation (the components of the respiratory chain).
- Lipid metabolism: uptake of lipids. Activation of fatty acids. Beta-oxidation of saturated fatty acids (regulation). Metabolism of propionilCoA. Biosynthesis of fatty acids (stages, meaning and regulation). Cholesterol metabolism.
- Amino acid catabolism: transamination, oxidative deamination. Metabolism of ammonia. Urea cycle
- Metabolism nitrogen compounds: Catabolism of porphyrins and biological amines.
The informational metabolism
- Replication of DNA: Reaction of DNA polymerase.
- The transcription of the DNA: RNA polymerase.
- Protein synthesis: ribosomes, tRNAs. Activation of amino acids. Post-translational modifications.
The molecular pathology
Tutorials: exercices - 1 CFU (12 hours):
pH and dissociation and buffers
Isoelectric point
Thermodynamics of biological reactions
Lessons Bioinformatics 3 CFU (24 hours):
Computational approaches for the biochemical investigations (Data banks, software, servers)
Exercises Bioinformatics: Practical use of data banks and software
Slides of lessons: from the Elearning website
Exercises: downloadable from Elearning
Lecture notes and papers (also for the laboratory): downloadable from Elearning site
Text book metabolism (one of the following):
Berg J., Timoczcko J.L., Stryer L., Biochimica (Zanichelli)
Voet D., Voet J.G. Pratt C.W., Fondamenti di biochimica (Zanichelli)
Nelson D.L., Cox M.M., I principi di biochimica di Lehninger (Zanichelli)
Garrett, Grisham, Principi di biochimica (PICCIN)
Matthews, Van Holde, Ahern, Biochimica (Casa Editrice Ambrosiana)
Baynes J.W., Dominiczak M.H., Biochimica per le discipline biomediche (Elsevier)
Campbell M.K., Farrell S.O., Biochimica 4a ed. (EdiSES)
Text book bioinformatics (one of the following):
Pascarella S., Alessandro P., Bioniformatica (Zanichelli)
Valle G., Helmer Citterich M., Attimonelli M., Pesole G., Introduzione alla bioinformatica (Zanichelli)
Tramontano A., “BIOINFORMATICA” (Zanichelli)
Module “Metabolism” Gianluca Molla: 7 CFU – 56 hours class (Lectures)
Module “Bioinformatisa” Gianluca Molla: 3 CFU – 24 hours class (Lectures)
Module “Tutorials" Gianluca Molla: 1 CFU – 24 hours lab (Tutorials)