CELLULAR BIOCHEMISTRY AND PROTEOMICS-DDP
- Overview
- Assessment methods
- Learning objectives
- Contents
- Full programme
- Bibliography
- Delivery method
- Teaching methods
- Contacts/Info
A solid background in Citology, Biochemistry and Molecular Biology.
The assessment of intended learning outcomes will be made with a final oral exam and it consists of two questions. The first aims at discussing a general cellular biochemistry content (normally the title of a lesson), in order to evaluate the autonomy to organize a scientific discussion, as well as knowledge and understanding. The second question is more specific and focused on a specific molecular pathway or a specific proteomics approach.
A mid-term written exam is planned. This intermediate test is NOT mandatory. It is organized into two questions. The first aims at discussing a general cellular biochemistry content (normally the title of a lesson), in order to evaluate the autonomy to organize a scientific discussion, as well as knowledge and understanding. The second question is more specific and focused on a specific molecular pathway or a specific proteomics approach. The mark should be higher than 18 to be further considered. The student can decide whether to keep the mark obtained (in this case the final oral exam will be only on the second part of the course and the final mark will be an average score of the two exams) or to do the final oral exam, without considering the intermediate test.
In cells every biochemical event or pathway is integrated in a network of reactions, underlying cell functions and integration into tissues. The course aims at clarifying the integration of main cellular components and biochemical reactions and to explore proteomics tools to investigate protein levels, localization and function. Therefore, the course aims at teaching fundamental basic topics, needed for the comprehension of other courses contents.
The main objectives of the course are:
-to understand the mechanisms of biochemical regulation of cell function (cellular biochemistry)
1. To be able to describe the main molecular factors and pathways discussed during lessons (e.g., protein targeting, autophagy, biosignalling)
2. To be able to report about complex cellular mechanisms, by selecting the most important information in scientific literature.
-to acquire knowledge about post-genomic methods in cellular biochemistry (proteomics).
3. To understand how cellular biochemistry can be studied by the mean of proteomics.
4. To be able to use technical terminology.
5. To be able to read and comprehend proteomics literature critically.
6. To apply theoretical knowledge during the lab experience integrated in the course.
CELLULAR BIOCHEMISTRY- 3,5 CFU, 32 HRS
• Introduction to cellular biochemistry. Course objectives and examination modes.
• Protein homeostasis: Protein synthesis. Post-translational translocation. Signal sequences. Intracellular protein trafficking. Quality control. UPS degradation. The secretory pathway. Molecular mechanisms of vesicular trafficking. Coating proteins and clathrin. Proteolytic processing of secreted proteins. Receptor-mediated endocytosis.
• Post-translational modifications. The ability of particular tags to regulate signaling and protein turnover, and to exert dynamic control over protein function in diverse cell biological contexts.
• Membranes and transport. Chemical components of membranes. Peripheral and integral proteins. Lipid rafts. Mechanisms of membrane fusion. Transport processes.
• The mitochondrion. Cell energetics. Mitochondrial biochemistry. Transport towards and across the inner membrane. Glucose and fatty acid metabolism. Biochemistry of the electron transport chain. Calcium ion homeostasis. Apoptosis regulation. Mitophagy. Organelles biosynthesis. Mitochondrial dynamics.
• Autophagy.
• Cytoskeleton. Three kinds of filaments building the cytoskeleton. Actin filaments: polymerization, dynamics, myosins, cell motility. Intermediate filaments: structure and mechanics. Intermediate filament associated proteins. Microtubules: molecular organization and polarization. Proteins regulating microtubule dynamics. Microtubule organization centers. Motor proteins: Kinesins and dyneins. The mitotic apparatus.
• Integration of cells into tissues. Adhesive junctions. Adhesive proteins. Biochemistry of cell junctions: adherent junctions, desmosomes, hemidesmosomes, tight junctions, gap junctions. The basal lamina. Proteins of the extracellular matrix.
• Biosignaling. Characteristics of a transduction system. Molecular mechanisms of signal recognition. Ligand gated ion channels (e.g., the nicotinic receptor, neuronal signaling). Receptors with intrinsic enzyme activity (e.g., glycogen synthesis). G-protein-coupled receptors (e.g., taste and smell transduction). Receptors linked to soluble kinases (e.g., the erythropoietin receptor). Guanylate cyclase activity and NO-synthase activation. Adhesion receptors. Intracellular receptors.
• Response to stress. Oxidative stress. Reactive oxygen species. Enzymatic control of ROS homeostasis. Iron homeostasis. Lipid oxidation. Protein oxidation. Unfolded protein response.
• Hormone regulation and metabolic control. Molecular aspects of hormone action. Peptide hormones. Catecholamines. Eicosanoids. Steroid hormones. Vitamin D. Retinoids. Thyroid hormones. The neuroendocrine system. Metabolic specialization of tissues: liver, muscle, brain and pancreas. The hypothalamus.
PROTEOMICS- 1,5 CFU + 1 CFU+1 CFU (12 HRS THEORETICAL LECTURES+ 16 HRS PRACTICAL ACTIVITIES + 16 HRS PRACTICAL ACTIVITIES FOR DD STUDENTS ONLY)
• Post-genomic methods in cellular biochemistry. The principles of the “a posteriori” hypothesis and the experimental design.
• Integrated Omics: Transcriptomics, Proteomics, Metabolomics.
• Proteomics approaches and technologies: In-gel and off-gel, quantitative analysis, statistical approaches, databases for protein identification. Post-translational modifications proteomics.
• Beyond proteomics. MALDI imaging, MALDI profiling, Metabolomics.
• Journal club: a group activity to read and critically interpret proteomics literature.
CELLULAR BIOCHEMISTRY- 3,5 CFU, 32 HRS
• Introduction to cellular biochemistry. Course objectives and examination modes.
• Protein homeostasis: Protein synthesis. Post-translational translocation. Signal sequences. Intracellular protein trafficking. Quality control. UPS degradation. The secretory pathway. Molecular mechanisms of vesicular trafficking. Coating proteins and clathrin. Proteolytic processing of secreted proteins. Receptor-mediated endocytosis.
• Post-translational modifications. The ability of particular tags to regulate signaling and protein turnover, and to exert dynamic control over protein function in diverse cell biological contexts.
• Membranes and transport. Chemical components of membranes. Peripheral and integral proteins. Lipid rafts. Mechanisms of membrane fusion. Transport processes.
• The mitochondrion. Cell energetics. Mitochondrial biochemistry. Transport towards and across the inner membrane. Glucose and fatty acid metabolism. Biochemistry of the electron transport chain. Calcium ion homeostasis. Apoptosis regulation. Mitophagy. Organelles biosynthesis. Mitochondrial dynamics.
• Autophagy.
• Cytoskeleton. Three kinds of filaments building the cytoskeleton. Actin filaments: polymerization, dynamics, myosins, cell motility. Intermediate filaments: structure and mechanics. Intermediate filament associated proteins. Microtubules: molecular organization and polarization. Proteins regulating microtubule dynamics. Microtubule organization centers. Motor proteins: Kinesins and dyneins. The mitotic apparatus.
• Integration of cells into tissues. Adhesive junctions. Adhesive proteins. Biochemistry of cell junctions: adherent junctions, desmosomes, hemidesmosomes, tight junctions, gap junctions. The basal lamina. Proteins of the extracellular matrix.
• Biosignaling. Characteristics of a transduction system. Molecular mechanisms of signal recognition. Ligand gated ion channels (e.g., the nicotinic receptor, neuronal signaling). Receptors with intrinsic enzyme activity (e.g., glycogen synthesis). G-protein-coupled receptors (e.g., taste and smell transduction). Receptors linked to soluble kinases (e.g., the erythropoietin receptor). Guanylate cyclase activity and NO-synthase activation. Adhesion receptors. Intracellular receptors.
• Response to stress. Oxidative stress. Reactive oxygen species. Enzymatic control of ROS homeostasis. Iron homeostasis. Lipid oxidation. Protein oxidation. Unfolded protein response.
• Hormone regulation and metabolic control. Molecular aspects of hormone action. Peptide hormones. Catecholamines. Eicosanoids. Steroid hormones. Vitamin D. Retinoids. Thyroid hormones. The neuroendocrine system. Metabolic specialization of tissues: liver, muscle, brain and pancreas. The hypothalamus.
PROTEOMICS- 1,5 CFU + 1 CFU+1 CFU (12 HRS THEORETICAL LECTURES+ 16 HRS PRACTICAL ACTIVITIES + 16 HRS PRACTICAL ACTIVITIES FOR DD STUDENTS ONLY)
• Post-genomic methods in cellular biochemistry. The principles of the “a posteriori” hypothesis and the experimental design.
• Integrated Omics: Transcriptomics, Proteomics, Metabolomics.
• Proteomics approaches and technologies: In-gel and off-gel, quantitative analysis, statistical approaches, databases for protein identification. Post-translational modifications proteomics.
• Beyond proteomics. MALDI imaging, MALDI profiling, Metabolomics.
• Journal club: a group activity to read and critically interpret proteomics literature.
All the presentations, reviews, research articles and relevant material will be loaded on the course e-learning platform.
Reference books of cell biology and biochemistry (e.g., Molecular biology of the cell, Lehninger Principles of Biochemistry) should be consulted for basic background knowledge.
Teaching activity consists of theoretical (32+12 hrs) and practical (32 hrs: 16 for all students + 16 for Double Degree students) lectures with hands-on activity. Seminars by experts in the field will be considered for particular topics. A lesson will be structured as a journal club, in order to read and critically interpret proteomics literature. A visit to a proteomics facility is planned, in order to see different technological platforms in the proteomics field.
Office hours and e-mail address: Upon appointment via e-mail, writing at tiziana.alberio@uninsubria.it
Professors
Borrowers
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Degree course in: BIOMEDICAL SCIENCES