Bioinformatics

Module I (First Semester) 1. Definition of life. Darwinian evolution: variation, heredity and fitness. Gene-centered view of evolution: replicators and vehicles. Origin of life: pre-biotic chemistry, RNA world. From molecules to the first cells. Prokaryotes, Eukaryotes. From single cells to multicellular organisms. Mutualistic symbiosis and complexity. Microscopy: light microscopy, fluorescence microscopy, confocal microscopy, electron microscopy. 2. Proteins: structure and functions. Enzymes and biological reactions. Endoergonic and exoergonic reactions. Coupled reactions. Energy carriers: ATP, NADH, NADPH. 3. Bio-membranes: Structural Organization and Functions. Phospholipids and membrane proteins. Principles of membrane transport: active/passive transport, carrier proteins, ion channels, electro-chemical properties of membranes. 4. Energy for cellular activities. Production of ATP. Structure and function of mitochondria. Glycolysis, Krebs cycle, electron transport chain. The mitochondrial ATP synthase, oxidative phosphorylation. Fermentation. Structure and function of Chloroplasts. Photosynthesis: photosystems, light reactions, dark reactions, Calvin cycle. 5. Nucleotides, RNA and DNA structures. DNA replication: replication origins, enzymes, proofreading activity of DNA polymerases. Leading strand and lagging strand. Brief introduction to DNA damage and repair. The cell nucleus and its organization. The nucleolus. Chromatin structure: histones, nucleosomes. Brief introduction to epigenetic modifications. 6. Transcription and translation. RNA transcription in prokaryotes. mRNA transcription and processing in eukaryotes. Brief introduction to splicing. tRNA, rRNA. tRNA activation. The genetic code. Protein synthesis: initiation, elongation and termination. Module II (Second Semester) 7. Regulation of gene expression. Control of transcription in prokaryotes: bacterial operons. Control of transcription in eukaryotes. Post-transcriptional and translational regulation. Non-coding RNAs, microRNAs. 11. Principles of cell signaling: G Protein–Coupled Receptors. Effectors and second messengers. Receptor Tyrosine Kinases, MAP Kinase Pathways. Steroid hormones receptors. 8. The genome and it evolution. Circular DNA and eukaryotic chromosomes. Repetitive DNA. brief introduction to gene duplication, gene families, pseudogenes. 9. Endomembrane system: endoplasmic reticulum, Golgi apparatus. Protein sorting to subcellular compartments. Post-translational modifications: phsphorylation, methylation, acetylation, ubiquitination and glycosylation. Brief introduction to peroxisomes. Endocytic pathways: pinocytosys, endocytosis, phagocytosis. Lysosomes. Autophagy. Exocytic pathways: controlled and costitutive secretion. 10. The cytoskeleton: microtubules, actin filaments, intermediate filaments. Dynamic instability of microtubules, centrosomes, centrioles, flagella and cilia. Prokaryotic flagella. Threadmilling of actin filaments. Vesicle trafficking and motor proteins. Extracellular matrix, connective tissue, epithelia. Epithelial to mesenchimal transition. Cell movements and adhesion. 12. Eukaryotic cell cycle. Cyclin-dependent protein kinases (CdKs). Cell cycle checkpoints. G1, G2, S and M phases of cell cycle. Mitosis. Cytokinesis. Apoptosis: caspases activation through intrinsic and extrinsic signalling. 13. Genetics of cancer. The hallmarks of cancer. Oncogenes and tumor suppressor genes. Gain of function and Loss of function mutations.Ras, p53, retinoblastoma. Somatic evolution in cancer.

Knowledge of basic principles of Chemistry is required

Alberts et al, Essential cell Biology, W.W. Norton.

Taught classes during which the students are encouraged to ask questions or further insights on specific topics. Exercises consisting in the development of simple python scripts to mimic key biological process (e.g. transcription, translation) During covid emergeny lectures will be streamed live on the meet platform. Furhter details are provided on the moodle page of the course

In person. Attendance of classes is optional

During the course the students will be encouraged to undertake informal in itinere assessments (whose results will not be taken into account for the final marks) aiming to help the student in identifying those topics in which their preparation is poor. In itinere assessments will consist in multiple choice questions. The final mark (module I and module II) will be assessed through an oral exam. Exams will start in June (after the end of the lessons of module II) and the dates will be timely published on Infostud website. The oral exam will consist in 3 or 4 questions about the topics listed in the syllabus of the course. Candidates should provide correct and complete answers with an appropriate language. The following criteria (all equally relevant) will be taken into account: 1) correctness and completeness of answers 2) comprehension of the chemical, molecular and evolutionary bases of biological processes 3) ability to put in the cell context biological processes, suggesting connections between different biological processes 4) appropriate language Candidates providing wrong or largely incomplete answers to more than one question will fail the exam. Marks over 25 will be awarded to those attaining a good level according to ALL the four criteria outlined above.

Taught classes during which the students are encouraged to ask questions or further insights on specific topics. Exercises consisting in the development of simple python scripts to mimic key biological process (e.g. transcription, translation) During covid emergeny lectures will be streamed live on the meet platform. Furhter details are provided on the moodle page of the course

1. Definition of life. Darwinian evolution: variation, heritability and fitness. Origin of life: prebiotic chemistry, RNA world. Gene-centered view of evolution: replicators and vehicles. From molecules from the first cells. From single cells to multicellular organisms. The tree of life. The major transitions in evolution: mutualistic symbiosis and complexity 2. Proteins: structure and functions. Enzymes and biological reactions. 3. Bio-membranes: Structural Organization and Functions. Principles of membrane transport: active/passive transport, carrier proteins, ion channels, electrical properties of membranes. 4. Biological order and energy. Energy for cellular activities. Production of ATP. Structure and function of mitochondria. Glycolysis, Krebs cycle, electron transport chain. The mitochondrial ATP synthase. 5. RNA and DNA structures. DNA replication and repair. The cell nucleus: chromatin structure, epigenetic modifications. 6. Transcription and translation. RNA transcription in prokaryotes. RNA transcription and processing in eukaryotes: mRNA, tRNA, rRNA. The genetic code. Protein synthesis: initiation, elongation and termination . 7. Regulation of gene expression. Control of transcription in prokaryotes: bacterial operons. Control of transcription in eukaryotes. Post-transcriptional and translational regulation. Non-coding RNAs, microRNAs. 8. The genome organization in prokaryotic and eukaryotic organisms. Mobile elements. Genome evolution. 9. Endomembrane system: endoplasmic reticulum, Golgi. Protein sorting and glycosylation. Lysosomes. Phagocytosis and Endocytosis. 10. Principles of cell signaling: G Protein–Coupled Receptors. Effectors and second messengers. Receptor Tyrosine Kinases, MAP Kinase Pathways. 11. Eukaryotic cell cycle. Phases of cell cycle. Cyclin-dependent protein kinases (CdKs). Cell cycle checkpoints. S phase. Mitosis. Cytokinesis. Apoptosis. 12. Genetics of cancer. The hallmarks of cancer. Oncogenes and tumor suppressor genes. Somatic evolution in cancer.

Suggested Textbooks: Essential Cell Biology, Fourth Edition. Alberts B. et al. Garland Science.

To pass the exam it is necessary to obtain a mark of not less than 18/30. The student must demonstrate that he/she has acquired sufficient knowledge of topics covered during the course. In order, to achieve a mark of 30/30 with honors, the student must instead prove that he/she has acquired excellent knowledge of all the topics covered during the course, being able to connect them in a logical and consistent way.