00061 - Biochemistry

Learning outcomes

At the end of the course, the student will show appreciation of general and metabolic biochemistry and will be able to apply some basic techniques of biochemistry.  In particular, the student will appreciate structure and function of the main biochemical molecules (sugars, proteins, lipids and nucleic acids), metabolic pathways of animal eukaryotic cells and their regulation. The student will acquire knowledge of the fundamental and unifying elements of metabolism and the integrated regulation of the various metabolic pathways.

Course contents

Lectures

1. MAIN BIOMOLECULES

1.1. Aminoacids and proteins: Structure and properties of amino acids, formula and nomenclature; structure, stability and formation of the peptide bond. Primary, secondary, tertiary and quaternary structure of proteins; introduction to prediction of protein structure.

1.2. Lipids and biological membranes: Saturated and unsaturated fatty acids, triglycerides (formula, properties and nomenclature), phospholipids and sphingolipids, cholesterol. Structure, composition and properties of biological membranes. Membrane proteins and lipid anchors. Lipids rafts.

1.3. Methods in protein analysis: the proteome, protein purification: subcellular fractionation, centrifugation, chromatographic techniques, electrophoresis, western blot, ELISA.

2. STRUCTURE AND FUNCTION OF PROTEINS

2.1. Myoglobin and hemoglobin: structure of heme, myoglobin and hemoglobin, oxygen binding, saturation curves,emoglobin S and sickle cell anemia

2.2. Enzymes: proteins as molecular catalysts, chemical reaction rates and the effects of catalysts, transition states, the enzyme-substrate complex, some general catalytic mechanisms. Introduction to kinetics of enzymatic catalysis: the Michaelis-Menten analysis, the significance of Km and Vmax. Rearrangement of Michaelis-Menten equation (Lineweaver-Burk plot). Enzyme inhibition: reversible and irreversible inhibition, competitive, non competitive and acompetitive inhibitors.

3. SIGNAL TRANSDUCTION PATHWAYS

3.1. Signalling strategies, first messengers, intracellular and membrane receptors. Membrane receptors types:

3.2. Intracellular receptors: structure and mechanisms

3.3. 7TM receptors: structure and examples; G proteins: activation/deactivation; effector systems: adenylate cyclase and phospholipase C; second messengers (cAMP, IP3, DAG e calcio), protein chinases and phosphatases, calcium binding proteins

Receptor with tyrosine kinase activity and SH2 domain-mediated signalling, Grb2, Ras and MAP kinases. Epidermal Growth Factor receptor signalling as a model for this class.

4. ENERGY CONVERSIONS AND BIOSYNTHESIS

4.1 Basic principles of metabolism: general aspects, anabolism and catabolism, coupled reactions, high energy compounds. The nucleotide. ATP and its peculiar chemical characteristics and other compounds with a high potential for phosphate group transfer. NADH and FADH2. Notes on vitamins and the main coenzymes that are involved in the metabolic pathways.

4.2. Glycolysis: general information; reactions of the glycolytic pathway with formulas, metabolic fate of pyruvate in the absence and presence of oxygen: alcoholic and lactic fermentation, transport into mitochondria and oxidation; regulation of glycolysis.

4.3. Citrate cycle: pyruvate dehydrogenase complex: structure, coenzymes and regulation. Overview of the reactions of the TCA cycle with formulas, regulation, energy yield. Anaplerotic reactions.

4.4. Oxidative phosphorylation: electron transport and ATP synthesis Ultrastructure of mitochondria; redox potentials of the components of the complexes, structure and function of the respiratory chain complexes (complexes I, II, III, CIV). ATP synthase or V complex: structure of the F1 and FO portions; main subunits and catalytic cycle. Inner membrane transporters, shuttle systems for reducing equivalent transport in mitochondria. Energy balance, inhibitors of complexes, decoupling.

4.5. Gluconeogenesis: pyruvate carboxylase; reactions with gluconeogenesis formulas; coordinated regulation of gluconeogenesis and glycolysis. Cori cycle. Synthesis and demolition of glycogen, glycogen phosphorylase: structure and regulation in muscle and liver.

4.6. Pentose-phosphate pathway: oxidative phase and non-oxidative phase: reactions with formulas. Adjustment. Production of NADPH by the biosynthetic pathways and glutathione.

4.7. Lipid metabolism: Catabolism: hydrolysis of triglycerides in animals; activation, transport (CPT I and CPTII) and oxidation of fatty acids in the mitochondrial matrix. The ketone bodies; synthesis and use. Biosynthesis of fatty acids: reactions and role of citrate, elongation; biosynthesis of complex lipids: biosynthesis of cholesterol.

4.8. Amino acid metabolism: digestion and absorption of proteins. Degradation of amino acids: fate of the amino group, urea cycle, relationship between urea cycle and TCA cycle.

Laboratory (1CFU)

The final part of the course (1 CFU) will be dedicated to carrying out laboratory activities for quantifying proteins using a microplate assay. There will also be an introductory bioinformatics session to proteome analysis. 

 

Readings/Bibliography

Introduction to Lehninger's Biochemistry. D. L. Nelson, M. M. Cox, sixth Italian edition, 2018, Zanichelli

Biochemistry. M. K. Campbell, S. O. Farrell, O. M. McDugal. Fifth edition, 2019, EdiSES

Biochemistry. J. M. Berg, J. L. Tymoczko, L. Stryer, 7th edition, 2012, Zanichelli

Principles of Biochemistry. TO THE. Lehninger, D.L. Nelson, M.M. Cox. 2009 Zanichelli

Fundamentals of Biochemistry. D.Voet, J.Voet, C.W. Pratt. 2013 Zanichelli.

Biochemistry. Molecules and metabolism. D.R. Appling, S.J Antony-Cahaill, C.K. Mathews. 2017 Pearson.

The lecturer will provide the PDF files of the slides projected in class through the virtual space of the course. The material provided is for personal use only. The slides are notes (titles, keywords) or illustrations and do not replace texts or other learning material (articles, websites, videos) that students are invited to consult for an in-depth study of the topics and their appreciation independently.

 

Teaching methods

During the lectures, the structure and function of the main molecules of biological interest are illustrated and discussed in detail and the main metabolic pathways and their integration analyzed. In some cases directions are provided for independent study of some topics and their application. The course is accompanied by a module of practical exercises in the laboratory.

 

Assessment methods

Evaluation To take the exam it is necessary to register on Almaesami, in compliance with the established deadlines. The assessment test is written.

The written exam includes:

Part A: QUIZ

- Questions: prevalence of multiple choice questions, but also short answer questions, short exercises (the relationship between these types of questions may vary with the same difficulty of the QUIZ);

- Topics: all the topics covered in class and during the experimental laboratory;

- Allotted time: 60 minutes

Part B: Open question

- The proposed topics concern metabolic pathways and require: (i) detailed description of relevant biochemical reactions; (ii) appreciation (in-depth knowledge of the subject).

- Allotted time: 30 minutes

 

Teaching tools

Powerpoint presentations.

Office hours

See the website of Elisabetta Verderio