Teaching code

4S02696

Credits

12

Coordinator

Paola Dominici

Language

Italian

Also offered in courses:

• Introduction to biochemistry of the course Bachelor's degree in Bioinformatics

Moodle Seminars 0

The teaching is organized as follows:

Learning outcomes

Biochemistry is a branch of life sciences which deals with the study of chemical reactions and their organization in living cells and organisms. It takes into account the studies related to the nature of the chemical constituents of living matter, their transformations in biological systems and the energy changes associated with these transformations. Students will be guided through the course to understand the relationships between structure and function of macromolecules, and the regulatory strategies, with particular focus on metabolic pathways. The experimental activities are aimed at understanding the rationale behind the basic biochemical protocols developed to investigate the macromolecules and their functions. Pratical knowledge of basic biochemical techniques by means of lessons and experiments. Students will gain a thorough competence on the main technique used in biochemistry labs, in particular they will learn isolation, identification and structure- function relationship of macromolecules, with a focus on proteins.

Program

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MM: BIOCHIMICA
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The properties that characterize living systems
Biological molecules: Hierarchy among biological molecules: simple molecules as units of complex structures
Water, pH and ionic balances
Amino acids. Acid-base properties of amino acids.
Proteins: biological functions and primary structure
Peptide bond. Architecture of protein molecules
The three-dimensional structure of proteins:
Secondary structure: description of helices and folded sheets. Ramachandran's graphs
Globular proteins: tertiary structure and functional diversity
Folding models. Factors determining secondary and tertiary structure Information and sensing thermodynamics.
Conformational diseases.
Quaternary structure of proteins
Enzymes: Catalytic power, specificity and regulation.
Enzyme kinetics: Free energy of activation and action of catalysts.
The Michaelis-Menten equation. Steady state assumption. The kinetic parameters. Linear graphical methods.
Enzyme inhibition: irreversible and reversible. Competitive and non-competitive.
Control mechanisms of enzymatic activity.
Oxygen transport and storage: the role of hemoglobin and myoglobin. Structure-function relationship of Mb and Hb
Hemoglobin: cooperative binding and allostery. Models for the allosteric transition in hemoglobin: the symmetric model and the sequential model. Homotropic and heterotropic effectors.
Bioenergetics. Basic thermodynamic concepts.
Entropy and free energy. The progress of a reaction, the change in standard free energy. Effect of pH and cancentration on standard free energies.
The importance of coupled processes in living systems.
ATP and high energy compounds: group transfer potential. The energetic charge.
Metabolism:
Central metabolic pathways and energy metabolism. Existence of independent degradative and biosynthetic pathways. Oxidations as a source of metabolic energy. Main mechanisms of metabolism control.
Glycolysis: General aspects. The importance of coupled reactions in glycolysis, reactions of glycolysis. The metabolic fates of NADH and pyruvate
The tricarboxylic acid cycle: The linking phase: the oxidative decarboxylation of pyruvate. The reactions of the cycle. The TCA cycle as a source of intermediates for biosynthetic pathways. Anaplerotic reactions.
Electron transport and oxidative phosphorylation: Reduction potentials. The complexes of the electron transport chain.
The thermodynamic approach to the chemiosmotic coupling hypothesis. ATP synthase. Shuttle systems for the transport of cytosolic NADH into the mitochondria.
Gluconeogenesis, glycogen metabolism and hormonal regulation. Hormones and second messengers: cAMP and G proteins.
The beta-oxidation of fatty acids with an equal number of saturated and monounsaturated C atoms.
The pentose phosphate pathway: reactions and control.
Nitrogen metabolism: Transamination reactions; Fate of the carbon skeleton of amino acids; fate of the amino group; urea cycle.
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MM: BIOCHIMICA ANALITICA
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Protein purification Ionic properties of amino acids and proteins. Isoelectric point. Sample preparation. Methods of cell disruption and production of the initial crude extracts. Protein solubilization methods. Saline swabs. Fractionation and precipitation techniques. Filtration, dialysis, sample concentration. Spectroscopic techniques. Properties of electromagnetic radiation. Light-matter interaction. States and processes involved in the phenomena of absorption, emission and decay. Absorption spectroscopy in ultraviolet and visible. Qualitative and quantitative aspects of light absorption. Colorimetric and spectroscopic methods applied to the determination of protein concentration. Spectrophotometers. Fluorescence and emission spectroscopy. Intrinsic and extrinsic fluorophores. Green fluorescent protein Spectrofluorimeters. Fluorescence resonance energy transfer (FRET). Circular dichroism. Chromatographic techniques. Principles of chromatography. The chromatogram. Parameters that determine the chromatographic performance. Van Deemter equation. Column chromatography: ion exchange, molecular exclusion, affinity, hydrophobic interaction and their applications. Purification of fusion proteins with Electrophoretic techniques. General principles and electrophoretic mobility. Support materials. Nucleic acid electrophoresis. Protein electrophoresis. SDS PAGE. Electrophoresis in native conditions. Protein coloring on gel. Protein blotting (western blotting). Isoelectrofocusing. Basics of: Capillary electrophoresis. Two-dimensional electrophoresis gel.

Bibliography

Examination Methods

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MM: BIOCHIMICA
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The final (oral) exam is divided into three questions on any topic covered in class
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MM: BIOCHIMICA ANALITICA
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The final (written) exam will focus on all the topics of the program. The student will have to demonstrate that they understand and be able to use the fundamental concepts of each topic.