Teaching code

4S02696

Teacher

Paola Dominici

Credits

8

Also offered in courses:

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

Language

Italian

Scientific Disciplinary Sector (SSD)

BIO/10 - BIOCHEMISTRY

Period

I semestre dal Oct 1, 2020 al Jan 29, 2021.

Lessons timetable Moodle Seminars 0

To show the organization of the course that includes this module, follow this link:  Course organization

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.

Program

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:
The secondary structure: description of helices and folded sheets. Ramachandran's graphs
Globular proteins: tertiary structure and functional diversity
Folding models. Factors determining the secondary and tertiary structure Information and thermodynamics of the survey.
Conformational diseases.
Quaternary structure of proteins
Lipids and membranes: Fatty acids. Triacylglycerols.
Membranes: Fluid mosaic model. Membrane transport
Nucleotides and nucleic acids. DNA and RNA. Properties of nucleotides. Stability and formation of the phosphodiester bond. DNA denaturation and renaturation.
Enzymes: catalytic power, specificity and regulation.
Enzymatic kinetics: Free energy of activation and action of catalysts.
The Michaelis-Menten equation. Steady state assumption. The kinetic parameters. Linear graphic methods.
Enzymatic 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 allosteria. Models for the transition to allosteria in hemoglobin: the symmetrical model and the sequential model. Homotropic and heterotropic effectors.
Bioenergetics. Basic thermodynamic concepts.
Entropy and free energy. The course of a reaction, the variation of 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 energy charge.
The metabolism.
The central metabolic pathways and energy metabolism. Existence of independent degradative and biosynthetic pathways. Oxidations as a source of metabolic energy. Main metabolism control mechanisms.
Glycolysis: General aspects. The importance of coupled reactions in glycolysis. reactions of glycolysis.
The metabolic fates of NADH and pyruvate
The cycle of tricarboxylic acids: The connection phase: the oxidative decarboxylation of pyruvate. The reactions of the cycle. The cycle of TCAs as a source of intermediates for the biosynthetic pathways. Anaplerotic reactions.
Electron transport and oxidative phosphorylation: Reduction potentials. The complexes of the electron transport chain.
The thermodynamic approach to the chemoosmotic coupling hypothesis. ATP synthase. Shuttle systems for the transport of cytosolic NADH into mitochondria.
Gluconeogenesis, glycogen metabolism and hormonal regulation. Hormones and second messengers: cAMP and G.
The beta-oxidation of fatty acids with an equal number of saturated C atoms.
The pentose phosphate pathway: reactions and control.
Nitrogen metabolism: Transamination reactions; Fate of the carbonaceous skeleton of amino acids; fate of the amino group; urea cycle.
NUCLEIC ACIDS: how the structure carries information. Structural levels of nucleic acids (DNA, RNA). DNA denaturation.
TRANSFER OF INFORMATION
DNA replication. Replication enzymology: structure / function of DNA polymerases. DNA replication fidelity.

Examination Methods

The objective of the exam is to verify the level of knowledge and depth of the topics of the course program and the reasoning skills developed by the student. The evaluation is expressed out of thirty (minimum grade 18).

The final exam (written for Bioinformatics students) will focus on all the topics of the program. The student will have to answer a series of open-ended questions, demonstrating that they understand and be able to use the fundamental concepts of each topic.

The final exam (oral for Biotechnology students) will focus on all the topics of the program. The student will have to answer a series of questions, demonstrating that they understand and be able to use the fundamental concepts of each topic.