00061 - Biochemistry

Learning outcomes

At the end of the course, the student will have knowledge of: biological processes at the molecular level; structure-function relationships of biomolecules, with particular focus on proteins; energy metabolism; an integrated view of signaling pathways and major metabolic processes; the fundamentals of structural biochemistry and enzymology; the main spectrophotometric methods for protein quantification; electrophoretic separation techniques and protein identification methods; the use of experimental protocols for calculating enzyme specific activity. Upon completion of the laboratory component, the student will also be able to critically evaluate the results obtained by preparing a report on the experiments performed.

Course contents

Module 1 (6 ECTS) BIOCHEMISTRY-Concettina Cappadone)

PROTEIN FUNCTION-Oxygen-binding proteins: haemoglobin and myoglobin. Structure of the heme group. Oxygen saturation curves and cooperativity. Allosteric effectors.

ENZYMES- Classification, structure, and general properties of enzymes. Cofactors and coenzymes. Activation energy. Mechanisms of enzyme catalysis. Enzyme kinetics. The Michaelis–Menten equation and double-reciprocal plots. Effects of pH and temperature on enzyme activity. Inhibition of enzyme activity: reversible and irreversible inhibition. Regulation of enzyme activity: allosteric enzymes, positive and negative modulators, reversible covalent modifications, zymogens, and isoenzymes.

CELL SIGNALLING-General features of signal transduction. G protein-coupled receptors and second messengers; receptors with tyrosine kinase activity and phosphorylation cascade mechanisms.

BIOENERGETICS AND METABOLISM- Thermodynamics and spontaneity of metabolic processes. Definition and biological significance of free energy; relationship between free energy, entropy, enthalpy, and the equilibrium constant. Mechanisms of energy transfer: coupled reactions. High-energy biological molecules: high-energy phosphorylated compounds and reduced nucleotides. ATP and phosphoryl-group transfer potential.

General organisation and compartmentalisation of metabolic pathways. Catabolism and anabolism. Definition of the committed step in a metabolic pathway, regulatory mechanisms, and the role of ATP in the thermodynamic feasibility of metabolic pathways. Directionality of metabolic pathways and regulation of metabolic flux.

CARBOHYDRATE METABOLISM- Glycolysis: reactions and regulation. Fate of pyruvate under aerobic and anaerobic conditions. Gluconeogenesis: substrates and reactions. Coordinated regulation of glycolysis and gluconeogenesis. Glucose oxidation through the pentose phosphate pathway. Glycogen metabolism: glycogen breakdown and synthesis. Coordinated regulation of glycogenolysis and glycogen synthesis.

THE CITRIC ACID CYCLE- Acetyl-coenzyme A production. The pyruvate dehydrogenase complex and its five cofactors. Regulatory mechanisms of pyruvate dehydrogenase. The citric acid cycle: reactions, regulatory mechanisms, and connections with other metabolic pathways, including the role of anaplerotic reactions.

LIPID METABOLISM- Digestion, mobilisation, and transport of fatty acids. Fatty acid catabolism: β-oxidation reactions and regulation. Formation and utilisation of ketone bodies. Fatty acid biosynthesis: reactions and regulation. Fatty acid elongation and desaturation. Overview of triglyceride and phospholipid biosynthesis. Cholesterol, steroids, and isoprenoids: biosynthesis, regulation, and transport.

OXIDATIVE PHOSPHORYLATION
Electron transport and oxidative phosphorylation: three-dimensional structure of electron carriers in the mitochondrial respiratory chain. ATP synthesis: role of the transmembrane proton gradient in ATP synthesis. Structure of ATP synthase. Regulation of oxidative phosphorylation: cellular energy demand and the role of uncoupling agents in thermogenesis.

AMINO ACID DEGRADATION AND UREA PRODUCTION
Metabolic fate of amino groups: transamination and oxidative deamination reactions. The urea cycle: cellular localisation of cycle reactions and connections between the urea cycle and the citric acid cycle.

Module 2 (2 ECTS credits) – BIOCHEMISTRY LABORATORY- Concettina Cappadone (Group A)

Module 3 (2 ECTS credits) – BIOCHEMISTRY LABORATORY- Laura Giusti (group B)

The 2 ECTS credits of the Biochemistry Laboratory module are integrated into the educational activities of the Biochemistry course. The laboratory is designed to provide students with the theoretical and practical foundations for studying enzymes and applying key biochemical methods to the analysis of cellular samples.

Students will learn how to determine the protein content of a cell lysate, calculate the specific activity of an enzyme, and assess the main parameters of enzyme kinetics. The effects of pH and substrate specificity on enzyme activity will also be investigated. Spectrophotometric and colorimetric methods for the study of biological molecules will be applied.

The laboratory activities include:

1. Determination of the protein content of a cellular extract using the Bradford method.
2. Determination of the specific activity of lactate dehydrogenase (LDH) in a muscle cell extract.
3. Determination of the kinetic parameters Km and Vmax of alkaline phosphatase.
4. Analysis of the effects of pH and substrate specificity on trypsin activity.
5. Experimental determination of the molar extinction coefficient of NADPH through analysis of the reaction catalysed by glucose-6-phosphate dehydrogenase.
6. Identification of reducing and non-reducing sugars using Fehling’s method.

At the end of the laboratory activities, a session will be devoted to the analysis of the data collected, both individually and in groups. The principles and format of scientific report writing will be discussed on the basis of the experimental results obtained. In addition to practical activities, short theoretical lectures will address protein extraction from biological samples, electrophoresis, and UV–Vis absorption spectroscopy.

Readings/Bibliography

1. Nelson, D. L., & Cox, M. M. (2021). I principi di Biochimica di Lehninger (VIII ed.). Zanichelli Editore.

2. Berg, J. M., Tymoczko, J. L., & Stryer, L. (2020). Biochimica (VIII ed.). Zanichelli Editore.

3. Appling, D. R., Anthony-Cahill, S. J., & Mathews, C. K. (2021). Biochimica. Molecole e metabolismo. Pearson Editore.

Laboratory Materials:

Students will be provided with handouts detailing the procedures for each individual experiment. All materials used during the theoretical lessons will also be made available. No specific textbook is required.

Teaching methods

Module 1: Lectures 
Module 2: Individual laboratory work and group data analysis. Attendance in the laboratory is mandatory.

 

 

"Given the nature of the activities and the teaching methods adopted, participation in this learning activity requires all students enrolled in Modules 1 and 2 to complete the e-learning course on safety and health in study and training environments [https://www.unibo.it/en/services-and-opportunities/health-and-assistance/health-and-safety/health-and-safety-in-study-and-training-places ]. Additionally, students must attend Module 3, a specific training course on safety and health in study environments. Information regarding the dates and attendance procedures for Module 3 is available in the dedicated section of the degree program website."

Assessment methods

The final assessment aims to evaluate the achievement of the following learning objectives:

Module 1 – Biochemistry

• Understanding the structure and function of the main biological macromolecules and the fundamental principles of enzymology.
• Understanding cellular bioenergetics, major metabolic pathways, and the underlying mechanisms of their regulation and signal transduction.
• Understanding the basic molecular mechanisms of living systems and the molecular logic behind their regulation.

Module 2 – Biochemistry Laboratory

• Knowledge of the main methods for protein quantification.
• Knowledge of experimental methods for evaluating enzyme activity.

 

The examination includes:

• A report on the laboratory activities of Module 2/3.
• An oral examination to assess Module 1 (Biochemistry).

The oral exam consists of three questions aimed at verifying the student’s theoretical understanding of the structure and function of biological macromolecules, metabolism, and its regulation.

Throughout the laboratory activities, students will be guided by the instructors of both modules and supported by tutors. Continuous interaction will be encouraged to clarify the analytical approach and individual experiments. To pass the laboratory module, students must submit a report based on the format presented during the final lab session. The final grade, expressed on a 30-point scale, will be the weighted average of the grades obtained in the two modules.

With regard to assessment, the use of artificial intelligence is prohibited. Any use of AI constitutes a violation of academic integrity.

Students with learning disorders and\or temporary or permanent disabilities: please, contact the office responsible (https://site.unibo.it/studenti-con-disabilita-e-dsa/en/for-students) as soon as possible so that they can propose acceptable adjustments. The request for adaptation must be submitted in advance (15 days before the exam date) to the lecturer, who will assess the appropriateness of the adjustments, taking into account the teaching objectives.

Teaching tools

Module 1: PowerPoint presentations.

Module 2: Practical laboratory equipped with spectrophotometers, thermostatic water baths, electrophoresis cells, and optical microscopes. Computer lab with individual workstations.

 

 

Office hours

See the website of Concettina Cappadone

See the website of Laura Giusti