BIOCHEMICAL SCIENCES APPLIED TO AGRICULTURAL BIOTECHNOLOGY 1

Module BIOCHIMICA GENERALE

Learning objectives based on the Dublin Descriptors

1. Knowledge and understanding

At the end of the course, the student will be able to:

- describe the molecular basis of biological systems through the study of the main classes of biomolecules;

- understand the relationship between chemical structure and biological function of biomolecules;

- know the fundamental principles of enzymatic catalysis, enzyme kinetics and metabolic regulation;

- understand the organization and integration of the main cellular metabolic processes;

- acquire familiarity with the scientific language of biochemistry.

2. Applying knowledge and understanding

The student will be able to:

- apply biochemical principles to interpret biological and molecular phenomena;

- correlate simple experimental data with the underlying biochemical mechanisms;

- understand the biochemical rationale of basic experimental techniques used in biotechnology;

- analyse and discuss basic experimental results, including those obtained from laboratory activities.

3. Making judgements

The student will be able to:

- critically analyse basic biochemical information and data;

- evaluate the consistency between experimental hypotheses, results and theoretical models;

- recognise the experimental and interpretative limits of the analysed data;

- develop an initial autonomous approach to scientific reasoning.

4. Communication skills

The student will be able to:

- clearly and correctly express concepts of general biochemistry;

- use appropriate scientific language, both in written and oral form;

- concisely describe experimental procedures and laboratory results;

- interact with peers and lecturers in scientific discussion contexts.

5. Learning skills

At the end of the course, the student will have acquired:

- the ability to independently learn progressively more complex biochemical contents;

- an appropriate study method for the analysis of scientific texts and experimental data;

- the foundations required to address subsequent courses in the biotechnological and molecular area.

Laboratory activities

Laboratory activities will contribute to the development of the ability to apply knowledge and independent judgement, enabling the student to:

- acquire familiarity with basic biochemical techniques;

- understand the link between theory and experimental practice;

- critically and consciously interpret experimental data.

Frontal lessons with learning tests at the end of the lesson. Theoretical-practical exercises and/or practical laboratory techniques.

In order to be able to understand and attend the course profitably, it is useful for the student to have a fair knowledge of the basic elements of general and inorganic chemistry, organic chemistry and cellular biology, as well as the basic foundations of general physics.

According to the degree course regulations.

Carbohydrates – Review of structure and function, monosaccharides, disaccharides. Homopolysaccharides and heteropolysaccharides. Glycoconjugates (proteoglycans, glycoproteins, glycolipids). Lipids – Review of structure and function. Storage lipids. Structural lipids. Sterols. Lipoproteins. Nitrogenous compounds: purine and pyrimidine bases and derived compounds. Amino acids – Review of structure and function, titration. Peptide bond and its characteristics. Proteins – Structure and function of proteins. Primary structure. Secondary structures: alpha-helix, beta-sheet. The Ramachandran diagram. Tertiary structure. Quaternary structure. Fibrous proteins. Globular proteins – Haemoproteins involved in the transport of gases (O2, CO2): myoglobin and haemoglobin: structures, function and regulation, degradation and disposal of haem. Haemoproteins involved in redox reactions. Cytochromes. - Biochemical catalysis. – Chemical catalysts and biological catalysts. Enzymes: classification. Coenzymes and vitamins. Michaelis-Menten equation. Km, Vmax, turnover number, Kcat/Km. The double reciprocal graph. Effect of pH and temperature on enzymatic activity. Irreversible inhibition. Reversible inhibition: competitive, non-competitive, incompetitive and mixed. Effect of different types of inhibitors on the double reciprocal graph. Multienzyme complexes. Allosteric regulation of enzymatic activity. Introduction to metabolism: general organization – Concept of metabolic pathways and maps. Degradative pathways (catabolism) and biosynthetic pathways (anabolism). Shuttle systems: metabolic functions and roles. Bioenergetics. Molecules of energy importance, production and use of biochemical energy in the cell. Biochemical roles of NADH and NADPH. General mechanisms of regulation of metabolism - hormonal control, feedback regulation, allosteric enzymes, zymogens, isoenzymes, cascade amplification, compartmentalization, gene regulation. Biochemical reactions of glycolysis - Regulation of glycolysis and regulatory steps. Oxidation of pyruvic acid: the multienzyme complex of pyruvic dehydrogenase and its reaction mechanism. Aerobic and anaerobic glycolysis. Reactions of the citric acid cycle and regulation of the cycle. Degradation of glycogen. Reactions of the pentose phosphate pathway - Oxidative phosphorylation - The mitochondrion as the powerhouse of the cell. Redox potential scales of molecules of biological importance. Machinery for electron transport: structure and functions of mitochondrial complexes. Electrochemical potentials in electron transport and role of oxygen. Reactions of beta-oxidation of fatty acids. Activation and transport in the mitochondrion: acyl-CoA synthetase, carnitine and the acylcarnitine-carnitine transporter. Control and energy yield. Cholesterol metabolism. Ketogenesis. Amino acid metabolism and fate of nitrogenous compounds: ammonia activation, transamination, oxidative deamination, urea cycle. Degradation and recovery of nucleotides. Biosynthetic pathways: glucose and glycogen biosynthesis. Notes on chromatographic separations and spectrophotometry

1) Nelson, M.M.Cox, Principi di Biochimica di Lehninger, Ed. Zanichelli 

2) Matthews, Van Holde et al., Biochimica, Ed. Piccin
3) D. Voet, J.G. Voet, Fondamenti di Biochimica, Ed. Zanichelli4) Campbell & Farrell, Biochimica, EdiSES

5) Garrett e Grisham, Principi di Biochimica, Ed. Piccin

6) Tinti B., Chimica organica – Biochimica – Biotecnologie- 2020, ed. Piccin

7) David Sadava David M. Hillis H. Craig Heller May R. Berenbaum , From Biochemistry to Biotechnology- 2014 Zanichelli

During the course, verification tests will be offered to evaluate progress

At the end of the course the exam will take place with a write and an oral exam.

The following parameters will be taken into account for the attribution of the final grade:

Score 29-30 cum laude: the student has an IN-DEPTH knowledge of the subject, has excellent communication skills and masters the technical-scientific language.

Score 26-28: the student has a GOOD knowledge of the subject and explains the topics clearly using appropriate technical-scientific language;

Score 22-25: the student has a DISCRETE knowledge of the subject, even if limited to the main topics and explains the topics quite clearly with a reasonable command of language;

Score 18-21: the student has the MINIMUM knowledge of the subject and explains the topics clearly enough although the language skills are poorly developed;

Exam not passed: the student DOES NOT HAVE THE MINIMUM KNOWLEDGE required of the main contents of the course. The ability to use specific language is very poor or non-existent and he is not able to apply the acquired knowledge independently.

Examples of questions for the written exam will be provided by the professor to students during the course, during ongoing assessments. The oral exam focuses on all parts of the program in order to verify the student's complete preparation and maturity in managing connections on different biochemical aspects
Examples of questions can be:
- Talk about carbohydrates
- Difference between epimers and enantiomers
- What type of bond is the peptide bond