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CODE 66895
ACADEMIC YEAR 2024/2025
CREDITS
SCIENTIFIC DISCIPLINARY SECTOR BIO/10
LANGUAGE Italian
TEACHING LOCATION
  • GENOVA
SEMESTER 1° Semester
PREREQUISITES
Propedeuticità in ingresso
Per sostenere l'esame di questo insegnamento è necessario aver sostenuto i seguenti esami:
Propedeuticità in uscita
Questo insegnamento è propedeutico per gli insegnamenti:
  • Biotechnology 8756 (coorte 2023/2024)
  • MOLECULAR BIOLOGY 31177
  • Biotechnology 8756 (coorte 2023/2024)
  • BIOINFORMATICS 80793
  • Biotechnology 8756 (coorte 2023/2024)
  • INDUSTRIAL MICROBIOLOGY, BIOTECHNOLOGY OF FERMENTATIONS AND LABORATORY COURSE 80798
TEACHING MATERIALS AULAWEB

OVERVIEW

Biochemistry studies biological processes at the molecular level, such as the structural, functional and regulatory properties of biological macromolecules and the dynamic characteristics of metabolic pathways in living organisms. Biochemistry plays a central role in biotechnology because it provides basic knowledge and study methods to understand and apply biological systems, from the simplest (enzyme) to the most complex (organism), in order to obtain goods and services.

AIMS AND CONTENT

LEARNING OUTCOMES

The aim of the course is to provide the students with detailed knowledge about the main biochemical processes and metabolic control systems  that take place in biological systems, to allow them to understand the cellular and organism responses in physiological conditions and their alterations in some pathological conditions used as models (diabetes, cancer).  The Laboratory module will provide students basic competences about the main biochemical techniques by means of practical experiences in the laboratory.

AIMS AND LEARNING OUTCOMES

At the end of the course, students should:

  • to know in depth the main macromolecules present within living organisms by demonstrating that you understand how chemical and physical properties affect their function;
  • apply the chemical-physical differences of macromolecules for their analysis and separation in laboratory practice;
  •  to recognize the main types of chemical reactions taking place within organisms, to explain their mechanisms and energy variations; to correctly draw the structural formulas of the main metabolic intermediates.
  • to know the mechanisms of catalysis and enzymatic kinetics and be able to apply them in laboratory practice
  • know the cellular bioenergetics and be able to critically analyse differences in different organisms (prokaryotes, animals and plants)
  • to know the main metabolic pathways, their functional significance and regulatory mechanisms
  • apply knowledge gained on general metabolic regulation mechanisms to explain the main differences between animal and plant cells
  • apply this knowledge to explain the cellular and organism responses in mammals in response to the action of hormones, during fasting and the fed state, and their alterations in some pathological states used as models (diabetes, cancer cells)
  • provide examples of biotechnological applications of biochemical processes
  • be able to describe biochemical processes in an appropriate way and with the correct terminology for molecule identification.

PREREQUISITES

Students must have adequate knowledge of general and organic chemistry. The examination of organic chemistry is preparatory to the examination of biochemistry.

TEACHING METHODS

The teaching consists of lectures on general biochemistry subjects by the Profs. Bruzzone and Tonetti, for a total of 64 hours, and part of the theoretical-practical workshop (32 hours).

The theoretical-practical workshop will be held by Prof. Sturla and Piacente, assisted by tutors, at the Biotec Pole. At the beginning of each laboratory activity a short theoretical introduction is provided with the aim of providing the basic principles on which the biochemical methodologies will be based for use in the practical part. In the practical part, students, divided into groups of two or three and with the support of teachers and tutors, will have to apply the experimental protocol provided, applying the methods described. The organization and dates of the laboratory activities will be communicated directly by the teacher at the beginning of the lessons.

Any Student with documented Specific Learning Disorders (SLD), or with any special needs, should contact the Lecturer(s) and to the dedicated SLD Representative in the Department before class begins, in order to liaise and arrange the specific teaching methods so that the learning aims and outcomes may be met.

SYLLABUS/CONTENT

General biochemistry

  • Part 1: The molecules of life

1. Reaction rate and reaction equilibrium. Energy of chemical reactions
2. Organic functional groups and their reactivity in biological systems
3. Major carbohydrates and lipids in biological systems
4. Amino acids: structure and reactivity
5. Peptides and peptide bond: binding characteristics
6. Proteins: primary, secondary, tertiary, quaternary structure
7. Proteins: classification and functions. Conjugated proteins: hemoglobin
8. Biological catalysts (enzymes): catalysis and classification mechanisms; enzymatic coenzymes and cofactors; enzymatic kinetics; enzymatic inhibition.

  • Part 2: Metabolism and the main metabolic pathways

1. Metabolism and bioenergetics: ATP, high-energy compounds, biological oxidoreduction reactions
2. General principles of enzyme control and metabolic pathway regulation. The role of allosteric enzymes in limiting stages of metabolic pathways. Reversible covalent modifications (phosphorylation/dephosphorylation)
3. Carbohydrate metabolism:
a. Glycolysis: functional role, reactions (with formulas) and regulation; aerobic and anaerobic glycolysis;
b. Gluconeogenesis: functional role, reactions (with formulas) and regulation; F2,6BP’s role in glycolysis/gluconeogenesis regulation;
c. Glycogen metabolism: pathways of synthesis and degradation, functional role and regulation; other polysaccharides of biological interest: starch, cellulose and peptidoglycan (notes);
d. Pentose phosphate cycle: reactions (with formulas), functional role and regulation; reactive oxygen species and mechanisms of defence against oxidative stress and genetic defect of G6PD; use of fructose and galactose
4. Pyruvate dehydrogenase: role and enzymatic mechanism (with formulas). Alcoholic fermentation.
5. Citric acid cycle: functional role, reactions (with formulas) and regulation
6. Oxidative phosphorylation: standard reduction potentials, Δ e and Δ g, proton gradient, structure and function of respiratory chain complexes, ATP-synthase, mitochondrial thermogenesis.
7. Lipid metabolism:
a. triglycerides, digestion and absorption, transport through lipoproteins; lipolysis in adipose tissue
b. fatty acid activation and transport to mitochondria; oxidation of fatty acids, functional role, reactions (with formulas) and regulation; degradation of unsaturated and C-chain fatty acids (C-chain);

 c. fatty acid synthesis: relationships between mitochondria and cytosol, synthesis reactions (with formulas), regulation;
 d. cholesterol synthesis and regulation (hints); cholesterol as a precursor for other molecules;
 e. synthesis of glycerophospholipids, phospholipase and their role in the generation of signal molecules; cyclooxygenases and eicosanoid synthesis (notes)

8. Ketone bodies: functional role, synthesis reactions (with formulas) and systems of use in peripheral tissues.
9. Amino acid metabolism:

    a. metabolic fate of amino, transaminase and glutamic dehydrogenase groups (with formulas);
    b. the transport of amino groups to the liver: glutamine and alanine-pyruvate cycle (reactions with formulas);
    c. urea cycle

10. Nucleotide metabolism:

    a. De novo and recovery synthesis of purine and pyrimidine nucleotides; the formation of diphosphate and triphosphate nucleotides;
    b. Degradation of purines and uric acid (notes);
    c. Deoxyribonucleotide formation: ribonucleotide reductase, thymidylate synthase;
    d. Folate cycle; SAM cycle
    e. Metabolism of dinucleotide coenzymes
    f. Nucleotide metabolism for therapeutic and biotechnological applications (TS and DHFR inhibitors, antiviral drugs, dUTPasis of bacteria, DHFR as selection marker)

11. Plant biochemistry: photosynthesis in prokaryotes and higher plants, the Rubisco and Calvin cycle; systems of enzymatic regulation by light; C3 and C4 plants (cenni); glioxalate cycle; major metabolic differences between animal and plant cells.

  • Part 3: Hormone regulation and metabolism integration in mammals

    1. Biosignaling and general signal transduction characteristics
    2. Receptors and mechanism of action of insulin, glucagon, adrenaline, steroid hormones
    3. Hormonal control of metabolism: effects of insulin, glucagon, steroid hormones, adipose tissue hormones; control of blood glucose, fasting and feeding status
    4. Metabolic organ interactions

  • Theoretical and practical workshop

   1. Calculation of concentrations (molarity, normality, percentages), dilutions, pH calculation, use of analytical balance, preparation of solutions.
   2. Separation of particles and molecules: centrifugation, ultrafiltration, dialysis, precipitation, extraction techniques.
   3. Spectrophotometry and spectrofluorimetry: basic principles and applications.
   4. Spectrophotometric assays of DNA and proteins.
   5. Enzymatic assays. Determination of the concentration of compounds by enzymatic tests.
   6. Purification of recombinant proteins by affinity chromatography.
   7. Protein electrophoresis: techniques and applications. Western blot: techniques and application.

RECOMMENDED READING/BIBLIOGRAPHY

All the slides used during the lessons and other teaching material will be available on Aulaweb. In general, the notes taken during the lessons and the material on Aulaweb are sufficient for the preparation of the exam.

The books below are suggested as supporting texts, but students may also use other university-level biochemistry texts, provided they are editions published in the last 5 years.

Nelson D.L., Cox M.M. - Introduzione alla biochimica di Lehninger. Zanichelli (Nelson-Cox copies are available for consultation at the Library of Medical and Pharmaceutical Sciences).

Appling et al. - Biochimica, molecole e metabolismo. Pearson.

Tymoczko J., Berg J., Stryer L. - Principi di Biochimica. Zanichelli.

TEACHERS AND EXAM BOARD

LESSONS

LESSONS START

I semester, in October.

EXAMS

EXAM DESCRIPTION

The examination consists of two written tests.

The first paper is related to the topics of the theoretical-practical workshop: it consists of a test with single answer questions, calculation exercises and problems.. Examples of problems and exercises will be provided during the workshop. The written text relating to the theoretical and practical workshop must be written before the second written test and may be supported either in previous appeals or in the same appeal in which the student intends to support the second written text. The result of the written test of the theoretical and practical laboratory will be considered valid only until the first call of the winter session of the following a.a. (first call of the winter session 2024 for the AA 2022/23). After this date, the student must take the examination again.

To take the second written test on general biochemistry students must have passed the written test with a minimum grade of 18/30. A multiple-choice test with 21 questions (max 21 points) and an open question will be proposed in which it will be asked to explain a metabolic pathway, including the formulas of the compounds (max 11 points).

The final grade will take into account the average of the evaluations obtained in the two written tests, weighted on the number of CFU (8 CFU General Biochemistry - 2 CFU Theoretical-practical Laboratory).

Three examination appeals will be available for the winter session (mid-January to February) and four for the summer session (June, July and September). No extraordinary appeals will be granted outside the periods indicated in the Course Regulations, except for students out of course.
 

ASSESSMENT METHODS

Details on how to prepare for the exam and how in-depth each topic will be provided during the lessons.

The written examination of the theoretical-practical laboratory will verify the actual acquisition of basic knowledge on some biochemical methodologies and their applications for the analysis, identification and separation of the main biomolecules.  The student should be able to link and integrate the knowledge acquired during the laboratory activities with that provided during the lectures. The problems will allow an assessment of the ability to use knowledge in practical situations that may occur in the laboratory, including with reference to safety measures and good laboratory practice.

The written examination in general biochemistry will cover the subjects covered during the lectures and will aim to assess not only whether the student has reached an adequate level of knowledge, If you have acquired the ability to critically analyse biochemical problems that will be posed during the examination. The student will also be asked to draw the biomolecules structure formulas and metabolic intermediates, identifying the types of reaction involved and the resulting energy variations. The student will also have to demonstrate that he or she has acquired the ability to describe biochemical processes in a clear and correct terminology. 

Exam schedule

Data appello Orario Luogo Degree type Note
17/01/2025 09:00 GENOVA Laboratorio
31/01/2025 09:00 GENOVA Laboratorio
21/02/2025 09:00 GENOVA Laboratorio
16/06/2025 09:00 GENOVA Laboratorio
18/07/2025 09:00 GENOVA Laboratorio
19/09/2025 09:00 GENOVA Laboratorio