Ateneo - UPO

Protein structure:·               Structure-function relationship in protein classes.·               Transporter proteins.·               Enzymes. Enzyme kinetics:·               Reaction speed.·               Regulatory mechanisms.·               Vitamins and cofactors.Signal Transduction:·               Classes of receptors.·               Signaling mechanisms. ·               Second messengers.Bioenergetics. Introduction to metabolism.Cellular respiration.

BIBLIOGRAPHY/STUDY MATERIALS Biochemistry with medical approach: • La Biochimica di Thomas M. Devlin di D' Andrea - Altieri - Baldanzi - Borriello - Devlin - AAVV 2023 Biochimica con taglio più generale: • David L Nelson Michael M Cox, I principi di biochimica di Lehninger. Ottava edizione italiana a cura di Edon Melloni 2022 (Esistono anche varie versioni riassunte e quindi non completissime quali «introduzione alla biochimica di Lehninger» stessi autori) • Jeremy M Berg John L Tymoczko Gregory J. Gatto Lubert Stryer, Biochimica. Ottava edizione italiana condotta sulla nona edizione americana 2020 AAVV Biochimica. Edi ERMES Per integrare: • Bruce Alberts, Rebecca Heald, Alexander Johnson. Biologia molecolare della cellula. Zanichelli, edizione 7° del 2025. Biochemistry with medical approach: • La Biochimica di Thomas M. Devlin di D' Andrea - Altieri - Baldanzi - Borriello - Devlin - AAVV 2023 Biochemistry with a more general approach: • David L Nelson Michael M Cox, I principi di biochimica di Lehninger. Ottava edizione italiana a cura di Edon Melloni 2022 (Esistono anche varie versioni riassunte e quindi non completissime quali «introduzione alla biochimica di Lehninger» stessi autori) • Jeremy M Berg John L Tymoczko Gregory J. Gatto Lubert Stryer, Biochimica. Ottava edizione italiana condotta sulla nona edizione americana 2020 AAVV Biochimica. Edi ERMES To integrate: • Bruce Alberts, Rebecca Heald, Alexander Johnson. Biologia molecolare della cellula. Zanichelli, edizione 7° del 2025

Knowledge and understanding.
At the end of the course the student will be able to:
• describe the structure of biological matter in molecular terms,
• define the structure-function relationship of biological macromolecules, in particular transporter proteins or proteins with enzymatic activity,
• describe the mechanisms of receptor-mediated signaling and intra-cellular signaling pathways,
• describe the organization of metabolism and the basics of bioenergetics with particular attention to the role of oxidative phosphorylation.

Ability to apply knowledge and understanding
At the end of the course the student will be able to:
• recognize the role of structure on the functionality of macromolecules,
• apply a molecular approach to physiology and pathology,
• discuss the functional role of receptors, second messengers and proteins involved in signal transduction,
• describe the organization of metabolism and related energy flows.

Making judgements
At the end of the course the student will be able to:
• critically evaluate information,
• formulate informed opinions,
• make autonomous decisions.

Communication skills:
At the end of the course the student will be able to:
• clearly and effectively express their information and knowledge

Learning skills
At the end of the course the student will be able to:
• learning autonomously and continuously,
• update their skills and knowledge.

Attended chemistry, physics and cell biology courses. Knowledge of the structure and reactivity of the main biological compounds (sugars, lipids, proteins, nucleic acids). Anatomy basics (structure and function of major human body systems). Principles of thermodynamics.

This module includes:- lectures with slide shows,- experimental simulations,- interactive multimedia materials (generally on DIR)
with online self-assessment tests,- some scientific articles,- student-led dissertations.
To prepare for the exam, students must use the textbooks and recommended readings to supplement the
materials provided by the instructor (PDF copies of the slides shown in class and any handouts that
explore the topics covered in the course).
PDF copies of the slides shown, additional material, and all information regarding the course and exam
procedures will be made available on the DIR (https://www.dir.uniupo.it/).
Ongoing learning will be monitored through group discussions of the syllabus topics and numerical
exercises proposed during the lectures. The DIR section also contains materials for students to assess
their initial preparation and ongoing learning. Discussion and study assignments for the topics covered
in the course are available. Tests with open-ended and multiple-choice questions and numerical
exercises are also available to assess student progress.

Students with physical disabilities, Learning Disabilities or Special Education Needs can request specific services and tools via the Staff Sviluppo e Coordinamento Carriere e Servizi alle Studentesse e agli Studenti, consulting the University webpage: https://www.uniupo.it/en/services/services-students-physical-or-learning-disabilities. Students with disabilities, learning disabilities or special education needs, once they have contacted the University Staff, can refer to the tutor in charge of the course to define the examination modalities, concerning academic aspects.

Numerous ongoing self-assessment tests are planned.
There will be a final written exam with multiple-choice answers on a computer, possibly with one or
more open-ended questions. The written exam questions include multiple-choice tests, molecular
structures, numerical exercises, and open-ended questions, covering all topics covered in the course
syllabus. Answers to the open-ended questions will be judged for both content and appropriate
language. Question scores are indicated in the assignment.
The final grade is calculated as a percentage of correct answers/total questions and may be
supplemented by any research and guided discussion activities undertaken by students during the course
and the results obtained in the DIR activities.
The test is designed to assess the student's level of knowledge and understanding of the course syllabus
topics and their developed reasoning skills.
The Biochemistry 1 interim exam results in a grade that remains valid until December of the current
academic year and allows students to proceed to the oral exam for Biochemistry 2. The overall grade
will take into account the evidence gathered by the commission in both the Biochemistry I written exam
and the grades for the molecular biology and oral exams for Biochemistry II.
The Biochemistry I written exam must always be retaken if the oral exam is not passed. A passing grade is achieved through a basic level of knowledge and understanding of the syllabus. An excellent grade is achieved by demonstrating a profound understanding of the syllabus and excellent communication skills.

Protein structure: primary structure, secondary structure (alpha helix and beta-sheet); tertiary and quaternary structure. Peptide bonding, steric encumbrance, weak interactions at the base of each structural layer, and disulfide bridge bonds. Protein denaturation and loss of function. Folding errors, protein aggregates, prion proteins and beta-amyloid peptides.

Glycated and lipid proteins.

Methods of studying polypeptides and proteins.

Structure-function relationship of different protein classes:

1. immunoglobulin.

2. muscle contractile proteins, morphological and molecular organization, biochemical mechanism of contraction with the role of ATP and calcium ions,

3. proteins of the intercellular matrix, collagen, laminin and fibronectin, integrin receptors and the role of integrins in matrix-cell communication,

4. cytoskeletal proteins, actin and tubulin with polymerization mechanism and hints on regulatory proteins; molecular motors (kinesines and dyneins with ATP-dependent structure and mechanism of advancement on the microtubule),

5. transporter proteins with particular attention to transporter proteins in plasma; process of recognition and binding (Ka, Kd, degree of saturation); O2-binding proteins, heme group with structure and interactions with the globin chain; myoglobin with structure, function, and saturation curve; hemoglobin with structure, saturation curve, T/R allostery, interaction between binding sites (cooperativity between equal binding sites belonging to the same oligomer protein, Hill coefficient); regulation of Hb affinity for its ligand by: O2, CO2, H+ and 2,3 bisphosphoglycerate, their role in the regulation of Hb affinity for O2 and in lung and tissue gas exchange; hemoglobin isoforms and maternal-fetal gas exchange; molecular basis of haemoglobinopathies (thalassemia and sickle cell anaemia).

· Enzymes with description of the general mechanism of action and classification; chemical transformations (thermodynamic aspects, Gibbs free energy, Van't Hoff equation, activation energy and its impact on reaction rate); reaction rate, rate constant and Arrhenius equation; structure and function of enzymes (pH and T effect on velocity).

Enzyme kinetics:

1. Steady-state hypothesis, Michaelis-Menten equation and Lineweaver-Burk representation;

2. fundamental kinetic parameters with meaning and calculation method (Km, Vmax, Kcat).

Mechanisms of enzyme regulation:

Mechanisms of catalysis: induced adaptation, entropic reduction, acid base, covalent.

Proteases as an example of enzymes: trypsin/chymotrypsin, HIV-protease, thrombin, caspase and metalloprotease.

Vitamins and their role as cofactors

Reporting mechanisms:

1. generalities; endocrine, paracrine, autocrine mechanisms; characteristics of signalling processes (specificity, affinity, cooperativity, amplification, integration); desensitization and threshold effect; calculation of the affinity and number of receptors (Scatchard plot)

2. Receptor classes:

1. receptors coupled to trimeric G proteins; downstream effector systems of trimeric G proteins;

2. adenylate cyclase and mechanism of action of toxins (cholera and whooping cough); beta adrenergic system; glucagon receptor and downstream signaling pathways;

3. phospholipase A-D-C; IP3 and diacylglycerol.

4. Ca-dependent reporting; CaMK, MLCK, cADPR and NAADP; PKC.

5. Voltage-gated and ligand-gated channels (voltage-gated neural channel for sodium, cholinergic receptor);

6. biochemical mechanisms of sensory perception.

7. receptor tyrosine kinases: structure and signaling mechanism;

8. via Ras/MAPK;

9. via PI3K/AKT;

10. Src and non-receptor tyrosine kinases;

11. Detailed description of insulin receptor and downstream signaling pathways.

12. negative regulation of TRKs, ubiquitination and Cbl;

13. receptors associated with tyrosine kinases; role of Jak-Stat, erythropoietin reporting;

14. tyrosine phosphatase with receptor-like structure;

15. serine/threonine kinase receptors and morphogenesis;

16. receptors with guanylate cyclase activity and cGMP-dependent signaling.

17. synthesis of NO and its role in the cardiovascular system;

18. Inside out and outside in signaling mediated by integrins.

Metabolism: general aspects of catabolism and anabolism. High energy molecules: NAD, NADP, FAD, FMN, ATP, phosphocreatine. Metabolic intermediates with high energy content. Esters and thioesters. Role of redox cofactors in catabolic and anabolic processes. Metabolic compartmentalization. Biochemical aspects of food digestion.

Bioenergetics:

1. basal metabolic rate;

2. energy requirements in relation to physical activity;

3. energy consumption by different tissues and organs.

Cellular respiration:

1. Molecular organization of mitochondria;

2. electron transport chain;

3. Mitchell's chemiosmotic theory;

ATP synthase: structure and rotational mechanism

It is intended that the student acquire:
- the typical language of biochemistry and its main formalisms (formulas)
- an in-depth knowledge of the structure-function relationship of biological molecules with particular emphasis on proteins
- the main signal transduction mechanisms that the student must be able to contextualize in the different biological contexts
The concept of bioenergetics and the key role of oxidative phosphorylation in animal metabolism
- the ability to understand and discuss physiological events at the molecular level.