Biochimica M - Z
Academic Year 2023/2024 - Teacher: ANGELA MARIA AMORINIExpected Learning Outcomes
To acquire the knowledge on structure, function and regulation of biological macromolecules. To understand the general mechanisms of regulation of metabolism. To acquire the knowledge on the main pathways and cycles of metabolism, with particular attentio to metabolism of carbohydrates, lipids and amino acids. To understand the general mechanisms of metabolic alterations under non-physiological conditions (prolonged starvation, physical stress).
Course Structure
Frontal lessons with practise on chemical formulae and metabolic cycles.
Should teaching be carried out in mixed mode or remotely, it may be necessary to introduce changes with respect to previous statements, in line with the programme planned and outlined in the syllabus.
Learning assessment may also be carried out on line, should the conditions require it.
Information for students with disabilities and / or SLD: To guarantee equal opportunities and in compliance with the laws in force, interested students can ask for a personal interview in order to plan any compensatory and / or dispensatory measures, based on the teaching objectives and specifications needs. It is also possible to contact the CInAP contact person (Center for Active and Participatory Integration - Services for Disabilities and / or SLD) of the Department.
Required Prerequisites
To be able to take the exam you must have passed the Organic Chemistry exam
The following knowledge is also required:
General Chemistry - Chemical bonds. Thermodynamics. Acids and bases. Properties of solutions: pH, pK, buffers, osmotic pressure. Oxide-reductions.
Recall of organic chemistry - Hybridization of carbon. Saturated, unsaturated and cilicic hydrocarbons. Heterocylic and aromatic compounds Electronic delocalization and resonance. Functional groups of greatest biochemical interest: -OH, -SH, -COOH, -COH, -CO, -CH3, -NH2, -NH3. Acidity and basicity of organic compounds. Isomerism.
Detailed Course Content
Recalls of inorganic and organic chemistry. Carbohydrates – structure and function. Lipids – structure and function. Purines and pyrimidines – structure and function. Amino acids – structure and function. Peptide bond and its characteristics. Peptides of biological relevance. Proteins – structure and function. Classification. Primary structure. Secondary structures: alfa-helix, beta-strand, collagen helix. Tertiary structure. Quaternary structure. Relationship between primary structure and conformation. Denaturation and renaturation. Protein folding. Fibrous proteins. Globular proteins. Hemoproteins involved in the transport of gases (O2, CO2). The heme group. Tridimensional structures of myoglobin and hemoglobin. Mechanism of oxygen binding to myoglobin and hemoglobin. Oxygen affinity. Saturation curves, Bohr effect, cooperativity, Hill plot, homotropic and heterotropic interactions. The effect of 2,3-DPG. The Monod-Wyman and Changeux (MWC) model and the sequential model. T and R states. Heterogeneity of circulating hemoglobin. Methemoglobin reductase, reduced glutathione (GSH) and NADPH for the maintenance of hemoglobin functions. Deficit of G-6-PDH, oxidation of hemoglobin, malaria. Molecular pathology of abnormal hemoglobin. Enzymes. Classification. Coenzymes and vitamins. Chemistry and biological catalysts. The Michaelis-Menten equation. Km, Vmax, turnover number, Kcat/Km. Reversible and irreversible inhibition. General mechanisms of enzyme catalysis (acid-base catalysis, covalent catalysis, state transition catalysis, metal ions catalysis). Multimeric enzymes and allosteric regulation. Multi-enzymatic complexes. Regulation of enzymatic activity. Examples of regulation of metabolic sequences. Feedback inhibition. Cascade amplification. Isoenzymes. Introduction to metabolism: its general organization. Understanding pathways and metabolic maps. Catabolism and anabolism. Bioenergetic. Energetically relevant molecules. Use of biochemical energy within the cell. Introduction to metabolism: its general organization. Understanding pathways and metabolic maps. Catabolism and anabolism. Bioenergetic. Energetically relevant molecules. Use of biochemical energy within the cell. The biochemical reactions of glycolysis – Regulation of glycolysis. Oxidation of pyruvate: the pyruvate dehydrogenase. Degradation of glycogen – The glycogen phosphorylase and its hormonal control. The transduction of the hormonal signal within the cell: G-proteins, cyclic AMP, adenylate cyclase, protein kinase. Reactions of the citric acid cycle – Regulation of the cycle. Reactions of the pentose phosphate shunt and its biochemical importance. Oxidative phosphorylation – The mitochondrion as the energetic plant of the cell. The scale of redox potential of biologically relevant molecules. The machinery for the electron transport: structure and function of the complexes I, II, III and IV. The sulphur-iron centers. The Q-cycle in the complex III. The transmembrane complexes in the electron transport. The electrochemical potential in electron transport. Oxygen utilization. The ATP synthase: structure and mechanism of action. Transport of nucleotides through mitochondria: the adenine nucleotides transporter. The beta-oxidation reactions. Absorption and transport of dietary lipids. Activation of lipolysis and transport of free fatty acids. Activation and transport in mitochondria. The four reactions of the beta-oxidation. Regulation and energy yield. Relationship with glucose metabolism. Ketogenesis. Transamination and transdeamination of amino acids. The urea cycle. Degradation of nucleotides. Catabolism of purines and pyrimidines. Degradation of heme: structure and function of biliary salts. Biosynthetic pathways. Gluconeogenesis. The reaction of carboxylation of pyruvate and the reactions of gluconeogenesis. Relationship between glycolysis and gluconeogenesis. Glycogen biosynthesis. Biosynthesis and recovery of purines and pyrimidines. Biosynthesis of heme. Biosynthesis of fatty acids. Biosynthesis of cholesterol. Mechanisms of regulation of metabolism.
Textbook Information
David L. Nelson, Michael M. Cox Lehninger Principles of Biochemistry Editor: W.H.Freeman & Co Ltd
BERG JM, TYMOZCKO JJL, STRYER L. Biochemistry Editor McMillan
VOET and VOET Biochemistry Editor Wiley
Course Planning
| Subjects | Text References | |
|---|---|---|
| 1 | Richiami di chimica generale - Legami chimici. Termodinamica. Caratteristiche chimico-fisiche dell’ acqua. Proprietà delle soluzioni: pH, pK, tamponi, pressione osmotica. Funzione dell’acqua nei sistemi biologici. Richiami di chimica organica – Ibridizzazione del carbonio. Gruppi funzionali di maggiore interesse biochimico: -OH, -SH, -COOH, -COH, -CO, -CH3, -NH2, -NH3. Acidità e basicità dei composti organici. Isomeria | 3,6,7 |
| 2 | Molecole di importanza biologica - Carboidrati - Struttura e funzione. Monosaccaridi: classificazione, formule di Fisher e di Haworth, ciclizzazione, mutarotazione, reazioni dei gruppi aldeidici e chetonici.. Il legame glicosidico. Oligosaccaridi. Omopolisaccaridi di struttura e di riserva. Eteropolisaccaridi. Proteoglicani, glicoproteine, glicosamminoglicani e glicolipidi. Lipidi - Struttura e funzione. Lipidi semplici: caratteristiche chimiche e chimico-fisiche degli acidi grassi. Lipidi complessi: neutri | da 1 a 9 |
| 3 | Amminoacidi – Struttura e funzione. Proprietà chimiche e chimico-fisiche. Punto isoelettrico. Classificazione e proprietà specifiche delle catene laterali. Legame peptidico e sue caratteristiche. Angoli fi e psi. Il grafico di Ramachandran. Peptidi di importanza biologica. Macromolecole di importanza biologica - Proteine - Struttura e funzione delle proteine. Classificazione. Cenni di purificazione di proteine (cromatografia, elettroforesi, determinazione del P.M.). Struttura primaria. Legami responsabili d | 1,2,4,5 |
| 4 | Biochimica comparata delle proteine respiratorie. Entalpia di ossigenazione dell’emoglobina e suo ruolo fisiopatologico. La catalisi biochimica. - Enzimi - Classificazione. Coenzimi e vitamine. Catalizzatori chimici e catalizzatori biologici. Equazione di Michaelis-Menten. Km, Vmax, numero di turnover, Kcat/Km. Il grafico dei doppi reciproci. Effetto del pH e della temperatura sull’attività enzimatica. Inibizione irreversibile. Inibizione reversibile: competitiva, non-competitiva, incompetitiva e mista. Eff | 1,2 |
| 5 | Concetto di vie e di mappe metaboliche. Vie degradative (catabolismo) e vie biosintetiche (anabolismo). Bioenergetica. Molecole energeticamente cariche. Utilizzo dell’energia biochimica nella cellula. Ruoli biochimici del NADH e del NADPH. Meccanismi generali di regolazione del metabolismo - controllo ormonale, regolazione a feedback, enzimi allosterici, zimogeni, isoenzimi, amplificazione a cascata, compartimentazione, regolazione genica. | da 1 a 9 |
| 6 | Le reazioni biochimiche della glicolisi – Regolazione della glicolisi: esochinasi, fosfofruttochinasi, GAPDH, piruvatochinasi. Ossidazione dell’acido piruvico: il complesso multienzimatico della piruvico deidrogenasi e il suo meccanismo di reazione. Riduzione dell’acido piruvico: la lattico deidrogenasi. Degradazione del glicogeno – La glicogeno fosforilasi: meccanismo di reazione e il suo controllo ormonale. | 1,2 |
| 7 | La trasduzione del segnale ormonale all’interno della cellula: le proteine G, l’AMP ciclico, l’adenilato ciclasi, le proteine chinasi. Glicogeno epatico e glicogeno muscolare: stessa molecola, due finalità metaboliche. | 1,2,8 |
| 8 | Reazioni del ciclo dell’acido citrico – Regolazione del ciclo. Reazioni della via dei pentosio fosfati – Significato biochimico. La fosforilazione ossidativa - Il mitocondrio come centrale energetica della cellula. Le scale di potenziali redox di molecole di importanza biologica. Macchinario per il trasporto degli elettroni: struttura e funzioni dei complessi I, II, III e IV. I centri ferro-zolfo. Il ciclo Q nel complesso III. I complessi trans-membrana e il trasporto dei protoni. | da 1 a 9 |
| 9 | I potenziali elettrochimici nel trasporto degli elettroni. Utilizzazione dell’ossigeno. L’ATP sintasi: struttura e meccanismo d’azione. Trasporto dei nucleotidi attraverso il mitocondrio: il trasportatore dei nucleotidi adenilici Reazioni della beta-ossidazione degli acidi grassi – Assorbimento e trasporto dei grassi alimentari. Attivazione della lipolisi e trasporto degli acidi grassi liberi. Attivazione e trasporto nel mitocondrio: l’acil-CoA sintetasi, la carnitina,trasportatore acilcarnitina-carnitina | da 1 a 9 |
| 10 | Le 4 reazioni della beta-ossidazione. Controllo e resa energetica. Degradazione degli acidi grassi insaturi e degli acidi grassi a numero dispari di atomi di carbonio. Interrelazioni col metabolismo del glucosio. Chetogenesi Reazioni di transamminazione degli amminoacidi. – Gli amminoacidi e i chetoacidi nelle transamminazioni. Le transaminasi: meccanismo di reazione. La navetta malato-aspartato: suo funzionamento e ruolo metabolico. La transdeamminazione ossidativa degli amminoacidi. | da 1 a 9 |
| 11 | Meccanismo di reazione della glutammato deidrogenasi. Ciclo dell’urea. – Attivazione dell’ammoniaca: la carbammilfosfato sintetasi. Le reazioni del ciclo e la sua compartimentazione. Degradazione dei nucleotidi – Catabolismo e vie di recupero delle purine e delle pirimidine. Degradazione dell’eme: struttura e funzione dei sali biliari.. Vie biosintetiche. La gluconeogenesi – La reazione di carbossilazione del piruvato e le reazioni della gluconeogenesi. | da 1 a 9 |
| 12 | Relazioni tra gluconeogenesi e glicolisi. Biosintesi del glicogeno. Biosintesi dell’eme. Biosintesi degli acidi grassi. Biosintesi del colesterolo. | 1,2,8 |
Learning Assessment
Learning Assessment Procedures
Written test without grade which consists in CORRECTLY writing the structural formulas of at least 4 compounds (out of 6) whose names are given. Demonstrated knowledge of the structural formulas of compounds of biochemical interest (monosaccharides, amino acids, nucleosides, nucleotides, purine and pyrimidine bases, coenzymes, intermediates of the planned metabolic cycles and pathways) allows access to the oral exam.
The grade is given on the basis of the knowledge and understanding of the subject demonstrated by the student during the oral test.
· Grade 29-30 with honors: The student has an in-depth knowledge of Biochemistry, can promptly and correctly integrate and critically analyze presented situations, autonomously solve complex problems, and has excellent communication skills while mastering medical-scientific language.
· Grade 26-28: The student has good knowledge of Biochemistry, can integrate and critically analyze presented situations in a linear manner, autonomously solve complex problems to some extent, and presents topics clearly using appropriate medical-scientific language.
· Grade 22-25: The student has a fair knowledge of Biochemistry, albeit limited to the main topics. They can integrate and critically analyze presented situations in a non-linear manner and present topics fairly clearly with moderate language proficiency.
· Grade 18-21: The student has minimal knowledge of Biochemistry, with limited ability to integrate and critically analyze presented situations. They present topics sufficiently clearly, although their language proficiency is not well-developed.
· Failed Examination: The student lacks the minimum required knowledge of the main course content. Their ability to use specific language is extremely limited or nonexistent, and they cannot apply acquired knowledge independently.