90968 - General and Molecular Biochemistry

Learning outcomes

The Course will provide a basic knowledge on the structure and functions of the major biological molecules (carbohydrates, lipids and proteins) and on enzymology. The main metabolic pathways will be discussed, together with their relations and regulation. Students will know the fundamental concepts of molecular biology and basic molecular mechanisms of living organisms such as replication, transcription, translation and transcription regulation.

Course contents

General and Molecular Biochemistry course consists of 10 (ECTS) credits, that are divided into 3 parts/modules:

- MODULE 1 - STRUCTURAL BIOCHEMISTRY (3 ECTS, 24h) Prof. C. Cappadone

Introduction to Biochemistry. Concepts from chemistry to explain the proprieties of biological molecules: chemical bonds; structure of water; First and Second Laws of Thermodynamics; principles of acid–base chemistry.

Aminoacids and proteins: characteristics and function. Primary structure of proteins: peptide bond formation; Phi and Psi angles; Ramachandran diagram.

Secondary structure: alpha-helix , beta-sheet beta-turns. Tertiary structure. Fibrous proteins. Globular proteins.

Quaternary structure of proteins. Myoglobin and Hemoglobin. Allosterism and cooperativity. Sickle Cell Anemia.

Enzymes: Catalytic power; Specificity Regulation. Ribozymes. Cofactors and Coenzymes. Enzyme kinetics- Michaelis-Menten Equation-K_M and Vmax significance.

Kinetic parameters are used to compare enzyme activities. Sequential reactions. Double-displacement reactions. Allosteric enzymes. Regulatory strategies.

Control of Enzyme Activity. Blood clotting. Haemophilia-Vitamin K.

Lipids and Membranes. Fatty acid in biological system: Phospholipids; Triglycerides; Sphingolipids; Steroids.

Lipid bilayers. Liposomes. Membrane proteins-.Fluid mosaic model.Lipid raft.

Bioenergetics. Free energy change- Reactions coupled. ATP. Electron Transport chain- Oxidative phosphorylation.

- MODULE 2 - METABOLISM (4 ECTS, 32h) Prof. C. Prata

1. Introduction to Metabolism - Anabolic and catabolic pathways.

2. Biosignallinig - Cell signalling, hormones and receptors - Protein G coupled receptors. Signal transduction mechanisms (the cAMP and phosphatidylinositol pathways). Receptor tyrosine kinases. Hormones. ROS, antioxidants and Redox signalling.

3. Glycolysis - Oxidation of glucose: the reactions of glycolysis and their regulation. The anaerobic metabolism of pyruvate: fermentations.

4.The citric acid cycle (Krebs Cycle)- Mitochondrial oxidation of pyruvate and synthesis of acetyl-Coenzyme A. Reactions of the citric acid cycle and its regulation. Reactions related to the citric acid cycle.

[Brief review of Electron transport chain and oxidative phosphorylation - Electron transporters in the mitochondrial respiratory chain, Oxidative phosphorylation and ATP synthesis. Regulation of oxidative phosphorylation. Uncoupling and inhibition of the oxidative phosphorylation system. Brown adipose tissue and thermogenesis].

5.Glycogen metabolism - glycogen synthesis, breakdown and their control.

6. Gluconeogenesis - reactions and regulation.

7. The Ketone bodies

8. The pentose phosphate pathway also called the phosphogluconate pathway and the hexose monophosphate shunt). It generates NADPH and pentoses (5-carbon sugars) as well as ribose 5-phosphate, a precursor for the synthesis of nucleotides

9. Fatty acids catabolism / oxidation - Lipid digestion, degradation, absorption and transport. Use of fatty acids for energy production: beta-oxidation. Formation and use of cholesterol. Characteristics, metabolism and functional role of polyunsaturated fatty acids.

10. Fatty acid biosynthesis - Palmitate synthesis: reactions and regulation. Biosynthesis of polyunsaturated fatty acids: elongation and desaturation. Essential fatty acids. Synthesis of triacylglycerols and glycerophospholipids. Synthesis of cholesterol: early steps. Regulation of fatty acid and cholesterol metabolism.

11. Aminoacid oxidation and urea production: protein degradation. Role of pyridoxal-phosphate in amino acid metabolism. Transamination and oxidative deamination reactions. Nitrogen excretion and urea cycle.

12. General overview on Regulation of metabolic pathways

- MODULE 3 - MOLECULAR BIOCHEMISTRY (3 ECTS, 24h) Prof. G. Farruggia

Purine and pyrimidine bases: structures, tautomeric forms and polarity

Nucleosides and nucleotides: structures and functions

Chemical structures of DNA and RNA: the phosphodiester bond, directionality and polarity of polynucleotide chains

Stability of DNA and RNA: spontaneous hydrolysis, nucleases, restriction endonucleases

Secondary structure of DNA: the Watson-Crick structure: the double helix, complementary base pairing, stability. DNA denaturation. DNA supercoiling. Topoisomerases. Organization of eukaryotic chromatin

Structure of RNA: modified bases. Hairpins and loops. Types of RNA and their functions

The central dogma

DNA replication in prokaryotes : DNA polimerase III in E. coli. The polymerization reaction. OriC. Leading and lagging strand. Roles of DNA polimerase I and ligase. Proof-reading of DNA polimerase I and III. DNA damage and mutations.

RNA transcription in prokaryotes: RNA polymerase in E. coli. The polymerization reaction. Promoters and consensus sequence. Steps of transcription in E. coli. Sigma subunits. Short information about eukaryotic transcription, transcription factors and enhancers. RNA processing. Reverse transcriptase

Regulation of gene expression in prokaryotes:different sigma factors. Operons. Lac operon regulation. Short information about gene expression in eukaryotes

Aminoacyl-tRNA synthethases: reaction, specificity and fidelity

The genetic code: definition, characteristics, codons, reading frame. Type of mutations. Codon-anticodon interactions. The"wobble" pairing. Isoaccepting tRNA. Methionine tRNA.

Protein synthesis in prokaryotes: ribosome structure. The Shine-Dalgarno sequence. Initiation. Chain elongation. Formation of a peptide bond. Chain termination.

Steps in DNA cloning

Readings/Bibliography

- Lehninger Principles of Biochemistry 7th edition

David L. Nelson and Michael M. Cox.

-Biochemistry

Reginald H. Garrett, Charles M. Grisham

- Biochemistry

Jeremy M. Berg, John L. Tymoczko, Lubert Stryer

- Textbook of Biochemistry with Clinical Correlations

Thomas M. Devlin

Teaching methods

Lectures with ppt presentations

Assessment methods

The single exam for all the 3 modules aims to assess the achievement of the following objectives:

- the structure and function of the main biological macromolecules and the fundamental notions of enzymology

- cellular bioenergetic, signal transduction, the main metabolic pathways and their regulation

- the bases of molecular biochemistry, molecular mechanisms of living systems and the molecular logic of their regulation

The exam consists of a written evaluation.

The exam is made up of multiple-choice questions and 3 open-ended questions.

Registration to AlmaEsami is required.

Teaching tools

The Teaching material consists of:

one of the recommended books,

lecture notes,

additional material provided on the “Virtuale” platform in pdf format or brief videos

Office hours

See the website of Cecilia Prata

See the website of Concettina Cappadone

See the website of Giovanna Farruggia