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

MODULE 1 - BIOCHEMISTRY (5 CFU, 40h) Prof Cappadone

1. Introduction to biochemistry. Chemical concepts to explain the properties of biological molecules: chemical bonds; water structure; Principles of Thermodynamic.

2. Bioenergetics. Free energy variation - Coupled reactions. ATP

3. Amino acids and proteins: characteristics and function. Primary structure of proteins: formation of the peptide bond; Phi and Psi angles; Ramachandran diagram.

4. Secondary structure: alpha-helix, beta-sheet, beta-turn. tertiary structure. Fibrous protein. Globular proteins.

5. Quaternary structure of proteins. Myoglobin and Hemoglobin. Allosterism and cooperation.

6. Enzymes: catalytic power; Specific regulation. Ribozymes. Cofactors and coenzymes. Enzyme kinetics - Michaelis-Menten equation

7. Kinetic parameters used to compare enzyme activities. sequential reactions. Double displacement reactions. Allosteric enzymes. Regulatory strategies.

8. Control of enzyme activity. Blood clotting and vitamin K.

9. Lipids and membrane. Fatty acids in the biological system: Phospholipids; Triglycerides; Sphingolipids; Steroids.

10. Lipid bilayers. Liposomes. membrane proteins. Fluid mosaic pattern. Lipid rafts.

11. Purine and pyrimidine bases. Nucleosides and nucleotides

12. Nucleic acid metabolism: biosynthesis and degradation

13. DNA structure: phosphodiester bond, directionality and polarity of polynucleotide chains. The Watson-Crick structure: double helix, complementary base pairing, stability. DNA denaturation. Supercoiling of DNA. Topoisomerase. Organization of eukaryotic chromatin

14. DNA Replication: DNA polymerase. Overhaul and repair. The central dogma

15. RNA structure: modified bases. Hairpin and loop structures. Types of RNA and their functions.

16. Transcription of RNA

MODULE 2 - BIOCHEMISTRY (5 CFU, 40h) Prof Prata

1. The genetic code: definition, characteristics, codons, reading frame. Type of mutations. Codon-anticodon interactions. The "swinging" coupling. methionine tRNA.

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

3. Introduction to metabolism - Anabolic and catabolic pathways.

4. Biosignalling - Cell signalling, hormones and receptors - G protein coupled receptors. Mechanisms of signal transduction (the cAMP and phosphatidylinositol pathways). Tyrosine kinase receptor. Hormones. ROS, antioxidants and redox signaling.

5. Glycolysis - Glucose oxidation: the reactions of glycolysis and their regulation. Anaerobic metabolism of pyruvate: fermentations.

6. 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.

7. Electron Transport Chain - Oxidative Phosphorylation. Regulation of oxidative phosphorylation. Uncoupling and inhibition of the oxidative phosphorylation system. Brown/beige adipose tissue and thermogenesis

8. Glycogen metabolism - synthesis, breakdown and control of glycogen.

9. Gluconeogenesis - reactions and regulation.

10. The pentose phosphate pathway (also called the phosphogluconate pathway or hexose monophosphate shunt). Generation of NADPH and pentoses (5-carbon sugars) as well as ribose 5-phosphate, a precursor for nucleotide synthesis

11. Catabolism/oxidation of fatty acids - Digestion, degradation, absorption and transport of lipids. Use of fatty acids for energy production: beta-oxidation. Formation and utilization of cholesterol. Characteristics, metabolism and functional role of polyunsaturated fatty acids.

12. Ketone bodies

13. Biosynthesis of fatty acids - Synthesis of palmitate: reactions and regulation. Biosynthesis of polyunsaturated fatty acids: elongation and desaturation. Essential fatty acids. Synthesis of triacylglycerols and glycerophospholipids. Cholesterol synthesis: first steps. Regulation of the metabolism of fatty acids and cholesterol.

14. Cholesterol

15. Amino acid oxidation and urea production: protein degradation. Role of pyridoxal phosphate in amino acid metabolism. Transamination reactions and oxidative deamination. Nitrogen excretion and the urea cycle.

16. General overview of the regulation of metabolic pathways between various organs

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 the two 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