44113 - Biochemistry Molecular Biology

Learning outcomes

The Course will provide a basic knowledge on the structure and functions of the major biological molecules (carbohydrates, lipids and proteins). 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 (8 ECTS) Prof. Natalia Calonghi

The molecules of life: properties of biomolecules. Energy and living systems. Covalent and non-covalent bonds. Role of weak bonds in biological molecules.

Amino acids and proteins: Structure and properties of amino acids. Peptide bonds and protein sequence. Secondary structure. Motifs and structural and functional domains in the tertiary structure. Quaternary structure. Protein folding and degradation. Fibrous proteins.

Physiological activities of proteins: Structure of myoglobin and hemoglobin.The heme group. Oxygen binding and cooperativity. Competitive inhibitors and allosteric ligands. Hemoglobin variants (embryonic, fetal and pathologic mutant forms).

Enzymes: Classification and general properties of enzymes. Activation energy. Catalytic mechanisms. Cofactors and prosthetic groups.

Kinetics of enzymatic reactions: Significance of kinetic data and kinetic parameters (Km, Vmax, kcat). The Michaelis-Menten equation. pH and temperature effect on enzyme activity. Enzyme inhibitors. Drugs as enzyme inhibitors. Control of enzyme activity: allosteric control and covalent modifications.

Carbohydrates: monosaccharides, disaccharides, polysaccharides and glycoproteins.

Lipids and biomembranes: Fatty acids, triacylglycerols, glycerophospholipids, sphingolipids and steroids. Bilayers. Membrane integral and peripheral proteins. Structural organization and basic functions of biomembranes. Fluidity of membranes. The fluid mosaic model and lipid rafts. Transport across cell membranes, kinetics and thermodynamics of transport. Passive diffusion, uniporter catalyzed transport, active transport by ATP-powered pumps, cotransport by simporters and antiporters.

Introduction to metabolic pathways: thermodynamics of metabolic pathways. Control of metabolic flux. ATP and “high-energy” compounds. Coupled reactions. Redox reactions.

Cellular energetics and glucose catabolism: Oxidation of glucose: the reactions of glycolisis. The anaerobic metabolism of pyruvate: fermentations. Regulation of glycolisis. Metabolism of hexoses other than glucose. The pentose phosphate pathway.

Glycogen metabolism and gluconeogenesis: glycogen breakdown, synthesis and control. Gluconeogenesis: reactions and regulation.

The citric acid 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.

Mitochondrial electron transport and oxidative phosphorylation: Electron transporters in mitochondria. Oxidative phosphorylation: the proton-motive force and the chemiosmotic theory. ATP synthase. Uncoupling and inhibition of electron transport. Control of oxidative metabolism. Brown fat mitochondria and thermogenesis.

Oxidation of fatty acids: Lipid digestion, degradation, absorption and transport. Fatty acid oxidation. Ketone bodies.

Fatty acid biosynthesis: palmitate synthesis: reactions and regulation. Biosynthesis of polyunsaturated fatty acids: elongation and desaturation. Essential fatty acids. Synthesis of triacilglycerols and glycerophospolipids. Synthesis of cholesterol: early steps. Regulation of fatty acid and cholesterol metabolism.

Catabolism of amino acids: Protein degradation. The aminotransferase reactions. Amino acid deamination. The urea cycle: reactions and regulation.

Cell-to cell signalling, hormones and receptors: Hormones. Receptor proteins and G proteins. Signal transduction mechanisms (the cAMP and phosphatidylinositol pathways). Receptor tyrosine kinases.

Module 2. Biochemistry of nucleic acids (3 ECTS) Prof. Romana Fato

Nucleotide, nucleoside and base. structures of the purines and pyrimidines. The synthesis of purines and pyrimidines. Synthesis of deoxyribonucleotides. Salvage of nucleotides — purine salvage and pyrimidine Salvage. Catabolism of bases - degradation to uric acid

Phosphodiester bond and nucleotide sequences. Base pairs and the general structure of DNA. Specific forms A-DNA, B-DNA and 2-DNA. DNA topology. Chromosome structure: histones, nucleosomes and chromatin.

DNA replication and enzymes involved in the process. Bacteria replicon. Replication origins.

Ribosomal, messanger and transfer RNAs. Primary, secondary and tertiary structures of RNA.

Procaryotic transcription. Procaryotic RNA polymerases. Promotor and cis elements. RNA polymerase subunits: sigma factor. End of transcription.

Regulation of gene expression. Bacterial Operon: trans factors. Lac and Trp operons. Attenuation and termination of transcription.

Genetic code: codon and anticodon. Genetic mutations and effects on AA sequence. mRNAs: structure and post-transcriptional modifications.

Structure and function of tRNAs. Aminoacil-tRNA sinthetases. Ribosome structure. Translation factors and mechanisms.

Structure of eucaryotic genes: intron and exon. cDNAs and reverse transcription.

Readings/Bibliography

D.L.Nelson and M.M. Cox - Lehninger principles of Biochemistry - Freeman

T.M. Devlin - Biochimica con aspetti clinico-farmaceutici- Edises

D.Voet, J.G.Voet and C.W.Pratt - Fundamentals of Biochemistry - Wiley

R. H. Garrett , C. M. Grisham –Biochemistry – Mary Finch

J.M. Berg, J.L. Tymoczko, L. Stayer-Biochemistry - Freeman

B. Lewin - Gene – Zanichelli

Teaching methods

Theoretical lessons

Assessment methods

Module 1 (Biochemistry).

The examination consists of an oral examination with three questions aimed at assessing the theoretical knowledge on the structure and function of biological macromolecules, metabolism and its regulation. Over the course a written test in progress can be set up "one-off" on the structure and function of biomolecules consisting of open-ended questions that if overcome with positive vote (>18) will count as the acquisition of knowledge and will contribute for 3/11 to the final vote. In this case, the oral examination will focus only on the metabolic pathways and their regulation and will consist of two questions.

Module 2 (Biochemistry of nucleic acids)

The final assessment will be given as written test that will consist of 10 multiple choice quizzes, 10 True/False questions in which the student has to explain his answer and 3 short answer questions. The test score (as a fraction of thirty from 18/30 to 30/30 cum laude) will contribute to the final evaluation of the course. The final grading will be done by the weighted average of the grades obtained in the two modules.

Teaching tools

PC and overhead projector for Powerpoint presentations.

Office hours

See the website of Natalia Calonghi

See the website of Romana Fato