84898 - 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

Section: Biochemistry 1 (6 ECTS) Prof. Silvana Hrelia

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 haemoglobin. 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.

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.

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.

Section: Biochemistry 2 (4 ECTS) Dr. Christian Bergamini

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.

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

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

D.L.Nelson and M.M. Cox - Lehninger principles of Biochemistry - 7th Edition, Freeman 2017

D.Voet, J.G.Voet and C.W.Pratt - Fundamentals of Biochemistry - 2nd Edition, Wiley 2006

R. H. Garrett , C. M. Grisham –Biochemistry – 4th edition, Mary Finch, 2010

J.M. Berg, J.L. Tymoczko, L. Stayer-Biochimica-7th edition, Freeman 2012

B. Lewin - Gene – Zanichelli

Teaching methods

Theoretical lessons

Assessment methods

The examination at the end of the course aims to assess the achievement of learning objectives

- to know the structure and function of the main biological macromolecules and the basis of enzymology.

- to know the cellular bioenergetics, the main metabolic pathways and the mechanisms underlying their regulation and signal transduction

- to know the fundamental concepts of molecular biology, the basic molecular mechanisms of living organisms and their regulation

The final examination consists of an evaluation of both modules, which can be broken down into separated moments of verification. Registration in Alma Esami is required for both modules.

Biochemistry 1 module: 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 can be set up "one-off" a written test in progress on the structure and function of biomolecules consisting of two open-ended questions that if overcome with positive vote will count as the acquisition of knowledge and will contribute for 50% to the vote of Biochemistry 1 module. In this case, the oral examination will focus only on the metabolic pathways and their regulation and will consist of two questions. The test is not compulsory, Students can decide for the oral examination.

Biochemistry 2 module: the verification test is written. The written test consists of multiple choice questions and open-ended questions on topics of molecular biology. For every correct answer is assigned a score indicated in the test sheet, for the open-ended questions a maximum score is indicated. No negative scores for wrong or unanswered questions is assigned. The test is passed if the score is at least 18.

The final vote of the course will be the weighted average of the marks obtained in the two modules (Biochemistry1 and Biochemistry 2)

Teaching tools

PC and overhead projector for Powerpoint presentations.

Office hours

See the website of Silvana Hrelia

See the website of Christian Bergamini