00061 - Biochemistry

Learning outcomes

The aim of the Course is to give a basic knowledge on the structure and functions of the major biological molecules. The main metabolic pathways will be discussed, together with their relations and regulation. General principles on DNA structure and information flow from DNA replication to RNA and protein synthesis will be discussed.

Course contents

Section: BIOCHIMICA I     (7 CFU)

Properties of biomolecules: Life obeys the laws of  thermodynamics. Role of weak bonds in biomolecules.

Amino acids and proteins: Structure and properties of amino acids. Peptide bonds and protein sequence. Secondary structure. Fibrous proteins. Tertiary and quaternary structure. Protein folding.

Physiological activities of proteins: oxygen binding to myoglobin and hemoglobin: the heme group. Structures of myoglobin and hemoglobin. Oxygen binding and cooperativity. Hemoglobin variants.

Properties and action of enzymes: Activation energy. General properties of enzymes. Catalytic mechanisms. Some enzymes require cofactors.

Kinetics, inhibition and control: Kinetic data and kinetic parameters (Km, Vmax, kcat). Enzyme inhibition. Drugs as enzyme inhibitors. Control of enzyme activity: allosteric control and covalent modifications.

Carbohydrates: monosaccharides, disaccharides, polysaccharides.

Nucleosides and nucleotides: ATP structure. Roles of nucleotides. Cyclic nucleotides.

Lipids, bilayers and membranes: Fatty acids, triacylglycerols, glycerophospholipids, sphingolipids, steroids. Bilayers. Membrane proteins. Membrane structure and assembly. The fluid mosaic model.

Membrane transport: Kinetics and thermodynamics of transport. Passive and active transport. Channels.

Overview of metabolism: Thermodynamics of metabolic pathways. Metabolic flux must be controlled. ATP and “high-energy” compounds. Coupled reactions. Redox reactions.

Glucose catabolism: The reactions of glycolisis. The anaerobic fate 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: Synthesis of acetyl-Coenzyme A. Reactions and regulation of the citric acid cycle. Reactions related to the citric acid cycle.

Electron transport and oxidative phosphorylation: The mitochondrion. Electron transporters. Oxidative phosphorylation: the chemiosmotic theory. Uncoupling and inhibition of electron transport. Control of oxidative metabolism.

Degradation of lipids: Lipid digestion, absorption and transport. Fatty acid oxidation. Ketone bodies.

Fatty acid biosynthesis: Palmitate synthesis: reactions and regulation. Fatty acids may be elongated and desaturated. Synthesis of triacilglycerols and glycerophospolipids. Synthesis of cholesterol: early steps. Regulation of fatty acid metabolism.

Cholesterol: Roles and biosynthesis of cholesterol. Regulation of HMG-CoA reductase and its inhibitors. Transport of cholesterol and lipoproteins.

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

Hormones and signal transduction: Hormones. Receptor tyrosine kinases. G proteins. Cyclic AMP pathway. The phosphoinositide pathway. Energy metabolism and hormone control: role of glucagon, epinephrine and insulin.

Vitamin K and blood clotting.

 

Section: BIOCHIMICA II   (3 CFU)

Purine and pyrimidine bases: structure, tautomeric forms and polarity

Nucleosides and nucleotides

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

Hydrolisis of DNA and RNA

Secondary structure of DNA: the double helix: The Watson-Crick structure: complementary base pairing. DNA denaturation. Supercoling. Topoisomerases. DNA damage. Chromatin structure in eukaryotes.

Secondary structure of RNA: modified bases. Hairpins and loops. Posttranscriptional processing of mRNA, tRNA and rRNA

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 - DNA Polimerases I and III can edit mistakes - Short informations on DNA repair and mitochondrial DNA.

RNA transcription in prokaryotes: RNA polymerase in E. coli. The polymerization reaction. Promoters. Chain initiation and sigma subunit. Chain elongation and termination.

Control of transcription in prokaryotes: Promoters. Different sigma factors. Lac operon regulation.

Transcription in eukaryotes: short accounts: transcription factors and enhancers. Steroid hormones.

Reverse transcriptase: properties of  reverse transcriptase - action mechanism  of AZT in AIDS treatment.

Posttranscriptional processing of RNA in prokaryotes: modifications of nucleosides. Ribosomes in prokaryotes and eukaryotes. Short accounts on posttranscriptional processing of RNA in eukaryotes.

Aminoacyl-tRNA synthethases: choice of the correct amino acid for covalent attachment to a tRNA. Proof-reading.

The genetic code: the nature of the code. Codons are triplets. Reading frames. The code is degenerate and widespread. Codon-anticodon interactions. The"wobble" pairing. Isoaccepting tRNA. Methionine tRNA.

Protein synthesis: Ribosomes structure. The Shine-Dalgarno sequence. Initiation. Chain elongation. Formation of a peptide bond. Chain termination. Posttranslational modifications. Protein folding.

Readings/Bibliography

M.K.Campbell and S.O.Farrell - Biochemistry - 3rd Edition, Thomson Brooks/Cole 2009

D.L.Nelson and M.M. Cox - Lehninger principles of Biochemistry -5th Edition, Freeman 2008

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

J.Berg, J.L.Tymoczko and L.Stryer, Biochemistry 6th Edition, Freeman 2007

Assessment methods

A multiple choice test on the section “Biochimica II” must be passed in order to take the final, oral examination. The written test stands for 1 year.

Teaching tools

PC and  overhead projector for Powerpoint presentations.

Updated slides are available at: http://campus.cib.unibo.it

Office hours

See the website of Diana Fiorentini