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: Biochemistry I  (7 CFU) Prof. Calonghi Natalia

Structure and properties of amino acids . Primary, secondary, tertiary and quaternary structure.

Fibrous proteins. Myoglobin and haemoglobin. The heme group. Oxygen binding and cooperativity. Competitive inhibitors and allosteric ligands.

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

Kinetics of enzymatic reactions : Km, Vmax, kcat. The Michaelis-Menten equation. pH and temperature effect on enzyme activity. Enzyme inhibitors. Control of enzyme activity: allosteric control and covalent modifications.

Lipids . Fatty acids, triacylglycerols, glycerophospholipids, sphingolipids and steroids. Biomembranes. Transport across cell membranes.

Carbohydrates . monosaccharides, disaccharides, polysaccharides.

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

Cellular energetics and glucose metabolism . Glycolisis. The anaerobic metabolism of pyruvate. Regulation of glycolisis.  The pentose phosphate pathway. Glycogen metabolism and gluconeogenesis: glycogen breakdown, synthesis and control. Gluconeogenesis: reactions and regulation.

The citric acid cycle and its regulation.

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.

Lipid metabolism . 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.

Signal trasduction . AMPc pathway. Phosphatidylinositole pathway. Tyrosine kinase receptors

Section: Biochemistry II (3 CFU)  Prof. Fiorentini Diana

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

- J.M Berg, J.L. Tymoczko, L. Stryer  “Biochimica”, VII edizione, Zanichelli, 2012

- M.K. Campbell, S.O. Farrell  “Biochimica”, IV edizione, EdiSES, 2012

- D.L.Nelson, M.M.Cox “Lehninger principles of Biochemistry”, V edizione, Zanichelli, 2010

Teaching methods

PC and overhead projector for Power Point presentations

Assessment methods

The learning assessment takes place with the final exam. The acquisition of the learning outcomes is ascertained by means of a written test of 1 hour, to be undertaken without the support of notes or textbooks, followed by an oral exam. A multiple choice test on the section “Biochimica II” must be passed in order to take the final, oral examination. A score of at least 18 in the written test is required to be admitted to the oral exam. Such an admission is valid for one solar year since the date of the positively evaluated written test; during this period the student can take the oral exam in any available session. Whether the student does not accept the score obtained in the written test, he will be allowed to perform another one and in this case the valid score will be that obtained in the latest test. The oral exam has an average duration of 20-30 minutes and consists of 2/3 questions on the section “Biochimica  I”. If the oral exam is failed the written test does not have to be repeated; the student can try the oral exam again in a later session, within the term of validity of the written test. The final mark is mainly determined from the outcome of the oral exam, taking into account, however, the score assigned to the written test.

Teaching tools

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

Office hours

See the website of Natalia Calonghi

See the website of Diana Fiorentini