BIOCHEMISTRY - channel 1

BIO/10 - 5 CFU - 2° Semester

Teaching Staff

DANIELE FILIPPO CONDORELLI
Email: daniele.condorelli@unict.it
Office: Torre Biologica, Via Santa Sofia 97, Catania
Phone: 095 478 1152
Office Hours: 9:00-11:00


Learning Objectives

Understanding of biological phenomena at the level of chemical reactions and molecular interactions.



Detailed Course Content

Topics already covered in Chemistry and Biochemistry Propaedeutics: free radicals, the structure of carbohydrates and lipids, enzymology, the structure of nucleotides and nucleic acids.

PROTEIN STRUCTURE.

Structure, classification and general properties of amino acids.

Peptide bond. Definition of the primary structure, secondary, tertiary, quaternary. Angles phi, psi, chi, omega. Ramachandran plot. Secondary structure: alpha-helix, beta-strand, beta sheets (parallel, antiparallel, mixed). Reverse turn. Supersecondary structures. Definition of protein domain. The bonds that stabilize the tertiary structure of proteins. Fibrous proteins and globular proteins. Structural classification of proteins. Fibrous proteins: keratin, silk fibroin, collagen, elastin. Collagen: primary structure, secondary structure (triple helix); synthesis and post-translational modifications (hydroxylation of proline and lysine, and the role of ascorbic acid, glycosylation, processing of pro-collagen; oxidation of lysine and formation of crosslinks).

Membrane proteins.

Folding and denaturation of proteins. Protein misfolding and human diseases.

Porphyrins and heme. Structure of myoglobin, hemoglobin and globin chains. Classification of globin chains. Saturation curve with oxygen in hemoglobin and myoglobin. Hemoglobin as allosteric protein. Oxyhemoglobin and deoxyhemoglobin structure. Bohr effect, 2.3 BPG. Hemoglobin and CO2. Hemoglobin and acid-base balance. Fetal hemoglobin. Molecular basis of hemoglobinopathies and thalassemias.

Fundamental principles of the techniques for protein purification and assay (precipitation, chromatography, electrophoresis, ultracentrifugation, immunoassays).

Basic principles of the techniques for sequencing and for the determination of the three-dimensional structure (X-ray crystallography, NMR) of proteins.

MITOCHONDRIAL BIOENERGETICS

Principles of chemical thermodynamics; ATP and high energy compounds; Role of ATP in bioenergetics. Relationship between variation of the standard free energy and standard redox potential.

Pyridin-nucleotide coenzymes: NAD and NADP; structure and function; nicotinic acid and nicotinamide (vitamin PP).

Mitochondrial electron transport chain: inner and outer mitochondrial membrane; standard redox potential of the components of the electron transport chain. Organization of the electron transport chain in the inner membrane lipoprotein complexes (complex I - II - III - IV) and mobile carriers (ubiquinone and cytochrome C). Flavin coenzymes (structure and function, FMN and FAD, riboflavin or vitamin B2); Iron-sulfur proteins; Structure and function of cytochromes. Structure and functions of Complex I (NADH-ubiquinone oxidoreductase), complex II (succinate-ubiquinone oxidoreductase), complex III (ubiquinol-cytochrome c oxidoreductase), complex IV (cytochrome oxidase). Inhibitors of electron transport.

Oxidative phosphorylation: mitochondrial ATP synthase (complex V): structure and function of the factors F1 and F0, P/O ratio; chemiosmotic coupling hypothesis, electrochemical proton gradient, respiratory control; uncoupling. Thermogenin and brown adipose tissue.

METABOLIC BIOCHEMISTRY

Vitamins and coenzymes.

Thiamine, riboflavin, pyridoxine, nicotinamide, pantothenic acid, coenzyme A, biotin, folic acid, retinol, calciferol, ascorbic acid, vitamin B12 functions

Glucidic metabolism

Biological importance of carbohydrates: glycogen, starch, disaccharides, monosaccharides.

Aerobic glycolysis and anaerobic: chemical reactions, enzymes and functional significance. Origin of lactic acid and lactate dehydrogenase (LDH). Alcoholic fermentation. Energy balance of glycolysis.

Oxidative decarboxylation of pyruvic acid.

The citric acid cycle or Krebs cycle: reactions and energy balance. Mitochondrial localization of enzymes.

Glycogen synthesis and glycogenolysis. Regulation of the metabolism of the liver and muscle glycogen.

Gluconeogenesis.

Mechanism of action of adrenaline, glucagon and insulin.

Metabolism of fructose, lactose and galactose.

Pentose pathway: role of NADPH in metabolism. Favism. Other mechanisms for NADP reduction (malic enzyme and transhydrogenase).

Lipid metabolism

beta-oxidation of fatty acids (role of carnitine, chemical reactions, energy yield, oxidation of fatty acids with odd number of carbon atoms and vitamin B12, oxidation of unsaturated fatty acids, peroxisomal beta-oxidation, alpha-oxidation). Lipolysis, hormone-sensitive lipase and its regulation.

Biosynthesis of ketone bodies; utilization of ketone bodies; diabetic ketoacidosis.

Fatty acid biosynthesis: transport of acetyl-CoA from the mitochondria to the cytoplasm (the role of citrate and carnitine), acetyl- carboxylase and biotin, fatty acid synthase, and acyl carrier protein, regulation of the synthesis of fatty acids, chain elongation reactions (microsomal and mitochondrial); mechanism of the desaturation; essential fatty acids; arachidonic acid derivatives (eicosanoids): prostaglandins, prostacyclin, thromboxanes, leukotrienes.

Biosynthesis of triglycerides. Metabolic pathways of conversion of sugar into fat.

Biosynthesis and degradation of phospholipids, sphingolipids, and glycolipids.

Digestion of lipids; pancreatic lipase, biliary salts; micelles and intestinal absorption of lipid; pancreatic juice, bile composition, cholecystokinin-pancreozymin, secretin, steatorrhea (pancreatic insufficiency and biliary insufficiency), biosynthesis of triglycerides in the intestine (monoglycerides pathway); chylomicrons; biosynthesis of triglycerides (liver and adipose tissue); methods of separation of lipoproteins (electrophoretic separation on agarose gel; separation by ultracentrifugation at increasing density); classification and chemical composition of lipoproteins (chylomicron, VLDL, LDL, HDL ); role of lipoproteins in the transport of exogenous and endogenous fat; lipoprotein lipase; blood transport of non-esterified fatty acids (NEFA) in the form of complexes with albumin; receptor-mediated endocytosis of LDL; regulation of the synthesis of cholesterol and LDL receptors by intracellular cholesterol. Cholesterol biosynthesis and its regulation; bile acid biosynthesis; enterohepatic circulation; biosynthesis of biliary acids; biosynthesis of vit. D; biosynthesis of steroid hormones.

Classification and molecular pathogenesis of hyperlipidemia.

Amino acid metabolism.

Digestion of proteins: mechanism of HCl secretion in the stomach; gastric protease (pepsin); pancreatic proteases (trypsin, chymotrypsin, elastase, carboxypeptidase); intestinal peptidases (aminopeptidase, tripeptidase, dipeptidase); intestinal absorption of amino acids

Essential and non-essential amino acids. Nitrogen balance, daily protein requirement, biological value of protein.

Catabolism of amino acids: oxidative deamination and transamination of amino acids, glutamine synthetase, glutaminase and functions of glutamine, "muscle-liver"alanine cycle; urea cycle; correlation between the urea cycle and tricarboxylic acid cycle, glucogenic and ketogenic amino acids.

Biosynthesis of nonessential amino acids.

Synthesis of serine from 3-phosphoglycerate; serine transhydroxymethylase and tetrahydrofolate; non-oxidative deamination of serine and threonine (serine threonine dehydratase)

Glycine: serine-glycine conversion, glycine synthase. Heme biosynthesis (see hemoglobin metabolism); role in the biosynthesis of creatine, glutathione and purine nucleotides.

Metabolism of phenylalanine and tyrosine: catabolism to fumarate and acetoacetate, biosynthesis of melanin, biosynthesis catecholamines (dopamine, noradrenaline and adrenaline). Degradation of catecholamines. Phenylketonuria, alkaptonuria, albinism.

Tryptophan metabolism; biogenesis of nicotinic acid. Biosynthesis and degradation of serotonin

Metabolism of methionine and S-adenosyl-methionine. Methyl cycle and role of folic acid and vitamin B12.

Decarboxylation of amino acids: biosynthesis of polyamines, catecholamines, serotonin, histamine and GABA.

Metabolism of cysteine (with taurine and glutathione synthesis)

Arginine metabolism and synthesis of NO.

Metabolism of branched chain amino acids (valine, isoleucine, leucine).

Biosynthesis, transport and degradation of proteins.

Integration and hormonal control of glucidic, lipid and protein metabolism during the fasting-feeding cycle.

Metabolism of hemoglobin.

Iron metabolism. Biosynthesis and catabolism of heme. Hyperbilirubinemia.

Nucleotide metabolism

Biosynthesis "de novo" of pyrimidine nucleotides and its regulation. De novo biosynthesis of purine nucleotides and interconversion. Conversion of ribonucleotides into deoxyribonucleotides. Salvage pathways. Purine catabolism and uric acid; hyperuricemia (primary and secondary gout).

Cell and tissue biochemistry.

Mechanisms of DNA repair and correlations with the phenomena of cellular aging and with human diseases (in particular with cancer).

Pathways of signal transduction.

Receptors with seven transmembrane domains, G proteins, enzyme effectors (adenylyl cyclase, phospholipase C), second messengers (cAMP, IP3, DAG, Ca+ +). Phosphoinositide cycle. PKA and PKC. Cyclic GMP and NO. Receptors with tyrosin kinase activity. Kinase cascades. Transduction pathways through PI3K/PKB. The MAP kinase pathway. JAK-STAT pathway.

Biochemical aspects of the cell cycle and apoptosis.

Biochemistry of metals

Iron and copper: cellular homeostasis and human diseases.

Endocrine biochemistry.

Biosynthesis and degradation, release, metabolic and other physiological effects, receptors, signal transduction pathways of the following hormones: glucagon, insulin, adrenaline and noradrenaline, hypothalamic and pituitary hormones, thyroid hormones, steroid hormones (glucocorticoids, mineralocorticoids, sex hormones), parathyroid hormone, calcitonin and vit D. Hormonal regulation of salt and water balance.

Blood biochemistry.

Plasma and serum. Plasma proteins. Blood clotting.

Biochemistry of the liver.

Metabolic roles. Detoxification processes. Reactions of phase 1: the cytochrome P450 CYP enzymes. Reactions of stage 2. Hepatic metabolism of ethanol.

Muscle tissue and biochemistry of physical exercise.

Classification of muscle fibers. Muscle bioenergetics: exoergonic mechanisms in muscle contraction: anaerobic (alactacid and lactacid) and aerobic metabolism. ATP, phosphocreatine and creatine kinase, adenylate kinase or miokinase, anaerobic threshold, anaerobic glycolysis and glycogen, beta-oxidation and carnitine; anaerobic and aerobic exercise, oxygen debt.

Principles of Neurochemistry

Neurotransmission: neurotransmitter, the synapse (presynaptic terminal, synaptic vesicles, mitochondria, pre-and post-synaptic membrane, synaptic cleft). Postsynaptic receptors: ionotropic receptors and receptors coupled to second messengers (metabotropic receptors).

Biosynthesis and functional aspects of noradrenaline, dopamine, serotonin, acetylcholine, glutamate, GABA.



Textbook Information

Siliprandi-Tettamanti. Biochimica Medica. Piccin.
Nelson Cox. I principi di Biochimica di Lehninger. Zanichelli




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