Dec 19, 2013 ... Teaching Medical biochemistry includes scope of cellular, physical and .....
Practical exam- test with multiple choice questions -max 2 points.
SYLLABUS OF MEDICAL BIOCHEMISTRY
Teaching Medical biochemistry includes scope of cellular, physical and genetic foundations of biochemistry, enzymes as catalysts, cellular bioenergetics, carbohydrate, protein and lipid metabolism, nitrogen metabolism, gene expression and protein synthesis, biosignaling, biochemical endocrinology, chemistry of blood, liver metabolism, biochemistry of muscle contraction, metabolism of nervous system, biochemistry of extracellular matrix and connective tissues, vitamins, minerals and trace elements and clinical enzymology. Medical Biochemistry course is organized in 20 weeks of teaching and starts 9 weeks after beginning of school year, following the chemistry course. The total of 166 hours of medical biochemistry course is organized as 3 hours of lectures, 3 hours of seminars and 3(2) hours of laboratory practice per week. During the course, continuous evaluation of students’ knowledge and activity is performed through quizzes, two colloquiums and activity on seminars.
LECTURES (60 hrs) BIOLOGICAL CATALYSIS (6 hrs) I
Enzymes as catalysts-general aspects. Definition, specificity, intracellular localization and classification of enzymes. Mechanisms of enzyme-catalyzed reactions: covalent and acid-base catalysis. Role of coenzymes and metals in catalysis. Mechanism-based inhibitors.
3
II
Regulation of enzyme activity: Enzyme kinetics as an approach to understanding mechanism. The Michaelis-Menten equation model. Enzyme inhibitors: irreversible and reversible competitive and non-competitive. Regulation of enzyme activity: allosteric enzymes, covalent modifications. Regulation of metabolic pathways.
3
CELLULAR BIOENERGETICS (9 hrs) III
Basic aspects of metabolism. Definition, sequence of metabolic reactions, metabolic pathways. Intermediary metabolism. Bioenergetics and thermodynamics. Chemical logic and common biochemical reactions. Phosphoryl group transfers and ATP. Biological oxidationreduction reactions. Digestion and absorption of carbohydrates, proteins and lipids.
3
IV
The respiratory chain and oxidative phosphorylation. Oxidation-reduction components of the electron transport chain. Coupling of electron transport and ATP synthesis. Chemical uncouplers. Transport through inner and outer mitochondrial membranes.
3
V
Tricarboxylic acid cycle. Pyruvate dehydrogenase complex. Reactions, energetics and regulation of tricarboxylic acid cycle. Precursors of acetyl-CoA. TCA cycle intermediates and anaplerotic reactions.
3
INTEGRATION OF METABOLISM (12 hrs) VI
Carbohydrate metabolism-part I. Glycolysis: reactions and regulation, oxidative fates of pyruvate and NADH, anaerobic glycolysis. Gluconeogenesis and maintenance of blood glucose level. Glycogen synthesis and degradation: reactions and regulation. Clinical aspects.
3
VII
Carbohydrate metabolism-part II. Pathways of sugar metabolism: pentose phosphate pathway, fructose and galactose metabolism. Reactions and regulation. Clinical aspects. Lipid metabolism- part I. Oxidation of saturated and unsaturated fatty acids. Alternative routes of fatty acid oxidation. Metabolism of ketone bodies. Reactions and regulation. Clinical aspects.
3
VIII
Lipid metabolism-part II. Biosynthesis of fatty acids, triacylglycerols and the major membrane lipids. Fatty acid synthase complex. Elongation and desaturation of fatty acids. Structure and function of phospholipids and sphingolipids. Cholesterol synthesis, transport and metabolic fate. Synthesis, role and metabolic fate of lipoproteins. Clinical aspects.
3
IX
Metabolism of amino acids. Synthesis and degradation of amino acids. Essential and nonessential amino acids. Glycogenic and ketogenic amino acids. The role of cofactors in amino acid metabolism. Fate of amino acid nitrogen: urea cycle, reactions and regulation. Intertissue relationships in the metabolism of amino acids. Disorders of amino acid metabolism.
3
INFORMATION PATHWAYS (9hrs) X
Purine and pyrimidine metabolism. De novo and “salvage” pathways for purine and pyrimidine synthesis. Degradation of purine and pyrimidine bases. Reactions and regulation. Metabolic disorders. DNA organization, replication and repair. DNA structure: primary, secondary and tertiary. DNA supercoiling. The structure of chromosomes. DNA replication. Repair mechanisms.
3
XI
RNA structure, synthesis and processing. Structure of RNA. Transcription of eukaryotic genes. Types of RNA polymerases. RNA processing.
3
XII
Protein synthesis and degradation. The genetic code. Formation of aminoacyl-tRNA. Process of translation: initiation, elongation and termination. Processing of proteins. Posttranslational modifications. Protein targeting and degradation. Clinical significance.
3
BIOSIGNALING. HORMONES. TISSUE METABOLISM (24 hrs) XIII
Biological membranes and transport. The composition and architecture of membranes. Membrane dynamics. Solute transport across the membranes. Membrane selectivity. Transport through plasma, nuclear and mitochondrial membranes. Hormones: diverse structures and diverse functions. Hormone classification according to structure, mechanisms of action, transport and storage.
3
XIV
Basic concept of hormone action. General features of signal transduction: G-protein-coupled receptors and second messenger, receptor tyrosine kinases, receptor guanylil cyclase, cGMP, Protein kinase G, gated ion channels. Regulation of transcription by steroid hormones.
3
XV
Structure, mechanism of action and effects of (1): insulin and glucagon, thyroid hormones, hormones involved in regulation of calcium metabolism.
3
XVI
Structure, mechanism of action and effects of (2): hormones of adrenal medulla and cortex, sex hormones. Endocrine role of kidney and adipose tissue.
3
XVII
Basic concept of cell structure. Intracellular components and compartments. Tissue metabolism 1. Biochemistry of blood cells. Porphyrins and bile pigments. Clinical aspects.
3
XVIII
Tissue metabolism 2. Liver metabolism. Biochemistry of muscle contraction. Metabolism of nervous system. Biochemistry of extracellular matrix and connective tissues. Clinical aspects
3
XIX
Vitamins and minerals. Classification and function. Vitamins as coenzymes; reactive oxygen species; oxidative stress; vitamins as antioxidans.
3
XX
Oncogenesis and cell cycle. Oncogenes and tumor suppressor genes. Cell cycle: regulation and disturbances. Regulation of the cell cycle by protein kinases. Programmed cell death.
3
SEMINARS (60 hrs) BIOLOGICAL CATALYSIS (9hrs) I
Proteins. The three-dimensional structure and function. Structure and function of oxygenbinding proteins (myoglobin and hemoglobin). Protein denaturation and folding. Ubiquitindependent proteolysis: proteasomes.
3
II
Mechanisms of enzyme catalysis. Functional groups in catalysis. Covalent and acid-base catalysis (lysozyme, chymotrypsin). Metal ions in catalysis: the importance of zinc ion in the active site of carbonanhydrase.
3
III
Clinical significance of enzymes. Isoenzymes, definition and clinical importance. Basic principles of enzyme activity determination in clinical diagnostics. Clinical significance of alkaline phosphatase, aspartate aminotransferase, alanine aminotransferase, creatine kinase, lactate dehydrogenase, γ-glutamyltransferase, amylase.
3
BIOENERGETICS (9hrs) IV
Regulation of metabolic pathways: covalent and non covalent mechanisms. Regulatory enzymes of metabolic pathways. Directing substrates by enzyme compartmentalization. The reciprocal regulation of metabolic pathways. Feed-forward and feed-back regulation.
3
V
Biological oxidation-reduction reaction and oxidative phosphorylation. Oxidoreducatases and their coenzymes. The shuttle systems: glycerophasphate and oxaloacetate-malate. Components of the respiratory chain. The coupling of respiration and ATP synthesis. Brown adipose tissue and thermogenin.
3
VI
The central role of tricarboxylic acid cycle in metabolism. Generation of acetyl CoA: pyruvate dehydrogenase complex, enzymes and coenzymes, regulation. TCA cycle: reactions and regulation. The central role of TCA cycle in catabolic pathways of carbohydrates, lipids and amino acids. Krebs cycle intermediates as starting compounds for a variety of biosynthetic products.
3
INTEGRATION OF METABOLISM - THE PROVISION OF METABOLIC FUELS (12 hrs) VII
Central role of glucose in carbohydrate metabolism. Maintenance of blood glucose level (after a meal, between meals and in fasting conditions). Glucose, fructose and galactose metabolism. Lactose intolerance. The formation of glucuronides. Carbohydrates as components of extracellular matrix.
3
VIII
Fatty acid synthase as a muticatalytic protein. Structure (domains and catalytic sites), and reactions. Sources of acetyl-CoA for the synthesis of fatty acids. Synthesis of fatty acids with more than 16C atoms. Mechanisms of fatty acid desaturation. Fatty acids as an energy reserve.
3
IX
Clinical significance of lipoproteins. Definition and classification. Classification of apolipoproteins. Clinical significance: increased production of lipoproteins/inadequate cellular download of lipoproteins: hypertriglyceridemia, hypercholesterolemia and familiar hyperlipidemia. The rationale of diet and the treatment of patients with increased cholesterol levels.
3
X
Amino acids important for the synthesis of some biologically important compounds and sources of biosynthetic units in biosynthetic reactions. Amino acids as precursors of creatine, beta-alanine, polyamines and glutathione. Biotin, tetrahydrofolate, vitamin B12, and S-adenosyl methionine as sources of biosynthetic units in biosynthetic reactions.
3
INFORMATION PATHWAYS (9 hrs) XI
Control of DNA replication fidelity, mismatch repair mechanisms. DNA replication. The role of DNA polymerase. Post-replication mechanisms: mismatch repair, base excision-repair, nucleotide excision-repair, double-strand break repair. Mutations.
3
XII
Regulation of gene expression. Different levels of control: genome, transcription, RNA processing and translocation, translation, posttranslational protein modification. Differences between control of gene expression in prokaryotes and eukaryotes.
3
XIII
Post-translational processing of proteins in endoplasmic reticulum and Golgi apparatus. Intracellular traffic and sorting of proteins: Folding, modification and targeting of the protein. The roles of chaperones in protein folding. Protein synthesis on rough endoplasmic reticulum. Processing of glycoproteins in Golgi cisterns. Diseases caused by disorders of intracellular synthesis and degradation.
3
BIOSIGNALING. HORMONES. TISSUE METABOLISM (21 hrs) XIV
Composition and architecture of biological membranes. Subcellular compartments and intracellular membrane systems. Pathological processes as a consequence of cell membrane damage. Inappropriate signal transduction. Apoptosis, necrosis and autophagy.
3
XV
Plasma membrane receptors and signal transduction. Basic mechanisms of signal transmission via membrane and intracellular receptors, signal transduction pathways. Intracellular transcription factor receptors.
3
XVI
Autocrine and paracrine hormones. Eicosanoid classification. Cyclooxygenase and lipooxygenase pathways. Gastrointestinal hormones: mechanisms of action.
3
XVII
Disorders caused by changes in hormonal status. Glucose intolerance/Diabetes Mellitus. Disorders of calcium metabolism. Osteoporosis. Chronic glucocorticoid tratement and its effects.
3
XVIII
Metabolic functions of the liver and ethanol metabolism. Detoxification of xenobiotics and metabolites in liver. Cytochrome P450 family. Ethanol oxidation; toxic effect of ethanol metabolism; ethanol and free radical formation. Biochemical disorders due to chronic ethanol abuse. Clinical aspects of metabolic disorders in various tissues. Disorders of liver dysfunction and metabolism. Erythrocyte metabolism disorders (anemia, reduced activity of glucose-6phosphate dehydrogenase). Oxygen toxicity and free radical injury: generation of reactive oxygen species, anti-oxidative cell protection: enzymatic and non-enzymatic. Muscle metabolism during aerobic and anaerobic exercise.
3
Hiper and hypovitaminosis. Definition and classification. Vitamin A deficiency as a cause of blindness. Vitamin D deficiency: rickets and osteomalatia. Hypervitaminosis A and D. Antioxidant role of vitamin C and E. Role of vitamin K in blood coagulation.
3
XIX
XX
3
LABORATORY EXCERSISES (46 hrs) I
General properties of enzymes and regulation of enzyme activity. Starch hydrolysis by salivary amylase and hydrochloric acid. Absolute substrate specificity of urease. Specificity of salivary α-amylase. Effects of changes in pH and temperature on enzymatic activity. Activators and inhibitors of α-amylase.
3
II
Enzyme kinetics. Determination of the kinetic parameters (Km, Vmax) of β-Dfructofuranosidase for sucrose. Determination of the concentration of reducing sugars by Folin-Wu’s method.
3
III
Diagnostic enzymology. Determination of alkaline phosphatase activity in blood serum (Raabe’s method). Determination of α-amylase activity in serum (Wohlgemuth’s method)
3
IV
Digestion. Pepsin activity in stomach mucosa extract. Hymosine activity. Trypsine activity in pancreas tissue extract. Lipase activity. Phospholipase activity
3
V
Oxidative phosphorylation. The electron transport chain.
3
VI
Carbohydrates – glucose. Quantitative determination of glucose in serum
3
VII
Carbohydrates – glycogen. Extraction of total amount of glycogen from rat liver tissue. Determination of total amount of glycogen in rat liver tissue.
2
VIII
Lipids. Quantitative determination of serum triacylglycerols. Quantitative determination of serum cholesterol. Determination of HDL and LDL cholesterol.
2
IX
Nonprotein nitrogen metabolites. Quantitative determination of urea in serum and urine (Berthelot’s method). Quantitative determination of uric acid in serum and urine by enzymecolorimetric method
2
X
Main recombinant DNA techniques used in medicine. Polymerase chain reaction (PCR). In situ hybridization. DNA analysis in practice.
2
XI
Plasma and serum proteins 1. Preparation of standard curve for determination of protein concentration –Biuret method.
2
XII
Plasma and serum proteins 2. Determination of total protein concentration in serum by the Biuret method. Determination of the concentration of albumin and globulins in blood serum by Biuret method. Determination of total protein concentration in serum by Philips van Slyke’s method.
2
XIII
Metabolites of porphyrins in serum and urine. Determination of iron concentration in serum. Determination of direct and indirect bilirubin in serum using Jendrassik-Grof method. Demonstration of urobilinogen in urine using Erlich’s reagent. Demonstration of presence of urobilin in urine.
2
XIV
Liver function examination. Determination of activity of alanine aminotransferase and aspartate aminotransferase.
2
XV
Electrolytes in serum 1. Determination of serum chloride concentration (Keler’s method). Determination of bicarbonate concentration in blood serum (Scribner’s method).
2
XVI
Electrolytes in serum 2. Determination of serum calcium concentration. Determination of inorganic phosphorus in serum by UV method. Determination of magnesium concentration in blood serum and urine.
2
XVII
Physico-chemical properties of urine. Determination of the specific gravity of urine. Analysis of morning urine using universal indicator paper. Urine sediment analysis.
2
XVIII
Biochemical properties of urine. Determination of creatinine concentration in urine (Jaffe’s method). Determination of urine chloride concentration (Volhard – Charpentie’s method).
2
XIX
Oxidative stress. Determination of the amount of lipid peroxides in liver tissue.
2
XX
Cellular defense against oxygen toxicity – antioxidant enzymes and nonenzymatic antioxidants. Determination of glutathione in red blood cells. Catalase activity in rat liver tissue.
2
TIME TABLE BIOCHEMISTRY- III SEMESTER 2013/14. December 18, 2013 14:15-16:30 Practical 1
December 19, 2013 8:00-09:45 Lecture 1 09:45-11:30
Lecture 2
14:15-16:30
Seminar 1
Week I General properties of enzymes and regulation of enzyme activity (dr Milica Velimirović/dr Anđelka Isaković)
Enzymes as catalysts-general aspects (Doc. dr Ana Savić-Radojević) Regulation of enzyme activity (Doc. dr Marija Matić)
Proteins: Structure and function. Ubiquitin-dependent proteolysis: proteasomes. (Ass dr Željka Stanojević /Ass dr Tatjana Nikolić) December 23, 2013- January 7, 2014 CHRISTMAS HOLIDAY January 08, 2014 Week III 14:15-16:30 Practical 2 Enzyme kinetics (dr Marija Dulović/ dr Vesna Ćorić) January 09, 2014 9:00-11:15 Lecture 3
Basic aspects of metabolism. Digestion and absorption of carbohydrates, protein and lipids (Prof. dr Ivanka Marković)
13:15-15:30
Seminar2
Mechanisms of enzyme catalysis (Prof dr Aleksandra Isaković/Doc dr Marija Matić )
15:30-17:45
Seminar 3
Clinical significance of enzymes (Ass dr Tatjana Đukić/Ass dr Tatjana Nikolić)
January 15, 2014 12:30-14:00 Biophysics` Seminar 1*
Week IV Biophysical methods in determination of structure of macromolecules (Prof. dr Nebojša Milošević/ Doc. dr Dejan Žikić)
14:15-16:30
Diagnostic enzymology (dr Marija Dulović/dr Tihomir Stojković)
Practical 3
January 16, 2014 9:00-11:15 Lecture 4
14:15-16:30
Seminar 4
January 22, 2014 14:15-16:30 Practical 4 January 23, 2014 9:00-11:15 Lecture 5
The respiratory chain and oxidative phosphorylation (Prof. dr Aleksandra Isaković) Regulation of metabolic pathways: covalent and noncovalent mechanisms (Doc dr Ana Savić Radojević/Ass dr Željka Stanojević) Week V Digestion (dr Milica Velimirović/dr Vesna Ćorić)
The tricarboxylic acid cycle- reactions and regulation (Prof. dr Nataša Petronijević)
14:15-16:30
Seminar 5
Biological oxidation-reduction reactions and oxidative phosphorylation (Doc dr Sonja Misirlić Denčić/ Ass dr Tatjana Đukić)
January 29, 2014 12:30-14:00 Biophysics` Seminar 2*
Week VI Thermodynamics (Prof. dr Nebojša Milošević /Doc .dr Mirjana Platiša)
14:15-16:30
Oxidative phosphorylation (dr Vesna Ćorić/ dr Tihomir Stojković)
Practical 5
January 30, 2014 9:00-11:15 Lecture 6 14:15-16:30
Seminar 6
Carbohydrate metabolism -part 1 (Prof dr Tatjana Simić) PDH complex. The central role of tricarboxylic acid cycle in metabolism (Prof. dr Ivanka Marković/Doc. dr Sonja Misirlić Denčić)
Lectures will be held in Head building and seminars and laboratory practicles at the Institute of
histophysiology (Biochemical rooms)
* Seminars from Biophysics will be held at the Institute of histophysiology (Rooms number 1 and 2, first floor)
GRADING POLICY
Chemistry mark - max 1 point (score ≥ 90/100 may improve final grade)
During academic year, continuous evaluation of students’ knowledge and activity is performed through ten laboratory quizzes, two colloquiums and activity on seminars (five short essay questions and two presentations)- max 2 points
Practical exam- test with multiple choice questions -max 2 points
Final exam- test with multiple choice questions-max 5 points
Medical Biochemistry Course Director Assistant Professor Ana Savic Radojevic Email:
[email protected]
