Biochemistry Biochemistry is a science concerning the chemical

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Biochemistry
Biochemistry is a science concerning the chemical reactions occuring in living cells and organisms.
Biochemistry in the medicine is mainly concerned with balance of biochemical reactions occuring in
the body, both in physiological state as in pathology.
The program of teaching biochemistry for medical students consists of lectures, seminars and
laboratory classes.
The main object comprises five sections: Structure and Function of Proteins and Enzymes,
Metabolism of Carbohydrates, Lipids of Physiological Significance, Nulceic Acids and special topics
(Nutrition, Digestion, Vitamins, Plasma Proteins, Immunoglobulins, Haemostasis, Xenobiotics). At the
end of the course students must take the final examination prepared by Board of Medical Examiners.
Teachers:
1. Prof. dr hab. med. Józef Kędziora
2. Dr Jolanta Czuczejko
3. Dr Karolina Szewczyk-Golec
4. Dr Mariusz Kozakiewicz
Contact: Jolanta Czuczejko [email protected], Karolina Szewczyk-Golec [email protected], Mariusz
Kozakiewicz [email protected]
Syllabus
I. Department of Biochemistry
II. Head of the Unit: prof. dr hab. med. Józef Kędziora
III. Faculty of Medicine, Medical Program, for:
- second semester (summer) of the first year
- first semester (winter) of the second year
IV. Course coordinator – prof. dr hab. Józef Kędziora
V. Form of the classes - lectures, tutorials, seminars
VI. Assessment - examination
VII. Subject hours:
-
second semester (summer) of the first year - 30 hours of lectures, 30 hours of practicals and
seminars
-
first semester (winter) of the second year - 30 hours of lectures, 30 hours of practicals and
seminars
VIII. Aim of the course:
Acquiring knowledge of the chemical processes occuring in human cells. Studying the chemical
constituents of human cells: structure, properties and function of proteins, saccharydes, lipids,
nucleic acids, vitamins and coenzymes. Studying biochemical aspects of metabolic disorders. Analysis
of the compartmentation, integration and regulation of metabolic pathways. Learning about the
metabolism of the main human organs. Emphasising the relationships between medicine and
biochemistry and the role of biochemical knowledge in medical diagnostics.
Amino acids, peptides, proteins.
1. Nature of Proteins
-
Function: Enzymatic catalysis, transport and storage of small molecules, structural
elements of cytoskeleton, immunity (immune defense system)
2. Amino Acids – fundamental units of proteins
-
Composition
-
Optical activity
-
Amphoteric properties
3. Peptides and polypeptides
-
Formation
-
Amphoteric properties
4. Purification of proteins
5. Conformation of proteins - primary, secondary, tertiary, quaternary structure
6. Protein Structure – Function Relationship
Oxygen transport proteins
A. Myoglobin and Hemoglobin Structure and Function
B. Hemoglobinopathies (HbS, HbC, HbM, thalassemias)
C. Humoral Immunity - five basic classes of immunoglobulin (structure and function): IgM,
IgD, IgG, IgE, IgA
D. Fibrous proteins - collagen
Enzymes, co-enzymes, vitamins.
1. General characteristics of enzyme
Differences between enzymes and chemical catalysts
-
Measures of enzyme activity
-
Enzymes nomenclature
2. Enzyme Kinetics
A.
Quantification of enzyme activity
B.
Quantification of chemical reaction by kinetic order
C
Michaelis – Menten kinetic theory of enzyme action
-significance of the Michaelis constant
-Lineweaver Burk transform
3. Enzyme Inhibition
A.
Competitive
B.
Uncompetitive
C.
Medical relevance of enzyme inhibitor
D.
Regulation of enzymes
4. Enzymes in clinical diagnosis
5. Nomenclature of vitamins - water soluble and fat soluble.
6. Coenzymes:
Nicotinamide-adenine dinukleotide (NAD+)
Nicotinamide – adenine dinukleotide phosphate (NADP+)
Flavin mononucleotide (FMN)
Flavin adenine dinukleotide (FAD)
CoA-SH, ACP
Folic acid
Pyridoxal phosphate (PLP)
Thiamin pyrophosphate (TPP)
Biotin
Cobalamine
Ascorbic acid
7. Cofactors: metal ions of Co, Cu, Mg, Mn, Se, Zn, Fe.
Saccharides, glycolysis pathway, tricarboxylic acid cycle, pentose phosphate pathway.
1. Structures of saccharides
A. Open chain form (asymmetric carbon, isomers, epimers, enantiomers, hemiacetals)
B. Cyclic form (acetals, glycosialles) polysacharydes
2. Carbohydrate derivates
A. Phosphoric acid esters of monosacharides
B. Amino sugars
C. Sugar acids
D. Deoxy sugars
3. Glycoproteins - physiologic functions
A. Glycosaminoglycans (heparin, chondroitin sulfate, dermatan sulfate, heparin sulfate,
keratin sulfate, hyaluronic acid)
4. Glycolysis - anaerobic glycolysis, aerobic glycolisys.
5. The pyruvate dehydrogenase (PDH) enzyme complex, PDH regulation
5. Pentose phosphate pathway
6. Uronic acid pathway (glucuronic acid cycle)
7. Citric acid cycle
Oxidative phosphorylation and biologic oxidation.
Mitochondrial Electron Transport
Localization of electron transport chain
1. The outer membrane
2. The itermembrane space present
3. The inner membrane
4. Organization of the electron transport chain - Complex I, II, III, IV
Lipids
1. Nomenclature of lipids and physiologic significance
2. Phospholipids and glycosphingolipids – structure, function and biosynthesis
3. Fatty acids chain biosynthesis
4. Desaturase & elongase enzyme systems
5. Eicosanoids biosynthesis and their physiologic role
6. Cholesterol biosynthesis (regulation of HMG-CoA reductase activity)
7. Cholesterol as a precursor of steroids (corticosteroids, sex hormones, bile acids, vitamin D)
8. Lipid and cholesterol transport and storage – plasma lipoproteins
9. β-oxidation of saturated, unsaturated and odd number of carbon atoms fatty acids
10. Ketogenesis
11. Lipid peroxidation
12. Interrelationships among carbohydrates and lipids metabolism
Nucleic acids – structure, function, organization. Molecular genetics.
1. Human genome – definition and structure. Nucleosome and chromatin package. Hetero –
and euchromatin. Structure of nucleic acids. Genetic information and genetic code. Organization
of genes, promoters, microsatellite DNA, pseudogenes.
2. DNA replication – DNA polymerases, start of replication, role of starters in DNA synthesis,
Okazaki fragments. Topology of DNA associated with replication and role of helicases.
3. Transcription of genetic information. RNA synthesis by DNA-dependent RNA polymerase.
Types of RNA and their function. Reverse transcriptase.
4. Translation of genetic information. Components of the translation apparatus. Protein
biosynthesis. Protein maturation and posttranslational modifications. Protein degradation and
turnover.
5. Epigenetics – DNA modifications, DNA methylation. Modulation of genes expression.
Epigenetics and cancer.
6. DNA damage and repair. DNA damage in the way of health & on the way to ageing. Oxidative
DNA damage and repair. Measurement of DNA damage. Biological consequences of oxidative
DNA damage. DNA repair pathways. Mutagenesis. Mutations and polymorphisms in genes
encoding DNA repair enzymes.
7. Mitochondrial genome and its metabolism. Organisation of the human mitochondrial
genome.
Maternal
inheritance.
Nutrition, digestion & absorption.
High
mutation
rate.
Mutations
in
mtDNA.
1. Macro- and micronutrients. Digestion and absorption of proteins, carbohydrates and lipids.
Vitamins. Bile acids metabolism.
2. Energy metabolism. Protein-energy intake. Malnutrition. Obesity. Assessment of nutritional
status.
Blood, hemostasis & thrombosis.
1. The composition of blood. Blood cells and plasma. Oxygenation of blood.
2. Mechanism of blood coagulation.
Excretory system.
1. Organs of the excretory system. Removal of carbon dioxide excess by lungs. Skin functions.
Break-down of proteins and urea production in liver. Urea cycle.
2. Kidney function. Hormonal control of water and salt
Detoxification processes – liver functions
1. The metabolism of the liver - amino acids, urea cycle, proteins, carbohydrates, lipids
2. Steps of detoxification – cytochrome P450, conjugation (role of reduced glutathione GSH –
biosynthesis of mercapturic acids)
3. Other role of GSH – peroxidase glutathione (GSH-Px), reductase glutathione (GR), transport of
amino acids
Metabolism of amino acids.
Deamination (role of Glu), transamination, decarboxylation, glucogenic and ketogenic
aminoacids, role of aminoacids on biosynthesis, essential and non-essential amino acids
Hormones and hormonal regulation.
Hormones and the hormonal cascade system. Major polypeptide hormones and their action.
Steroid hormones. Hormone receptors and intracellular hormone signalling.
Practical 1 Chemical properties of amino acids
The aim of the class: studies on selected properties of amino acids
Theoretical basis: general structure of amino acids, the names (full names and their three-letter
abbrevations) and structures of protein amino acids, characteristics of the chemical groups attached to
amino acid chain (like carboxylic, amino, imino, sulphydryl, imidazol, guanidine, hydroxyl groups),
amphoteric properties of amino acids, classification of amino acids according to the chemical
properties of their side chains (charged, nonpolar hydrophobic, uncharged polar; aliphatic, cyclic,
aromatic; acidic, basic)
Practical 2 Some properties of peptides and proteins
The aim of the class: Some physical and chemical properties of peptides and proteins
Theoretical basis: structure and characteristics of the peptide bond, classification of peptides according
to their structures, the physiologic significance of some peptides in human body, the characteristics of
primary, secondary, tertiary and quaternary structures of proteins, classification of proteins according
to their structures, properties and functions, the amphoteric properties of proteins (the isoelectric
point of proteins)
Practical 3 Blood proteins
The aim of the class: Some properties of blood proteins
Theoretical basis: the constituents of the blood, the compositions of blood plasma and blood serum,
characteristics of main blood plasma proteins: albumins, globulins and fibrinogen, electrophoresis as
an important method of plasma (or serum) protein fractionation, the characteristics of individual
protein fractions,
Practical 4 Quantitative methods for determination of proteins
The aim of the class: Assessment of some quantitative methods for determination of total
protein concentration.
Theoretical basis: The physiologic and pathological concentrations of blood plasma protein, the
diagnostic role of alterations in the amount of total proteins and in mutual quantitative relationships
between individual fractions, examples of methods for protein concentration determination (biuret
protein assay, Lowry protein assay, Bradford protein assay)
SEMINAR / TEST I Amino acids, peptides, proteins
The key problems: The structure of protein amino acids. The classification of amino acids according to
both the polarity and the structural features of their side chains (e. g. polar, nonpolar; aliphatic,
aromatic; sulfur-containing; charged, uncharged; acidic, basic). The amphoteric properties of amino
acids, zwitterions. The structure of some modified amino acids (as selenocysteine, 4-hydroxyproline, 5hydroxylysine). The structure of some physiologically important nonprotein amino acids.
The formation, structure and properties of the peptide bond. Some important peptides in the
human organism (glutathione, peptide hormones). The insulin synthesis.
The classification of proteins according to their structure, properties and functions. The
characteristics of primary, secondary, tertiary and quaternary structures of proteins. The interactions
involved in a protein folding into its final conformation (e. g. the attraction between positively and
negatively charged molecules, the hydrophobic effect, hydrogen bonding, and van der Waals
interactions). Posttranslational modifications of amino acids in proteins. Structure – function
relationships in myoglobin, hemoglobin and immunoglobulins. The structure and synthesis of collagen.
Rybonuclease renaturation as an example of the importance of primary protein structure. The prions
as an example of medical importance of proper protein folding.
Practical 5 Preparation and purification of saccharase.
The aim of the class: the isolation and purification of yeast saccharase
Theoretical basis: the structure of enzymes, classification of enzymes, the enzymes names, the
methods of isolation and purification of enzymes from biological materials.
Practical 6 The kinetics of the enzymatic reaction
The aim of the class: the determination of the initial velocity and Michaelis constant in reaction
catalysed by saccharase
Theoretical basis: the enzyme-catalyzed reaction, the definitions of initial velocity, maximal velocity
and Michaelis constant, the Michaelis-Menten equation, the standard units of enzymatic activity (katal,
international unit), the influence of some factors on the enzyme activity (e. g. temperature, pH, the
concentration of substrate and enzyme, competitive and noncompetitive inhibitors).
Practical 7 Properties of vitamins A, C, D in biological materials
The aim of the class: Properties of retinol, ascorbic acid and cholecalciferol in different biological
materials
Theoretical basis: classification, structure and functions of water and fat soluble vitamins, classification,
structure and functions of coenzymes.
SEMINAR / TEST II Enzymes and coenzymes
The key problems: The definitions: enzyme, coenzyme, cofactor. The isoenzymes of the diagnostic
importance (lactate dehydrogenase (LDH), creatine phosphokinase (CPK)). The structure of the active
site and models for substrate binding. The specificity of enzymes to the substrates and the catalysed
reaction.
The catalytic mechanisms of the enzymatic reactions. The influence of physical and chemical factors on
the enzyme activity (temperature, pH, the enzyme concentration, the substrate concentration, the
product concentration).
The kinetics of enzymatic reaction: the initial and maximal velocities,
Michaelis constant, the Michaelis-Menten equation, the Lineweaver-Burk plot.
Regulation of enzyme activity: allosteric enzymes (allosteric activators and inhibitors, the
examples of allosteric enzymes, the sequential and concerted models for an allosteric enzyme, the
kinetics of allosteric enzyme reaction), feedback regulation and its examples in the human organism,
covalent modification of enzymes (phosphorylation), proteolytic cleavage (proenzymes, zymogens,
autocatalysis), reversible inhibition (competitive and noncompetitive inhibitors, the mechanism of the
inhibition, the kinetics of competitive and noncompetitive inhibitions, medical significance of
inhibition: acetylsalicylic acid, Fluorouracil, methotrexate, penicillin, allopurinol).
The standard units of enzymatic activity (katal, the international unit, the specific activity of an
enzyme). The classes of enzymes (oxidoreductases, transferases, hydrolases, lyases, isomerases,
ligases).
Coenzymes: their structrures and functions in the reactions. Water-soluble and fat-soluble vitamins:
their structures and functions. The trace elements: some enzymatic reactions that involve the iron,
cobalt, zinc, or copper ions.
Practical 8 Some properties of monosaccharides
The aim of the class: some chemical properties of monosaccharides
Theoretical basis: nomenclature of monosaccharides and their isomerism, the structure of
monosaccharides (Fischer projection and cyclic structure), the
chemical properties of
monosaccharides, the examples of biologically important monosaccharides.
Practical 9 Some properties of di- and polysaccharides
The aim of the class: some properties of biologically important disaccharides and
polysaccharides
Theoretical basis: nomenclature of disaccharides and polysaccharides, their structure and properties,
the examples of biologically important di- and polysaccharides, physiologically significant saccharide
derivatives (e. g. heparine) and glycoproteins
1. Iodine test – the detection of starch.
Practical 10 Saccharides of physiological importance
The aim of the class: preparation of glucose tolerance curve, the estimation of sialic acids
concentration in the blood serum
Theoretical basis: the glucose concentration in the blood, the maintenance of blood glucose levels,
regulation of blood glucose level by hormones, the glucose levels in diabetes mellitus, glucose
tolerance test in healthy persons and diabetes mellitus patients, the physiologic role of sialic acid
SEMINAR / TEST III Saccharides
The key problems: Classification of monosaccharides by both the number of contained carbon atoms
(e. g. triose, tetrose etc.) and the type of contained carbonyl group (aldose, ketose), and their
isomerism. Common disaccharides. The structure of important polysaccharides (starch and glycogen).
Physiologically significant saccharide derivatives (especially amino sugars). Synthesis and functions of
sialic acids.
Generation of ATP from glucose: glycolysis (reactions of glycolytic pathway, substrate-level
phosphorylation, regulation of glycolysis). Synthesis of 2,3-bis-phosphoglycerate in a “side reaction” of
the glycolytic pathway. Anaerobic glycolysis – (lactate fermentation, tissues dependent on anaerobic
glycolysis, fate of lactate – Cori cycle, lactic acidemia, ethanol fermentation). Fructose and galactose
metabolisms. Synthesis and degradation of lactose. Formation and degradation of glycogen. Disorders
of metabolisms of fructose, galactose and glycogen. The pentose phosphate pathway. The directions of
the pentose phosphate pathway reactions due to the cellular needs. Hemolysis caused by reactive
oxygen species in the conditions of glucose-6-phosphate dehydrogenase deficiency. Gluconeogenesis.
The maintenance of blood glucose levels by hormones (regulation of glycolysis and gluconeogenesis, as
well as formation and degradation of glycogen by insulin, glucagon and noradrenaline).
Practical 11 The electron-transport chain.
The aim of the class: studies on selected enzymes of the electron-transport chain and some
enzymes of antioxidative properties.
Theoretical basis: the oxidative-reduction components of the electron-transport chain and their
structures, the electron-transport chain as a major source of the free radicals in the cell, the
antioxidative defense in the human organism, the enzymatic and non-enzymatic components of the
antioxidative defense
SEMINAR / TEST IV Oxidative phosphorylation and tricarboxylic acid cycle
The key problems: Oxidative fates of pyruvate – oxidation of pyruvate to acetyl CoA by pyruvate
dehydrogenase. The tricarboxylic acid (TCA) cycle (reaction, enzymes, coenzymes, regulation of this
cycle). The energetics of the TCA cycle. Cellular bioenergetics: the compounds containing high-energy
bonds (ATP and the others nucleoside triphosphates, creatine phosphate, 1,3-bis-phosphoglycerate,
acetyl CoA). Oxidative fates of NADH, produced from glycolysis (glycerol 3-phosphate shuttle and
malate-aspartate shuttle). Transfer of compounds through the inner and outer mitochondrial
membranes. The generation of ATP from glucose (complete aerobic oxidation of glucose, anaerobic
glycolysis).
Oxidative phosphorylation. The electron-transport chain. Chemiosmotic model of ATP synthesis.
The structure of protein complexes of the electron-transport chain. Respiratory chain inhibitors,
chemical uncouplers of oxidative phosphorylation. The generation of reactive oxygen species (ROS) in
the cell (the mitochondrial electron-transport chain and other sources). ROS-mediated cellular injury.
Formation of free radicals during phagocytosis and inflammation. Cellular defences against oxygen
toxicity.
Practical 1 Some properties of lipids.
The aim of the class: some chemical properties of lipids, lipids of physiologic significance.
Theoretical basis: categories of lipids, the nomenclature of both saturated and unsaturated fatty acids,
examples of biologically important fatty acids, the structure of glycerolipids, the structure of
sphingolipids, the role of some important lipids in the human organism, the lipid peroxidation, the
structure of cholesterol, the physiological blood concentrations of both cholesterol and triacylglycerols,
the diagnostic significance of cholesterol, triacylglycerols and lipoproteins levels in the blood.
SEMINAR / TEST I Lipids
The key problems: Saturated and unsaturated fatty acids, their nomenclature and structure.
Acylglycerols, phosphoacylglycerols, sphingolipids, steroids, eicosanoids. Structure and functions of
cholesterol. The cholesterol derivatives (vitamin D, steroid hormones, the bile acids) and their role in
the organism. Transport of cholesterol by the blood lipoproteins. The cholesterol synthesis and its
regulation. Medical significance of elevated cholesterol blood levels. Dyslipoproteinemias.
Activation of long-chain fatty acids and their transport into mitochondria. β-oxidation of long-chain
fatty acids, oxidation of unsaturated fatty acids. Energy yield of β-oxidation. Odd-chain-lenght fatty
acids oxidation. Conversion of propionyl CoA to succinyl CoA. Metabolism of ketone bodies.
The acetyl CoA transport from mitochondria into cytosol (role of citrate). The sources of NADPH for
fatty acid synthesis. Fatty acid synthesis. Elongation of fatty acids. Desaturation of fatty acids.
Conversion of linoleic acid to arachidonic acid. The synthesis of eicosanoids and their physiologic
significance. Synthesis of triacylglycerols. Synthesis of glycerophospholipids and sphingolipids.
Integration of carbohydrate and lipid metabolism.
Practical 2 Nucleic acids extraction from yeast
The aim of the class: isolation of nucleic acids from yeast.
Theoretical basis: the structure and nomenclature of nucletides, the structure of nucleic acids: DNA
and RNA, the conditions of nucleic acid separation from yeast
Practical 3 Some properties of nucleic acids
The aim of the class: studies on the composition and some properties of nucleic acids
Theoretical basis: characteristics of nucleic acids, their structure, metabolism and functions in the
human body
SEMINAR / TEST II Nucleic acids and their metabolism
The key problems: The nomenclature and structure of purine and pirymidine bases. The structure of
nucleotides. Purine and pyrimidine synthesis and its regulation. The purine nucleotide salvage
pathway. The formation of deoxyribonucleotides. Degradation of purine and pyrimidine bases. LeschNyhan syndrome, sever combined immunodeficiency disease (SCID), hyperuricemia.
The structure of the nucleic acids. Synthesis of DNA. Transcription: synthesis of RNA. Translation:
synthesis of proteins. Regulation of gene expression. Use of recombinant DNA techniques in medicine.
The molecular biology of cancer.
Practical 4 Enzymes of digestive tract
The aim of the class: studies on some properties of digestive juices
Theoretical basis: the composition of digestive juices, the physical and chemical properties of digestive
juices, the role of the components of digestive juices in the digestion process. The characteristics of
digestive enzymes.
Practical 5 The constituents of the blood
The aim of the class: studies on some properties of some constituents of the blood
Theoretical basis: the constituents of both cellular and noncellular fractions of the blood, major
functions of the blood, the structure of hemoglobin and its role in the respiration (oxygen and carbon
dioxide transport), the oxygen-binding curve of hemoglobin, the allosteric effectors for oxygen binding
to hemoglobin (pH, carbon dioxide, 2,3-bisphosphoglycerate), the Bohr effect, some examples of
hemoglobinopathies (hemoglobin M, hemoglobin S, thalassemias), the role of the blood proteins in the
maintenance of homeostasis, the functions of inorganic compounds in the blood
Practical 6 The blood serum enzymes used in clinical diagnosis
The aim of the class: the analysis of some serum enzymes activities and its role in the diagnosis
of disease processes
Theoretical basis: classification of blood diagnostic enzymes, the major enzymes used in clinical
diagnosis, the role of diagnostic enzymology in diagnosis of myocardial infarction and some liver
diseases, absorption spectra of NAD+ and NADH, the usage of these spectra for the assays of
dehydrogenases activities, the coupled enzyme assays
Laboratory tests:
SEMINAR / TEST III The blood. Nutrition, digestion, and absorption
The key problems: The composition of digestive juices, the enzymes of digestive tract. Digestion and
absorption of carbohydrates, lipids, proteins, vitamins and minerals. The role of hydrochloric acid and
the bile salts in digestion processes. The production of hydrochloric acid by parietal cell of the stomach.
The biosynthesis and degradation of bile salts. The enterohepatic bile salts circulation.
Synthesis of heme and regulation of this process. Catabolism of heme. The fates of bilirubin:
transport to the liver, conjugation with glukuronic acid, secretion into bile, reduction to urobilinogen.
The enterohepatic urobilinogen cycle. Hyperbilirubinemias, different causes of jaundice (hemolytic
anemia, hepatitis, obstructive jaundice), the laboratory tests important in helping to distinguish
between prehepatic, hepatic and posthepatic causes of jaundice.
The major functions of the blood, the constituents of the blood. The organic and inorganic
constituents of the blood plasma. The characteristics and functions of plasma proteins. Structure and
functions of red blood cells. Metabolism of the red cell. Reaction of importance in relation to oxidative
stress in blood cells. System for reducing heme Fe3+ back to the Fe2+ state in the red blood cell.
Physiologic roles of hemoglobin and mioglobin, the oxygen dissociation curves for myoglobin and
hemoglobin. The mechanism of binding O2 to myoglobin and hemoglobin. The cooperative interactions
infuencing the binding O2 to hemoglobing, the changes of oxygen-binding curve of hemoglobin (effect
of temperature, pH, carbon dioxide concentration, 2,3-bis-phosphoglycerate concentration). The Bohr
effect. The carbon dioxide transport in the blood. Binding CO to hemoglobin. Changes of the subunit
composition of hemoglobin tetramers during development (embryonic, fetal and adult subunits).
Abnormal hemoglobines. Anemia. The classification of the causes of anemia.
Practical 7 Urine physiologic parameters
The aim of the class: the analysis of some substances extreted by the kidney from the body via
the urine during physiologic conditions
Theoretical basis: the functions of the kidney (excretion of waste products produced by metabolism,
acid-base homeostasis, osmolality regulation, the blood pressure regulation, hormone secretion), the
production of urine, characteristics and composition of the urine, glomerular filtration rate (GFR),
creatinine clearance as a creatinine-based approximation of GFR
Practical 8 Diagnostic chemical markers in human urine
The aim of the class: the analysis of some substances excreted by the kidney from the body via
the urine during pathologic conditions
Theoretical basis: the role of the urine analysis in the medical examination, the substances excreted by
the kidney via the urine in selected disease processes, diagnostic urine stripes as a rapid method of
urine analysis.
SEMINAR / TEST IV Metabolism of amino acids.
The key problems: Fate of amino acid nitrogen. Enzymes important in the process of interconverting
amino acids and in removing nitrogen (dehydratases, transaminases, glutamate dehydrogenase,
glutaminase, deaminases). The convertion of amino acid nitrogen to urea – the urea cycle.
Degradation of amino acid: fate of amino acid carbon skeletons. Glucogenic and ketogenic
amino acids. The role of pyridoxal phosphate, tetrahydrofolate and tetrahydrobiopterin coenzymes in
amino acid metabolism. Some disorders of amino acid catabolism: alkaptonuria, phenylketonuria,
maple syrup urine disease.
The biosyntheses of biologically important compounds from amino acids (sphingosine, choline,
taurine, creatine, catecholamines, hippuric acid, nitric oxide, glutathione, glycerophospholipids,
purines, pirymidines, carnosine, anserine, bile salts, hem, serotonin, melatonin, nicotinin acid,
coenzyme A). Biosynthetic decarboxylations of amino acids to amines – the biogenic amines and their
biological functions.
The one-carbon carriers in the body: tetrahydrofolate (FH4), vitamin B12, S-adenosylmethionine
(SAM). Sources and recipients of one-carbon FH4 pool.The methyl-trap hypothesis. The role of SAM in
the biosynthesis of the compounds of biological importance (creatine, phosphatidylcholine, adrenaline,
melatonin, methylated nucleotides, methylated DNA).
Essential and nonessential amino acids. The synthesis of nonessential amino acids in the human
organism.
SEMINAR / TEST V Integrative seminar 1 – Metabolism of tissues and organs.
The key problems: Carbohydrate, lipid and amino acid metabolism of liver, brain, skeletal muscle,
cardiac muscle cells, and kidney. The sources of ATP for skeletal muscle cells (e. g. creatine phosphate,
purine nucleotide cycle). Major functions of the kidney (excretion of waste products produced by
metabolism, acid-base homeostasis, osmolality regulation, the blood pressure regulation, hormone
secretion, γ-glutamyl cycle). The substances excreted via the urine in normal and pathologic conditions.
The metabolism of liver (detoxification of drugs and metabolites, glutathione S-transferases,
metabolism of ethanol). The functions of glutathione in the organism. Intertissue relationships in the
metabolism of carbohydrates, lipids and amino acids.
Classification of hormones according to their structure, a type of hormone receptor, and a
second messenger. The synthesis of thyroid hormones. The hormones involved in the glucose
maintenance in the blood. The major hormones influencing nutrient metabolism and their actions on
muscle, liver, and adipose tissue. The changes in the fuel metabolism during fasting state and
starvation. The metabolism of carbohydrates, lipids, and amino acids in the diabetes mellitus type I and
type II.
Practical 20 End-of-year practical
Booklist:
1. Lieberman M, Marks AD "Marks` Basic Medical Biochemistry a Clinical Approach". 3rd edition
2. Murray RK, Bender DA et al. "Harper`s Illustrated Biochemistry" 28th edition
3. Devlin Thomas M. Textbook of Biochemistry with Clinical Correlations, Seventh Edition WileyBlackwell 2010
Rules and regulations
The main objective of the course is to provide an understanding of biochemical processes
and to gain relevant basic laboratory skills according to the educational requirement defined in the
program of teaching biochemistry for medical students.
The program (120 hrs) consists of lectures (60 hrs), practical classes (60 hrs), and a closing
test. All classes are compulsory. Students should check the schedule carefully and be on time. If
students cannot attend class they must have sick note and arrange for an alternative date to carry
out the lab/seminar.
The performance during each laboratory class will be evaluated by the quality of theoretical
preparation, laboratory skills and written protocol from the experiments.
Seminars: Students must be prepared to give a short presentations of topics which will be
given to them by the teacher after each part of material.
Tests: One-choice tests (50 questions, graded 1 point for a correct answer) will be held at the
end of the each part of the material.
Final examination: Students who has earned credit must take the final examination (100
questions, one-choice questions test, graded 1 point for a correct answer).
The final examination and partial tests can be retaken according to the schedule and the
percentage of the points according to the following system:
60-67 % - satisfactory
68-75 % - fairly good
76 - 83 % - good
84 - 90% - better than good
90 - 100 % - very good
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